Starting phenix.real_space_refine on Thu Sep 18 04:26:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxt_43639/09_2025/8vxt_43639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxt_43639/09_2025/8vxt_43639.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/8vxt_43639/09_2025/8vxt_43639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxt_43639/09_2025/8vxt_43639.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxt_43639/09_2025/8vxt_43639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxt_43639/09_2025/8vxt_43639.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= 0.002 sd= 0.031 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 18 5.49 5 S 96 5.16 5 C 8664 2.51 5 N 2424 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13896 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2285 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.30, per 1000 atoms: 0.17 Number of scatterers: 13896 At special positions: 0 Unit cell: (124.2, 117.72, 125.28, 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 96 16.00 P 18 15.00 O 2694 8.00 N 2424 7.00 C 8664 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=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 580.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 6 sheets defined 64.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE A 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 113 removed outlier: 3.956A pdb=" N LEU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.582A pdb=" N GLU A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 205 through 226 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE B 93 " --> pdb=" O TRP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU B 118 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 184 removed outlier: 4.356A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 205 through 226 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 261 through 274 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'C' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE C 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.956A pdb=" N LEU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU C 118 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 205 through 226 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE D 93 " --> pdb=" O TRP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.584A pdb=" N GLU D 118 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.798A pdb=" N GLY D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 205 through 226 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'E' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE E 93 " --> pdb=" O TRP E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU E 118 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 205 through 226 Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU E 320 " --> pdb=" O ASN E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'F' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS F 79 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE F 93 " --> pdb=" O TRP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.582A pdb=" N GLU F 118 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.798A pdb=" N GLY F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 168 through 184 removed outlier: 4.356A pdb=" N LYS F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 205 through 226 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 261 through 274 Processing helix chain 'F' and resid 284 through 291 Processing helix chain 'F' and resid 295 through 320 removed outlier: 4.177A pdb=" N GLU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 190 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER A 187 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET A 234 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 189 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 236 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 191 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 237 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 130 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE B 190 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 187 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET B 234 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 189 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA B 236 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 191 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 237 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 130 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE C 190 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 187 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET C 234 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 189 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA C 236 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 191 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 237 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 130 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE D 190 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER D 187 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET D 234 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE D 189 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA D 236 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 191 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 237 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 130 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE E 190 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 191 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 237 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 130 " --> pdb=" O PHE E 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE F 190 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER F 187 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET F 234 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE F 189 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA F 236 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 191 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 237 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU F 130 " --> pdb=" O PHE F 255 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2052 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: 2.02 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4806 1.37 - 1.52: 3716 1.52 - 1.66: 5464 1.66 - 1.80: 101 1.80 - 1.95: 55 Bond restraints: 14142 Sorted by residual: bond pdb=" CZ ARG E 304 " pdb=" NH2 ARG E 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.87e+00 bond pdb=" CZ ARG F 304 " pdb=" NH2 ARG F 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.84e+00 bond pdb=" CZ ARG C 304 " pdb=" NH2 ARG C 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.83e+00 bond pdb=" CZ ARG A 304 " pdb=" NH2 ARG A 304 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.30e-02 5.92e+03 1.80e+00 bond pdb=" CZ ARG D 304 " pdb=" NH2 ARG D 304 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.30e-02 5.92e+03 1.73e+00 ... (remaining 14137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 18836 2.24 - 4.48: 262 4.48 - 6.72: 30 6.72 - 8.96: 12 8.96 - 11.20: 6 Bond angle restraints: 19146 Sorted by residual: angle pdb=" C3' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" C5' AGS D 401 " ideal model delta sigma weight residual 115.29 126.49 -11.20 1.82e+00 3.02e-01 3.79e+01 angle pdb=" C3' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" C5' AGS B 401 " ideal model delta sigma weight residual 115.29 126.48 -11.19 1.82e+00 3.02e-01 3.78e+01 angle pdb=" C3' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" C5' AGS F 401 " ideal model delta sigma weight residual 115.29 126.46 -11.17 1.82e+00 3.02e-01 3.77e+01 angle pdb=" C3' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" C5' AGS E 401 " ideal model delta sigma weight residual 115.29 126.45 -11.16 1.82e+00 3.02e-01 3.76e+01 angle pdb=" C3' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" C5' AGS C 401 " ideal model delta sigma weight residual 115.29 126.45 -11.16 1.82e+00 3.02e-01 3.76e+01 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 7752 15.59 - 31.17: 816 31.17 - 46.76: 138 46.76 - 62.35: 42 62.35 - 77.94: 36 Dihedral angle restraints: 8784 sinusoidal: 3678 harmonic: 5106 Sorted by residual: dihedral pdb=" CA ARG E 121 " pdb=" C ARG E 121 " pdb=" N LEU E 122 " pdb=" CA LEU E 122 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG A 121 " pdb=" C ARG A 121 " pdb=" N LEU A 122 " pdb=" CA LEU A 122 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N LEU B 122 " pdb=" CA LEU B 122 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 8781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2184 0.246 - 0.492: 0 0.492 - 0.739: 0 0.739 - 0.985: 0 0.985 - 1.231: 6 Chirality restraints: 2190 Sorted by residual: chirality pdb=" C4' AGS B 401 " pdb=" C3' AGS B 401 " pdb=" C5' AGS B 401 " pdb=" O4' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" C4' AGS A 401 " pdb=" C3' AGS A 401 " pdb=" C5' AGS A 401 " pdb=" O4' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" C4' AGS E 401 " pdb=" C3' AGS E 401 " pdb=" C5' AGS E 401 " pdb=" O4' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.78e+01 ... (remaining 2187 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 239 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO E 240 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 239 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 240 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 239 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 240 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2358 2.76 - 3.29: 15121 3.29 - 3.83: 22334 3.83 - 4.36: 26719 4.36 - 4.90: 42491 Nonbonded interactions: 109023 Sorted by model distance: nonbonded pdb=" NZ LYS A 139 " pdb=" O1B AGS A 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS C 139 " pdb=" O1B AGS C 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS D 139 " pdb=" O1B AGS D 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS B 139 " pdb=" O1B AGS B 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS F 139 " pdb=" O1B AGS F 401 " model vdw 2.224 3.120 ... (remaining 109018 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 11.910 Find NCS groups from input model: 0.120 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14142 Z= 0.156 Angle : 0.708 11.204 19146 Z= 0.412 Chirality : 0.076 1.231 2190 Planarity : 0.005 0.060 2448 Dihedral : 14.079 77.936 5436 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.21), residues: 1728 helix: 0.74 (0.17), residues: 888 sheet: 0.37 (0.38), residues: 198 loop : 0.10 (0.28), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 304 TYR 0.009 0.002 TYR C 314 PHE 0.009 0.001 PHE D 178 TRP 0.019 0.003 TRP D 166 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00303 (14142) covalent geometry : angle 0.70848 (19146) hydrogen bonds : bond 0.14727 ( 738) hydrogen bonds : angle 5.66385 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 0.563 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: 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: 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: A 82 ASP cc_start: 0.7802 (t70) cc_final: 0.7391 (t0) REVERT: A 85 ASN cc_start: 0.8106 (p0) cc_final: 0.7693 (p0) REVERT: A 90 TRP cc_start: 0.7886 (m100) cc_final: 0.7576 (m100) REVERT: A 109 LEU cc_start: 0.8672 (mt) cc_final: 0.8257 (mt) REVERT: A 114 LYS cc_start: 0.8106 (tptm) cc_final: 0.7888 (tptm) REVERT: A 117 PHE cc_start: 0.7726 (m-10) cc_final: 0.7456 (m-10) REVERT: A 118 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6747 (mt-10) REVERT: A 125 PRO cc_start: 0.8015 (Cg_endo) cc_final: 0.7726 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8226 (tttt) cc_final: 0.7642 (ttmt) REVERT: A 154 PHE cc_start: 0.7644 (t80) cc_final: 0.6906 (t80) REVERT: A 157 LEU cc_start: 0.7960 (tp) cc_final: 0.7548 (tp) REVERT: A 158 GLN cc_start: 0.6839 (pm20) cc_final: 0.6182 (pm20) REVERT: A 193 GLU cc_start: 0.7632 (tt0) cc_final: 0.7330 (tt0) REVERT: A 206 HIS cc_start: 0.8184 (p90) cc_final: 0.7605 (p90) REVERT: A 211 MET cc_start: 0.8133 (mmp) cc_final: 0.7338 (mmt) REVERT: A 212 MET cc_start: 0.7964 (mmp) cc_final: 0.7751 (mmp) REVERT: A 213 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7817 (mtmt) REVERT: A 215 GLN cc_start: 0.7579 (tp-100) cc_final: 0.6871 (tp-100) REVERT: A 217 MET cc_start: 0.8014 (mpp) cc_final: 0.7646 (mpp) REVERT: A 232 ILE cc_start: 0.8142 (mt) cc_final: 0.7734 (pt) REVERT: A 240 PRO cc_start: 0.7974 (Cg_endo) cc_final: 0.7642 (Cg_exo) REVERT: A 248 MET cc_start: 0.7476 (mtp) cc_final: 0.7260 (mtp) REVERT: A 286 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 341 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 342 LYS cc_start: 0.8672 (mptt) cc_final: 0.8138 (mptt) REVERT: A 347 LYS cc_start: 0.9119 (mptt) cc_final: 0.8533 (mptt) REVERT: B 74 MET cc_start: 0.8169 (mtm) cc_final: 0.7440 (mtm) REVERT: B 82 ASP cc_start: 0.7935 (t70) cc_final: 0.7707 (t0) REVERT: B 85 ASN cc_start: 0.8217 (p0) cc_final: 0.7951 (p0) REVERT: B 86 MET cc_start: 0.8042 (mtp) cc_final: 0.7747 (mtp) REVERT: B 102 ASP cc_start: 0.8110 (m-30) cc_final: 0.7781 (m-30) REVERT: B 109 LEU cc_start: 0.8629 (mt) cc_final: 0.8215 (mt) REVERT: B 113 LYS cc_start: 0.8017 (tppp) cc_final: 0.7734 (mmmm) REVERT: B 117 PHE cc_start: 0.7587 (m-10) cc_final: 0.7331 (m-10) REVERT: B 148 LYS cc_start: 0.8374 (tttt) cc_final: 0.7877 (ttmt) REVERT: B 149 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 154 PHE cc_start: 0.7653 (t80) cc_final: 0.7188 (t80) REVERT: B 157 LEU cc_start: 0.7835 (tp) cc_final: 0.7396 (tp) REVERT: B 158 GLN cc_start: 0.6820 (pm20) cc_final: 0.6232 (pm20) REVERT: B 193 GLU cc_start: 0.7532 (tt0) cc_final: 0.7193 (tt0) REVERT: B 211 MET cc_start: 0.8081 (mmp) cc_final: 0.7608 (mmp) REVERT: B 212 MET cc_start: 0.7959 (mmp) cc_final: 0.7736 (mmp) REVERT: B 213 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7665 (mtmt) REVERT: B 215 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6744 (tp-100) REVERT: B 232 ILE cc_start: 0.8129 (mt) cc_final: 0.7846 (mt) REVERT: B 240 PRO cc_start: 0.8343 (Cg_endo) cc_final: 0.7501 (Cg_exo) REVERT: B 243 LEU cc_start: 0.8406 (mt) cc_final: 0.8161 (mt) REVERT: B 259 GLN cc_start: 0.7585 (mt0) cc_final: 0.7204 (mt0) REVERT: B 273 LEU cc_start: 0.8114 (mm) cc_final: 0.7893 (mm) REVERT: B 286 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6929 (mm-30) REVERT: B 299 LEU cc_start: 0.8657 (mt) cc_final: 0.8418 (mt) REVERT: B 331 VAL cc_start: 0.7609 (t) cc_final: 0.7368 (t) REVERT: B 341 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 342 LYS cc_start: 0.8703 (mptt) cc_final: 0.7956 (mptt) REVERT: B 343 MET cc_start: 0.8260 (tpt) cc_final: 0.8045 (tpt) REVERT: C 74 MET cc_start: 0.5899 (mtm) cc_final: 0.5253 (mtm) REVERT: C 132 TYR cc_start: 0.6485 (p90) cc_final: 0.6251 (p90) REVERT: C 211 MET cc_start: 0.6721 (mmp) cc_final: 0.6433 (mmp) REVERT: C 212 MET cc_start: 0.6911 (mmp) cc_final: 0.6357 (mmp) REVERT: C 239 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7052 (mtt90) REVERT: C 248 MET cc_start: 0.7551 (mtp) cc_final: 0.7013 (mtp) REVERT: C 298 ASP cc_start: 0.7728 (m-30) cc_final: 0.7337 (m-30) REVERT: C 299 LEU cc_start: 0.8550 (mt) cc_final: 0.8335 (mt) REVERT: C 301 GLU cc_start: 0.8333 (tt0) cc_final: 0.8051 (tt0) REVERT: C 304 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7862 (mmm-85) REVERT: C 336 LEU cc_start: 0.8585 (mp) cc_final: 0.8299 (mp) REVERT: C 343 MET cc_start: 0.8441 (tpt) cc_final: 0.8112 (tpt) REVERT: C 344 LYS cc_start: 0.8784 (mttm) cc_final: 0.8524 (mttm) REVERT: D 74 MET cc_start: 0.7528 (mtm) cc_final: 0.7220 (mtm) REVERT: D 89 THR cc_start: 0.7547 (p) cc_final: 0.7221 (p) REVERT: D 96 LEU cc_start: 0.7683 (mt) cc_final: 0.7437 (mt) REVERT: D 104 LYS cc_start: 0.8262 (tttt) cc_final: 0.8037 (ttmt) REVERT: D 139 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7588 (mtmm) REVERT: D 149 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6708 (mm-30) REVERT: D 199 ARG cc_start: 0.6102 (tpp80) cc_final: 0.5023 (tpp80) REVERT: D 212 MET cc_start: 0.7788 (mmp) cc_final: 0.7422 (mmp) REVERT: D 248 MET cc_start: 0.7198 (mtp) cc_final: 0.6751 (mtp) REVERT: D 250 ARG cc_start: 0.6713 (mtt-85) cc_final: 0.6491 (tpp-160) REVERT: D 294 PHE cc_start: 0.6810 (m-10) cc_final: 0.5728 (m-10) REVERT: D 300 LYS cc_start: 0.8288 (tptm) cc_final: 0.7724 (tptm) REVERT: D 302 MET cc_start: 0.7281 (tmm) cc_final: 0.6973 (tmm) REVERT: D 337 HIS cc_start: 0.7511 (m170) cc_final: 0.7277 (m90) REVERT: E 191 ILE cc_start: 0.6401 (mt) cc_final: 0.6177 (mt) REVERT: E 211 MET cc_start: 0.6846 (mmp) cc_final: 0.6458 (mmp) REVERT: E 212 MET cc_start: 0.7083 (mmp) cc_final: 0.6218 (mmp) REVERT: E 213 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7492 (mtmt) REVERT: E 248 MET cc_start: 0.7603 (mtp) cc_final: 0.7059 (mtp) REVERT: E 285 LEU cc_start: 0.8558 (mt) cc_final: 0.8317 (mt) REVERT: E 290 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 298 ASP cc_start: 0.7631 (m-30) cc_final: 0.7283 (m-30) REVERT: E 336 LEU cc_start: 0.8581 (mp) cc_final: 0.8343 (mp) REVERT: E 340 ILE cc_start: 0.8528 (mt) cc_final: 0.8033 (mt) REVERT: E 341 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7951 (mm-30) REVERT: E 343 MET cc_start: 0.8479 (tpt) cc_final: 0.8172 (tpt) REVERT: F 74 MET cc_start: 0.7680 (mtm) cc_final: 0.7390 (mtm) REVERT: F 82 ASP cc_start: 0.6771 (t70) cc_final: 0.6230 (t0) REVERT: F 85 ASN cc_start: 0.8163 (p0) cc_final: 0.7646 (p0) REVERT: F 104 LYS cc_start: 0.8311 (tttt) cc_final: 0.8079 (ttmm) REVERT: F 139 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7611 (mtmm) REVERT: F 149 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6827 (mm-30) REVERT: F 199 ARG cc_start: 0.6181 (tpp80) cc_final: 0.4963 (tpp80) REVERT: F 211 MET cc_start: 0.7309 (mmp) cc_final: 0.6775 (mmp) REVERT: F 212 MET cc_start: 0.8011 (mmp) cc_final: 0.7572 (mmp) REVERT: F 241 GLN cc_start: 0.7715 (mm110) cc_final: 0.7366 (mm-40) REVERT: F 248 MET cc_start: 0.7346 (mtp) cc_final: 0.6939 (mtp) REVERT: F 294 PHE cc_start: 0.6863 (m-10) cc_final: 0.5580 (m-10) REVERT: F 300 LYS cc_start: 0.8108 (tptm) cc_final: 0.7899 (tptm) REVERT: F 302 MET cc_start: 0.7292 (tmm) cc_final: 0.6952 (tmm) REVERT: F 337 HIS cc_start: 0.7500 (m170) cc_final: 0.7294 (m90) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.1223 time to fit residues: 100.7916 Evaluate side-chains 552 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 264 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 230 GLN F 259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133049 restraints weight = 30102.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137655 restraints weight = 18569.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140875 restraints weight = 12809.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143109 restraints weight = 9467.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144907 restraints weight = 7433.977| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14142 Z= 0.163 Angle : 0.678 9.322 19146 Z= 0.355 Chirality : 0.045 0.150 2190 Planarity : 0.005 0.052 2448 Dihedral : 11.081 97.205 1962 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.20), residues: 1728 helix: 0.92 (0.16), residues: 906 sheet: 0.76 (0.39), residues: 192 loop : 0.11 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 304 TYR 0.015 0.003 TYR C 132 PHE 0.030 0.002 PHE D 294 TRP 0.018 0.002 TRP D 220 HIS 0.013 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00339 (14142) covalent geometry : angle 0.67779 (19146) hydrogen bonds : bond 0.05207 ( 738) hydrogen bonds : angle 4.69374 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 560 time to evaluate : 0.488 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8136 (mtm) cc_final: 0.7769 (mtm) REVERT: A 85 ASN cc_start: 0.8006 (p0) cc_final: 0.7739 (p0) REVERT: A 86 MET cc_start: 0.7667 (mtm) cc_final: 0.7290 (mtm) REVERT: A 90 TRP cc_start: 0.7927 (m100) cc_final: 0.7718 (m100) REVERT: A 101 THR cc_start: 0.8382 (p) cc_final: 0.8005 (t) REVERT: A 114 LYS cc_start: 0.7921 (tptm) cc_final: 0.7398 (tptm) REVERT: A 117 PHE cc_start: 0.7885 (m-10) cc_final: 0.7659 (m-10) REVERT: A 122 LEU cc_start: 0.7570 (pt) cc_final: 0.7091 (tt) REVERT: A 125 PRO cc_start: 0.8156 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7558 (mtmm) REVERT: A 141 LEU cc_start: 0.8427 (tp) cc_final: 0.8187 (tp) REVERT: A 146 THR cc_start: 0.8220 (p) cc_final: 0.7938 (p) REVERT: A 148 LYS cc_start: 0.8240 (tttt) cc_final: 0.7783 (ttmt) REVERT: A 154 PHE cc_start: 0.7692 (t80) cc_final: 0.7059 (t80) REVERT: A 157 LEU cc_start: 0.8034 (tp) cc_final: 0.7693 (tp) REVERT: A 193 GLU cc_start: 0.7657 (tt0) cc_final: 0.7423 (tt0) REVERT: A 199 ARG cc_start: 0.7193 (tpp80) cc_final: 0.6464 (tpp80) REVERT: A 206 HIS cc_start: 0.7988 (p90) cc_final: 0.7347 (p90) REVERT: A 211 MET cc_start: 0.8036 (mmp) cc_final: 0.7336 (mmt) REVERT: A 212 MET cc_start: 0.7898 (mmp) cc_final: 0.7590 (mmp) REVERT: A 213 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7645 (mtmt) REVERT: A 215 GLN cc_start: 0.7583 (tp-100) cc_final: 0.6343 (tp-100) REVERT: A 217 MET cc_start: 0.8032 (mpp) cc_final: 0.7555 (mpp) REVERT: A 219 LEU cc_start: 0.8668 (mt) cc_final: 0.7544 (mt) REVERT: A 232 ILE cc_start: 0.8309 (mt) cc_final: 0.8021 (mt) REVERT: A 237 THR cc_start: 0.7840 (t) cc_final: 0.7110 (m) REVERT: A 259 GLN cc_start: 0.7345 (mt0) cc_final: 0.6943 (mt0) REVERT: A 273 LEU cc_start: 0.8161 (mm) cc_final: 0.7942 (mm) REVERT: A 305 ASP cc_start: 0.8205 (t0) cc_final: 0.7916 (m-30) REVERT: A 341 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 342 LYS cc_start: 0.8593 (mptt) cc_final: 0.8080 (mptt) REVERT: A 343 MET cc_start: 0.8197 (tpt) cc_final: 0.7929 (tpt) REVERT: B 74 MET cc_start: 0.8008 (mtm) cc_final: 0.7309 (mtm) REVERT: B 85 ASN cc_start: 0.8035 (p0) cc_final: 0.7803 (p0) REVERT: B 86 MET cc_start: 0.7772 (mtp) cc_final: 0.7563 (mtp) REVERT: B 117 PHE cc_start: 0.7681 (m-10) cc_final: 0.7382 (m-10) REVERT: B 148 LYS cc_start: 0.8428 (tttt) cc_final: 0.7782 (ttmt) REVERT: B 149 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 157 LEU cc_start: 0.8065 (tp) cc_final: 0.7657 (tp) REVERT: B 158 GLN cc_start: 0.6978 (pm20) cc_final: 0.6211 (pm20) REVERT: B 193 GLU cc_start: 0.7559 (tt0) cc_final: 0.7223 (tt0) REVERT: B 211 MET cc_start: 0.8007 (mmp) cc_final: 0.7610 (mmp) REVERT: B 212 MET cc_start: 0.7950 (mmp) cc_final: 0.7678 (mmp) REVERT: B 213 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7585 (mtmt) REVERT: B 215 GLN cc_start: 0.7505 (tp-100) cc_final: 0.6620 (tp-100) REVERT: B 217 MET cc_start: 0.8071 (mpp) cc_final: 0.7259 (mpp) REVERT: B 221 ASP cc_start: 0.7092 (m-30) cc_final: 0.6858 (m-30) REVERT: B 231 VAL cc_start: 0.7875 (t) cc_final: 0.7589 (p) REVERT: B 232 ILE cc_start: 0.8303 (mt) cc_final: 0.8044 (mt) REVERT: B 243 LEU cc_start: 0.8425 (mt) cc_final: 0.8155 (mt) REVERT: B 259 GLN cc_start: 0.7581 (mt0) cc_final: 0.7229 (mt0) REVERT: B 266 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6923 (tm-30) REVERT: B 270 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7742 (mmtm) REVERT: B 273 LEU cc_start: 0.8167 (mm) cc_final: 0.7945 (mm) REVERT: B 286 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 295 SER cc_start: 0.6817 (p) cc_final: 0.6493 (p) REVERT: B 299 LEU cc_start: 0.8641 (mt) cc_final: 0.8301 (mt) REVERT: B 311 VAL cc_start: 0.8191 (t) cc_final: 0.7981 (t) REVERT: B 338 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8226 (mtp85) REVERT: B 341 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 342 LYS cc_start: 0.8493 (mptt) cc_final: 0.7671 (mptt) REVERT: B 345 LYS cc_start: 0.8762 (pptt) cc_final: 0.8454 (pptt) REVERT: C 74 MET cc_start: 0.5658 (mtm) cc_final: 0.5185 (mtm) REVERT: C 184 LEU cc_start: 0.6177 (mm) cc_final: 0.5777 (mt) REVERT: C 190 PHE cc_start: 0.6471 (t80) cc_final: 0.6194 (t80) REVERT: C 199 ARG cc_start: 0.6028 (tpp80) cc_final: 0.5780 (tpp80) REVERT: C 211 MET cc_start: 0.7164 (mmp) cc_final: 0.6917 (mmp) REVERT: C 212 MET cc_start: 0.7579 (mmp) cc_final: 0.6756 (mmp) REVERT: C 239 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7254 (mtt90) REVERT: C 248 MET cc_start: 0.7579 (mtp) cc_final: 0.7005 (mtp) REVERT: C 251 MET cc_start: 0.6382 (mmt) cc_final: 0.5817 (mmt) REVERT: C 264 GLN cc_start: 0.8276 (mp10) cc_final: 0.8073 (mp10) REVERT: C 289 GLN cc_start: 0.8312 (mt0) cc_final: 0.8081 (mt0) REVERT: C 299 LEU cc_start: 0.8576 (mt) cc_final: 0.8371 (mt) REVERT: C 308 LEU cc_start: 0.8600 (tp) cc_final: 0.8390 (tp) REVERT: C 335 ASP cc_start: 0.7879 (m-30) cc_final: 0.7615 (m-30) REVERT: C 336 LEU cc_start: 0.8655 (mp) cc_final: 0.8394 (mp) REVERT: C 343 MET cc_start: 0.8288 (tpt) cc_final: 0.7446 (tpt) REVERT: C 344 LYS cc_start: 0.8954 (mttm) cc_final: 0.8598 (mttm) REVERT: C 347 LYS cc_start: 0.8146 (mptt) cc_final: 0.7883 (mptt) REVERT: D 82 ASP cc_start: 0.7660 (t0) cc_final: 0.7038 (t70) REVERT: D 89 THR cc_start: 0.7694 (p) cc_final: 0.7488 (p) REVERT: D 90 TRP cc_start: 0.7851 (m100) cc_final: 0.6964 (m100) REVERT: D 104 LYS cc_start: 0.8293 (tttt) cc_final: 0.7996 (tttm) REVERT: D 132 TYR cc_start: 0.7283 (p90) cc_final: 0.7019 (p90) REVERT: D 139 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7195 (mtmm) REVERT: D 149 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6254 (mm-30) REVERT: D 173 LEU cc_start: 0.8261 (tp) cc_final: 0.8046 (tp) REVERT: D 196 SER cc_start: 0.7168 (t) cc_final: 0.6872 (p) REVERT: D 212 MET cc_start: 0.7853 (mmp) cc_final: 0.6999 (mmp) REVERT: D 217 MET cc_start: 0.6959 (mmp) cc_final: 0.6526 (mmt) REVERT: D 237 THR cc_start: 0.7143 (t) cc_final: 0.6515 (m) REVERT: D 241 GLN cc_start: 0.8209 (mp-120) cc_final: 0.7329 (mm110) REVERT: D 248 MET cc_start: 0.7003 (mtp) cc_final: 0.6570 (mtp) REVERT: D 300 LYS cc_start: 0.8436 (tptm) cc_final: 0.8106 (tptm) REVERT: D 305 ASP cc_start: 0.7456 (t0) cc_final: 0.7097 (t0) REVERT: D 337 HIS cc_start: 0.7603 (m170) cc_final: 0.7311 (m90) REVERT: E 155 ILE cc_start: 0.7213 (pt) cc_final: 0.6404 (tp) REVERT: E 171 GLN cc_start: 0.8541 (mm110) cc_final: 0.8151 (mm-40) REVERT: E 205 ASP cc_start: 0.4623 (m-30) cc_final: 0.4340 (m-30) REVERT: E 212 MET cc_start: 0.7633 (mmp) cc_final: 0.6756 (mmp) REVERT: E 248 MET cc_start: 0.7682 (mtp) cc_final: 0.7161 (mtp) REVERT: E 251 MET cc_start: 0.5703 (mmt) cc_final: 0.5332 (mmt) REVERT: E 265 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7595 (mtt180) REVERT: E 286 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7575 (mm-30) REVERT: E 290 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7670 (mm-30) REVERT: E 298 ASP cc_start: 0.7697 (m-30) cc_final: 0.7339 (m-30) REVERT: E 304 ARG cc_start: 0.8623 (mtp180) cc_final: 0.8247 (mtp-110) REVERT: E 336 LEU cc_start: 0.8620 (mp) cc_final: 0.8405 (mp) REVERT: E 341 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7786 (mm-30) REVERT: E 343 MET cc_start: 0.8449 (tpt) cc_final: 0.7477 (tpt) REVERT: E 347 LYS cc_start: 0.8202 (mptt) cc_final: 0.7981 (mmtt) REVERT: F 74 MET cc_start: 0.7409 (mtm) cc_final: 0.7073 (mtm) REVERT: F 87 HIS cc_start: 0.7586 (m-70) cc_final: 0.6918 (m-70) REVERT: F 102 ASP cc_start: 0.7968 (m-30) cc_final: 0.7665 (m-30) REVERT: F 104 LYS cc_start: 0.8323 (tttt) cc_final: 0.8007 (tttm) REVERT: F 115 HIS cc_start: 0.5848 (OUTLIER) cc_final: 0.5513 (p90) REVERT: F 139 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7352 (mtmm) REVERT: F 183 LYS cc_start: 0.8569 (mptt) cc_final: 0.8307 (mptt) REVERT: F 199 ARG cc_start: 0.6049 (tpp80) cc_final: 0.4885 (tpp80) REVERT: F 211 MET cc_start: 0.7248 (mmp) cc_final: 0.6904 (mmp) REVERT: F 212 MET cc_start: 0.7961 (mmp) cc_final: 0.7551 (mmp) REVERT: F 215 GLN cc_start: 0.6972 (tp-100) cc_final: 0.6722 (tp-100) REVERT: F 219 LEU cc_start: 0.7579 (mt) cc_final: 0.6808 (mt) REVERT: F 237 THR cc_start: 0.7062 (t) cc_final: 0.6400 (m) REVERT: F 241 GLN cc_start: 0.7994 (mm110) cc_final: 0.7536 (mm-40) REVERT: F 248 MET cc_start: 0.7111 (mtp) cc_final: 0.6631 (mtp) REVERT: F 270 LYS cc_start: 0.8281 (pttp) cc_final: 0.7858 (ptmm) REVERT: F 300 LYS cc_start: 0.8239 (tptm) cc_final: 0.7932 (tptm) REVERT: F 302 MET cc_start: 0.7653 (tmm) cc_final: 0.7321 (tmm) REVERT: F 337 HIS cc_start: 0.7696 (m170) cc_final: 0.7381 (m170) outliers start: 2 outliers final: 0 residues processed: 561 average time/residue: 0.1180 time to fit residues: 92.2885 Evaluate side-chains 554 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 171 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS F 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.159963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132629 restraints weight = 30106.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137242 restraints weight = 18746.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140512 restraints weight = 12943.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142803 restraints weight = 9590.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144567 restraints weight = 7537.708| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14142 Z= 0.148 Angle : 0.615 10.286 19146 Z= 0.324 Chirality : 0.045 0.290 2190 Planarity : 0.004 0.072 2448 Dihedral : 10.876 100.784 1962 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.13 % Allowed : 2.35 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.21), residues: 1728 helix: 1.03 (0.16), residues: 972 sheet: 1.01 (0.40), residues: 192 loop : 0.35 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 199 TYR 0.014 0.002 TYR C 132 PHE 0.029 0.002 PHE D 294 TRP 0.028 0.002 TRP D 220 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00314 (14142) covalent geometry : angle 0.61505 (19146) hydrogen bonds : bond 0.04539 ( 738) hydrogen bonds : angle 4.41715 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 563 time to evaluate : 0.506 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: 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: 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: symmetry clash REVERT: A 74 MET cc_start: 0.8131 (mtm) cc_final: 0.7747 (mtm) REVERT: A 85 ASN cc_start: 0.7917 (p0) cc_final: 0.7658 (p0) REVERT: A 96 LEU cc_start: 0.7482 (mt) cc_final: 0.7186 (mt) REVERT: A 101 THR cc_start: 0.8351 (p) cc_final: 0.7977 (t) REVERT: A 114 LYS cc_start: 0.7856 (tptm) cc_final: 0.7285 (tptm) REVERT: A 125 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7881 (Cg_exo) REVERT: A 141 LEU cc_start: 0.8382 (tp) cc_final: 0.8176 (tp) REVERT: A 148 LYS cc_start: 0.8343 (tttt) cc_final: 0.7900 (ttmt) REVERT: A 154 PHE cc_start: 0.7740 (t80) cc_final: 0.7164 (t80) REVERT: A 157 LEU cc_start: 0.8068 (tp) cc_final: 0.7759 (tp) REVERT: A 199 ARG cc_start: 0.7248 (tpp80) cc_final: 0.6426 (tpp80) REVERT: A 206 HIS cc_start: 0.7985 (p90) cc_final: 0.7248 (p90) REVERT: A 211 MET cc_start: 0.7961 (mmp) cc_final: 0.7397 (mmp) REVERT: A 212 MET cc_start: 0.7798 (mmp) cc_final: 0.7516 (mmp) REVERT: A 213 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7777 (mtmt) REVERT: A 217 MET cc_start: 0.8017 (mpp) cc_final: 0.7582 (mpp) REVERT: A 219 LEU cc_start: 0.8689 (mt) cc_final: 0.8332 (mt) REVERT: A 251 MET cc_start: 0.7749 (mmm) cc_final: 0.7087 (mmm) REVERT: A 259 GLN cc_start: 0.7438 (mt0) cc_final: 0.7065 (mt0) REVERT: A 305 ASP cc_start: 0.8236 (t0) cc_final: 0.7951 (m-30) REVERT: A 341 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 342 LYS cc_start: 0.8658 (mptt) cc_final: 0.8193 (mptt) REVERT: B 74 MET cc_start: 0.7950 (mtm) cc_final: 0.7231 (mtm) REVERT: B 82 ASP cc_start: 0.7890 (t70) cc_final: 0.7599 (t70) REVERT: B 85 ASN cc_start: 0.8036 (p0) cc_final: 0.7813 (p0) REVERT: B 90 TRP cc_start: 0.8080 (m100) cc_final: 0.7777 (m100) REVERT: B 146 THR cc_start: 0.8273 (p) cc_final: 0.7726 (p) REVERT: B 148 LYS cc_start: 0.8507 (tttt) cc_final: 0.7922 (ttmt) REVERT: B 157 LEU cc_start: 0.8122 (tp) cc_final: 0.7893 (tp) REVERT: B 199 ARG cc_start: 0.7429 (tpp80) cc_final: 0.6514 (tpp80) REVERT: B 211 MET cc_start: 0.7923 (mmp) cc_final: 0.7540 (mmp) REVERT: B 213 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7601 (mtmt) REVERT: B 215 GLN cc_start: 0.7423 (tp-100) cc_final: 0.6514 (tp-100) REVERT: B 217 MET cc_start: 0.8072 (mpp) cc_final: 0.7671 (mpp) REVERT: B 243 LEU cc_start: 0.8326 (mt) cc_final: 0.8071 (mt) REVERT: B 259 GLN cc_start: 0.7660 (mt0) cc_final: 0.7262 (mt0) REVERT: B 266 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 270 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7858 (mmtm) REVERT: B 273 LEU cc_start: 0.8128 (mm) cc_final: 0.7922 (mm) REVERT: B 286 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 295 SER cc_start: 0.6991 (p) cc_final: 0.6674 (p) REVERT: B 299 LEU cc_start: 0.8693 (mt) cc_final: 0.8261 (mt) REVERT: B 305 ASP cc_start: 0.8038 (t0) cc_final: 0.7774 (m-30) REVERT: B 342 LYS cc_start: 0.8513 (mptt) cc_final: 0.7645 (mptt) REVERT: B 343 MET cc_start: 0.8116 (tpt) cc_final: 0.6517 (tpt) REVERT: B 345 LYS cc_start: 0.8760 (pptt) cc_final: 0.8406 (pptt) REVERT: B 346 SER cc_start: 0.8572 (p) cc_final: 0.8349 (p) REVERT: B 347 LYS cc_start: 0.8855 (mptt) cc_final: 0.8334 (mptt) REVERT: C 158 GLN cc_start: 0.8373 (pm20) cc_final: 0.8062 (pm20) REVERT: C 171 GLN cc_start: 0.8328 (mm110) cc_final: 0.7903 (mm-40) REVERT: C 212 MET cc_start: 0.7527 (mmp) cc_final: 0.6907 (mmp) REVERT: C 239 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7104 (mtt90) REVERT: C 248 MET cc_start: 0.7685 (mtp) cc_final: 0.7117 (mtp) REVERT: C 251 MET cc_start: 0.6412 (mmt) cc_final: 0.5810 (mmt) REVERT: C 264 GLN cc_start: 0.8263 (mp10) cc_final: 0.8037 (mp10) REVERT: C 289 GLN cc_start: 0.8228 (mt0) cc_final: 0.7890 (mt0) REVERT: C 295 SER cc_start: 0.8019 (p) cc_final: 0.7761 (p) REVERT: C 299 LEU cc_start: 0.8609 (mt) cc_final: 0.8250 (mt) REVERT: C 302 MET cc_start: 0.7945 (tmm) cc_final: 0.7709 (tmm) REVERT: C 304 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8172 (mmm-85) REVERT: C 308 LEU cc_start: 0.8599 (tp) cc_final: 0.8338 (tp) REVERT: C 309 LEU cc_start: 0.8764 (tp) cc_final: 0.8421 (tp) REVERT: C 313 GLU cc_start: 0.8000 (pt0) cc_final: 0.7792 (pt0) REVERT: C 343 MET cc_start: 0.8227 (tpt) cc_final: 0.7357 (tpt) REVERT: C 344 LYS cc_start: 0.8957 (mttm) cc_final: 0.8622 (mttm) REVERT: D 82 ASP cc_start: 0.7913 (t0) cc_final: 0.7365 (t70) REVERT: D 89 THR cc_start: 0.7821 (p) cc_final: 0.7615 (p) REVERT: D 104 LYS cc_start: 0.8322 (tttt) cc_final: 0.7968 (tttm) REVERT: D 132 TYR cc_start: 0.7347 (p90) cc_final: 0.7071 (p90) REVERT: D 139 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7034 (mtmm) REVERT: D 183 LYS cc_start: 0.8573 (mptt) cc_final: 0.8215 (mptt) REVERT: D 196 SER cc_start: 0.7187 (t) cc_final: 0.6803 (p) REVERT: D 215 GLN cc_start: 0.7451 (pt0) cc_final: 0.7034 (pt0) REVERT: D 241 GLN cc_start: 0.8168 (mp-120) cc_final: 0.7250 (mm-40) REVERT: D 248 MET cc_start: 0.7041 (mtp) cc_final: 0.6527 (mtp) REVERT: D 259 GLN cc_start: 0.8319 (mp10) cc_final: 0.8086 (mp10) REVERT: D 300 LYS cc_start: 0.8498 (tptm) cc_final: 0.8126 (tptm) REVERT: D 302 MET cc_start: 0.7709 (tmm) cc_final: 0.7485 (tmm) REVERT: D 305 ASP cc_start: 0.7536 (t0) cc_final: 0.7161 (t0) REVERT: D 337 HIS cc_start: 0.7455 (m170) cc_final: 0.7243 (m90) REVERT: E 171 GLN cc_start: 0.8403 (mm110) cc_final: 0.7893 (mm-40) REVERT: E 193 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7054 (mt-10) REVERT: E 212 MET cc_start: 0.7524 (mmp) cc_final: 0.6573 (mmp) REVERT: E 248 MET cc_start: 0.7766 (mtp) cc_final: 0.7246 (mtp) REVERT: E 290 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7581 (mm-30) REVERT: E 298 ASP cc_start: 0.7613 (m-30) cc_final: 0.7271 (m-30) REVERT: E 299 LEU cc_start: 0.8680 (mt) cc_final: 0.8464 (mt) REVERT: E 300 LYS cc_start: 0.8680 (tttt) cc_final: 0.8478 (tttt) REVERT: E 304 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8199 (mtp-110) REVERT: E 340 ILE cc_start: 0.8447 (mt) cc_final: 0.8246 (mt) REVERT: E 341 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7709 (mm-30) REVERT: F 74 MET cc_start: 0.7408 (mtm) cc_final: 0.7103 (mtm) REVERT: F 82 ASP cc_start: 0.7929 (t0) cc_final: 0.7079 (t70) REVERT: F 85 ASN cc_start: 0.8323 (p0) cc_final: 0.7901 (p0) REVERT: F 102 ASP cc_start: 0.7921 (m-30) cc_final: 0.7602 (m-30) REVERT: F 104 LYS cc_start: 0.8355 (tttt) cc_final: 0.7997 (tttm) REVERT: F 139 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7255 (mtmm) REVERT: F 183 LYS cc_start: 0.8568 (mptt) cc_final: 0.8296 (mptt) REVERT: F 199 ARG cc_start: 0.6026 (tpp80) cc_final: 0.4894 (tpp80) REVERT: F 211 MET cc_start: 0.7247 (mmp) cc_final: 0.6974 (mmp) REVERT: F 212 MET cc_start: 0.7862 (mmp) cc_final: 0.7516 (mmp) REVERT: F 215 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6641 (tp-100) REVERT: F 217 MET cc_start: 0.7348 (mmt) cc_final: 0.6975 (mmt) REVERT: F 219 LEU cc_start: 0.7531 (mt) cc_final: 0.6777 (mt) REVERT: F 237 THR cc_start: 0.7069 (t) cc_final: 0.6398 (m) REVERT: F 241 GLN cc_start: 0.7912 (mm110) cc_final: 0.7504 (mm-40) REVERT: F 248 MET cc_start: 0.6904 (mtp) cc_final: 0.6352 (mtp) REVERT: F 263 LYS cc_start: 0.7119 (mtmm) cc_final: 0.6890 (mmmm) REVERT: F 270 LYS cc_start: 0.8333 (pttp) cc_final: 0.7890 (ptmm) REVERT: F 300 LYS cc_start: 0.8222 (tptm) cc_final: 0.7882 (tptm) REVERT: F 302 MET cc_start: 0.7624 (tmm) cc_final: 0.7252 (tmm) REVERT: F 337 HIS cc_start: 0.7688 (m170) cc_final: 0.7408 (m170) outliers start: 2 outliers final: 0 residues processed: 565 average time/residue: 0.1231 time to fit residues: 96.6243 Evaluate side-chains 539 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 241 GLN A 256 HIS A 275 ASN B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN F 256 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.118464 restraints weight = 30813.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123064 restraints weight = 18462.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126250 restraints weight = 12462.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128437 restraints weight = 9150.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130090 restraints weight = 7186.709| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14142 Z= 0.287 Angle : 0.787 10.309 19146 Z= 0.420 Chirality : 0.049 0.255 2190 Planarity : 0.006 0.061 2448 Dihedral : 11.574 107.671 1962 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1728 helix: 0.51 (0.16), residues: 942 sheet: 0.86 (0.40), residues: 186 loop : 0.20 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 304 TYR 0.020 0.003 TYR B 314 PHE 0.030 0.003 PHE C 216 TRP 0.028 0.003 TRP D 90 HIS 0.016 0.002 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00551 (14142) covalent geometry : angle 0.78735 (19146) hydrogen bonds : bond 0.05433 ( 738) hydrogen bonds : angle 5.08302 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 617 time to evaluate : 0.564 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: 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: 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: A 74 MET cc_start: 0.8239 (mtm) cc_final: 0.7825 (mtm) REVERT: A 101 THR cc_start: 0.8269 (p) cc_final: 0.7894 (p) REVERT: A 104 LYS cc_start: 0.8614 (tttt) cc_final: 0.8218 (tttt) REVERT: A 114 LYS cc_start: 0.8008 (tptm) cc_final: 0.7640 (tptm) REVERT: A 118 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6572 (mt-10) REVERT: A 124 GLN cc_start: 0.8185 (pp30) cc_final: 0.7875 (pp30) REVERT: A 125 PRO cc_start: 0.8648 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: A 157 LEU cc_start: 0.7996 (tp) cc_final: 0.7722 (tp) REVERT: A 169 GLU cc_start: 0.7923 (tt0) cc_final: 0.7638 (tt0) REVERT: A 179 SER cc_start: 0.8850 (t) cc_final: 0.8558 (p) REVERT: A 206 HIS cc_start: 0.8154 (p90) cc_final: 0.7437 (p90) REVERT: A 211 MET cc_start: 0.7936 (mmp) cc_final: 0.7391 (mmp) REVERT: A 212 MET cc_start: 0.8052 (mmp) cc_final: 0.7807 (mmp) REVERT: A 213 LYS cc_start: 0.8404 (mtmt) cc_final: 0.7845 (mtmt) REVERT: A 217 MET cc_start: 0.8083 (mpp) cc_final: 0.7679 (mpp) REVERT: A 218 SER cc_start: 0.8670 (p) cc_final: 0.8455 (p) REVERT: A 219 LEU cc_start: 0.8775 (mt) cc_final: 0.8525 (mt) REVERT: A 251 MET cc_start: 0.7749 (mmm) cc_final: 0.7183 (mmm) REVERT: A 259 GLN cc_start: 0.7541 (mt0) cc_final: 0.7321 (mt0) REVERT: A 266 GLU cc_start: 0.7915 (tp30) cc_final: 0.7713 (tp30) REVERT: A 270 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8279 (mmtt) REVERT: A 304 ARG cc_start: 0.7861 (mmp-170) cc_final: 0.7615 (mmm160) REVERT: A 305 ASP cc_start: 0.8394 (t0) cc_final: 0.8145 (m-30) REVERT: A 341 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 342 LYS cc_start: 0.8828 (mptt) cc_final: 0.8526 (mptt) REVERT: B 74 MET cc_start: 0.8105 (mtm) cc_final: 0.7395 (mtm) REVERT: B 101 THR cc_start: 0.8558 (t) cc_final: 0.7921 (p) REVERT: B 104 LYS cc_start: 0.8541 (tttt) cc_final: 0.8175 (tttt) REVERT: B 131 LEU cc_start: 0.8048 (mp) cc_final: 0.7725 (tp) REVERT: B 148 LYS cc_start: 0.8461 (tttt) cc_final: 0.8009 (ttmt) REVERT: B 154 PHE cc_start: 0.7740 (t80) cc_final: 0.7017 (t80) REVERT: B 157 LEU cc_start: 0.8131 (tp) cc_final: 0.7816 (tp) REVERT: B 158 GLN cc_start: 0.7420 (pm20) cc_final: 0.6550 (pm20) REVERT: B 167 TYR cc_start: 0.7076 (m-10) cc_final: 0.6869 (m-10) REVERT: B 211 MET cc_start: 0.7954 (mmp) cc_final: 0.7603 (mmp) REVERT: B 213 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7613 (mtmt) REVERT: B 215 GLN cc_start: 0.7542 (tp-100) cc_final: 0.6653 (tp-100) REVERT: B 217 MET cc_start: 0.8221 (mpp) cc_final: 0.7574 (mpp) REVERT: B 243 LEU cc_start: 0.8583 (mt) cc_final: 0.8281 (mt) REVERT: B 250 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7183 (mtt180) REVERT: B 259 GLN cc_start: 0.7828 (mt0) cc_final: 0.7509 (mt0) REVERT: B 266 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 295 SER cc_start: 0.7023 (p) cc_final: 0.6767 (p) REVERT: B 299 LEU cc_start: 0.8791 (mt) cc_final: 0.8543 (mt) REVERT: B 304 ARG cc_start: 0.7900 (mmp-170) cc_final: 0.7483 (mmm160) REVERT: B 331 VAL cc_start: 0.7697 (t) cc_final: 0.7395 (t) REVERT: B 338 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8106 (mtp85) REVERT: B 342 LYS cc_start: 0.8702 (mptt) cc_final: 0.7897 (mptt) REVERT: B 343 MET cc_start: 0.8242 (tpt) cc_final: 0.6868 (tpt) REVERT: B 345 LYS cc_start: 0.8799 (pptt) cc_final: 0.8518 (pptt) REVERT: B 347 LYS cc_start: 0.8891 (mptt) cc_final: 0.8339 (mptt) REVERT: C 74 MET cc_start: 0.5751 (mtm) cc_final: 0.5528 (mtm) REVERT: C 86 MET cc_start: 0.5659 (pmm) cc_final: 0.5299 (pmm) REVERT: C 158 GLN cc_start: 0.7900 (pm20) cc_final: 0.7554 (pm20) REVERT: C 171 GLN cc_start: 0.8369 (mm110) cc_final: 0.7884 (mp10) REVERT: C 212 MET cc_start: 0.7551 (mmp) cc_final: 0.7163 (mmp) REVERT: C 215 GLN cc_start: 0.8131 (tp-100) cc_final: 0.7532 (tm-30) REVERT: C 239 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7586 (mtt90) REVERT: C 248 MET cc_start: 0.7959 (mtp) cc_final: 0.7305 (mtp) REVERT: C 251 MET cc_start: 0.6515 (mmt) cc_final: 0.5876 (mmt) REVERT: C 270 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7643 (mmmt) REVERT: C 289 GLN cc_start: 0.8247 (mt0) cc_final: 0.7897 (mt0) REVERT: C 299 LEU cc_start: 0.8712 (mt) cc_final: 0.8321 (mt) REVERT: C 302 MET cc_start: 0.8250 (tmm) cc_final: 0.7940 (tmm) REVERT: C 304 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8346 (mmm160) REVERT: C 308 LEU cc_start: 0.8644 (tp) cc_final: 0.8349 (tp) REVERT: C 313 GLU cc_start: 0.8142 (pt0) cc_final: 0.7878 (pt0) REVERT: C 335 ASP cc_start: 0.8051 (m-30) cc_final: 0.7794 (m-30) REVERT: C 344 LYS cc_start: 0.8812 (mttm) cc_final: 0.8490 (mttm) REVERT: D 82 ASP cc_start: 0.8196 (t0) cc_final: 0.7858 (t70) REVERT: D 90 TRP cc_start: 0.8212 (m100) cc_final: 0.7996 (m100) REVERT: D 104 LYS cc_start: 0.8392 (tttt) cc_final: 0.8102 (tttm) REVERT: D 131 LEU cc_start: 0.8455 (mp) cc_final: 0.8027 (mt) REVERT: D 139 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7394 (mtmm) REVERT: D 183 LYS cc_start: 0.8479 (mptt) cc_final: 0.8038 (mptt) REVERT: D 191 ILE cc_start: 0.7955 (mt) cc_final: 0.7582 (mm) REVERT: D 212 MET cc_start: 0.7635 (mmp) cc_final: 0.7246 (mmp) REVERT: D 215 GLN cc_start: 0.7858 (pt0) cc_final: 0.7166 (pt0) REVERT: D 217 MET cc_start: 0.6905 (mmt) cc_final: 0.6622 (mmt) REVERT: D 241 GLN cc_start: 0.8183 (mp-120) cc_final: 0.7135 (mm-40) REVERT: D 250 ARG cc_start: 0.7629 (ptp-170) cc_final: 0.7407 (tpp-160) REVERT: D 251 MET cc_start: 0.7664 (mpp) cc_final: 0.6975 (mpp) REVERT: D 291 THR cc_start: 0.6602 (p) cc_final: 0.6224 (t) REVERT: D 300 LYS cc_start: 0.8624 (tptm) cc_final: 0.8344 (tptm) REVERT: D 302 MET cc_start: 0.7826 (tmm) cc_final: 0.7573 (tmm) REVERT: D 305 ASP cc_start: 0.7657 (t0) cc_final: 0.7304 (t0) REVERT: D 309 LEU cc_start: 0.8490 (tp) cc_final: 0.8179 (tp) REVERT: D 312 ARG cc_start: 0.8283 (mtp180) cc_final: 0.8031 (mtp180) REVERT: D 337 HIS cc_start: 0.7745 (m170) cc_final: 0.7446 (m-70) REVERT: E 158 GLN cc_start: 0.7946 (pm20) cc_final: 0.7643 (pm20) REVERT: E 171 GLN cc_start: 0.8584 (mm110) cc_final: 0.8151 (mp10) REVERT: E 193 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7430 (mt-10) REVERT: E 212 MET cc_start: 0.7783 (mmp) cc_final: 0.7152 (mmp) REVERT: E 215 GLN cc_start: 0.7878 (tp-100) cc_final: 0.7022 (tm-30) REVERT: E 219 LEU cc_start: 0.7437 (mt) cc_final: 0.6898 (mt) REVERT: E 239 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7936 (mtt90) REVERT: E 248 MET cc_start: 0.7942 (mtp) cc_final: 0.7355 (mtp) REVERT: E 251 MET cc_start: 0.6023 (mmt) cc_final: 0.5603 (mmt) REVERT: E 264 GLN cc_start: 0.8562 (mp10) cc_final: 0.8307 (mp10) REVERT: E 266 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7558 (tm-30) REVERT: E 270 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7450 (mmmt) REVERT: E 290 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7717 (mm-30) REVERT: E 298 ASP cc_start: 0.7407 (m-30) cc_final: 0.6958 (m-30) REVERT: E 299 LEU cc_start: 0.8780 (mt) cc_final: 0.8364 (mt) REVERT: E 300 LYS cc_start: 0.8782 (tttt) cc_final: 0.8523 (tttt) REVERT: E 302 MET cc_start: 0.8222 (tmm) cc_final: 0.7926 (tmm) REVERT: E 309 LEU cc_start: 0.8806 (tp) cc_final: 0.8564 (tp) REVERT: E 313 GLU cc_start: 0.8395 (pt0) cc_final: 0.8186 (pt0) REVERT: E 335 ASP cc_start: 0.8055 (m-30) cc_final: 0.7755 (m-30) REVERT: E 341 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7774 (mm-30) REVERT: F 74 MET cc_start: 0.7737 (mtm) cc_final: 0.7090 (mtm) REVERT: F 82 ASP cc_start: 0.8273 (t0) cc_final: 0.7779 (t0) REVERT: F 90 TRP cc_start: 0.8244 (m100) cc_final: 0.7721 (m100) REVERT: F 100 ILE cc_start: 0.8446 (mm) cc_final: 0.8179 (mm) REVERT: F 102 ASP cc_start: 0.8015 (m-30) cc_final: 0.7665 (m-30) REVERT: F 104 LYS cc_start: 0.8405 (tttt) cc_final: 0.8072 (ttmt) REVERT: F 124 GLN cc_start: 0.7606 (pp30) cc_final: 0.7260 (pp30) REVERT: F 131 LEU cc_start: 0.8378 (mp) cc_final: 0.7933 (mt) REVERT: F 139 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7464 (mtmm) REVERT: F 180 LEU cc_start: 0.8241 (tt) cc_final: 0.7979 (tt) REVERT: F 183 LYS cc_start: 0.8537 (mptt) cc_final: 0.8109 (mptt) REVERT: F 211 MET cc_start: 0.7355 (mmp) cc_final: 0.6937 (mmp) REVERT: F 212 MET cc_start: 0.8005 (mmp) cc_final: 0.7710 (mmp) REVERT: F 215 GLN cc_start: 0.7127 (tp-100) cc_final: 0.6822 (tp-100) REVERT: F 217 MET cc_start: 0.7478 (mmt) cc_final: 0.6806 (mmt) REVERT: F 219 LEU cc_start: 0.7902 (mt) cc_final: 0.7265 (mt) REVERT: F 248 MET cc_start: 0.6949 (mtp) cc_final: 0.6400 (mtp) REVERT: F 270 LYS cc_start: 0.8461 (pttp) cc_final: 0.8018 (ptmm) REVERT: F 291 THR cc_start: 0.7052 (p) cc_final: 0.6628 (p) REVERT: F 300 LYS cc_start: 0.8371 (tptm) cc_final: 0.7991 (tptm) REVERT: F 302 MET cc_start: 0.7914 (tmm) cc_final: 0.7654 (tmm) REVERT: F 337 HIS cc_start: 0.7846 (m170) cc_final: 0.7506 (m170) outliers start: 2 outliers final: 2 residues processed: 619 average time/residue: 0.1208 time to fit residues: 105.1852 Evaluate side-chains 579 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 577 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 132 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 149 optimal weight: 0.0070 chunk 162 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.153478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126497 restraints weight = 29901.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131153 restraints weight = 18035.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134247 restraints weight = 12240.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136576 restraints weight = 9057.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138306 restraints weight = 7055.007| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14142 Z= 0.135 Angle : 0.621 11.706 19146 Z= 0.325 Chirality : 0.045 0.308 2190 Planarity : 0.004 0.054 2448 Dihedral : 11.455 107.644 1962 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.21), residues: 1728 helix: 1.09 (0.16), residues: 936 sheet: 0.61 (0.40), residues: 192 loop : 0.56 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 199 TYR 0.015 0.002 TYR C 132 PHE 0.040 0.002 PHE C 216 TRP 0.019 0.002 TRP C 220 HIS 0.012 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00282 (14142) covalent geometry : angle 0.62116 (19146) hydrogen bonds : bond 0.04259 ( 738) hydrogen bonds : angle 4.47448 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 0.529 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8124 (mtm) cc_final: 0.7734 (mtm) REVERT: A 96 LEU cc_start: 0.7539 (mt) cc_final: 0.7337 (mt) REVERT: A 100 ILE cc_start: 0.8028 (mm) cc_final: 0.7705 (mm) REVERT: A 102 ASP cc_start: 0.7790 (m-30) cc_final: 0.7555 (m-30) REVERT: A 104 LYS cc_start: 0.8630 (tttt) cc_final: 0.8220 (tttt) REVERT: A 114 LYS cc_start: 0.7848 (tptm) cc_final: 0.7555 (tptm) REVERT: A 118 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6496 (mt-10) REVERT: A 124 GLN cc_start: 0.8212 (pp30) cc_final: 0.7954 (pp30) REVERT: A 125 PRO cc_start: 0.8616 (Cg_endo) cc_final: 0.8074 (Cg_exo) REVERT: A 146 THR cc_start: 0.8416 (p) cc_final: 0.8122 (p) REVERT: A 148 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7926 (ttmt) REVERT: A 157 LEU cc_start: 0.7944 (tp) cc_final: 0.7565 (tp) REVERT: A 169 GLU cc_start: 0.7755 (tt0) cc_final: 0.7106 (tt0) REVERT: A 179 SER cc_start: 0.8842 (t) cc_final: 0.8530 (p) REVERT: A 193 GLU cc_start: 0.7769 (tt0) cc_final: 0.7537 (tt0) REVERT: A 206 HIS cc_start: 0.8083 (p90) cc_final: 0.7406 (p90) REVERT: A 211 MET cc_start: 0.7860 (mmp) cc_final: 0.7289 (mmp) REVERT: A 212 MET cc_start: 0.7779 (mmp) cc_final: 0.7530 (mmp) REVERT: A 213 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7719 (mtmt) REVERT: A 215 GLN cc_start: 0.7636 (tp-100) cc_final: 0.6485 (tp-100) REVERT: A 217 MET cc_start: 0.8061 (mpp) cc_final: 0.7670 (mpp) REVERT: A 218 SER cc_start: 0.8677 (p) cc_final: 0.8223 (p) REVERT: A 219 LEU cc_start: 0.8787 (mt) cc_final: 0.7746 (mt) REVERT: A 251 MET cc_start: 0.7423 (mmm) cc_final: 0.7058 (mmm) REVERT: A 259 GLN cc_start: 0.7609 (mt0) cc_final: 0.7279 (mt0) REVERT: A 263 LYS cc_start: 0.7769 (mttp) cc_final: 0.7547 (mttp) REVERT: A 270 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8119 (mmtt) REVERT: A 305 ASP cc_start: 0.8251 (t0) cc_final: 0.7877 (m-30) REVERT: A 341 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 342 LYS cc_start: 0.8727 (mptt) cc_final: 0.8350 (mptt) REVERT: B 74 MET cc_start: 0.7981 (mtm) cc_final: 0.7269 (mtm) REVERT: B 85 ASN cc_start: 0.7958 (p0) cc_final: 0.7552 (p0) REVERT: B 90 TRP cc_start: 0.7795 (m100) cc_final: 0.7095 (m100) REVERT: B 104 LYS cc_start: 0.8498 (tttt) cc_final: 0.8137 (tttt) REVERT: B 129 VAL cc_start: 0.6855 (t) cc_final: 0.6619 (t) REVERT: B 131 LEU cc_start: 0.8076 (mp) cc_final: 0.7806 (tp) REVERT: B 157 LEU cc_start: 0.8070 (tp) cc_final: 0.7718 (tp) REVERT: B 158 GLN cc_start: 0.7335 (pm20) cc_final: 0.6520 (pm20) REVERT: B 211 MET cc_start: 0.7918 (mmp) cc_final: 0.7550 (mmp) REVERT: B 213 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7683 (mtmt) REVERT: B 215 GLN cc_start: 0.7504 (tp-100) cc_final: 0.6204 (tp-100) REVERT: B 217 MET cc_start: 0.8107 (mpp) cc_final: 0.7665 (mpp) REVERT: B 219 LEU cc_start: 0.8778 (mt) cc_final: 0.7747 (mt) REVERT: B 243 LEU cc_start: 0.8503 (mt) cc_final: 0.8279 (mt) REVERT: B 259 GLN cc_start: 0.7843 (mt0) cc_final: 0.7440 (mt0) REVERT: B 266 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7038 (tm-30) REVERT: B 270 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7872 (mptt) REVERT: B 286 GLU cc_start: 0.6923 (pm20) cc_final: 0.6628 (pm20) REVERT: B 304 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.6984 (tpm170) REVERT: B 338 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7949 (mtp85) REVERT: B 341 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 342 LYS cc_start: 0.8583 (mptt) cc_final: 0.7906 (mptt) REVERT: B 343 MET cc_start: 0.8185 (tpt) cc_final: 0.6722 (tpt) REVERT: B 347 LYS cc_start: 0.8894 (mptt) cc_final: 0.8329 (mptt) REVERT: C 74 MET cc_start: 0.5740 (mtm) cc_final: 0.5496 (mtm) REVERT: C 86 MET cc_start: 0.5670 (pmm) cc_final: 0.5469 (pmm) REVERT: C 158 GLN cc_start: 0.8084 (pm20) cc_final: 0.7599 (pm20) REVERT: C 167 TYR cc_start: 0.7392 (m-10) cc_final: 0.7006 (m-10) REVERT: C 170 SER cc_start: 0.7977 (p) cc_final: 0.7385 (p) REVERT: C 171 GLN cc_start: 0.8357 (mm110) cc_final: 0.7877 (mp10) REVERT: C 212 MET cc_start: 0.7572 (mmp) cc_final: 0.7208 (mmp) REVERT: C 215 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7436 (tm-30) REVERT: C 217 MET cc_start: 0.8561 (mmm) cc_final: 0.8256 (tpp) REVERT: C 248 MET cc_start: 0.7859 (mtp) cc_final: 0.7317 (mtp) REVERT: C 264 GLN cc_start: 0.8340 (mp10) cc_final: 0.8037 (mp10) REVERT: C 270 LYS cc_start: 0.8554 (mmmt) cc_final: 0.7598 (mmmt) REVERT: C 289 GLN cc_start: 0.8068 (mt0) cc_final: 0.7681 (mt0) REVERT: C 299 LEU cc_start: 0.8619 (mt) cc_final: 0.8273 (mt) REVERT: C 300 LYS cc_start: 0.8848 (tttp) cc_final: 0.8607 (tttp) REVERT: C 302 MET cc_start: 0.8144 (tmm) cc_final: 0.7815 (tmm) REVERT: C 304 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8007 (mtp85) REVERT: C 308 LEU cc_start: 0.8555 (tp) cc_final: 0.8282 (tp) REVERT: C 309 LEU cc_start: 0.8734 (tp) cc_final: 0.8371 (tp) REVERT: C 312 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7944 (mtp-110) REVERT: C 313 GLU cc_start: 0.8135 (pt0) cc_final: 0.7839 (pt0) REVERT: C 344 LYS cc_start: 0.8945 (mttm) cc_final: 0.8638 (mttm) REVERT: D 82 ASP cc_start: 0.8250 (t0) cc_final: 0.7888 (t70) REVERT: D 90 TRP cc_start: 0.8259 (m100) cc_final: 0.7698 (m100) REVERT: D 104 LYS cc_start: 0.8320 (tttt) cc_final: 0.8054 (ttmt) REVERT: D 131 LEU cc_start: 0.8508 (mp) cc_final: 0.8098 (mt) REVERT: D 139 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7221 (mtmm) REVERT: D 179 SER cc_start: 0.8131 (p) cc_final: 0.7859 (p) REVERT: D 180 LEU cc_start: 0.8031 (tt) cc_final: 0.7823 (tt) REVERT: D 183 LYS cc_start: 0.8364 (mptt) cc_final: 0.8004 (mptt) REVERT: D 212 MET cc_start: 0.7518 (mmp) cc_final: 0.7205 (mmp) REVERT: D 215 GLN cc_start: 0.7738 (pt0) cc_final: 0.7156 (pt0) REVERT: D 217 MET cc_start: 0.6774 (mmt) cc_final: 0.6397 (mmt) REVERT: D 241 GLN cc_start: 0.8142 (mp-120) cc_final: 0.7165 (mm-40) REVERT: D 250 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7248 (ptp-170) REVERT: D 263 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7654 (mmmm) REVERT: D 300 LYS cc_start: 0.8547 (tptm) cc_final: 0.8240 (tptm) REVERT: D 305 ASP cc_start: 0.7526 (t0) cc_final: 0.7170 (t0) REVERT: D 337 HIS cc_start: 0.7580 (m170) cc_final: 0.7243 (m90) REVERT: E 139 LYS cc_start: 0.8205 (ptpp) cc_final: 0.7884 (pttm) REVERT: E 158 GLN cc_start: 0.8052 (pm20) cc_final: 0.7734 (pm20) REVERT: E 167 TYR cc_start: 0.7188 (m-10) cc_final: 0.6797 (m-10) REVERT: E 171 GLN cc_start: 0.8441 (mm110) cc_final: 0.8024 (mp10) REVERT: E 178 PHE cc_start: 0.6013 (m-80) cc_final: 0.5783 (m-80) REVERT: E 193 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7224 (mt-10) REVERT: E 212 MET cc_start: 0.7736 (mmp) cc_final: 0.7134 (mmp) REVERT: E 215 GLN cc_start: 0.7821 (tp-100) cc_final: 0.6734 (tm-30) REVERT: E 219 LEU cc_start: 0.7433 (mt) cc_final: 0.6627 (mt) REVERT: E 239 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7398 (ttp-110) REVERT: E 248 MET cc_start: 0.7890 (mtp) cc_final: 0.7307 (mtp) REVERT: E 256 HIS cc_start: 0.7688 (t70) cc_final: 0.7308 (t70) REVERT: E 259 GLN cc_start: 0.7448 (tt0) cc_final: 0.7150 (tp40) REVERT: E 264 GLN cc_start: 0.8486 (mp10) cc_final: 0.8148 (mp10) REVERT: E 266 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7410 (tm-30) REVERT: E 270 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7416 (mmmt) REVERT: E 290 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 298 ASP cc_start: 0.7333 (m-30) cc_final: 0.6867 (m-30) REVERT: E 299 LEU cc_start: 0.8712 (mt) cc_final: 0.8284 (mt) REVERT: E 300 LYS cc_start: 0.8675 (tttt) cc_final: 0.8382 (tttt) REVERT: E 301 GLU cc_start: 0.8345 (tt0) cc_final: 0.7980 (tt0) REVERT: E 302 MET cc_start: 0.8035 (tmm) cc_final: 0.7780 (tmm) REVERT: E 313 GLU cc_start: 0.8397 (pt0) cc_final: 0.8115 (pt0) REVERT: E 341 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7726 (mm-30) REVERT: F 74 MET cc_start: 0.7541 (mtm) cc_final: 0.7126 (mtm) REVERT: F 82 ASP cc_start: 0.8307 (t0) cc_final: 0.7921 (t0) REVERT: F 90 TRP cc_start: 0.8237 (m100) cc_final: 0.7556 (m100) REVERT: F 102 ASP cc_start: 0.7931 (m-30) cc_final: 0.7584 (m-30) REVERT: F 104 LYS cc_start: 0.8355 (tttt) cc_final: 0.8035 (ttmt) REVERT: F 112 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7475 (mtmt) REVERT: F 124 GLN cc_start: 0.7579 (pp30) cc_final: 0.7276 (pp30) REVERT: F 131 LEU cc_start: 0.8452 (mp) cc_final: 0.8224 (mt) REVERT: F 180 LEU cc_start: 0.8149 (tt) cc_final: 0.7887 (tt) REVERT: F 183 LYS cc_start: 0.8461 (mptt) cc_final: 0.8038 (mptt) REVERT: F 211 MET cc_start: 0.7264 (mmp) cc_final: 0.6890 (mmp) REVERT: F 212 MET cc_start: 0.7931 (mmp) cc_final: 0.7591 (mmp) REVERT: F 215 GLN cc_start: 0.6955 (tp-100) cc_final: 0.6661 (tp-100) REVERT: F 217 MET cc_start: 0.7461 (mmt) cc_final: 0.6853 (mmt) REVERT: F 219 LEU cc_start: 0.7824 (mt) cc_final: 0.7167 (mt) REVERT: F 241 GLN cc_start: 0.7839 (mm110) cc_final: 0.7288 (mm110) REVERT: F 244 ASP cc_start: 0.7702 (p0) cc_final: 0.7409 (p0) REVERT: F 248 MET cc_start: 0.7079 (mtp) cc_final: 0.6515 (mtp) REVERT: F 250 ARG cc_start: 0.7784 (ttt-90) cc_final: 0.7022 (ttt180) REVERT: F 270 LYS cc_start: 0.8405 (pttp) cc_final: 0.7962 (ptmm) REVERT: F 291 THR cc_start: 0.7093 (p) cc_final: 0.6772 (t) REVERT: F 300 LYS cc_start: 0.8330 (tptm) cc_final: 0.7863 (tptm) REVERT: F 302 MET cc_start: 0.7635 (tmm) cc_final: 0.7236 (tmm) REVERT: F 337 HIS cc_start: 0.7653 (m170) cc_final: 0.7343 (m170) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.1135 time to fit residues: 98.9355 Evaluate side-chains 588 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 0.0970 chunk 16 optimal weight: 0.0970 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 chunk 133 optimal weight: 0.0050 chunk 163 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.1828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128632 restraints weight = 29821.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133336 restraints weight = 17984.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136520 restraints weight = 12175.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138939 restraints weight = 8967.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140556 restraints weight = 6951.835| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14142 Z= 0.123 Angle : 0.611 12.545 19146 Z= 0.315 Chirality : 0.043 0.254 2190 Planarity : 0.004 0.051 2448 Dihedral : 11.317 109.582 1962 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1728 helix: 1.17 (0.16), residues: 972 sheet: 0.66 (0.41), residues: 192 loop : 0.49 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 199 TYR 0.013 0.002 TYR A 72 PHE 0.029 0.002 PHE C 216 TRP 0.021 0.002 TRP A 220 HIS 0.010 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00258 (14142) covalent geometry : angle 0.61125 (19146) hydrogen bonds : bond 0.03845 ( 738) hydrogen bonds : angle 4.26491 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 0.511 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8111 (mtm) cc_final: 0.7635 (mtm) REVERT: A 102 ASP cc_start: 0.7719 (m-30) cc_final: 0.7516 (m-30) REVERT: A 104 LYS cc_start: 0.8642 (tttt) cc_final: 0.8249 (tttt) REVERT: A 114 LYS cc_start: 0.7761 (tptm) cc_final: 0.7463 (tptm) REVERT: A 118 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6317 (mt-10) REVERT: A 123 LEU cc_start: 0.8366 (tp) cc_final: 0.8160 (tp) REVERT: A 124 GLN cc_start: 0.8174 (pp30) cc_final: 0.7908 (pp30) REVERT: A 125 PRO cc_start: 0.8609 (Cg_endo) cc_final: 0.8066 (Cg_exo) REVERT: A 146 THR cc_start: 0.8365 (p) cc_final: 0.7909 (p) REVERT: A 148 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7903 (ttmt) REVERT: A 157 LEU cc_start: 0.7879 (tp) cc_final: 0.7543 (tp) REVERT: A 158 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 169 GLU cc_start: 0.7153 (tt0) cc_final: 0.6817 (tt0) REVERT: A 179 SER cc_start: 0.8858 (t) cc_final: 0.8534 (p) REVERT: A 206 HIS cc_start: 0.8056 (p90) cc_final: 0.7403 (p90) REVERT: A 211 MET cc_start: 0.7853 (mmp) cc_final: 0.7225 (mmp) REVERT: A 212 MET cc_start: 0.7795 (mmp) cc_final: 0.7537 (mmp) REVERT: A 213 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7763 (mtmt) REVERT: A 215 GLN cc_start: 0.7480 (tp-100) cc_final: 0.6355 (tp-100) REVERT: A 217 MET cc_start: 0.8058 (mpp) cc_final: 0.7684 (mpp) REVERT: A 218 SER cc_start: 0.8639 (p) cc_final: 0.8225 (p) REVERT: A 219 LEU cc_start: 0.8765 (mt) cc_final: 0.7693 (mt) REVERT: A 251 MET cc_start: 0.7576 (mmm) cc_final: 0.7009 (mmm) REVERT: A 259 GLN cc_start: 0.7576 (mt0) cc_final: 0.7236 (mt0) REVERT: A 266 GLU cc_start: 0.7882 (tp30) cc_final: 0.7602 (tp30) REVERT: A 270 LYS cc_start: 0.8379 (mmtt) cc_final: 0.8094 (mmtt) REVERT: A 273 LEU cc_start: 0.8328 (mm) cc_final: 0.8124 (mm) REVERT: A 305 ASP cc_start: 0.8234 (t0) cc_final: 0.7765 (m-30) REVERT: A 338 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7862 (mtp85) REVERT: A 341 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 342 LYS cc_start: 0.8683 (mptt) cc_final: 0.8298 (mptt) REVERT: B 74 MET cc_start: 0.7968 (mtm) cc_final: 0.7270 (mtm) REVERT: B 90 TRP cc_start: 0.7751 (m100) cc_final: 0.6430 (m100) REVERT: B 104 LYS cc_start: 0.8481 (tttt) cc_final: 0.8178 (tttt) REVERT: B 131 LEU cc_start: 0.8202 (mp) cc_final: 0.7862 (tp) REVERT: B 157 LEU cc_start: 0.8002 (tp) cc_final: 0.7706 (tp) REVERT: B 158 GLN cc_start: 0.7389 (pm20) cc_final: 0.6480 (pm20) REVERT: B 211 MET cc_start: 0.7920 (mmp) cc_final: 0.7534 (mmp) REVERT: B 213 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7687 (mtmt) REVERT: B 215 GLN cc_start: 0.7508 (tp-100) cc_final: 0.6230 (tp-100) REVERT: B 217 MET cc_start: 0.8104 (mpp) cc_final: 0.7640 (mpp) REVERT: B 219 LEU cc_start: 0.8718 (mt) cc_final: 0.7690 (mt) REVERT: B 234 MET cc_start: 0.7153 (ttm) cc_final: 0.6868 (ttm) REVERT: B 243 LEU cc_start: 0.8488 (mt) cc_final: 0.8223 (mt) REVERT: B 250 ARG cc_start: 0.7794 (tpp80) cc_final: 0.7407 (tpp80) REVERT: B 259 GLN cc_start: 0.7835 (mt0) cc_final: 0.7411 (mt0) REVERT: B 266 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6945 (tm-30) REVERT: B 270 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7846 (mptt) REVERT: B 286 GLU cc_start: 0.6930 (pm20) cc_final: 0.6616 (pm20) REVERT: B 299 LEU cc_start: 0.8757 (mt) cc_final: 0.8393 (mp) REVERT: B 304 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6953 (tpm170) REVERT: B 305 ASP cc_start: 0.8129 (m-30) cc_final: 0.7853 (m-30) REVERT: B 338 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7937 (mtp85) REVERT: B 341 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 342 LYS cc_start: 0.8566 (mptt) cc_final: 0.7878 (mptt) REVERT: B 343 MET cc_start: 0.8184 (tpt) cc_final: 0.6709 (tpt) REVERT: B 347 LYS cc_start: 0.8924 (mptt) cc_final: 0.8397 (mptt) REVERT: C 74 MET cc_start: 0.5695 (mtm) cc_final: 0.5431 (mtm) REVERT: C 86 MET cc_start: 0.5683 (pmm) cc_final: 0.5475 (pmm) REVERT: C 158 GLN cc_start: 0.8088 (pm20) cc_final: 0.7635 (pm20) REVERT: C 167 TYR cc_start: 0.7230 (m-10) cc_final: 0.6907 (m-10) REVERT: C 170 SER cc_start: 0.8024 (p) cc_final: 0.7412 (p) REVERT: C 171 GLN cc_start: 0.8404 (mm110) cc_final: 0.7961 (mp10) REVERT: C 212 MET cc_start: 0.7546 (mmp) cc_final: 0.7206 (mmp) REVERT: C 215 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7402 (tm-30) REVERT: C 217 MET cc_start: 0.8560 (mmm) cc_final: 0.8206 (tpp) REVERT: C 248 MET cc_start: 0.7760 (mtp) cc_final: 0.7195 (mtp) REVERT: C 264 GLN cc_start: 0.8338 (mp10) cc_final: 0.8041 (mp10) REVERT: C 270 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7558 (mmmt) REVERT: C 289 GLN cc_start: 0.8076 (mt0) cc_final: 0.7666 (mt0) REVERT: C 299 LEU cc_start: 0.8633 (mt) cc_final: 0.8419 (mt) REVERT: C 300 LYS cc_start: 0.8810 (tttp) cc_final: 0.8570 (tttp) REVERT: C 302 MET cc_start: 0.8126 (tmm) cc_final: 0.7783 (tmm) REVERT: C 304 ARG cc_start: 0.8493 (mtp85) cc_final: 0.7961 (mtp85) REVERT: C 309 LEU cc_start: 0.8654 (tp) cc_final: 0.8344 (tp) REVERT: C 313 GLU cc_start: 0.8156 (pt0) cc_final: 0.7799 (pt0) REVERT: C 344 LYS cc_start: 0.8919 (mttm) cc_final: 0.8457 (mttm) REVERT: D 82 ASP cc_start: 0.8224 (t0) cc_final: 0.7819 (t70) REVERT: D 90 TRP cc_start: 0.8269 (m100) cc_final: 0.7630 (m100) REVERT: D 104 LYS cc_start: 0.8325 (tttt) cc_final: 0.7962 (ttmt) REVERT: D 124 GLN cc_start: 0.7545 (pp30) cc_final: 0.7248 (pp30) REVERT: D 131 LEU cc_start: 0.8502 (mp) cc_final: 0.8020 (mt) REVERT: D 132 TYR cc_start: 0.7525 (p90) cc_final: 0.7304 (p90) REVERT: D 139 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7241 (mtmm) REVERT: D 180 LEU cc_start: 0.8001 (tt) cc_final: 0.7750 (tt) REVERT: D 183 LYS cc_start: 0.8371 (mptt) cc_final: 0.8052 (mptt) REVERT: D 196 SER cc_start: 0.7302 (t) cc_final: 0.6786 (p) REVERT: D 212 MET cc_start: 0.7470 (mmp) cc_final: 0.7184 (mmp) REVERT: D 217 MET cc_start: 0.6895 (mmt) cc_final: 0.6557 (mmt) REVERT: D 234 MET cc_start: 0.7525 (mtp) cc_final: 0.7319 (mtp) REVERT: D 250 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.7339 (ptp-170) REVERT: D 251 MET cc_start: 0.7356 (mpp) cc_final: 0.6573 (mpp) REVERT: D 263 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7555 (mmmm) REVERT: D 265 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7042 (ptp-110) REVERT: D 300 LYS cc_start: 0.8585 (tptm) cc_final: 0.8245 (tptm) REVERT: D 305 ASP cc_start: 0.7568 (t0) cc_final: 0.7224 (t0) REVERT: D 337 HIS cc_start: 0.7597 (m170) cc_final: 0.7362 (m90) REVERT: E 139 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7876 (ptpt) REVERT: E 158 GLN cc_start: 0.8089 (pm20) cc_final: 0.7715 (pm20) REVERT: E 167 TYR cc_start: 0.7054 (m-10) cc_final: 0.6726 (m-10) REVERT: E 171 GLN cc_start: 0.8353 (mm110) cc_final: 0.7934 (mp10) REVERT: E 193 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7150 (mt-10) REVERT: E 212 MET cc_start: 0.7750 (mmp) cc_final: 0.7069 (mmp) REVERT: E 215 GLN cc_start: 0.7820 (tp-100) cc_final: 0.6730 (tm-30) REVERT: E 219 LEU cc_start: 0.7391 (mt) cc_final: 0.6597 (mt) REVERT: E 239 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7330 (ttp-110) REVERT: E 248 MET cc_start: 0.7849 (mtp) cc_final: 0.7283 (mtp) REVERT: E 256 HIS cc_start: 0.7687 (t70) cc_final: 0.7292 (t70) REVERT: E 264 GLN cc_start: 0.8450 (mp10) cc_final: 0.8091 (mp10) REVERT: E 266 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7427 (tm-30) REVERT: E 270 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7428 (mmmt) REVERT: E 290 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7608 (mm-30) REVERT: E 298 ASP cc_start: 0.7481 (m-30) cc_final: 0.6993 (m-30) REVERT: E 299 LEU cc_start: 0.8696 (mt) cc_final: 0.8345 (mt) REVERT: E 300 LYS cc_start: 0.8608 (tttt) cc_final: 0.8352 (tttt) REVERT: E 301 GLU cc_start: 0.8403 (tt0) cc_final: 0.7967 (tt0) REVERT: E 302 MET cc_start: 0.8008 (tmm) cc_final: 0.7755 (tmm) REVERT: E 313 GLU cc_start: 0.8475 (pt0) cc_final: 0.8180 (pt0) REVERT: E 335 ASP cc_start: 0.8234 (m-30) cc_final: 0.7937 (m-30) REVERT: E 341 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 343 MET cc_start: 0.8224 (tpt) cc_final: 0.7995 (tpt) REVERT: F 68 LYS cc_start: 0.7445 (mppt) cc_final: 0.7012 (mppt) REVERT: F 74 MET cc_start: 0.7483 (mtm) cc_final: 0.7081 (mtm) REVERT: F 82 ASP cc_start: 0.8295 (t0) cc_final: 0.7986 (t0) REVERT: F 90 TRP cc_start: 0.8156 (m100) cc_final: 0.7483 (m100) REVERT: F 102 ASP cc_start: 0.7897 (m-30) cc_final: 0.7607 (m-30) REVERT: F 104 LYS cc_start: 0.8351 (tttt) cc_final: 0.7945 (ttmt) REVERT: F 112 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7427 (mtmt) REVERT: F 124 GLN cc_start: 0.7566 (pp30) cc_final: 0.7241 (pp30) REVERT: F 131 LEU cc_start: 0.8448 (mp) cc_final: 0.8024 (mt) REVERT: F 139 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7223 (mtmm) REVERT: F 180 LEU cc_start: 0.8125 (tt) cc_final: 0.7881 (tt) REVERT: F 183 LYS cc_start: 0.8459 (mptt) cc_final: 0.8072 (mptt) REVERT: F 211 MET cc_start: 0.7302 (mmp) cc_final: 0.6953 (mmp) REVERT: F 212 MET cc_start: 0.7885 (mmp) cc_final: 0.7575 (mmp) REVERT: F 215 GLN cc_start: 0.6837 (tp-100) cc_final: 0.6428 (tp-100) REVERT: F 217 MET cc_start: 0.7327 (mmt) cc_final: 0.6664 (mmt) REVERT: F 219 LEU cc_start: 0.7743 (mt) cc_final: 0.7109 (mt) REVERT: F 248 MET cc_start: 0.6954 (mtp) cc_final: 0.6543 (mtp) REVERT: F 251 MET cc_start: 0.7901 (mpp) cc_final: 0.6878 (mpp) REVERT: F 265 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.6814 (mtm-85) REVERT: F 270 LYS cc_start: 0.8394 (pttp) cc_final: 0.7907 (ptmm) REVERT: F 291 THR cc_start: 0.7239 (p) cc_final: 0.6632 (t) REVERT: F 298 ASP cc_start: 0.8117 (m-30) cc_final: 0.7911 (m-30) REVERT: F 300 LYS cc_start: 0.8374 (tptm) cc_final: 0.7953 (tptm) REVERT: F 302 MET cc_start: 0.7647 (tmm) cc_final: 0.7250 (tmm) REVERT: F 337 HIS cc_start: 0.7652 (m170) cc_final: 0.7301 (m170) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.1219 time to fit residues: 102.5360 Evaluate side-chains 578 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 0.0060 chunk 129 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126929 restraints weight = 29979.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131503 restraints weight = 18019.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134786 restraints weight = 12201.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137019 restraints weight = 8940.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138656 restraints weight = 6989.430| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14142 Z= 0.136 Angle : 0.611 12.977 19146 Z= 0.319 Chirality : 0.044 0.251 2190 Planarity : 0.004 0.065 2448 Dihedral : 11.232 110.341 1962 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 1.50 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1728 helix: 1.32 (0.17), residues: 942 sheet: 0.68 (0.41), residues: 192 loop : 0.74 (0.30), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 199 TYR 0.013 0.002 TYR E 72 PHE 0.034 0.002 PHE A 216 TRP 0.023 0.003 TRP B 90 HIS 0.014 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00282 (14142) covalent geometry : angle 0.61131 (19146) hydrogen bonds : bond 0.03865 ( 738) hydrogen bonds : angle 4.35375 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 0.573 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8141 (mtm) cc_final: 0.7666 (mtm) REVERT: A 90 TRP cc_start: 0.7789 (m100) cc_final: 0.6795 (m100) REVERT: A 104 LYS cc_start: 0.8637 (tttt) cc_final: 0.8187 (tttt) REVERT: A 118 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 123 LEU cc_start: 0.8413 (tp) cc_final: 0.8209 (tp) REVERT: A 125 PRO cc_start: 0.8602 (Cg_endo) cc_final: 0.8125 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8343 (mp) cc_final: 0.7997 (tp) REVERT: A 148 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7829 (ttmt) REVERT: A 154 PHE cc_start: 0.7772 (t80) cc_final: 0.7326 (t80) REVERT: A 157 LEU cc_start: 0.7958 (tp) cc_final: 0.7616 (tp) REVERT: A 158 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 169 GLU cc_start: 0.7146 (tt0) cc_final: 0.6844 (tt0) REVERT: A 179 SER cc_start: 0.8893 (t) cc_final: 0.8575 (p) REVERT: A 199 ARG cc_start: 0.7314 (tpp80) cc_final: 0.6349 (tpp80) REVERT: A 206 HIS cc_start: 0.8100 (p90) cc_final: 0.7433 (p90) REVERT: A 211 MET cc_start: 0.7913 (mmp) cc_final: 0.7257 (mmp) REVERT: A 212 MET cc_start: 0.7803 (mmp) cc_final: 0.7577 (mmp) REVERT: A 213 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7791 (mtmt) REVERT: A 215 GLN cc_start: 0.7428 (tp-100) cc_final: 0.6286 (tp-100) REVERT: A 217 MET cc_start: 0.8105 (mpp) cc_final: 0.7561 (mpp) REVERT: A 218 SER cc_start: 0.8608 (p) cc_final: 0.8163 (p) REVERT: A 219 LEU cc_start: 0.8787 (mt) cc_final: 0.7622 (mt) REVERT: A 230 GLN cc_start: 0.5931 (mm-40) cc_final: 0.5594 (mm110) REVERT: A 250 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.7156 (mtt-85) REVERT: A 251 MET cc_start: 0.7364 (mmm) cc_final: 0.6864 (mmm) REVERT: A 259 GLN cc_start: 0.7649 (mt0) cc_final: 0.7288 (mt0) REVERT: A 270 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8114 (mmtt) REVERT: A 305 ASP cc_start: 0.8220 (t0) cc_final: 0.7894 (m-30) REVERT: A 338 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7766 (mtp85) REVERT: A 341 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 342 LYS cc_start: 0.8728 (mptt) cc_final: 0.8144 (mptt) REVERT: A 345 LYS cc_start: 0.8755 (pptt) cc_final: 0.8552 (pptt) REVERT: B 74 MET cc_start: 0.8039 (mtm) cc_final: 0.7303 (mtm) REVERT: B 85 ASN cc_start: 0.7874 (p0) cc_final: 0.7608 (p0) REVERT: B 86 MET cc_start: 0.7636 (mtm) cc_final: 0.7427 (mtm) REVERT: B 96 LEU cc_start: 0.7614 (mt) cc_final: 0.7335 (mm) REVERT: B 154 PHE cc_start: 0.7641 (t80) cc_final: 0.7063 (t80) REVERT: B 157 LEU cc_start: 0.8022 (tp) cc_final: 0.7694 (tp) REVERT: B 158 GLN cc_start: 0.7359 (pm20) cc_final: 0.6489 (pm20) REVERT: B 211 MET cc_start: 0.7982 (mmp) cc_final: 0.7632 (mmp) REVERT: B 213 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7717 (mtmt) REVERT: B 215 GLN cc_start: 0.7535 (tp-100) cc_final: 0.6286 (tp-100) REVERT: B 217 MET cc_start: 0.8156 (mpp) cc_final: 0.7672 (mpp) REVERT: B 219 LEU cc_start: 0.8770 (mt) cc_final: 0.7764 (mt) REVERT: B 234 MET cc_start: 0.7195 (ttm) cc_final: 0.6911 (ttm) REVERT: B 259 GLN cc_start: 0.7835 (mt0) cc_final: 0.7368 (mt0) REVERT: B 266 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 268 ILE cc_start: 0.8143 (mm) cc_final: 0.7776 (mm) REVERT: B 270 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7867 (mptt) REVERT: B 271 LEU cc_start: 0.8672 (tp) cc_final: 0.8408 (pp) REVERT: B 272 ILE cc_start: 0.8382 (mt) cc_final: 0.8135 (mt) REVERT: B 286 GLU cc_start: 0.6776 (pm20) cc_final: 0.6536 (pm20) REVERT: B 299 LEU cc_start: 0.8759 (mt) cc_final: 0.8453 (mp) REVERT: B 304 ARG cc_start: 0.7260 (mmp-170) cc_final: 0.6974 (tpm170) REVERT: B 338 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7918 (mtp85) REVERT: B 341 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 342 LYS cc_start: 0.8575 (mptt) cc_final: 0.8118 (mptt) REVERT: B 343 MET cc_start: 0.8208 (tpt) cc_final: 0.6802 (tpt) REVERT: B 344 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7255 (pttt) REVERT: B 347 LYS cc_start: 0.8942 (mptt) cc_final: 0.8398 (mptt) REVERT: C 74 MET cc_start: 0.5680 (mtm) cc_final: 0.5455 (mtm) REVERT: C 86 MET cc_start: 0.5644 (pmm) cc_final: 0.5422 (pmm) REVERT: C 158 GLN cc_start: 0.7988 (pm20) cc_final: 0.7555 (pm20) REVERT: C 167 TYR cc_start: 0.7302 (m-10) cc_final: 0.6967 (m-10) REVERT: C 170 SER cc_start: 0.8073 (p) cc_final: 0.7477 (p) REVERT: C 171 GLN cc_start: 0.8451 (mm110) cc_final: 0.8060 (mp10) REVERT: C 212 MET cc_start: 0.7650 (mmp) cc_final: 0.7281 (mmp) REVERT: C 215 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7431 (tm-30) REVERT: C 217 MET cc_start: 0.8597 (mmm) cc_final: 0.8233 (tpp) REVERT: C 219 LEU cc_start: 0.7369 (mt) cc_final: 0.7050 (mt) REVERT: C 229 CYS cc_start: 0.7469 (t) cc_final: 0.7246 (t) REVERT: C 245 SER cc_start: 0.8026 (t) cc_final: 0.7697 (t) REVERT: C 248 MET cc_start: 0.7862 (mtp) cc_final: 0.7236 (mtp) REVERT: C 264 GLN cc_start: 0.8349 (mp10) cc_final: 0.8054 (mp10) REVERT: C 270 LYS cc_start: 0.8590 (mmmt) cc_final: 0.7637 (mmmt) REVERT: C 289 GLN cc_start: 0.8036 (mt0) cc_final: 0.7629 (mt0) REVERT: C 299 LEU cc_start: 0.8637 (mt) cc_final: 0.8395 (mt) REVERT: C 300 LYS cc_start: 0.8817 (tttp) cc_final: 0.8561 (tttp) REVERT: C 302 MET cc_start: 0.8109 (tmm) cc_final: 0.7842 (tmm) REVERT: C 304 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7940 (mtp85) REVERT: C 309 LEU cc_start: 0.8653 (tp) cc_final: 0.8387 (tp) REVERT: C 313 GLU cc_start: 0.8190 (pt0) cc_final: 0.7827 (pt0) REVERT: C 343 MET cc_start: 0.8246 (tpp) cc_final: 0.8004 (tpp) REVERT: C 344 LYS cc_start: 0.9029 (mttm) cc_final: 0.8607 (mttm) REVERT: D 82 ASP cc_start: 0.8152 (t0) cc_final: 0.7904 (t70) REVERT: D 90 TRP cc_start: 0.8284 (m100) cc_final: 0.7591 (m100) REVERT: D 104 LYS cc_start: 0.8347 (tttt) cc_final: 0.8123 (tttt) REVERT: D 131 LEU cc_start: 0.8478 (mp) cc_final: 0.8028 (mt) REVERT: D 139 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7372 (mtmm) REVERT: D 183 LYS cc_start: 0.8396 (mptt) cc_final: 0.8079 (mptt) REVERT: D 212 MET cc_start: 0.7501 (mmp) cc_final: 0.7172 (mmp) REVERT: D 213 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7361 (mtmm) REVERT: D 217 MET cc_start: 0.6867 (mmt) cc_final: 0.6547 (mmt) REVERT: D 250 ARG cc_start: 0.7377 (ptp-170) cc_final: 0.6953 (ptp-170) REVERT: D 251 MET cc_start: 0.7290 (mpp) cc_final: 0.6904 (mpp) REVERT: D 265 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7326 (ptp-170) REVERT: D 300 LYS cc_start: 0.8583 (tptm) cc_final: 0.8265 (tptm) REVERT: D 305 ASP cc_start: 0.7562 (t0) cc_final: 0.7115 (t0) REVERT: D 308 LEU cc_start: 0.8180 (pp) cc_final: 0.7828 (pp) REVERT: D 337 HIS cc_start: 0.7668 (m170) cc_final: 0.7340 (m90) REVERT: E 139 LYS cc_start: 0.8274 (ptpp) cc_final: 0.7845 (ptpt) REVERT: E 158 GLN cc_start: 0.7955 (pm20) cc_final: 0.7607 (pm20) REVERT: E 167 TYR cc_start: 0.7025 (m-10) cc_final: 0.6751 (m-10) REVERT: E 171 GLN cc_start: 0.8504 (mm110) cc_final: 0.8122 (mp10) REVERT: E 193 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7194 (mt-10) REVERT: E 212 MET cc_start: 0.7771 (mmp) cc_final: 0.7152 (mmp) REVERT: E 215 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7076 (tm-30) REVERT: E 248 MET cc_start: 0.7669 (mtp) cc_final: 0.7111 (mtp) REVERT: E 256 HIS cc_start: 0.7678 (t70) cc_final: 0.7269 (t70) REVERT: E 264 GLN cc_start: 0.8486 (mp10) cc_final: 0.8139 (mp10) REVERT: E 266 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7478 (tm-30) REVERT: E 270 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7458 (mmmt) REVERT: E 290 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7647 (mm-30) REVERT: E 295 SER cc_start: 0.7608 (p) cc_final: 0.7318 (p) REVERT: E 298 ASP cc_start: 0.7342 (m-30) cc_final: 0.7058 (m-30) REVERT: E 299 LEU cc_start: 0.8686 (mt) cc_final: 0.8375 (mt) REVERT: E 300 LYS cc_start: 0.8633 (tttt) cc_final: 0.8359 (tttt) REVERT: E 301 GLU cc_start: 0.8419 (tt0) cc_final: 0.7961 (tt0) REVERT: E 302 MET cc_start: 0.8061 (tmm) cc_final: 0.7823 (tmm) REVERT: E 312 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7946 (mtp-110) REVERT: E 313 GLU cc_start: 0.8493 (pt0) cc_final: 0.8198 (pt0) REVERT: E 335 ASP cc_start: 0.8136 (m-30) cc_final: 0.7934 (m-30) REVERT: E 341 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 343 MET cc_start: 0.8271 (tpt) cc_final: 0.7982 (tpt) REVERT: F 68 LYS cc_start: 0.7505 (mppt) cc_final: 0.7084 (mppt) REVERT: F 74 MET cc_start: 0.7545 (mtm) cc_final: 0.7099 (mtm) REVERT: F 82 ASP cc_start: 0.8305 (t0) cc_final: 0.8062 (t0) REVERT: F 90 TRP cc_start: 0.8187 (m100) cc_final: 0.7437 (m100) REVERT: F 102 ASP cc_start: 0.7889 (m-30) cc_final: 0.7629 (m-30) REVERT: F 104 LYS cc_start: 0.8356 (tttt) cc_final: 0.8056 (ttmt) REVERT: F 112 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7544 (mtmt) REVERT: F 124 GLN cc_start: 0.7620 (pp30) cc_final: 0.7315 (pp30) REVERT: F 131 LEU cc_start: 0.8446 (mp) cc_final: 0.7980 (mt) REVERT: F 139 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7264 (mtmm) REVERT: F 180 LEU cc_start: 0.8228 (tt) cc_final: 0.8014 (tt) REVERT: F 183 LYS cc_start: 0.8491 (mptt) cc_final: 0.8183 (mptt) REVERT: F 211 MET cc_start: 0.7358 (mmp) cc_final: 0.6994 (mmp) REVERT: F 212 MET cc_start: 0.7945 (mmp) cc_final: 0.7580 (mmp) REVERT: F 215 GLN cc_start: 0.6901 (tp-100) cc_final: 0.6549 (tp-100) REVERT: F 217 MET cc_start: 0.7406 (mmt) cc_final: 0.6817 (mmt) REVERT: F 219 LEU cc_start: 0.7841 (mt) cc_final: 0.7197 (mt) REVERT: F 248 MET cc_start: 0.6996 (mtp) cc_final: 0.6698 (mtp) REVERT: F 250 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.6951 (ttt-90) REVERT: F 270 LYS cc_start: 0.8365 (pttp) cc_final: 0.7892 (ptmm) REVERT: F 300 LYS cc_start: 0.8393 (tptm) cc_final: 0.7952 (tptm) REVERT: F 302 MET cc_start: 0.7670 (tmm) cc_final: 0.7332 (tmm) REVERT: F 337 HIS cc_start: 0.7691 (m170) cc_final: 0.7395 (m170) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.1214 time to fit residues: 102.9662 Evaluate side-chains 585 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 275 ASN C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 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 = 0.4085 r_free = 0.4085 target = 0.153905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126813 restraints weight = 29741.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131445 restraints weight = 17882.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134656 restraints weight = 12100.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136811 restraints weight = 8882.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.138554 restraints weight = 7010.696| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14142 Z= 0.141 Angle : 0.618 13.354 19146 Z= 0.321 Chirality : 0.044 0.216 2190 Planarity : 0.004 0.051 2448 Dihedral : 11.124 107.981 1962 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.07 % Allowed : 1.24 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.21), residues: 1728 helix: 1.39 (0.17), residues: 936 sheet: 0.91 (0.42), residues: 186 loop : 0.63 (0.30), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 199 TYR 0.020 0.002 TYR F 72 PHE 0.036 0.002 PHE A 216 TRP 0.028 0.003 TRP B 220 HIS 0.007 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00295 (14142) covalent geometry : angle 0.61751 (19146) hydrogen bonds : bond 0.03819 ( 738) hydrogen bonds : angle 4.33656 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 605 time to evaluate : 0.472 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8185 (mtm) cc_final: 0.7722 (mtm) REVERT: A 102 ASP cc_start: 0.7759 (m-30) cc_final: 0.7556 (m-30) REVERT: A 118 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6956 (mt-10) REVERT: A 124 GLN cc_start: 0.8249 (pp30) cc_final: 0.7990 (pp30) REVERT: A 125 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8172 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8313 (mp) cc_final: 0.7997 (tp) REVERT: A 148 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7843 (ttmt) REVERT: A 154 PHE cc_start: 0.7777 (t80) cc_final: 0.7334 (t80) REVERT: A 157 LEU cc_start: 0.8016 (tp) cc_final: 0.7622 (tp) REVERT: A 158 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6686 (tm-30) REVERT: A 169 GLU cc_start: 0.7161 (tt0) cc_final: 0.6901 (tt0) REVERT: A 179 SER cc_start: 0.8914 (t) cc_final: 0.8532 (p) REVERT: A 199 ARG cc_start: 0.7359 (tpp80) cc_final: 0.6344 (tpp80) REVERT: A 206 HIS cc_start: 0.8094 (p90) cc_final: 0.7473 (p90) REVERT: A 211 MET cc_start: 0.7987 (mmp) cc_final: 0.7323 (mmp) REVERT: A 212 MET cc_start: 0.7797 (mmp) cc_final: 0.7540 (mmp) REVERT: A 213 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7791 (mtmt) REVERT: A 216 PHE cc_start: 0.7962 (t80) cc_final: 0.7738 (t80) REVERT: A 217 MET cc_start: 0.8157 (mpp) cc_final: 0.7687 (mpp) REVERT: A 218 SER cc_start: 0.8588 (p) cc_final: 0.8368 (p) REVERT: A 219 LEU cc_start: 0.8780 (mt) cc_final: 0.8504 (mt) REVERT: A 230 GLN cc_start: 0.6015 (mm-40) cc_final: 0.5709 (mm110) REVERT: A 251 MET cc_start: 0.7369 (mmm) cc_final: 0.6883 (mmm) REVERT: A 259 GLN cc_start: 0.7676 (mt0) cc_final: 0.7300 (mt0) REVERT: A 268 ILE cc_start: 0.8166 (mm) cc_final: 0.7858 (mm) REVERT: A 270 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8055 (mmtt) REVERT: A 271 LEU cc_start: 0.8877 (tp) cc_final: 0.8538 (pp) REVERT: A 272 ILE cc_start: 0.8562 (mt) cc_final: 0.8226 (mt) REVERT: A 283 ASP cc_start: 0.6977 (p0) cc_final: 0.6685 (p0) REVERT: A 305 ASP cc_start: 0.8244 (t0) cc_final: 0.7804 (m-30) REVERT: A 338 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7853 (mtp85) REVERT: A 341 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 342 LYS cc_start: 0.8783 (mptt) cc_final: 0.8190 (mptt) REVERT: B 74 MET cc_start: 0.8075 (mtm) cc_final: 0.7361 (mtm) REVERT: B 96 LEU cc_start: 0.7593 (mt) cc_final: 0.7158 (tp) REVERT: B 154 PHE cc_start: 0.7615 (t80) cc_final: 0.7089 (t80) REVERT: B 157 LEU cc_start: 0.8055 (tp) cc_final: 0.7657 (tp) REVERT: B 158 GLN cc_start: 0.7358 (pm20) cc_final: 0.6489 (pm20) REVERT: B 211 MET cc_start: 0.8040 (mmp) cc_final: 0.7700 (mmp) REVERT: B 213 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7711 (mtmt) REVERT: B 215 GLN cc_start: 0.7531 (tp-100) cc_final: 0.6200 (tp-100) REVERT: B 217 MET cc_start: 0.8212 (mpp) cc_final: 0.7496 (mpp) REVERT: B 219 LEU cc_start: 0.8772 (mt) cc_final: 0.7713 (mt) REVERT: B 220 TRP cc_start: 0.7755 (m-10) cc_final: 0.6866 (m-10) REVERT: B 234 MET cc_start: 0.7115 (ttm) cc_final: 0.6805 (ttm) REVERT: B 250 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7207 (mtt180) REVERT: B 259 GLN cc_start: 0.7741 (mt0) cc_final: 0.7323 (mt0) REVERT: B 266 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 268 ILE cc_start: 0.8162 (mm) cc_final: 0.7803 (mm) REVERT: B 270 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7859 (mptt) REVERT: B 271 LEU cc_start: 0.8687 (tp) cc_final: 0.8409 (pp) REVERT: B 272 ILE cc_start: 0.8364 (mt) cc_final: 0.8072 (mt) REVERT: B 286 GLU cc_start: 0.6890 (pm20) cc_final: 0.6609 (pm20) REVERT: B 304 ARG cc_start: 0.7189 (mmp-170) cc_final: 0.6876 (tpm170) REVERT: B 338 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8006 (mtp85) REVERT: B 341 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7062 (mm-30) REVERT: B 342 LYS cc_start: 0.8595 (mptt) cc_final: 0.8157 (mptt) REVERT: B 343 MET cc_start: 0.8251 (tpt) cc_final: 0.6907 (tpt) REVERT: B 344 LYS cc_start: 0.8001 (ptpp) cc_final: 0.7304 (pttt) REVERT: B 347 LYS cc_start: 0.8939 (mptt) cc_final: 0.8410 (mptt) REVERT: C 74 MET cc_start: 0.5698 (mtm) cc_final: 0.5446 (mtm) REVERT: C 86 MET cc_start: 0.5678 (pmm) cc_final: 0.5423 (pmm) REVERT: C 167 TYR cc_start: 0.7423 (m-10) cc_final: 0.7017 (m-10) REVERT: C 170 SER cc_start: 0.8044 (p) cc_final: 0.7451 (p) REVERT: C 171 GLN cc_start: 0.8455 (mm110) cc_final: 0.8067 (mp10) REVERT: C 212 MET cc_start: 0.7694 (mmp) cc_final: 0.7370 (mmp) REVERT: C 215 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7441 (tm-30) REVERT: C 217 MET cc_start: 0.8625 (mmm) cc_final: 0.8247 (tpp) REVERT: C 219 LEU cc_start: 0.7270 (mt) cc_final: 0.6907 (mt) REVERT: C 239 ARG cc_start: 0.7925 (mtt90) cc_final: 0.6995 (ttm110) REVERT: C 248 MET cc_start: 0.7853 (mtp) cc_final: 0.7276 (mtp) REVERT: C 264 GLN cc_start: 0.8419 (mp10) cc_final: 0.8106 (mp10) REVERT: C 270 LYS cc_start: 0.8635 (mmmt) cc_final: 0.7671 (mmmt) REVERT: C 289 GLN cc_start: 0.8156 (mt0) cc_final: 0.7872 (mt0) REVERT: C 299 LEU cc_start: 0.8662 (mt) cc_final: 0.8211 (mt) REVERT: C 300 LYS cc_start: 0.8798 (tttp) cc_final: 0.8531 (tttp) REVERT: C 301 GLU cc_start: 0.8550 (tt0) cc_final: 0.8142 (tt0) REVERT: C 302 MET cc_start: 0.8234 (tmm) cc_final: 0.7986 (tmm) REVERT: C 303 CYS cc_start: 0.8641 (m) cc_final: 0.8129 (m) REVERT: C 304 ARG cc_start: 0.8529 (mtp85) cc_final: 0.7983 (mtp85) REVERT: C 309 LEU cc_start: 0.8670 (tp) cc_final: 0.8408 (tp) REVERT: C 313 GLU cc_start: 0.8235 (pt0) cc_final: 0.7880 (pt0) REVERT: C 335 ASP cc_start: 0.8269 (m-30) cc_final: 0.8024 (m-30) REVERT: C 343 MET cc_start: 0.8324 (tpp) cc_final: 0.7944 (tpp) REVERT: C 344 LYS cc_start: 0.8994 (mttm) cc_final: 0.8522 (mttm) REVERT: D 82 ASP cc_start: 0.8140 (t0) cc_final: 0.7859 (t70) REVERT: D 104 LYS cc_start: 0.8355 (tttt) cc_final: 0.8023 (ttmt) REVERT: D 124 GLN cc_start: 0.7631 (pp30) cc_final: 0.7379 (pp30) REVERT: D 131 LEU cc_start: 0.8483 (mp) cc_final: 0.7950 (mt) REVERT: D 132 TYR cc_start: 0.7525 (p90) cc_final: 0.7264 (p90) REVERT: D 139 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7432 (mtmm) REVERT: D 179 SER cc_start: 0.8261 (p) cc_final: 0.8040 (p) REVERT: D 180 LEU cc_start: 0.8227 (tt) cc_final: 0.7955 (tt) REVERT: D 183 LYS cc_start: 0.8445 (mptt) cc_final: 0.8093 (mptt) REVERT: D 212 MET cc_start: 0.7535 (mmp) cc_final: 0.7223 (mmp) REVERT: D 213 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7414 (mtmm) REVERT: D 217 MET cc_start: 0.6915 (mmt) cc_final: 0.6556 (mmt) REVERT: D 220 TRP cc_start: 0.6413 (t-100) cc_final: 0.5651 (t60) REVERT: D 251 MET cc_start: 0.7566 (mpp) cc_final: 0.6674 (mpp) REVERT: D 265 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7187 (ptp-170) REVERT: D 300 LYS cc_start: 0.8621 (tptm) cc_final: 0.8320 (tptm) REVERT: D 305 ASP cc_start: 0.7633 (t0) cc_final: 0.7171 (t0) REVERT: D 337 HIS cc_start: 0.7751 (m170) cc_final: 0.7410 (m90) REVERT: E 139 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7804 (ptpt) REVERT: E 158 GLN cc_start: 0.7866 (pm20) cc_final: 0.7514 (pm20) REVERT: E 167 TYR cc_start: 0.7223 (m-10) cc_final: 0.6827 (m-10) REVERT: E 171 GLN cc_start: 0.8524 (mm110) cc_final: 0.8105 (mp10) REVERT: E 193 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7267 (mt-10) REVERT: E 212 MET cc_start: 0.7845 (mmp) cc_final: 0.7214 (mmp) REVERT: E 215 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7076 (tm-30) REVERT: E 239 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7329 (ttp-110) REVERT: E 248 MET cc_start: 0.7860 (mtp) cc_final: 0.7364 (mtp) REVERT: E 256 HIS cc_start: 0.7710 (t70) cc_final: 0.7316 (t70) REVERT: E 266 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 270 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7469 (mmmt) REVERT: E 279 ASP cc_start: 0.7349 (p0) cc_final: 0.6922 (t0) REVERT: E 286 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7612 (mm-30) REVERT: E 290 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7667 (mm-30) REVERT: E 298 ASP cc_start: 0.7349 (m-30) cc_final: 0.6872 (m-30) REVERT: E 299 LEU cc_start: 0.8690 (mt) cc_final: 0.8279 (mt) REVERT: E 300 LYS cc_start: 0.8627 (tttt) cc_final: 0.8358 (tttt) REVERT: E 301 GLU cc_start: 0.8412 (tt0) cc_final: 0.7952 (tt0) REVERT: E 303 CYS cc_start: 0.8594 (m) cc_final: 0.8021 (m) REVERT: E 313 GLU cc_start: 0.8490 (pt0) cc_final: 0.8222 (pt0) REVERT: E 335 ASP cc_start: 0.8272 (m-30) cc_final: 0.7860 (m-30) REVERT: E 341 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7747 (mm-30) REVERT: E 343 MET cc_start: 0.8356 (tpt) cc_final: 0.8101 (tpt) REVERT: F 68 LYS cc_start: 0.7545 (mppt) cc_final: 0.7122 (mppt) REVERT: F 74 MET cc_start: 0.7643 (mtm) cc_final: 0.7194 (mtm) REVERT: F 82 ASP cc_start: 0.8309 (t0) cc_final: 0.8085 (t0) REVERT: F 90 TRP cc_start: 0.8221 (m100) cc_final: 0.7366 (m100) REVERT: F 102 ASP cc_start: 0.7940 (m-30) cc_final: 0.7668 (m-30) REVERT: F 104 LYS cc_start: 0.8390 (tttt) cc_final: 0.8086 (ttmt) REVERT: F 112 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7610 (mtmt) REVERT: F 124 GLN cc_start: 0.7612 (pp30) cc_final: 0.7277 (pp30) REVERT: F 131 LEU cc_start: 0.8369 (mp) cc_final: 0.7803 (mt) REVERT: F 139 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7309 (mtmm) REVERT: F 183 LYS cc_start: 0.8501 (mptt) cc_final: 0.8177 (mptt) REVERT: F 211 MET cc_start: 0.7458 (mmp) cc_final: 0.7017 (mmp) REVERT: F 212 MET cc_start: 0.7972 (mmp) cc_final: 0.7697 (mmp) REVERT: F 215 GLN cc_start: 0.6999 (tp-100) cc_final: 0.6633 (tp-100) REVERT: F 217 MET cc_start: 0.7437 (mmt) cc_final: 0.6855 (mmt) REVERT: F 219 LEU cc_start: 0.7860 (mt) cc_final: 0.7200 (mt) REVERT: F 248 MET cc_start: 0.7181 (mtp) cc_final: 0.6715 (mtp) REVERT: F 250 ARG cc_start: 0.7622 (ttt-90) cc_final: 0.7068 (ttt180) REVERT: F 251 MET cc_start: 0.7873 (mpp) cc_final: 0.7441 (mpp) REVERT: F 263 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7753 (mmmm) REVERT: F 270 LYS cc_start: 0.8363 (pttp) cc_final: 0.7845 (ptmm) REVERT: F 298 ASP cc_start: 0.8178 (m-30) cc_final: 0.7951 (m-30) REVERT: F 300 LYS cc_start: 0.8398 (tptm) cc_final: 0.7932 (tptm) REVERT: F 302 MET cc_start: 0.7708 (tmm) cc_final: 0.7434 (tmm) REVERT: F 337 HIS cc_start: 0.7790 (m170) cc_final: 0.7458 (m170) outliers start: 1 outliers final: 0 residues processed: 606 average time/residue: 0.1218 time to fit residues: 104.0317 Evaluate side-chains 586 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 275 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.153484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126554 restraints weight = 29771.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131123 restraints weight = 17810.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134326 restraints weight = 12029.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136617 restraints weight = 8821.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.138263 restraints weight = 6899.159| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14142 Z= 0.139 Angle : 0.628 13.769 19146 Z= 0.327 Chirality : 0.044 0.205 2190 Planarity : 0.004 0.051 2448 Dihedral : 11.058 107.317 1962 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1728 helix: 1.38 (0.17), residues: 936 sheet: 0.62 (0.41), residues: 192 loop : 0.72 (0.30), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 312 TYR 0.025 0.002 TYR D 72 PHE 0.026 0.002 PHE A 216 TRP 0.021 0.003 TRP A 220 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00287 (14142) covalent geometry : angle 0.62812 (19146) hydrogen bonds : bond 0.03879 ( 738) hydrogen bonds : angle 4.35160 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 614 time to evaluate : 0.491 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: 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: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8209 (mtm) cc_final: 0.7700 (mtm) REVERT: A 90 TRP cc_start: 0.8053 (m100) cc_final: 0.6831 (m100) REVERT: A 92 ASP cc_start: 0.7580 (m-30) cc_final: 0.7343 (m-30) REVERT: A 102 ASP cc_start: 0.7708 (m-30) cc_final: 0.7444 (m-30) REVERT: A 104 LYS cc_start: 0.8630 (tttt) cc_final: 0.8246 (tttt) REVERT: A 118 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6938 (mt-10) REVERT: A 124 GLN cc_start: 0.8232 (pp30) cc_final: 0.8008 (pp30) REVERT: A 125 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8164 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8302 (mp) cc_final: 0.7958 (tp) REVERT: A 148 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7811 (ttmt) REVERT: A 154 PHE cc_start: 0.7767 (t80) cc_final: 0.7353 (t80) REVERT: A 157 LEU cc_start: 0.8041 (tp) cc_final: 0.7659 (tp) REVERT: A 158 GLN cc_start: 0.7413 (tm-30) cc_final: 0.6694 (tm-30) REVERT: A 169 GLU cc_start: 0.7195 (tt0) cc_final: 0.6904 (tt0) REVERT: A 179 SER cc_start: 0.8894 (t) cc_final: 0.8546 (p) REVERT: A 199 ARG cc_start: 0.7384 (tpp80) cc_final: 0.6347 (tpp80) REVERT: A 206 HIS cc_start: 0.8089 (p90) cc_final: 0.7461 (p90) REVERT: A 211 MET cc_start: 0.7987 (mmp) cc_final: 0.7335 (mmp) REVERT: A 212 MET cc_start: 0.7854 (mmp) cc_final: 0.7590 (mmp) REVERT: A 213 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7777 (mtmt) REVERT: A 216 PHE cc_start: 0.8068 (t80) cc_final: 0.7840 (t80) REVERT: A 217 MET cc_start: 0.8163 (mpp) cc_final: 0.7521 (mpp) REVERT: A 218 SER cc_start: 0.8577 (p) cc_final: 0.8308 (p) REVERT: A 219 LEU cc_start: 0.8800 (mt) cc_final: 0.8512 (mt) REVERT: A 230 GLN cc_start: 0.6019 (mm-40) cc_final: 0.5720 (mm110) REVERT: A 248 MET cc_start: 0.7669 (mtp) cc_final: 0.7440 (mtp) REVERT: A 251 MET cc_start: 0.7375 (mmm) cc_final: 0.7058 (mmm) REVERT: A 258 ASN cc_start: 0.8288 (p0) cc_final: 0.8007 (p0) REVERT: A 259 GLN cc_start: 0.7667 (mt0) cc_final: 0.7069 (mt0) REVERT: A 268 ILE cc_start: 0.8245 (mm) cc_final: 0.7932 (mm) REVERT: A 270 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8107 (mmtt) REVERT: A 271 LEU cc_start: 0.8875 (tp) cc_final: 0.8541 (pp) REVERT: A 272 ILE cc_start: 0.8531 (mt) cc_final: 0.8205 (mt) REVERT: A 286 GLU cc_start: 0.7732 (pm20) cc_final: 0.7361 (pm20) REVERT: A 301 GLU cc_start: 0.8010 (tt0) cc_final: 0.7013 (tt0) REVERT: A 305 ASP cc_start: 0.8260 (t0) cc_final: 0.7811 (m-30) REVERT: A 338 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7846 (mtp85) REVERT: A 341 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7217 (mm-30) REVERT: A 342 LYS cc_start: 0.8784 (mptt) cc_final: 0.8183 (mptt) REVERT: A 343 MET cc_start: 0.8111 (mmm) cc_final: 0.7591 (mmm) REVERT: B 74 MET cc_start: 0.8080 (mtm) cc_final: 0.7361 (mtm) REVERT: B 85 ASN cc_start: 0.7882 (p0) cc_final: 0.7617 (p0) REVERT: B 86 MET cc_start: 0.7715 (mtm) cc_final: 0.7515 (mtm) REVERT: B 99 VAL cc_start: 0.8181 (t) cc_final: 0.7891 (m) REVERT: B 154 PHE cc_start: 0.7608 (t80) cc_final: 0.7079 (t80) REVERT: B 157 LEU cc_start: 0.8063 (tp) cc_final: 0.7709 (tp) REVERT: B 158 GLN cc_start: 0.7341 (pm20) cc_final: 0.6611 (pm20) REVERT: B 211 MET cc_start: 0.8033 (mmp) cc_final: 0.7717 (mmp) REVERT: B 213 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7735 (mtmt) REVERT: B 215 GLN cc_start: 0.7537 (tp-100) cc_final: 0.6194 (tp-100) REVERT: B 217 MET cc_start: 0.8140 (mpp) cc_final: 0.7624 (mpp) REVERT: B 219 LEU cc_start: 0.8801 (mt) cc_final: 0.7698 (mt) REVERT: B 234 MET cc_start: 0.7141 (ttm) cc_final: 0.6802 (ttm) REVERT: B 237 THR cc_start: 0.8381 (t) cc_final: 0.7821 (m) REVERT: B 259 GLN cc_start: 0.7737 (mt0) cc_final: 0.7296 (mt0) REVERT: B 266 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 270 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7840 (mptt) REVERT: B 304 ARG cc_start: 0.7142 (mmp-170) cc_final: 0.6798 (tpm170) REVERT: B 338 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8012 (mtp85) REVERT: B 341 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7029 (mm-30) REVERT: B 342 LYS cc_start: 0.8607 (mptt) cc_final: 0.7763 (mptt) REVERT: B 343 MET cc_start: 0.8240 (tpt) cc_final: 0.6889 (tpt) REVERT: B 344 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7233 (pttt) REVERT: B 345 LYS cc_start: 0.8687 (pptt) cc_final: 0.8323 (pptt) REVERT: B 347 LYS cc_start: 0.8897 (mptt) cc_final: 0.8397 (mptt) REVERT: C 74 MET cc_start: 0.5669 (mtm) cc_final: 0.5415 (mtm) REVERT: C 86 MET cc_start: 0.5775 (pmm) cc_final: 0.5539 (pmm) REVERT: C 167 TYR cc_start: 0.7398 (m-10) cc_final: 0.7022 (m-10) REVERT: C 170 SER cc_start: 0.8052 (p) cc_final: 0.7468 (p) REVERT: C 171 GLN cc_start: 0.8445 (mm110) cc_final: 0.8078 (mp10) REVERT: C 190 PHE cc_start: 0.6987 (t80) cc_final: 0.6776 (t80) REVERT: C 212 MET cc_start: 0.7704 (mmp) cc_final: 0.7388 (mmp) REVERT: C 215 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7548 (tm-30) REVERT: C 217 MET cc_start: 0.8598 (mmm) cc_final: 0.8211 (tpp) REVERT: C 219 LEU cc_start: 0.7285 (mt) cc_final: 0.7013 (mt) REVERT: C 239 ARG cc_start: 0.7838 (mtt90) cc_final: 0.6913 (ttm110) REVERT: C 248 MET cc_start: 0.7825 (mtp) cc_final: 0.7203 (mtp) REVERT: C 264 GLN cc_start: 0.8470 (mp10) cc_final: 0.8145 (mp10) REVERT: C 270 LYS cc_start: 0.8602 (mmmt) cc_final: 0.7633 (mmmt) REVERT: C 289 GLN cc_start: 0.8094 (mt0) cc_final: 0.7774 (mt0) REVERT: C 299 LEU cc_start: 0.8647 (mt) cc_final: 0.8107 (mt) REVERT: C 300 LYS cc_start: 0.8779 (tttp) cc_final: 0.8533 (tttp) REVERT: C 301 GLU cc_start: 0.8528 (tt0) cc_final: 0.8092 (tt0) REVERT: C 302 MET cc_start: 0.8220 (tmm) cc_final: 0.7999 (tmm) REVERT: C 303 CYS cc_start: 0.8636 (m) cc_final: 0.8133 (m) REVERT: C 304 ARG cc_start: 0.8511 (mtp85) cc_final: 0.7955 (mtp85) REVERT: C 309 LEU cc_start: 0.8658 (tp) cc_final: 0.8402 (tp) REVERT: C 313 GLU cc_start: 0.8237 (pt0) cc_final: 0.7883 (pt0) REVERT: C 343 MET cc_start: 0.8369 (tpp) cc_final: 0.7970 (tpp) REVERT: C 344 LYS cc_start: 0.9005 (mttm) cc_final: 0.8524 (mttm) REVERT: D 82 ASP cc_start: 0.8235 (t0) cc_final: 0.7912 (t70) REVERT: D 104 LYS cc_start: 0.8337 (tttt) cc_final: 0.8040 (ttmt) REVERT: D 124 GLN cc_start: 0.7665 (pp30) cc_final: 0.7391 (pp30) REVERT: D 131 LEU cc_start: 0.8384 (mp) cc_final: 0.7901 (mt) REVERT: D 132 TYR cc_start: 0.7403 (p90) cc_final: 0.7147 (p90) REVERT: D 139 LYS cc_start: 0.7819 (mtmm) cc_final: 0.7442 (mtmm) REVERT: D 183 LYS cc_start: 0.8431 (mptt) cc_final: 0.8071 (mptt) REVERT: D 212 MET cc_start: 0.7504 (mmp) cc_final: 0.7239 (mmp) REVERT: D 213 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7389 (mtmm) REVERT: D 217 MET cc_start: 0.6905 (mmt) cc_final: 0.6461 (mmt) REVERT: D 241 GLN cc_start: 0.8216 (mp-120) cc_final: 0.7411 (mp-120) REVERT: D 251 MET cc_start: 0.7418 (mpp) cc_final: 0.6524 (mpp) REVERT: D 300 LYS cc_start: 0.8616 (tptm) cc_final: 0.8301 (tptm) REVERT: D 305 ASP cc_start: 0.7619 (t0) cc_final: 0.7178 (t0) REVERT: D 337 HIS cc_start: 0.7763 (m170) cc_final: 0.7433 (m90) REVERT: E 139 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7841 (ptpt) REVERT: E 158 GLN cc_start: 0.7815 (pm20) cc_final: 0.7458 (pm20) REVERT: E 167 TYR cc_start: 0.7229 (m-10) cc_final: 0.6866 (m-10) REVERT: E 171 GLN cc_start: 0.8474 (mm110) cc_final: 0.8105 (mp10) REVERT: E 193 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7260 (mt-10) REVERT: E 212 MET cc_start: 0.7942 (mmp) cc_final: 0.7226 (mmp) REVERT: E 215 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7092 (tm-30) REVERT: E 239 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7327 (ttp-110) REVERT: E 248 MET cc_start: 0.7901 (mtp) cc_final: 0.7340 (mtp) REVERT: E 250 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7613 (mmm160) REVERT: E 256 HIS cc_start: 0.7663 (t70) cc_final: 0.7291 (t70) REVERT: E 264 GLN cc_start: 0.8520 (mp10) cc_final: 0.8180 (mp10) REVERT: E 266 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 270 LYS cc_start: 0.8491 (mmmt) cc_final: 0.7481 (mmmt) REVERT: E 279 ASP cc_start: 0.7368 (p0) cc_final: 0.6861 (t0) REVERT: E 290 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7749 (mm-30) REVERT: E 299 LEU cc_start: 0.8725 (mt) cc_final: 0.8300 (mt) REVERT: E 300 LYS cc_start: 0.8637 (tttt) cc_final: 0.8369 (tttt) REVERT: E 301 GLU cc_start: 0.8423 (tt0) cc_final: 0.7919 (tt0) REVERT: E 303 CYS cc_start: 0.8593 (m) cc_final: 0.8073 (m) REVERT: E 312 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7846 (mtp-110) REVERT: E 313 GLU cc_start: 0.8489 (pt0) cc_final: 0.8229 (pt0) REVERT: E 335 ASP cc_start: 0.8323 (m-30) cc_final: 0.8114 (m-30) REVERT: E 340 ILE cc_start: 0.8501 (mt) cc_final: 0.8260 (mt) REVERT: E 341 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 343 MET cc_start: 0.8395 (tpt) cc_final: 0.8158 (tpt) REVERT: F 68 LYS cc_start: 0.7565 (mppt) cc_final: 0.7122 (mppt) REVERT: F 74 MET cc_start: 0.7701 (mtm) cc_final: 0.7188 (mtm) REVERT: F 82 ASP cc_start: 0.8338 (t0) cc_final: 0.8106 (t70) REVERT: F 90 TRP cc_start: 0.8218 (m100) cc_final: 0.7288 (m100) REVERT: F 102 ASP cc_start: 0.7994 (m-30) cc_final: 0.7584 (m-30) REVERT: F 104 LYS cc_start: 0.8368 (tttt) cc_final: 0.8069 (ttmt) REVERT: F 112 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7614 (mtmt) REVERT: F 119 ASN cc_start: 0.7579 (p0) cc_final: 0.7320 (t0) REVERT: F 124 GLN cc_start: 0.7603 (pp30) cc_final: 0.7282 (pp30) REVERT: F 131 LEU cc_start: 0.8358 (mp) cc_final: 0.8130 (mt) REVERT: F 180 LEU cc_start: 0.8369 (tt) cc_final: 0.8154 (tt) REVERT: F 183 LYS cc_start: 0.8519 (mptt) cc_final: 0.8165 (mptt) REVERT: F 211 MET cc_start: 0.7506 (mmp) cc_final: 0.7041 (mmp) REVERT: F 212 MET cc_start: 0.7997 (mmp) cc_final: 0.7701 (mmp) REVERT: F 215 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6703 (tp-100) REVERT: F 217 MET cc_start: 0.7469 (mmt) cc_final: 0.6873 (mmt) REVERT: F 219 LEU cc_start: 0.7905 (mt) cc_final: 0.7206 (mt) REVERT: F 234 MET cc_start: 0.7338 (ttp) cc_final: 0.7017 (ttp) REVERT: F 248 MET cc_start: 0.7221 (mtp) cc_final: 0.6775 (mtp) REVERT: F 250 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7104 (ttt180) REVERT: F 251 MET cc_start: 0.7804 (mpp) cc_final: 0.7320 (mpp) REVERT: F 263 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7720 (mmmm) REVERT: F 265 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7547 (ptp-170) REVERT: F 270 LYS cc_start: 0.8355 (pttp) cc_final: 0.7843 (ptmm) REVERT: F 300 LYS cc_start: 0.8402 (tptm) cc_final: 0.7969 (tptm) REVERT: F 302 MET cc_start: 0.7742 (tmm) cc_final: 0.7450 (tmm) REVERT: F 337 HIS cc_start: 0.7812 (m170) cc_final: 0.7472 (m170) outliers start: 1 outliers final: 1 residues processed: 615 average time/residue: 0.1187 time to fit residues: 103.2742 Evaluate side-chains 593 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 67 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125803 restraints weight = 29998.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130315 restraints weight = 17860.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133461 restraints weight = 12059.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135644 restraints weight = 8841.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137180 restraints weight = 6949.975| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14142 Z= 0.139 Angle : 0.624 13.993 19146 Z= 0.321 Chirality : 0.044 0.199 2190 Planarity : 0.004 0.053 2448 Dihedral : 10.978 105.728 1962 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1728 helix: 1.47 (0.17), residues: 906 sheet: 0.47 (0.41), residues: 192 loop : 0.50 (0.29), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 199 TYR 0.011 0.002 TYR F 72 PHE 0.021 0.002 PHE A 216 TRP 0.034 0.003 TRP A 220 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00290 (14142) covalent geometry : angle 0.62433 (19146) hydrogen bonds : bond 0.03820 ( 738) hydrogen bonds : angle 4.31022 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 614 time to evaluate : 0.578 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: 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: symmetry clash REVERT: A 74 MET cc_start: 0.8219 (mtm) cc_final: 0.7686 (mtm) REVERT: A 92 ASP cc_start: 0.7624 (m-30) cc_final: 0.7401 (m-30) REVERT: A 102 ASP cc_start: 0.7742 (m-30) cc_final: 0.7540 (m-30) REVERT: A 118 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6978 (mt-10) REVERT: A 124 GLN cc_start: 0.8208 (pp30) cc_final: 0.7997 (pp30) REVERT: A 125 PRO cc_start: 0.8696 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8314 (mp) cc_final: 0.7997 (tp) REVERT: A 148 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7900 (ttmt) REVERT: A 154 PHE cc_start: 0.7721 (t80) cc_final: 0.7362 (t80) REVERT: A 157 LEU cc_start: 0.8024 (tp) cc_final: 0.7635 (tp) REVERT: A 158 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 169 GLU cc_start: 0.7249 (tt0) cc_final: 0.6923 (tt0) REVERT: A 179 SER cc_start: 0.8888 (t) cc_final: 0.8508 (p) REVERT: A 193 GLU cc_start: 0.7725 (tt0) cc_final: 0.7516 (tt0) REVERT: A 199 ARG cc_start: 0.7394 (tpp80) cc_final: 0.6360 (tpp80) REVERT: A 206 HIS cc_start: 0.8092 (p90) cc_final: 0.7462 (p90) REVERT: A 211 MET cc_start: 0.7998 (mmp) cc_final: 0.7346 (mmp) REVERT: A 212 MET cc_start: 0.7842 (mmp) cc_final: 0.7590 (mmp) REVERT: A 213 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7779 (mtmt) REVERT: A 216 PHE cc_start: 0.7990 (t80) cc_final: 0.7762 (t80) REVERT: A 217 MET cc_start: 0.7979 (mpp) cc_final: 0.7581 (mpp) REVERT: A 218 SER cc_start: 0.8510 (p) cc_final: 0.8266 (p) REVERT: A 219 LEU cc_start: 0.8784 (mt) cc_final: 0.8497 (mt) REVERT: A 230 GLN cc_start: 0.6074 (mm-40) cc_final: 0.5767 (mm110) REVERT: A 241 GLN cc_start: 0.8409 (mm110) cc_final: 0.8063 (mm-40) REVERT: A 248 MET cc_start: 0.7770 (mtp) cc_final: 0.7543 (mtp) REVERT: A 251 MET cc_start: 0.7319 (mmm) cc_final: 0.7118 (mmm) REVERT: A 258 ASN cc_start: 0.8316 (p0) cc_final: 0.7975 (p0) REVERT: A 259 GLN cc_start: 0.7681 (mt0) cc_final: 0.7086 (mt0) REVERT: A 270 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8121 (mmtt) REVERT: A 271 LEU cc_start: 0.8869 (tp) cc_final: 0.8536 (pp) REVERT: A 272 ILE cc_start: 0.8545 (mt) cc_final: 0.8185 (mt) REVERT: A 286 GLU cc_start: 0.7691 (pm20) cc_final: 0.7339 (pm20) REVERT: A 301 GLU cc_start: 0.8097 (tt0) cc_final: 0.7093 (tt0) REVERT: A 305 ASP cc_start: 0.8319 (t0) cc_final: 0.7984 (m-30) REVERT: A 338 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7839 (mtp85) REVERT: A 341 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 342 LYS cc_start: 0.8783 (mptt) cc_final: 0.8223 (mptt) REVERT: A 343 MET cc_start: 0.8117 (mmm) cc_final: 0.7541 (mmm) REVERT: A 345 LYS cc_start: 0.8664 (pptt) cc_final: 0.8457 (pptt) REVERT: B 74 MET cc_start: 0.8037 (mtm) cc_final: 0.7358 (mtm) REVERT: B 99 VAL cc_start: 0.8171 (t) cc_final: 0.7888 (m) REVERT: B 114 LYS cc_start: 0.7521 (ptmm) cc_final: 0.7316 (ptmm) REVERT: B 132 TYR cc_start: 0.7261 (p90) cc_final: 0.6659 (p90) REVERT: B 139 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7627 (pttm) REVERT: B 157 LEU cc_start: 0.8065 (tp) cc_final: 0.7686 (tp) REVERT: B 158 GLN cc_start: 0.7343 (pm20) cc_final: 0.6505 (pm20) REVERT: B 211 MET cc_start: 0.8053 (mmp) cc_final: 0.7740 (mmp) REVERT: B 213 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7701 (mtmt) REVERT: B 215 GLN cc_start: 0.7615 (tp-100) cc_final: 0.6328 (tp-100) REVERT: B 217 MET cc_start: 0.8173 (mpp) cc_final: 0.7695 (mpp) REVERT: B 219 LEU cc_start: 0.8794 (mt) cc_final: 0.7759 (mt) REVERT: B 234 MET cc_start: 0.7121 (ttm) cc_final: 0.6742 (ttm) REVERT: B 237 THR cc_start: 0.8454 (t) cc_final: 0.7922 (m) REVERT: B 259 GLN cc_start: 0.7783 (mt0) cc_final: 0.7365 (mt0) REVERT: B 266 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 268 ILE cc_start: 0.8141 (mm) cc_final: 0.7781 (mm) REVERT: B 270 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7863 (mptt) REVERT: B 271 LEU cc_start: 0.8688 (tp) cc_final: 0.8416 (pp) REVERT: B 272 ILE cc_start: 0.8331 (mt) cc_final: 0.8094 (mt) REVERT: B 286 GLU cc_start: 0.6868 (pm20) cc_final: 0.6626 (pm20) REVERT: B 299 LEU cc_start: 0.8785 (mt) cc_final: 0.8440 (mt) REVERT: B 304 ARG cc_start: 0.7228 (mmp-170) cc_final: 0.6737 (tpm170) REVERT: B 338 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8034 (mtp85) REVERT: B 341 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6990 (mm-30) REVERT: B 342 LYS cc_start: 0.8614 (mptt) cc_final: 0.7784 (mptt) REVERT: B 343 MET cc_start: 0.8219 (tpt) cc_final: 0.6883 (tpt) REVERT: B 344 LYS cc_start: 0.7895 (ptpp) cc_final: 0.7161 (pttt) REVERT: B 345 LYS cc_start: 0.8681 (pptt) cc_final: 0.8325 (pptt) REVERT: B 347 LYS cc_start: 0.8897 (mptt) cc_final: 0.8381 (mptt) REVERT: C 74 MET cc_start: 0.5656 (mtm) cc_final: 0.5424 (mtm) REVERT: C 86 MET cc_start: 0.5789 (pmm) cc_final: 0.5522 (pmm) REVERT: C 167 TYR cc_start: 0.7335 (m-10) cc_final: 0.6896 (m-10) REVERT: C 170 SER cc_start: 0.8042 (p) cc_final: 0.7467 (p) REVERT: C 171 GLN cc_start: 0.8412 (mm110) cc_final: 0.8098 (mp10) REVERT: C 212 MET cc_start: 0.7690 (mmp) cc_final: 0.7450 (mmp) REVERT: C 215 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7537 (tm-30) REVERT: C 217 MET cc_start: 0.8624 (mmm) cc_final: 0.8246 (tpp) REVERT: C 219 LEU cc_start: 0.7299 (mt) cc_final: 0.7035 (mt) REVERT: C 229 CYS cc_start: 0.7686 (t) cc_final: 0.6769 (p) REVERT: C 239 ARG cc_start: 0.7886 (mtt90) cc_final: 0.6961 (ttm110) REVERT: C 248 MET cc_start: 0.7817 (mtp) cc_final: 0.7187 (mtp) REVERT: C 264 GLN cc_start: 0.8426 (mp10) cc_final: 0.8114 (mp10) REVERT: C 270 LYS cc_start: 0.8635 (mmmt) cc_final: 0.7699 (mmmt) REVERT: C 289 GLN cc_start: 0.8056 (mt0) cc_final: 0.7722 (mt0) REVERT: C 299 LEU cc_start: 0.8658 (mt) cc_final: 0.8201 (mt) REVERT: C 300 LYS cc_start: 0.8774 (tttp) cc_final: 0.8533 (tttp) REVERT: C 301 GLU cc_start: 0.8547 (tt0) cc_final: 0.8115 (tt0) REVERT: C 302 MET cc_start: 0.8187 (tmm) cc_final: 0.7980 (tmm) REVERT: C 303 CYS cc_start: 0.8691 (m) cc_final: 0.8191 (m) REVERT: C 304 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7923 (mtp85) REVERT: C 309 LEU cc_start: 0.8641 (tp) cc_final: 0.8397 (tp) REVERT: C 313 GLU cc_start: 0.8328 (pt0) cc_final: 0.7961 (pt0) REVERT: C 335 ASP cc_start: 0.8332 (m-30) cc_final: 0.7959 (m-30) REVERT: C 343 MET cc_start: 0.8410 (tpp) cc_final: 0.8017 (tpp) REVERT: C 344 LYS cc_start: 0.9010 (mttm) cc_final: 0.8551 (mttm) REVERT: D 82 ASP cc_start: 0.8144 (t0) cc_final: 0.7870 (t70) REVERT: D 97 ASP cc_start: 0.7586 (p0) cc_final: 0.7367 (p0) REVERT: D 104 LYS cc_start: 0.8331 (tttt) cc_final: 0.8048 (ttmt) REVERT: D 131 LEU cc_start: 0.8333 (mp) cc_final: 0.7860 (mt) REVERT: D 132 TYR cc_start: 0.7327 (p90) cc_final: 0.7112 (p90) REVERT: D 139 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7455 (mtmm) REVERT: D 180 LEU cc_start: 0.8281 (tt) cc_final: 0.8069 (tt) REVERT: D 183 LYS cc_start: 0.8395 (mptt) cc_final: 0.8009 (mptt) REVERT: D 212 MET cc_start: 0.7563 (mmp) cc_final: 0.7340 (mmp) REVERT: D 213 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7410 (mtmm) REVERT: D 217 MET cc_start: 0.6831 (mmt) cc_final: 0.6401 (mmt) REVERT: D 241 GLN cc_start: 0.8206 (mp-120) cc_final: 0.7397 (mp-120) REVERT: D 251 MET cc_start: 0.7540 (mpp) cc_final: 0.6738 (mpp) REVERT: D 300 LYS cc_start: 0.8631 (tptm) cc_final: 0.8333 (tptm) REVERT: D 305 ASP cc_start: 0.7622 (t0) cc_final: 0.7199 (t0) REVERT: D 337 HIS cc_start: 0.7793 (m170) cc_final: 0.7427 (m90) REVERT: E 139 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7873 (ptpt) REVERT: E 158 GLN cc_start: 0.7781 (pm20) cc_final: 0.7411 (pm20) REVERT: E 167 TYR cc_start: 0.7292 (m-10) cc_final: 0.6830 (m-10) REVERT: E 171 GLN cc_start: 0.8461 (mm110) cc_final: 0.8060 (mp10) REVERT: E 193 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 212 MET cc_start: 0.7968 (mmp) cc_final: 0.7300 (mmp) REVERT: E 215 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7074 (tm-30) REVERT: E 239 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7254 (ttp-110) REVERT: E 248 MET cc_start: 0.7839 (mtp) cc_final: 0.7319 (mtp) REVERT: E 250 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7564 (mmm160) REVERT: E 256 HIS cc_start: 0.7660 (t70) cc_final: 0.7332 (t70) REVERT: E 264 GLN cc_start: 0.8518 (mp10) cc_final: 0.8207 (mp10) REVERT: E 266 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 270 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7461 (mmmt) REVERT: E 279 ASP cc_start: 0.7431 (p0) cc_final: 0.6884 (t0) REVERT: E 290 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7753 (mm-30) REVERT: E 299 LEU cc_start: 0.8702 (mt) cc_final: 0.8272 (mt) REVERT: E 300 LYS cc_start: 0.8646 (tttt) cc_final: 0.8404 (tttt) REVERT: E 301 GLU cc_start: 0.8466 (tt0) cc_final: 0.7952 (tt0) REVERT: E 303 CYS cc_start: 0.8650 (m) cc_final: 0.8096 (m) REVERT: E 312 ARG cc_start: 0.8182 (mtp-110) cc_final: 0.7835 (mtp-110) REVERT: E 313 GLU cc_start: 0.8503 (pt0) cc_final: 0.8243 (pt0) REVERT: E 335 ASP cc_start: 0.8301 (m-30) cc_final: 0.8044 (m-30) REVERT: E 341 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7751 (mm-30) REVERT: E 343 MET cc_start: 0.8437 (tpt) cc_final: 0.8191 (tpt) REVERT: F 73 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8140 (mt-10) REVERT: F 74 MET cc_start: 0.7683 (mtm) cc_final: 0.7163 (mtm) REVERT: F 90 TRP cc_start: 0.8244 (m100) cc_final: 0.7273 (m100) REVERT: F 102 ASP cc_start: 0.7960 (m-30) cc_final: 0.7565 (m-30) REVERT: F 104 LYS cc_start: 0.8372 (tttt) cc_final: 0.8051 (ttmt) REVERT: F 112 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7621 (mtmt) REVERT: F 119 ASN cc_start: 0.7683 (p0) cc_final: 0.7432 (t0) REVERT: F 124 GLN cc_start: 0.7575 (pp30) cc_final: 0.7238 (pp30) REVERT: F 131 LEU cc_start: 0.8371 (mp) cc_final: 0.8049 (mt) REVERT: F 183 LYS cc_start: 0.8527 (mptt) cc_final: 0.8171 (mptt) REVERT: F 211 MET cc_start: 0.7501 (mmp) cc_final: 0.6978 (mmp) REVERT: F 212 MET cc_start: 0.7953 (mmp) cc_final: 0.7677 (mmp) REVERT: F 215 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6687 (tp-100) REVERT: F 217 MET cc_start: 0.7463 (mmt) cc_final: 0.6867 (mmt) REVERT: F 219 LEU cc_start: 0.7931 (mt) cc_final: 0.7211 (mt) REVERT: F 234 MET cc_start: 0.7359 (ttp) cc_final: 0.7018 (ttp) REVERT: F 248 MET cc_start: 0.7298 (mtp) cc_final: 0.6829 (mtp) REVERT: F 250 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7097 (ttt180) REVERT: F 251 MET cc_start: 0.7810 (mpp) cc_final: 0.7329 (mpp) REVERT: F 263 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7773 (mmmm) REVERT: F 270 LYS cc_start: 0.8339 (pttp) cc_final: 0.7891 (ptmm) REVERT: F 300 LYS cc_start: 0.8355 (tptm) cc_final: 0.7914 (tptm) REVERT: F 302 MET cc_start: 0.7771 (tmm) cc_final: 0.7507 (tmm) REVERT: F 337 HIS cc_start: 0.7843 (m170) cc_final: 0.7499 (m170) outliers start: 1 outliers final: 0 residues processed: 615 average time/residue: 0.1173 time to fit residues: 101.8400 Evaluate side-chains 588 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 31 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 88 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127876 restraints weight = 29697.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132404 restraints weight = 17709.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.135577 restraints weight = 11970.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137708 restraints weight = 8764.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139320 restraints weight = 6862.885| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14142 Z= 0.116 Angle : 0.613 14.259 19146 Z= 0.317 Chirality : 0.044 0.238 2190 Planarity : 0.004 0.052 2448 Dihedral : 10.864 104.943 1962 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.22), residues: 1728 helix: 1.23 (0.17), residues: 954 sheet: 0.49 (0.44), residues: 156 loop : 0.45 (0.30), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 199 TYR 0.014 0.002 TYR B 132 PHE 0.026 0.002 PHE A 216 TRP 0.040 0.003 TRP A 90 HIS 0.003 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00243 (14142) covalent geometry : angle 0.61302 (19146) hydrogen bonds : bond 0.03584 ( 738) hydrogen bonds : angle 4.21618 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.32 seconds wall clock time: 44 minutes 42.39 seconds (2682.39 seconds total)