Starting phenix.real_space_refine on Fri Jul 3 08:54:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363.map" model { file = "/net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xoy_33363/07_2026/7xoy_33363_trim.cif" } resolution = 4.25 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= 0.004 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 4 5.49 5 S 52 5.16 5 C 8336 2.51 5 N 2336 2.21 5 O 2536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13264 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3294 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 29, 'TRANS': 428} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13264 At special positions: 0 Unit cell: (104.13, 143.91, 81.9, 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 52 16.00 P 4 15.00 O 2536 8.00 N 2336 7.00 C 8336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 44.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.749A pdb=" N VAL B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.789A pdb=" N ASN B 150 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.618A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.913A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 248 through 263 removed outlier: 4.000A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.722A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.705A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.818A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.561A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 388 through 396 removed outlier: 3.947A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 450 through 460 removed outlier: 3.501A pdb=" N GLY B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.788A pdb=" N ASN A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.606A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 183 through 198 removed outlier: 3.914A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.999A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.725A pdb=" N GLY A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.706A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.818A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.539A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.947A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.592A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.725A pdb=" N ASN C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.602A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 184 through 198 removed outlier: 4.061A pdb=" N GLY C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 248 through 263 removed outlier: 4.017A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.726A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.670A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.841A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 removed outlier: 3.689A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 388 through 396 removed outlier: 3.935A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 450 through 460 removed outlier: 3.533A pdb=" N GLY C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.724A pdb=" N ASN D 150 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.621A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 184 through 198 removed outlier: 3.811A pdb=" N GLY D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 248 through 263 removed outlier: 4.017A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.725A pdb=" N GLY D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 removed outlier: 3.667A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.842A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.610A pdb=" N VAL D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 388 through 396 removed outlier: 3.940A pdb=" N PHE D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'D' and resid 450 through 460 removed outlier: 3.533A pdb=" N GLY D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.718A pdb=" N ALA B 31 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 294 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 33 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N HIS B 175 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 293 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 203 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY B 205 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.484A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 367 through 370 Processing sheet with id=AA4, first strand: chain 'B' and resid 416 through 417 removed outlier: 3.796A pdb=" N VAL B 439 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.691A pdb=" N ALA A 31 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU A 294 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 33 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS A 175 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU A 293 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 203 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 244 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLY A 205 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.478A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 367 through 370 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 417 removed outlier: 3.795A pdb=" N VAL A 439 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.703A pdb=" N ALA C 31 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU C 294 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS C 33 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS C 175 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N LEU C 293 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 203 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE C 244 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY C 205 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.481A pdb=" N ILE C 67 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 367 through 370 Processing sheet with id=AB3, first strand: chain 'C' and resid 416 through 417 removed outlier: 3.784A pdb=" N VAL C 439 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 18 removed outlier: 6.703A pdb=" N ALA D 31 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 294 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 33 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS D 175 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU D 293 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 203 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 244 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLY D 205 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.483A pdb=" N ILE D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 367 through 370 Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 417 removed outlier: 3.784A pdb=" N VAL D 439 " --> pdb=" O ILE D 417 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2830 1.33 - 1.45: 2924 1.45 - 1.57: 7690 1.57 - 1.69: 4 1.69 - 1.81: 88 Bond restraints: 13536 Sorted by residual: bond pdb=" C PRO A 70 " pdb=" O PRO A 70 " ideal model delta sigma weight residual 1.235 1.205 0.030 7.90e-03 1.60e+04 1.41e+01 bond pdb=" C3 PLS B 501 " pdb=" O3 PLS B 501 " ideal model delta sigma weight residual 1.333 1.400 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C3 PLS A 501 " pdb=" O3 PLS A 501 " ideal model delta sigma weight residual 1.333 1.399 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C3 PLS C 601 " pdb=" O3 PLS C 601 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C3 PLS D 501 " pdb=" O3 PLS D 501 " ideal model delta sigma weight residual 1.333 1.397 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17774 1.97 - 3.95: 602 3.95 - 5.92: 41 5.92 - 7.89: 15 7.89 - 9.86: 8 Bond angle restraints: 18440 Sorted by residual: angle pdb=" C GLY C 76 " pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta sigma weight residual 120.88 113.82 7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" N THR C 75 " pdb=" CA THR C 75 " pdb=" C THR C 75 " ideal model delta sigma weight residual 111.07 105.64 5.43 1.07e+00 8.73e-01 2.58e+01 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.18 107.49 5.69 1.21e+00 6.83e-01 2.21e+01 angle pdb=" N THR C 182 " pdb=" CA THR C 182 " pdb=" C THR C 182 " ideal model delta sigma weight residual 113.19 107.76 5.43 1.19e+00 7.06e-01 2.08e+01 angle pdb=" C ALA C 343 " pdb=" CA ALA C 343 " pdb=" CB ALA C 343 " ideal model delta sigma weight residual 116.54 111.46 5.08 1.15e+00 7.56e-01 1.95e+01 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 7460 16.68 - 33.37: 362 33.37 - 50.05: 141 50.05 - 66.74: 54 66.74 - 83.42: 3 Dihedral angle restraints: 8020 sinusoidal: 2916 harmonic: 5104 Sorted by residual: dihedral pdb=" CA LYS C 97 " pdb=" C LYS C 97 " pdb=" N VAL C 98 " pdb=" CA VAL C 98 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG D 335 " pdb=" CB ARG D 335 " pdb=" CG ARG D 335 " pdb=" CD ARG D 335 " ideal model delta sinusoidal sigma weight residual 60.00 119.92 -59.92 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 335 " pdb=" CB ARG A 335 " pdb=" CG ARG A 335 " pdb=" CD ARG A 335 " ideal model delta sinusoidal sigma weight residual 60.00 119.71 -59.71 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1478 0.052 - 0.103: 477 0.103 - 0.155: 86 0.155 - 0.206: 20 0.206 - 0.258: 7 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2065 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 277 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ALA D 277 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA D 277 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU D 278 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 277 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ALA C 277 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA C 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 278 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 277 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C ALA A 277 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA A 277 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 3548 2.78 - 3.31: 14375 3.31 - 3.84: 21655 3.84 - 4.37: 25093 4.37 - 4.90: 39628 Nonbonded interactions: 104299 Sorted by model distance: nonbonded pdb=" N GLN C 147 " pdb=" OE1 GLN C 147 " model vdw 2.255 3.120 nonbonded pdb=" N GLN D 147 " pdb=" OE1 GLN D 147 " model vdw 2.261 3.120 nonbonded pdb=" N LYS B 401 " pdb=" OD2 ASP B 404 " model vdw 2.274 3.120 nonbonded pdb=" N LYS A 401 " pdb=" OD2 ASP A 404 " model vdw 2.277 3.120 nonbonded pdb=" OD1 ASP D 250 " pdb=" NH1 ARG D 318 " model vdw 2.278 3.120 ... (remaining 104294 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.009 0.684 13537 Z= 0.710 Angle : 0.790 9.863 18440 Z= 0.477 Chirality : 0.053 0.258 2068 Planarity : 0.004 0.041 2440 Dihedral : 12.491 83.421 4804 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 45.00 Ramachandran Plot: Outliers : 1.15 % Allowed : 10.20 % Favored : 88.65 % Rotamer: Outliers : 8.23 % Allowed : 7.76 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.20), residues: 1824 helix: -0.75 (0.20), residues: 700 sheet: -2.22 (0.39), residues: 176 loop : -2.52 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.011 0.001 TYR A 451 PHE 0.011 0.001 PHE C 316 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.40 (13536) covalent geometry : angle 0.78953 / 0.48 (18440) hydrogen bonds : bond 0.18637 / 12.95 ( 539) hydrogen bonds : angle 8.39436 / 6.03 ( 1473) Misc. bond : bond 0.68428 / 36.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 310 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 HIS cc_start: 0.8743 (m-70) cc_final: 0.8502 (m-70) REVERT: B 316 PHE cc_start: 0.8906 (p90) cc_final: 0.8394 (p90) REVERT: A 97 LYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4423 (mptt) REVERT: A 316 PHE cc_start: 0.8824 (p90) cc_final: 0.8313 (p90) REVERT: C 38 ASN cc_start: 0.9366 (m-40) cc_final: 0.8711 (m-40) REVERT: C 224 GLU cc_start: 0.8923 (tt0) cc_final: 0.8432 (mp0) REVERT: C 368 MET cc_start: 0.8913 (ptm) cc_final: 0.8292 (ptm) REVERT: C 456 PHE cc_start: 0.8550 (t80) cc_final: 0.7682 (t80) REVERT: D 38 ASN cc_start: 0.9334 (m-40) cc_final: 0.8692 (m-40) REVERT: D 112 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7304 (mt-10) REVERT: D 185 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8279 (m) REVERT: D 224 GLU cc_start: 0.8978 (tt0) cc_final: 0.8508 (mp0) REVERT: D 368 MET cc_start: 0.8723 (ptm) cc_final: 0.8269 (ptm) outliers start: 106 outliers final: 24 residues processed: 380 average time/residue: 0.1056 time to fit residues: 56.4071 Evaluate side-chains 225 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083083 restraints weight = 29017.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085922 restraints weight = 16934.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087914 restraints weight = 11457.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089328 restraints weight = 8633.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090338 restraints weight = 7021.209| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13537 Z= 0.194 Angle : 0.736 9.304 18440 Z= 0.373 Chirality : 0.048 0.179 2068 Planarity : 0.006 0.043 2440 Dihedral : 5.710 60.516 2008 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.88 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.20), residues: 1824 helix: -0.67 (0.19), residues: 720 sheet: -2.72 (0.33), residues: 204 loop : -2.11 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 335 TYR 0.016 0.002 TYR D 451 PHE 0.018 0.002 PHE B 230 TRP 0.034 0.002 TRP B 143 HIS 0.008 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (13536) covalent geometry : angle 0.73621 / 0.37 (18440) hydrogen bonds : bond 0.04663 / 3.20 ( 539) hydrogen bonds : angle 5.99288 / 4.30 ( 1473) Misc. bond : bond 0.00145 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.8176 (m-40) cc_final: 0.7955 (m-40) REVERT: B 38 ASN cc_start: 0.8900 (t0) cc_final: 0.8560 (t0) REVERT: B 45 ASP cc_start: 0.8670 (p0) cc_final: 0.7926 (p0) REVERT: B 51 MET cc_start: 0.9238 (mtm) cc_final: 0.9037 (mtm) REVERT: B 264 MET cc_start: 0.8956 (mmm) cc_final: 0.8721 (mtp) REVERT: B 307 ASN cc_start: 0.8757 (t0) cc_final: 0.8431 (t0) REVERT: B 311 MET cc_start: 0.9016 (tpp) cc_final: 0.8686 (tpp) REVERT: B 336 ARG cc_start: 0.6192 (tpt170) cc_final: 0.5988 (tpt170) REVERT: B 385 SER cc_start: 0.8227 (p) cc_final: 0.8005 (m) REVERT: A 20 ASN cc_start: 0.8129 (m-40) cc_final: 0.7913 (m-40) REVERT: A 38 ASN cc_start: 0.8956 (t0) cc_final: 0.8486 (t0) REVERT: A 45 ASP cc_start: 0.8642 (p0) cc_final: 0.7861 (p0) REVERT: A 51 MET cc_start: 0.9265 (mtm) cc_final: 0.8770 (mtm) REVERT: A 197 SER cc_start: 0.8492 (t) cc_final: 0.8266 (t) REVERT: A 224 GLU cc_start: 0.8204 (tp30) cc_final: 0.7816 (tm-30) REVERT: A 264 MET cc_start: 0.8998 (mmm) cc_final: 0.8744 (mtp) REVERT: A 272 MET cc_start: 0.9072 (ttp) cc_final: 0.8867 (tmm) REVERT: A 307 ASN cc_start: 0.8779 (t0) cc_final: 0.8447 (t0) REVERT: A 385 SER cc_start: 0.8174 (p) cc_final: 0.7968 (m) REVERT: C 35 GLU cc_start: 0.7446 (tp30) cc_final: 0.7191 (tm-30) REVERT: C 224 GLU cc_start: 0.8789 (tt0) cc_final: 0.8466 (mp0) REVERT: C 368 MET cc_start: 0.8960 (ptm) cc_final: 0.8256 (ptm) REVERT: C 456 PHE cc_start: 0.8251 (t80) cc_final: 0.7807 (t80) REVERT: D 35 GLU cc_start: 0.7403 (tp30) cc_final: 0.7168 (tm-30) REVERT: D 47 ILE cc_start: 0.9249 (mt) cc_final: 0.9022 (mt) REVERT: D 224 GLU cc_start: 0.8791 (tt0) cc_final: 0.8427 (mp0) REVERT: D 368 MET cc_start: 0.8886 (ptm) cc_final: 0.8251 (ptm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.0955 time to fit residues: 35.5397 Evaluate side-chains 185 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086699 restraints weight = 28555.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089691 restraints weight = 16341.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091779 restraints weight = 10943.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093107 restraints weight = 8179.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094279 restraints weight = 6697.742| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13537 Z= 0.124 Angle : 0.633 7.969 18440 Z= 0.320 Chirality : 0.045 0.155 2068 Planarity : 0.005 0.048 2440 Dihedral : 5.513 62.379 2008 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.20), residues: 1824 helix: -0.18 (0.19), residues: 704 sheet: -2.47 (0.30), residues: 224 loop : -1.65 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 86 TYR 0.011 0.001 TYR C 88 PHE 0.013 0.002 PHE A 316 TRP 0.017 0.001 TRP A 143 HIS 0.005 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13536) covalent geometry : angle 0.63309 / 0.32 (18440) hydrogen bonds : bond 0.03866 / 2.66 ( 539) hydrogen bonds : angle 5.43686 / 3.89 ( 1473) Misc. bond : bond 0.00149 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.8094 (m-40) cc_final: 0.7646 (m-40) REVERT: B 38 ASN cc_start: 0.9112 (t0) cc_final: 0.8544 (t0) REVERT: B 45 ASP cc_start: 0.8669 (p0) cc_final: 0.7749 (p0) REVERT: B 143 TRP cc_start: 0.8235 (t60) cc_final: 0.8008 (t60) REVERT: B 168 ASP cc_start: 0.8364 (m-30) cc_final: 0.8003 (m-30) REVERT: B 307 ASN cc_start: 0.8641 (t0) cc_final: 0.8287 (t0) REVERT: B 311 MET cc_start: 0.9013 (tpp) cc_final: 0.8623 (tpp) REVERT: B 351 GLU cc_start: 0.8225 (tt0) cc_final: 0.7983 (tt0) REVERT: A 20 ASN cc_start: 0.8030 (m-40) cc_final: 0.7571 (m-40) REVERT: A 38 ASN cc_start: 0.9055 (t0) cc_final: 0.8701 (t0) REVERT: A 45 ASP cc_start: 0.8545 (p0) cc_final: 0.7867 (p0) REVERT: A 51 MET cc_start: 0.9388 (mtm) cc_final: 0.8769 (mtm) REVERT: A 143 TRP cc_start: 0.8244 (t60) cc_final: 0.7987 (t60) REVERT: A 168 ASP cc_start: 0.8365 (m-30) cc_final: 0.8009 (m-30) REVERT: A 197 SER cc_start: 0.8473 (t) cc_final: 0.8225 (t) REVERT: A 207 ASP cc_start: 0.8908 (t70) cc_final: 0.8703 (t0) REVERT: A 224 GLU cc_start: 0.8140 (tp30) cc_final: 0.7916 (tm-30) REVERT: A 254 MET cc_start: 0.9075 (tpt) cc_final: 0.8721 (tpp) REVERT: A 264 MET cc_start: 0.8755 (mmm) cc_final: 0.8511 (mtp) REVERT: A 307 ASN cc_start: 0.8638 (t0) cc_final: 0.8407 (t0) REVERT: A 311 MET cc_start: 0.8925 (tpp) cc_final: 0.8558 (tpp) REVERT: C 38 ASN cc_start: 0.8931 (m-40) cc_final: 0.8676 (m110) REVERT: C 84 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8200 (mm-40) REVERT: C 209 GLU cc_start: 0.7606 (pm20) cc_final: 0.7235 (pm20) REVERT: C 219 ARG cc_start: 0.7048 (ttp-170) cc_final: 0.6459 (ttp-170) REVERT: C 224 GLU cc_start: 0.8713 (tt0) cc_final: 0.8378 (mp0) REVERT: C 456 PHE cc_start: 0.8159 (t80) cc_final: 0.7726 (t80) REVERT: D 38 ASN cc_start: 0.8977 (m-40) cc_final: 0.8671 (m110) REVERT: D 84 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8115 (mm110) REVERT: D 224 GLU cc_start: 0.8689 (tt0) cc_final: 0.8226 (mp0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.0896 time to fit residues: 32.6436 Evaluate side-chains 187 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085575 restraints weight = 28378.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088455 restraints weight = 16464.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.090454 restraints weight = 11081.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091873 restraints weight = 8342.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092818 restraints weight = 6797.764| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13537 Z= 0.130 Angle : 0.624 8.137 18440 Z= 0.315 Chirality : 0.045 0.179 2068 Planarity : 0.005 0.046 2440 Dihedral : 5.297 62.174 2008 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.20), residues: 1824 helix: -0.14 (0.18), residues: 744 sheet: -1.92 (0.35), residues: 188 loop : -1.46 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 335 TYR 0.012 0.001 TYR C 451 PHE 0.012 0.002 PHE D 316 TRP 0.011 0.001 TRP A 143 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13536) covalent geometry : angle 0.62380 / 0.31 (18440) hydrogen bonds : bond 0.03667 / 2.52 ( 539) hydrogen bonds : angle 5.22755 / 3.74 ( 1473) Misc. bond : bond 0.00180 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.7974 (m-40) cc_final: 0.7485 (m-40) REVERT: B 45 ASP cc_start: 0.8558 (p0) cc_final: 0.8280 (p0) REVERT: B 51 MET cc_start: 0.9372 (mtt) cc_final: 0.8969 (mtt) REVERT: B 143 TRP cc_start: 0.8229 (t60) cc_final: 0.7964 (t60) REVERT: B 307 ASN cc_start: 0.8594 (t0) cc_final: 0.8268 (t0) REVERT: B 351 GLU cc_start: 0.8281 (tt0) cc_final: 0.7971 (tt0) REVERT: B 368 MET cc_start: 0.8056 (tmm) cc_final: 0.7846 (tmm) REVERT: B 430 LEU cc_start: 0.9314 (mp) cc_final: 0.9081 (mp) REVERT: B 443 LYS cc_start: 0.8636 (mttt) cc_final: 0.8352 (ptmt) REVERT: A 20 ASN cc_start: 0.7974 (m-40) cc_final: 0.7583 (m-40) REVERT: A 45 ASP cc_start: 0.8537 (p0) cc_final: 0.8122 (p0) REVERT: A 143 TRP cc_start: 0.8294 (t60) cc_final: 0.8015 (t60) REVERT: A 254 MET cc_start: 0.9104 (tpt) cc_final: 0.8729 (tpp) REVERT: A 307 ASN cc_start: 0.8590 (t0) cc_final: 0.8230 (t0) REVERT: C 35 GLU cc_start: 0.8090 (tp30) cc_final: 0.7811 (tp30) REVERT: C 38 ASN cc_start: 0.9216 (m-40) cc_final: 0.8750 (m110) REVERT: C 84 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8219 (mm-40) REVERT: C 219 ARG cc_start: 0.7418 (ttp-170) cc_final: 0.6492 (ttp-170) REVERT: C 224 GLU cc_start: 0.8760 (tt0) cc_final: 0.8357 (mp0) REVERT: C 264 MET cc_start: 0.9080 (mmm) cc_final: 0.8792 (mtp) REVERT: C 388 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 410 MET cc_start: 0.8350 (ptm) cc_final: 0.8085 (ptm) REVERT: C 451 TYR cc_start: 0.8708 (t80) cc_final: 0.8498 (t80) REVERT: C 456 PHE cc_start: 0.8150 (t80) cc_final: 0.7605 (t80) REVERT: D 11 ILE cc_start: 0.9106 (pt) cc_final: 0.8854 (pt) REVERT: D 38 ASN cc_start: 0.9267 (m-40) cc_final: 0.8726 (m110) REVERT: D 264 MET cc_start: 0.9026 (mmm) cc_final: 0.8712 (mtp) REVERT: D 388 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 410 MET cc_start: 0.8325 (ptm) cc_final: 0.8039 (ptm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.0997 time to fit residues: 34.0951 Evaluate side-chains 182 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 156 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 169 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084654 restraints weight = 28502.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087545 restraints weight = 16446.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089560 restraints weight = 11069.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090996 restraints weight = 8310.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091922 restraints weight = 6749.836| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13537 Z= 0.156 Angle : 0.642 7.923 18440 Z= 0.324 Chirality : 0.046 0.160 2068 Planarity : 0.005 0.044 2440 Dihedral : 5.220 59.905 2008 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1824 helix: 0.01 (0.19), residues: 736 sheet: -1.64 (0.36), residues: 188 loop : -1.27 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 86 TYR 0.014 0.001 TYR A 213 PHE 0.012 0.002 PHE D 316 TRP 0.010 0.001 TRP A 143 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (13536) covalent geometry : angle 0.64156 / 0.32 (18440) hydrogen bonds : bond 0.03735 / 2.56 ( 539) hydrogen bonds : angle 5.19244 / 3.72 ( 1473) Misc. bond : bond 0.00160 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.9095 (t0) cc_final: 0.8819 (t0) REVERT: B 45 ASP cc_start: 0.8497 (p0) cc_final: 0.8038 (p0) REVERT: B 60 GLN cc_start: 0.8472 (pm20) cc_final: 0.8268 (pm20) REVERT: B 72 SER cc_start: 0.8504 (m) cc_final: 0.8156 (t) REVERT: B 264 MET cc_start: 0.8616 (mmm) cc_final: 0.8328 (mtp) REVERT: B 307 ASN cc_start: 0.8671 (t0) cc_final: 0.8408 (t0) REVERT: B 351 GLU cc_start: 0.8239 (tt0) cc_final: 0.8024 (tt0) REVERT: B 385 SER cc_start: 0.7709 (m) cc_final: 0.7504 (m) REVERT: B 430 LEU cc_start: 0.9351 (mp) cc_final: 0.9082 (mp) REVERT: B 443 LYS cc_start: 0.8692 (mttt) cc_final: 0.8418 (ptmt) REVERT: A 52 ILE cc_start: 0.9360 (mm) cc_final: 0.9136 (mm) REVERT: A 143 TRP cc_start: 0.8399 (t60) cc_final: 0.8095 (t60) REVERT: A 207 ASP cc_start: 0.8486 (t0) cc_final: 0.8224 (t0) REVERT: A 254 MET cc_start: 0.9081 (tpt) cc_final: 0.8737 (tpp) REVERT: A 307 ASN cc_start: 0.8659 (t0) cc_final: 0.8400 (t0) REVERT: C 11 ILE cc_start: 0.9216 (pt) cc_final: 0.8980 (pt) REVERT: C 38 ASN cc_start: 0.9253 (m-40) cc_final: 0.8745 (m110) REVERT: C 146 ASP cc_start: 0.7573 (t0) cc_final: 0.7366 (t0) REVERT: C 388 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 451 TYR cc_start: 0.8772 (t80) cc_final: 0.8530 (t80) REVERT: D 35 GLU cc_start: 0.8135 (tp30) cc_final: 0.7351 (tp30) REVERT: D 38 ASN cc_start: 0.9309 (m-40) cc_final: 0.8636 (m110) REVERT: D 84 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8299 (mm110) REVERT: D 336 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7921 (ttp80) REVERT: D 388 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7918 (tm-30) REVERT: D 451 TYR cc_start: 0.8766 (t80) cc_final: 0.8469 (t80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0929 time to fit residues: 30.0620 Evaluate side-chains 176 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085927 restraints weight = 28431.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.088833 restraints weight = 16429.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090886 restraints weight = 11041.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092228 restraints weight = 8261.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093297 restraints weight = 6756.472| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13537 Z= 0.133 Angle : 0.627 8.156 18440 Z= 0.315 Chirality : 0.045 0.219 2068 Planarity : 0.005 0.045 2440 Dihedral : 5.172 72.562 2008 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1824 helix: 0.14 (0.19), residues: 736 sheet: -0.94 (0.41), residues: 148 loop : -1.30 (0.22), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 336 TYR 0.013 0.001 TYR C 451 PHE 0.012 0.002 PHE D 316 TRP 0.010 0.001 TRP A 143 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (13536) covalent geometry : angle 0.62723 / 0.31 (18440) hydrogen bonds : bond 0.03474 / 2.38 ( 539) hydrogen bonds : angle 5.05683 / 3.62 ( 1473) Misc. bond : bond 0.00224 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.8172 (m-40) cc_final: 0.7811 (m-40) REVERT: B 38 ASN cc_start: 0.9081 (t0) cc_final: 0.8759 (t0) REVERT: B 60 GLN cc_start: 0.8455 (pm20) cc_final: 0.8212 (pm20) REVERT: B 72 SER cc_start: 0.8567 (m) cc_final: 0.7966 (t) REVERT: B 143 TRP cc_start: 0.8422 (t60) cc_final: 0.8060 (t60) REVERT: B 264 MET cc_start: 0.8580 (mmm) cc_final: 0.8336 (mtp) REVERT: B 307 ASN cc_start: 0.8661 (t0) cc_final: 0.8263 (t0) REVERT: B 368 MET cc_start: 0.8192 (tmm) cc_final: 0.7989 (tmm) REVERT: A 51 MET cc_start: 0.9215 (mtt) cc_final: 0.8984 (mtm) REVERT: A 60 GLN cc_start: 0.8386 (pm20) cc_final: 0.8168 (pm20) REVERT: A 143 TRP cc_start: 0.8439 (t60) cc_final: 0.8105 (t60) REVERT: A 254 MET cc_start: 0.9159 (tpt) cc_final: 0.8777 (tpp) REVERT: A 262 GLU cc_start: 0.7492 (mp0) cc_final: 0.7276 (mp0) REVERT: A 307 ASN cc_start: 0.8621 (t0) cc_final: 0.8251 (t0) REVERT: A 351 GLU cc_start: 0.7978 (tt0) cc_final: 0.7739 (tt0) REVERT: C 11 ILE cc_start: 0.9195 (pt) cc_final: 0.8975 (pt) REVERT: C 35 GLU cc_start: 0.8115 (tp30) cc_final: 0.7304 (tp30) REVERT: C 38 ASN cc_start: 0.9295 (m-40) cc_final: 0.8684 (m110) REVERT: C 146 ASP cc_start: 0.7466 (t0) cc_final: 0.7265 (t0) REVERT: C 228 GLU cc_start: 0.7689 (tp30) cc_final: 0.7486 (tp30) REVERT: C 246 VAL cc_start: 0.9105 (p) cc_final: 0.8813 (m) REVERT: C 388 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 451 TYR cc_start: 0.8811 (t80) cc_final: 0.8553 (t80) REVERT: D 11 ILE cc_start: 0.9184 (pt) cc_final: 0.8919 (pt) REVERT: D 35 GLU cc_start: 0.8143 (tp30) cc_final: 0.7383 (tp30) REVERT: D 38 ASN cc_start: 0.9300 (m-40) cc_final: 0.8623 (m110) REVERT: D 228 GLU cc_start: 0.7697 (tp30) cc_final: 0.7431 (tp30) REVERT: D 388 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 456 PHE cc_start: 0.8350 (t80) cc_final: 0.7708 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0849 time to fit residues: 29.5453 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 168 optimal weight: 0.0470 chunk 32 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.087522 restraints weight = 28156.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090479 restraints weight = 16285.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092558 restraints weight = 10946.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094022 restraints weight = 8216.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095049 restraints weight = 6667.751| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13537 Z= 0.113 Angle : 0.615 8.158 18440 Z= 0.308 Chirality : 0.044 0.167 2068 Planarity : 0.005 0.069 2440 Dihedral : 5.089 76.467 2008 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 are not related in a simple way. whole: -0.87 (0.20), residues: 1824 helix: 0.24 (0.19), residues: 736 sheet: -0.65 (0.37), residues: 188 loop : -1.22 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 336 TYR 0.020 0.001 TYR D 451 PHE 0.012 0.001 PHE D 316 TRP 0.009 0.001 TRP B 143 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13536) covalent geometry : angle 0.61459 / 0.31 (18440) hydrogen bonds : bond 0.03269 / 2.23 ( 539) hydrogen bonds : angle 4.97772 / 3.58 ( 1473) Misc. bond : bond 0.00190 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 ASN cc_start: 0.8039 (m-40) cc_final: 0.7725 (m-40) REVERT: B 38 ASN cc_start: 0.9034 (t0) cc_final: 0.8701 (t0) REVERT: B 60 GLN cc_start: 0.8410 (pm20) cc_final: 0.8159 (pm20) REVERT: B 72 SER cc_start: 0.8602 (m) cc_final: 0.8020 (t) REVERT: B 143 TRP cc_start: 0.8342 (t60) cc_final: 0.7958 (t60) REVERT: B 264 MET cc_start: 0.8435 (mmm) cc_final: 0.8089 (mtp) REVERT: B 307 ASN cc_start: 0.8633 (t0) cc_final: 0.8295 (t0) REVERT: B 368 MET cc_start: 0.8327 (tmm) cc_final: 0.7856 (tmm) REVERT: A 51 MET cc_start: 0.9187 (mtt) cc_final: 0.8967 (mtm) REVERT: A 60 GLN cc_start: 0.8451 (pm20) cc_final: 0.8098 (pm20) REVERT: A 143 TRP cc_start: 0.8432 (t60) cc_final: 0.8122 (t60) REVERT: A 254 MET cc_start: 0.9168 (tpt) cc_final: 0.8726 (tpp) REVERT: A 262 GLU cc_start: 0.7514 (mp0) cc_final: 0.7254 (mp0) REVERT: A 351 GLU cc_start: 0.7926 (tt0) cc_final: 0.7707 (tt0) REVERT: C 11 ILE cc_start: 0.9176 (pt) cc_final: 0.8950 (pt) REVERT: C 35 GLU cc_start: 0.8241 (tp30) cc_final: 0.7526 (tp30) REVERT: C 38 ASN cc_start: 0.9315 (m-40) cc_final: 0.8721 (m110) REVERT: C 146 ASP cc_start: 0.7469 (t0) cc_final: 0.7220 (t0) REVERT: C 197 SER cc_start: 0.7839 (p) cc_final: 0.7592 (t) REVERT: C 388 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7783 (tm-30) REVERT: C 451 TYR cc_start: 0.8765 (t80) cc_final: 0.8480 (t80) REVERT: C 456 PHE cc_start: 0.8177 (t80) cc_final: 0.7649 (t80) REVERT: D 11 ILE cc_start: 0.9135 (pt) cc_final: 0.8887 (pt) REVERT: D 35 GLU cc_start: 0.8134 (tp30) cc_final: 0.7590 (tp30) REVERT: D 38 ASN cc_start: 0.9293 (m-40) cc_final: 0.8672 (m110) REVERT: D 84 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8310 (mm-40) REVERT: D 264 MET cc_start: 0.8995 (mmm) cc_final: 0.8671 (mtp) REVERT: D 388 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7617 (tm-30) REVERT: D 456 PHE cc_start: 0.8414 (t80) cc_final: 0.7764 (t80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0877 time to fit residues: 29.3555 Evaluate side-chains 181 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.0060 chunk 157 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089297 restraints weight = 27938.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092246 restraints weight = 16224.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094354 restraints weight = 10911.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095812 restraints weight = 8144.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096898 restraints weight = 6588.593| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13537 Z= 0.110 Angle : 0.629 8.252 18440 Z= 0.311 Chirality : 0.044 0.163 2068 Planarity : 0.006 0.069 2440 Dihedral : 5.003 75.959 2008 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1824 helix: 0.33 (0.19), residues: 736 sheet: -0.63 (0.36), residues: 224 loop : -1.13 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 361 TYR 0.010 0.001 TYR B 88 PHE 0.023 0.002 PHE D 316 TRP 0.008 0.001 TRP B 143 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13536) covalent geometry : angle 0.62856 / 0.31 (18440) hydrogen bonds : bond 0.03151 / 2.16 ( 539) hydrogen bonds : angle 4.87478 / 3.51 ( 1473) Misc. bond : bond 0.00167 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.9050 (t0) cc_final: 0.8724 (t0) REVERT: B 45 ASP cc_start: 0.8237 (p0) cc_final: 0.7931 (p0) REVERT: B 60 GLN cc_start: 0.8562 (pm20) cc_final: 0.8201 (pm20) REVERT: B 72 SER cc_start: 0.8636 (m) cc_final: 0.8038 (t) REVERT: B 143 TRP cc_start: 0.8316 (t60) cc_final: 0.7962 (t60) REVERT: B 264 MET cc_start: 0.8335 (mmm) cc_final: 0.7981 (mtp) REVERT: B 307 ASN cc_start: 0.8611 (t0) cc_final: 0.8397 (t0) REVERT: B 367 GLN cc_start: 0.8673 (mm110) cc_final: 0.8444 (mm-40) REVERT: B 368 MET cc_start: 0.8120 (tmm) cc_final: 0.7591 (tmm) REVERT: A 60 GLN cc_start: 0.8417 (pm20) cc_final: 0.8059 (pm20) REVERT: A 143 TRP cc_start: 0.8407 (t60) cc_final: 0.8072 (t60) REVERT: A 254 MET cc_start: 0.9235 (tpt) cc_final: 0.8830 (tpp) REVERT: A 307 ASN cc_start: 0.8568 (t0) cc_final: 0.8257 (t0) REVERT: A 351 GLU cc_start: 0.7914 (tt0) cc_final: 0.7678 (tt0) REVERT: A 385 SER cc_start: 0.8123 (m) cc_final: 0.7789 (m) REVERT: A 437 MET cc_start: 0.7498 (mtt) cc_final: 0.7113 (mtm) REVERT: C 11 ILE cc_start: 0.9177 (pt) cc_final: 0.8913 (pt) REVERT: C 35 GLU cc_start: 0.8222 (tp30) cc_final: 0.7576 (tp30) REVERT: C 38 ASN cc_start: 0.9305 (m-40) cc_final: 0.8759 (m110) REVERT: C 84 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8186 (mm-40) REVERT: C 146 ASP cc_start: 0.7368 (t0) cc_final: 0.7134 (t0) REVERT: C 228 GLU cc_start: 0.7636 (tp30) cc_final: 0.7398 (tp30) REVERT: C 388 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 451 TYR cc_start: 0.8754 (t80) cc_final: 0.8406 (t80) REVERT: C 456 PHE cc_start: 0.8113 (t80) cc_final: 0.7629 (t80) REVERT: D 11 ILE cc_start: 0.9178 (pt) cc_final: 0.8941 (pt) REVERT: D 35 GLU cc_start: 0.8181 (tp30) cc_final: 0.6787 (tm-30) REVERT: D 38 ASN cc_start: 0.9286 (m-40) cc_final: 0.8776 (m110) REVERT: D 84 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8289 (mm110) REVERT: D 264 MET cc_start: 0.8975 (mmm) cc_final: 0.8678 (mtp) REVERT: D 456 PHE cc_start: 0.8254 (t80) cc_final: 0.7655 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0850 time to fit residues: 29.4619 Evaluate side-chains 184 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 169 optimal weight: 0.0970 chunk 138 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 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 = 0.3467 r_free = 0.3467 target = 0.108993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090343 restraints weight = 28153.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093337 restraints weight = 16152.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095431 restraints weight = 10783.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096964 restraints weight = 8039.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098028 restraints weight = 6449.308| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13537 Z= 0.108 Angle : 0.625 8.581 18440 Z= 0.309 Chirality : 0.044 0.160 2068 Planarity : 0.005 0.061 2440 Dihedral : 4.853 73.277 2008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1824 helix: 0.39 (0.19), residues: 736 sheet: -0.42 (0.36), residues: 224 loop : -1.05 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 256 TYR 0.010 0.001 TYR B 88 PHE 0.021 0.001 PHE D 316 TRP 0.009 0.001 TRP A 143 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13536) covalent geometry : angle 0.62478 / 0.31 (18440) hydrogen bonds : bond 0.03090 / 2.12 ( 539) hydrogen bonds : angle 4.85731 / 3.49 ( 1473) Misc. bond : bond 0.00155 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASN cc_start: 0.9035 (t0) cc_final: 0.8680 (t0) REVERT: B 45 ASP cc_start: 0.8335 (p0) cc_final: 0.7973 (p0) REVERT: B 60 GLN cc_start: 0.8529 (pm20) cc_final: 0.8148 (pm20) REVERT: B 143 TRP cc_start: 0.8291 (t60) cc_final: 0.7893 (t60) REVERT: B 264 MET cc_start: 0.8213 (mmm) cc_final: 0.7831 (mtp) REVERT: B 367 GLN cc_start: 0.8729 (mm110) cc_final: 0.8462 (mm-40) REVERT: B 368 MET cc_start: 0.8264 (tmm) cc_final: 0.7799 (tmm) REVERT: A 143 TRP cc_start: 0.8400 (t60) cc_final: 0.8034 (t60) REVERT: A 254 MET cc_start: 0.9211 (tpt) cc_final: 0.8744 (tpp) REVERT: A 307 ASN cc_start: 0.8547 (t0) cc_final: 0.8267 (t0) REVERT: A 351 GLU cc_start: 0.7879 (tt0) cc_final: 0.7662 (tt0) REVERT: C 11 ILE cc_start: 0.9186 (pt) cc_final: 0.8928 (pt) REVERT: C 35 GLU cc_start: 0.8229 (tp30) cc_final: 0.7601 (tp30) REVERT: C 38 ASN cc_start: 0.9359 (m-40) cc_final: 0.8838 (m110) REVERT: C 44 LYS cc_start: 0.7781 (tttt) cc_final: 0.7475 (ttmt) REVERT: C 84 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8231 (mm110) REVERT: C 146 ASP cc_start: 0.7242 (t0) cc_final: 0.6997 (t0) REVERT: C 228 GLU cc_start: 0.7580 (tp30) cc_final: 0.7347 (tp30) REVERT: C 264 MET cc_start: 0.8938 (mmm) cc_final: 0.8581 (mtp) REVERT: C 452 ASP cc_start: 0.8586 (m-30) cc_final: 0.8384 (m-30) REVERT: C 456 PHE cc_start: 0.8049 (t80) cc_final: 0.7577 (t80) REVERT: D 11 ILE cc_start: 0.9169 (pt) cc_final: 0.8952 (pt) REVERT: D 35 GLU cc_start: 0.8157 (tp30) cc_final: 0.6860 (tm-30) REVERT: D 38 ASN cc_start: 0.9319 (m-40) cc_final: 0.8825 (m110) REVERT: D 84 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8315 (mm110) REVERT: D 228 GLU cc_start: 0.7973 (tp30) cc_final: 0.7717 (mm-30) REVERT: D 272 MET cc_start: 0.8779 (ttp) cc_final: 0.8553 (tmm) REVERT: D 456 PHE cc_start: 0.8202 (t80) cc_final: 0.7602 (t80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0913 time to fit residues: 31.5271 Evaluate side-chains 180 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 49 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 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 = 0.3447 r_free = 0.3447 target = 0.107959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089356 restraints weight = 28119.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092260 restraints weight = 16311.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094368 restraints weight = 10954.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095830 restraints weight = 8152.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096758 restraints weight = 6593.416| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13537 Z= 0.117 Angle : 0.629 9.606 18440 Z= 0.311 Chirality : 0.045 0.165 2068 Planarity : 0.006 0.059 2440 Dihedral : 4.841 72.577 2008 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1824 helix: 0.42 (0.19), residues: 736 sheet: -0.38 (0.35), residues: 240 loop : -1.00 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 256 TYR 0.017 0.001 TYR C 128 PHE 0.021 0.002 PHE D 316 TRP 0.011 0.001 TRP D 310 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13536) covalent geometry : angle 0.62947 / 0.31 (18440) hydrogen bonds : bond 0.03160 / 2.17 ( 539) hydrogen bonds : angle 4.86280 / 3.50 ( 1473) Misc. bond : bond 0.00145 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ASP cc_start: 0.8369 (p0) cc_final: 0.8157 (p0) REVERT: B 60 GLN cc_start: 0.8413 (pm20) cc_final: 0.8015 (pm20) REVERT: B 264 MET cc_start: 0.8286 (mmm) cc_final: 0.7919 (mtp) REVERT: B 307 ASN cc_start: 0.8536 (t0) cc_final: 0.8326 (t0) REVERT: B 367 GLN cc_start: 0.8786 (mm110) cc_final: 0.8536 (mm-40) REVERT: B 368 MET cc_start: 0.8238 (tmm) cc_final: 0.7791 (tmm) REVERT: A 254 MET cc_start: 0.9209 (tpt) cc_final: 0.8786 (tpp) REVERT: A 307 ASN cc_start: 0.8545 (t0) cc_final: 0.8240 (t0) REVERT: C 35 GLU cc_start: 0.8263 (tp30) cc_final: 0.7733 (tp30) REVERT: C 44 LYS cc_start: 0.7815 (tttt) cc_final: 0.7398 (ttmt) REVERT: C 84 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8311 (mm110) REVERT: C 146 ASP cc_start: 0.7281 (t0) cc_final: 0.7019 (t0) REVERT: C 228 GLU cc_start: 0.7689 (tp30) cc_final: 0.7463 (tp30) REVERT: C 264 MET cc_start: 0.8989 (mmm) cc_final: 0.8672 (mtp) REVERT: C 451 TYR cc_start: 0.8659 (t80) cc_final: 0.8332 (t80) REVERT: C 452 ASP cc_start: 0.8645 (m-30) cc_final: 0.8340 (m-30) REVERT: C 456 PHE cc_start: 0.8049 (t80) cc_final: 0.7518 (t80) REVERT: D 35 GLU cc_start: 0.8173 (tp30) cc_final: 0.7129 (tm-30) REVERT: D 228 GLU cc_start: 0.7907 (tp30) cc_final: 0.7647 (mm-30) REVERT: D 264 MET cc_start: 0.8863 (mmm) cc_final: 0.8547 (mtp) REVERT: D 272 MET cc_start: 0.8880 (ttp) cc_final: 0.8514 (tmm) REVERT: D 388 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 456 PHE cc_start: 0.8226 (t80) cc_final: 0.7611 (t80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0903 time to fit residues: 29.7891 Evaluate side-chains 173 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.084116 restraints weight = 28986.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086977 restraints weight = 16751.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089040 restraints weight = 11279.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090479 restraints weight = 8439.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091517 restraints weight = 6831.951| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13537 Z= 0.173 Angle : 0.674 10.941 18440 Z= 0.336 Chirality : 0.046 0.162 2068 Planarity : 0.006 0.058 2440 Dihedral : 5.135 84.799 2008 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1824 helix: 0.44 (0.19), residues: 736 sheet: -0.09 (0.37), residues: 224 loop : -1.05 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 256 TYR 0.015 0.001 TYR D 36 PHE 0.024 0.002 PHE D 316 TRP 0.011 0.001 TRP A 143 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (13536) covalent geometry : angle 0.67359 / 0.34 (18440) hydrogen bonds : bond 0.03702 / 2.53 ( 539) hydrogen bonds : angle 4.97929 / 3.58 ( 1473) Misc. bond : bond 0.00121 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.05 seconds wall clock time: 29 minutes 29.22 seconds (1769.22 seconds total)