Starting phenix.real_space_refine on Fri Jul 3 11:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_43639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_43639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_43639.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_43639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxt_43639/07_2026/8vxt_43639.map" } 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-dev-6108/lib/python3.11/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: 1.79, per 1000 atoms: 0.13 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: 1.22 Conformation dependent library (CDL) restraints added in 587.9 milliseconds 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: 0.28 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: 1.47 Time building geometry restraints manager: 1.60 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=" O3B AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3B AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 14137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18810 2.43 - 4.85: 251 4.85 - 7.28: 31 7.28 - 9.70: 41 9.70 - 12.13: 13 Bond angle restraints: 19146 Sorted by residual: angle pdb=" N GLY A 168 " pdb=" CA GLY A 168 " pdb=" C GLY A 168 " ideal model delta sigma weight residual 114.67 109.78 4.89 1.10e+00 8.26e-01 1.98e+01 angle pdb=" N GLY F 168 " pdb=" CA GLY F 168 " pdb=" C GLY F 168 " ideal model delta sigma weight residual 114.40 109.72 4.68 1.11e+00 8.12e-01 1.78e+01 angle pdb=" N GLY C 168 " pdb=" CA GLY C 168 " pdb=" C GLY C 168 " ideal model delta sigma weight residual 114.40 109.74 4.66 1.11e+00 8.12e-01 1.76e+01 angle pdb=" N GLY D 168 " pdb=" CA GLY D 168 " pdb=" C GLY D 168 " ideal model delta sigma weight residual 114.40 109.75 4.65 1.11e+00 8.12e-01 1.76e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 114.40 109.76 4.64 1.11e+00 8.12e-01 1.74e+01 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 7742 15.10 - 30.20: 832 30.20 - 45.29: 168 45.29 - 60.39: 77 60.39 - 75.49: 73 Dihedral angle restraints: 8892 sinusoidal: 3786 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 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 2166 0.231 - 0.462: 6 0.462 - 0.692: 0 0.692 - 0.923: 0 0.923 - 1.154: 6 Chirality restraints: 2178 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 -2.41 -1.26 -1.15 2.00e-01 2.50e+01 3.33e+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 -2.41 -1.26 -1.15 2.00e-01 2.50e+01 3.33e+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 -2.41 -1.26 -1.15 2.00e-01 2.50e+01 3.32e+01 ... (remaining 2175 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: 0.03 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.610 Find NCS groups from input model: 0.080 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 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 : 0.005 0.094 14142 Z= 0.237 Angle : 0.856 12.127 19146 Z= 0.421 Chirality : 0.074 1.154 2178 Planarity : 0.005 0.060 2448 Dihedral : 15.595 75.492 5544 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 are 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/Z covalent geometry : bond 0.00468 / 0.24 (14142) covalent geometry : angle 0.85601 / 0.42 (19146) hydrogen bonds : bond 0.14727 / 9.85 ( 738) hydrogen bonds : angle 5.66385 / 4.08 ( 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 : 0.526 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: 0.8225 (tttt) cc_final: 0.7642 (ttmt) REVERT: A 154 PHE cc_start: 0.7643 (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: 0.7580 (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: 0.7654 (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: 0.8656 (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: 0.7907 (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: 0.7053 (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: 0.8334 (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: 0.6845 (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: 0.8559 (mt) cc_final: 0.8317 (mt) REVERT: E 290 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7515 (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: 0.8478 (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: 0.8162 (p0) cc_final: 0.7645 (p0) REVERT: F 104 LYS cc_start: 0.8311 (tttt) cc_final: 0.8078 (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: 0.4964 (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: 0.6953 (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: 0.1275 time to fit residues: 106.3273 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 : 0.519 ------------------------------------------------------------------------------- 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... A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 275 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4114 r_free = 0.4114 target = 0.156777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.129773 restraints weight = 30099.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134448 restraints weight = 18331.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137641 restraints weight = 12450.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140013 restraints weight = 9187.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141630 restraints weight = 7155.049| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14142 Z= 0.148 Angle : 0.628 9.872 19146 Z= 0.325 Chirality : 0.044 0.152 2178 Planarity : 0.004 0.054 2448 Dihedral : 9.878 57.947 2070 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.20 % Allowed : 2.55 % Favored : 97.25 % 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 are not related in a simple way. whole: 1.31 (0.21), residues: 1728 helix: 1.21 (0.16), residues: 972 sheet: 0.93 (0.39), residues: 186 loop : 0.47 (0.30), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 304 TYR 0.013 0.002 TYR B 314 PHE 0.018 0.002 PHE D 197 TRP 0.014 0.002 TRP D 90 HIS 0.008 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (14142) covalent geometry : angle 0.62775 / 0.32 (19146) hydrogen bonds : bond 0.04307 / 2.81 ( 738) hydrogen bonds : angle 4.33330 / 3.08 ( 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 595 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 592 time to evaluate : 0.513 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: 0.8063 (mtm) cc_final: 0.7617 (mtm) REVERT: A 85 ASN cc_start: 0.7963 (p0) cc_final: 0.7736 (p0) REVERT: A 86 MET cc_start: 0.7594 (mtm) cc_final: 0.7388 (mtm) REVERT: A 90 TRP cc_start: 0.7958 (m100) cc_final: 0.6986 (m100) REVERT: A 101 THR cc_start: 0.8368 (p) cc_final: 0.8007 (t) REVERT: A 104 LYS cc_start: 0.8662 (tttt) cc_final: 0.8261 (tttt) REVERT: A 114 LYS cc_start: 0.7794 (tptm) cc_final: 0.7338 (tptm) REVERT: A 124 GLN cc_start: 0.8051 (pp30) cc_final: 0.7729 (pp30) REVERT: A 125 PRO cc_start: 0.8307 (Cg_endo) cc_final: 0.7777 (Cg_exo) REVERT: A 132 TYR cc_start: 0.7397 (p90) cc_final: 0.6598 (p90) REVERT: A 141 LEU cc_start: 0.8495 (tp) cc_final: 0.8290 (tp) REVERT: A 148 LYS cc_start: 0.8368 (tttt) cc_final: 0.8013 (ttmt) REVERT: A 157 LEU cc_start: 0.7983 (tp) cc_final: 0.7683 (tp) REVERT: A 177 VAL cc_start: 0.8732 (t) cc_final: 0.8499 (t) REVERT: A 179 SER cc_start: 0.8877 (t) cc_final: 0.8619 (p) REVERT: A 199 ARG cc_start: 0.7177 (tpp80) cc_final: 0.6380 (tpp80) REVERT: A 206 HIS cc_start: 0.8067 (p90) cc_final: 0.7298 (p90) REVERT: A 211 MET cc_start: 0.7908 (mmp) cc_final: 0.7213 (mmt) REVERT: A 213 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7728 (mtmt) REVERT: A 215 GLN cc_start: 0.7639 (tp-100) cc_final: 0.6382 (tp-100) REVERT: A 217 MET cc_start: 0.7949 (mpp) cc_final: 0.7544 (mpp) REVERT: A 219 LEU cc_start: 0.8752 (mt) cc_final: 0.7779 (mt) REVERT: A 232 ILE cc_start: 0.8427 (mt) cc_final: 0.8063 (mt) REVERT: A 243 LEU cc_start: 0.8166 (mt) cc_final: 0.7924 (mt) REVERT: A 259 GLN cc_start: 0.7447 (mt0) cc_final: 0.7087 (mt0) REVERT: A 266 GLU cc_start: 0.7641 (tp30) cc_final: 0.7418 (tp30) REVERT: A 286 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 301 GLU cc_start: 0.8103 (tt0) cc_final: 0.6699 (tt0) REVERT: A 305 ASP cc_start: 0.8259 (t0) cc_final: 0.8018 (m-30) REVERT: A 338 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7686 (mtp85) REVERT: A 341 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 342 LYS cc_start: 0.8663 (mptt) cc_final: 0.8221 (mptt) REVERT: A 343 MET cc_start: 0.8145 (tpt) cc_final: 0.7763 (tpt) REVERT: B 74 MET cc_start: 0.7920 (mtm) cc_final: 0.7173 (mtm) REVERT: B 90 TRP cc_start: 0.8101 (m100) cc_final: 0.7787 (m100) REVERT: B 122 LEU cc_start: 0.7921 (pt) cc_final: 0.7594 (tp) REVERT: B 148 LYS cc_start: 0.8417 (tttt) cc_final: 0.7859 (ttmt) REVERT: B 157 LEU cc_start: 0.8052 (tp) cc_final: 0.7798 (tp) REVERT: B 211 MET cc_start: 0.7925 (mmp) cc_final: 0.7597 (mmp) REVERT: B 213 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7676 (mtmt) REVERT: B 215 GLN cc_start: 0.7550 (tp-100) cc_final: 0.6588 (tp-100) REVERT: B 217 MET cc_start: 0.8037 (mpp) cc_final: 0.7523 (mpp) REVERT: B 231 VAL cc_start: 0.7843 (t) cc_final: 0.7617 (p) REVERT: B 232 ILE cc_start: 0.8348 (mt) cc_final: 0.8005 (mt) REVERT: B 243 LEU cc_start: 0.8386 (mt) cc_final: 0.8095 (mt) REVERT: B 259 GLN cc_start: 0.7649 (mt0) cc_final: 0.7261 (mt0) REVERT: B 266 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 295 SER cc_start: 0.7040 (p) cc_final: 0.6696 (p) REVERT: B 299 LEU cc_start: 0.8780 (mt) cc_final: 0.8464 (mt) REVERT: B 331 VAL cc_start: 0.7630 (t) cc_final: 0.7394 (m) REVERT: B 341 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 342 LYS cc_start: 0.8594 (mptt) cc_final: 0.7841 (mptt) REVERT: B 343 MET cc_start: 0.8116 (tpt) cc_final: 0.6792 (tpt) REVERT: B 345 LYS cc_start: 0.8815 (pptt) cc_final: 0.8582 (pptt) REVERT: B 347 LYS cc_start: 0.8835 (mptt) cc_final: 0.8369 (mptt) REVERT: C 158 GLN cc_start: 0.8192 (pm20) cc_final: 0.7942 (pm20) REVERT: C 171 GLN cc_start: 0.7954 (mp10) cc_final: 0.7611 (mp10) REVERT: C 199 ARG cc_start: 0.6260 (tpp80) cc_final: 0.5905 (tpp80) REVERT: C 212 MET cc_start: 0.7468 (mmp) cc_final: 0.7027 (mmp) REVERT: C 239 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7055 (mtt90) REVERT: C 248 MET cc_start: 0.7827 (mtp) cc_final: 0.7262 (mtp) REVERT: C 251 MET cc_start: 0.6451 (mmt) cc_final: 0.5925 (mmt) REVERT: C 264 GLN cc_start: 0.8293 (mp10) cc_final: 0.8072 (mp10) REVERT: C 270 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7555 (mmmt) REVERT: C 284 LEU cc_start: 0.8639 (mt) cc_final: 0.8249 (mt) REVERT: C 289 GLN cc_start: 0.8091 (mt0) cc_final: 0.7814 (mt0) REVERT: C 299 LEU cc_start: 0.8616 (mt) cc_final: 0.8355 (mt) REVERT: C 302 MET cc_start: 0.8020 (tmm) cc_final: 0.7707 (tmm) REVERT: C 308 LEU cc_start: 0.8526 (tp) cc_final: 0.8277 (tp) REVERT: C 313 GLU cc_start: 0.8039 (pt0) cc_final: 0.7816 (pt0) REVERT: C 335 ASP cc_start: 0.7804 (m-30) cc_final: 0.7516 (m-30) REVERT: C 343 MET cc_start: 0.8310 (tpt) cc_final: 0.7354 (tpt) REVERT: C 344 LYS cc_start: 0.9043 (mttm) cc_final: 0.8635 (mttm) REVERT: D 82 ASP cc_start: 0.8104 (t0) cc_final: 0.7608 (t70) REVERT: D 90 TRP cc_start: 0.7863 (m100) cc_final: 0.7196 (m100) REVERT: D 104 LYS cc_start: 0.8285 (tttt) cc_final: 0.7935 (tttm) REVERT: D 131 LEU cc_start: 0.8415 (mp) cc_final: 0.8191 (mp) REVERT: D 132 TYR cc_start: 0.7403 (p90) cc_final: 0.7098 (p90) REVERT: D 139 LYS cc_start: 0.7526 (mtmm) cc_final: 0.6631 (mtmm) REVERT: D 183 LYS cc_start: 0.8485 (mptt) cc_final: 0.8102 (mptt) REVERT: D 212 MET cc_start: 0.7882 (mmp) cc_final: 0.7597 (mmp) REVERT: D 217 MET cc_start: 0.6842 (mmp) cc_final: 0.6492 (mmp) REVERT: D 248 MET cc_start: 0.6998 (mtp) cc_final: 0.6507 (mtp) REVERT: D 300 LYS cc_start: 0.8534 (tptm) cc_final: 0.8231 (tptm) REVERT: D 302 MET cc_start: 0.7709 (tmm) cc_final: 0.7407 (tmm) REVERT: D 305 ASP cc_start: 0.7499 (t0) cc_final: 0.7103 (t0) REVERT: D 312 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7797 (ptm-80) REVERT: D 337 HIS cc_start: 0.7510 (m170) cc_final: 0.7175 (m-70) REVERT: E 155 ILE cc_start: 0.7040 (pt) cc_final: 0.6040 (tp) REVERT: E 171 GLN cc_start: 0.8483 (mm110) cc_final: 0.8132 (mm-40) REVERT: E 212 MET cc_start: 0.7637 (mmp) cc_final: 0.6875 (mmp) REVERT: E 213 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7672 (mtmt) REVERT: E 248 MET cc_start: 0.7793 (mtp) cc_final: 0.7227 (mtp) REVERT: E 270 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7462 (mmmt) REVERT: E 272 ILE cc_start: 0.8865 (mm) cc_final: 0.8665 (tp) REVERT: E 286 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 290 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7476 (mm-30) REVERT: E 299 LEU cc_start: 0.8614 (mt) cc_final: 0.8292 (mt) REVERT: E 302 MET cc_start: 0.7984 (tmm) cc_final: 0.7681 (tmm) REVERT: E 304 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8219 (mtp-110) REVERT: E 312 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8076 (mtp-110) REVERT: E 328 ILE cc_start: 0.6703 (mm) cc_final: 0.6276 (mp) REVERT: E 341 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7729 (mm-30) REVERT: E 343 MET cc_start: 0.8362 (tpt) cc_final: 0.7448 (tpt) REVERT: F 74 MET cc_start: 0.7459 (mtm) cc_final: 0.7111 (mtm) REVERT: F 75 SER cc_start: 0.8161 (p) cc_final: 0.7935 (p) REVERT: F 82 ASP cc_start: 0.7773 (t70) cc_final: 0.7484 (t0) REVERT: F 90 TRP cc_start: 0.7874 (m100) cc_final: 0.7150 (m100) REVERT: F 102 ASP cc_start: 0.7915 (m-30) cc_final: 0.7570 (m-30) REVERT: F 104 LYS cc_start: 0.8306 (tttt) cc_final: 0.8038 (ttmt) REVERT: F 132 TYR cc_start: 0.7516 (p90) cc_final: 0.7121 (p90) REVERT: F 139 LYS cc_start: 0.7499 (mtmm) cc_final: 0.6456 (mtmm) REVERT: F 149 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6913 (mm-30) REVERT: F 183 LYS cc_start: 0.8617 (mptt) cc_final: 0.8251 (mptt) REVERT: F 211 MET cc_start: 0.7267 (mmp) cc_final: 0.7037 (mmp) REVERT: F 212 MET cc_start: 0.7940 (mmp) cc_final: 0.7513 (mmp) REVERT: F 215 GLN cc_start: 0.6922 (tp-100) cc_final: 0.6682 (tp-100) REVERT: F 217 MET cc_start: 0.6984 (mpp) cc_final: 0.5931 (mpp) REVERT: F 219 LEU cc_start: 0.7806 (mt) cc_final: 0.6887 (mt) REVERT: F 241 GLN cc_start: 0.7817 (mm110) cc_final: 0.7447 (mm-40) REVERT: F 248 MET cc_start: 0.6827 (mtp) cc_final: 0.6313 (mtp) REVERT: F 250 ARG cc_start: 0.7528 (ptp-170) cc_final: 0.6424 (mtm180) REVERT: F 251 MET cc_start: 0.7108 (mmt) cc_final: 0.6869 (mmt) REVERT: F 270 LYS cc_start: 0.8285 (pttp) cc_final: 0.7853 (ptmm) REVERT: F 300 LYS cc_start: 0.8349 (tptm) cc_final: 0.7998 (tptm) REVERT: F 302 MET cc_start: 0.7713 (tmm) cc_final: 0.7419 (tmm) REVERT: F 304 ARG cc_start: 0.7163 (tpp-160) cc_final: 0.6827 (tpp-160) REVERT: F 337 HIS cc_start: 0.7667 (m170) cc_final: 0.7348 (m170) outliers start: 3 outliers final: 1 residues processed: 593 average time/residue: 0.1256 time to fit residues: 105.3432 Evaluate side-chains 564 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 563 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 5.9990 chunk 108 optimal weight: 0.0060 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 HIS A 241 GLN A 275 ASN ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125437 restraints weight = 29976.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130100 restraints weight = 17899.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133313 restraints weight = 12057.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135533 restraints weight = 8826.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137230 restraints weight = 6921.045| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4413 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= 0.157 Angle : 0.610 10.785 19146 Z= 0.315 Chirality : 0.044 0.501 2178 Planarity : 0.004 0.054 2448 Dihedral : 9.636 59.485 2070 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.20 % Allowed : 3.86 % Favored : 95.95 % 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 are not related in a simple way. whole: 1.85 (0.21), residues: 1728 helix: 1.54 (0.16), residues: 948 sheet: 0.69 (0.40), residues: 198 loop : 1.14 (0.31), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 304 TYR 0.013 0.001 TYR B 314 PHE 0.020 0.002 PHE F 178 TRP 0.016 0.002 TRP D 90 HIS 0.013 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (14142) covalent geometry : angle 0.61049 / 0.31 (19146) hydrogen bonds : bond 0.04235 / 2.78 ( 738) hydrogen bonds : angle 4.27357 / 3.06 ( 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 623 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 620 time to evaluate : 0.499 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: 0.8133 (mtm) cc_final: 0.7762 (mtm) REVERT: A 90 TRP cc_start: 0.7957 (m100) cc_final: 0.6938 (m100) REVERT: A 96 LEU cc_start: 0.7564 (mt) cc_final: 0.7150 (mt) REVERT: A 99 VAL cc_start: 0.8197 (t) cc_final: 0.7917 (m) REVERT: A 100 ILE cc_start: 0.8121 (mm) cc_final: 0.7685 (mm) REVERT: A 101 THR cc_start: 0.8259 (p) cc_final: 0.7853 (t) REVERT: A 104 LYS cc_start: 0.8685 (tttt) cc_final: 0.8285 (tttt) REVERT: A 114 LYS cc_start: 0.7771 (tptm) cc_final: 0.7208 (tptm) REVERT: A 124 GLN cc_start: 0.8150 (pp30) cc_final: 0.7873 (pp30) REVERT: A 125 PRO cc_start: 0.8596 (Cg_endo) cc_final: 0.7968 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8372 (tttt) cc_final: 0.8160 (tttt) REVERT: A 154 PHE cc_start: 0.7755 (t80) cc_final: 0.7144 (t80) REVERT: A 157 LEU cc_start: 0.7946 (tp) cc_final: 0.7611 (tp) REVERT: A 169 GLU cc_start: 0.7781 (tt0) cc_final: 0.7259 (tt0) REVERT: A 170 SER cc_start: 0.8592 (p) cc_final: 0.8152 (p) REVERT: A 179 SER cc_start: 0.8879 (t) cc_final: 0.8574 (p) REVERT: A 199 ARG cc_start: 0.7334 (tpp80) cc_final: 0.6400 (tpp80) REVERT: A 206 HIS cc_start: 0.8080 (p90) cc_final: 0.7353 (p90) REVERT: A 211 MET cc_start: 0.7887 (mmp) cc_final: 0.7299 (mmp) REVERT: A 213 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7725 (mtmt) REVERT: A 215 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7019 (tp-100) REVERT: A 217 MET cc_start: 0.8083 (mpp) cc_final: 0.7618 (mpp) REVERT: A 218 SER cc_start: 0.8634 (p) cc_final: 0.8379 (p) REVERT: A 251 MET cc_start: 0.7709 (mmm) cc_final: 0.7211 (mmm) REVERT: A 259 GLN cc_start: 0.7626 (mt0) cc_final: 0.7274 (mt0) REVERT: A 263 LYS cc_start: 0.7916 (mttp) cc_final: 0.7712 (mttp) REVERT: A 266 GLU cc_start: 0.7798 (tp30) cc_final: 0.7347 (tp30) REVERT: A 301 GLU cc_start: 0.8079 (tt0) cc_final: 0.6978 (tt0) REVERT: A 341 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 342 LYS cc_start: 0.8769 (mptt) cc_final: 0.8374 (mptt) REVERT: A 343 MET cc_start: 0.8222 (tpt) cc_final: 0.7877 (tpt) REVERT: B 74 MET cc_start: 0.8030 (mtm) cc_final: 0.7343 (mtm) REVERT: B 86 MET cc_start: 0.7816 (mtm) cc_final: 0.7528 (mtm) REVERT: B 90 TRP cc_start: 0.8206 (m100) cc_final: 0.7099 (m100) REVERT: B 102 ASP cc_start: 0.7883 (m-30) cc_final: 0.7682 (m-30) REVERT: B 104 LYS cc_start: 0.8560 (tttt) cc_final: 0.8189 (tttt) REVERT: B 114 LYS cc_start: 0.7780 (tptm) cc_final: 0.7519 (tptm) REVERT: B 115 HIS cc_start: 0.8712 (p90) cc_final: 0.8248 (p90) REVERT: B 123 LEU cc_start: 0.8316 (tp) cc_final: 0.8011 (tp) REVERT: B 124 GLN cc_start: 0.8114 (pp30) cc_final: 0.7747 (pp30) REVERT: B 144 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8338 (mtpt) REVERT: B 148 LYS cc_start: 0.8442 (tttt) cc_final: 0.8070 (ttmt) REVERT: B 154 PHE cc_start: 0.7668 (t80) cc_final: 0.7120 (t80) REVERT: B 157 LEU cc_start: 0.8215 (tp) cc_final: 0.7889 (tp) REVERT: B 158 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 177 VAL cc_start: 0.8683 (t) cc_final: 0.8471 (m) REVERT: B 211 MET cc_start: 0.7916 (mmp) cc_final: 0.7251 (mmp) REVERT: B 213 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7619 (mtmt) REVERT: B 215 GLN cc_start: 0.7633 (tp-100) cc_final: 0.6417 (tp-100) REVERT: B 217 MET cc_start: 0.8100 (mpp) cc_final: 0.7638 (mpp) REVERT: B 219 LEU cc_start: 0.8770 (mt) cc_final: 0.7800 (mt) REVERT: B 234 MET cc_start: 0.7061 (ttm) cc_final: 0.6820 (ttm) REVERT: B 243 LEU cc_start: 0.8524 (mt) cc_final: 0.8241 (mt) REVERT: B 251 MET cc_start: 0.7318 (mmm) cc_final: 0.6919 (mmm) REVERT: B 259 GLN cc_start: 0.7841 (mt0) cc_final: 0.7453 (mt0) REVERT: B 266 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 299 LEU cc_start: 0.8843 (mt) cc_final: 0.8547 (mt) REVERT: B 305 ASP cc_start: 0.8297 (m-30) cc_final: 0.7741 (m-30) REVERT: B 338 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7973 (mtp-110) REVERT: B 341 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 342 LYS cc_start: 0.8704 (mptt) cc_final: 0.7981 (mptt) REVERT: B 343 MET cc_start: 0.8193 (tpt) cc_final: 0.6791 (tpt) REVERT: B 345 LYS cc_start: 0.8751 (pptt) cc_final: 0.8485 (pptt) REVERT: B 347 LYS cc_start: 0.8916 (mptt) cc_final: 0.8382 (mptt) REVERT: C 74 MET cc_start: 0.5697 (mtm) cc_final: 0.5436 (mtm) REVERT: C 86 MET cc_start: 0.5522 (pmm) cc_final: 0.5269 (pmm) REVERT: C 158 GLN cc_start: 0.8014 (pm20) cc_final: 0.7538 (pm20) REVERT: C 170 SER cc_start: 0.7910 (p) cc_final: 0.7502 (p) REVERT: C 171 GLN cc_start: 0.8185 (mp10) cc_final: 0.7845 (mp10) REVERT: C 199 ARG cc_start: 0.5633 (tpp80) cc_final: 0.5211 (tpp80) REVERT: C 212 MET cc_start: 0.7648 (mmp) cc_final: 0.7362 (mmp) REVERT: C 215 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7514 (tm-30) REVERT: C 239 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7657 (mtt90) REVERT: C 248 MET cc_start: 0.7773 (mtp) cc_final: 0.7216 (mtp) REVERT: C 250 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6420 (mmm160) REVERT: C 270 LYS cc_start: 0.8554 (mmmt) cc_final: 0.7764 (mmmt) REVERT: C 289 GLN cc_start: 0.8071 (mt0) cc_final: 0.7664 (mt0) REVERT: C 299 LEU cc_start: 0.8685 (mt) cc_final: 0.8413 (mt) REVERT: C 300 LYS cc_start: 0.8898 (tttt) cc_final: 0.8619 (tttt) REVERT: C 302 MET cc_start: 0.8193 (tmm) cc_final: 0.7923 (tmm) REVERT: C 309 LEU cc_start: 0.8703 (tp) cc_final: 0.8450 (tp) REVERT: C 313 GLU cc_start: 0.8150 (pt0) cc_final: 0.7820 (pt0) REVERT: C 335 ASP cc_start: 0.8015 (m-30) cc_final: 0.7746 (m-30) REVERT: C 336 LEU cc_start: 0.8921 (mp) cc_final: 0.8676 (mp) REVERT: C 343 MET cc_start: 0.8241 (tpt) cc_final: 0.7468 (tpt) REVERT: C 344 LYS cc_start: 0.9043 (mttm) cc_final: 0.8647 (mttm) REVERT: D 82 ASP cc_start: 0.8217 (t0) cc_final: 0.7888 (t70) REVERT: D 97 ASP cc_start: 0.7541 (p0) cc_final: 0.7336 (p0) REVERT: D 102 ASP cc_start: 0.7878 (m-30) cc_final: 0.7506 (m-30) REVERT: D 104 LYS cc_start: 0.8313 (tttt) cc_final: 0.7949 (ttmt) REVERT: D 131 LEU cc_start: 0.8418 (mp) cc_final: 0.8176 (mt) REVERT: D 132 TYR cc_start: 0.7707 (p90) cc_final: 0.7377 (p90) REVERT: D 139 LYS cc_start: 0.7659 (mtmm) cc_final: 0.6862 (mtmm) REVERT: D 183 LYS cc_start: 0.8431 (mptt) cc_final: 0.8097 (mptt) REVERT: D 212 MET cc_start: 0.7968 (mmp) cc_final: 0.7206 (mmp) REVERT: D 217 MET cc_start: 0.7118 (mmp) cc_final: 0.6469 (mmp) REVERT: D 241 GLN cc_start: 0.8201 (mp-120) cc_final: 0.7114 (mm-40) REVERT: D 243 LEU cc_start: 0.8392 (mt) cc_final: 0.8020 (tt) REVERT: D 248 MET cc_start: 0.7299 (mtp) cc_final: 0.6762 (mtp) REVERT: D 251 MET cc_start: 0.7432 (mmt) cc_final: 0.7083 (mmm) REVERT: D 284 LEU cc_start: 0.8372 (mt) cc_final: 0.8158 (mt) REVERT: D 291 THR cc_start: 0.6870 (p) cc_final: 0.6290 (t) REVERT: D 300 LYS cc_start: 0.8600 (tptm) cc_final: 0.8263 (tptm) REVERT: D 305 ASP cc_start: 0.7571 (t0) cc_final: 0.7178 (t0) REVERT: D 312 ARG cc_start: 0.8060 (ptm-80) cc_final: 0.7732 (ptm-80) REVERT: D 337 HIS cc_start: 0.7652 (m170) cc_final: 0.7371 (m90) REVERT: E 139 LYS cc_start: 0.8375 (ptpp) cc_final: 0.8093 (pttm) REVERT: E 158 GLN cc_start: 0.7907 (pm20) cc_final: 0.7677 (pm20) REVERT: E 167 TYR cc_start: 0.7219 (m-10) cc_final: 0.6909 (m-10) REVERT: E 171 GLN cc_start: 0.8566 (mm110) cc_final: 0.8145 (mp10) REVERT: E 191 ILE cc_start: 0.7188 (mt) cc_final: 0.6931 (mm) REVERT: E 193 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7302 (mt-10) REVERT: E 212 MET cc_start: 0.7837 (mmp) cc_final: 0.7355 (mmp) REVERT: E 213 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7737 (mtmt) REVERT: E 215 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7294 (tm-30) REVERT: E 248 MET cc_start: 0.7832 (mtp) cc_final: 0.7352 (mtp) REVERT: E 250 ARG cc_start: 0.5960 (mmm160) cc_final: 0.5516 (mmm160) REVERT: E 251 MET cc_start: 0.6982 (mmm) cc_final: 0.6352 (mmm) REVERT: E 266 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7482 (tm-30) REVERT: E 270 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7446 (mmmt) REVERT: E 286 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7509 (mm-30) REVERT: E 290 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 298 ASP cc_start: 0.7460 (m-30) cc_final: 0.6870 (m-30) REVERT: E 299 LEU cc_start: 0.8685 (mt) cc_final: 0.8347 (mt) REVERT: E 300 LYS cc_start: 0.8657 (tttt) cc_final: 0.8391 (tttt) REVERT: E 301 GLU cc_start: 0.8292 (tt0) cc_final: 0.7730 (tt0) REVERT: E 302 MET cc_start: 0.8164 (tmm) cc_final: 0.7848 (tmm) REVERT: E 304 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8300 (mmm-85) REVERT: E 313 GLU cc_start: 0.8506 (pt0) cc_final: 0.8224 (pt0) REVERT: E 341 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7756 (mm-30) REVERT: E 343 MET cc_start: 0.8351 (tpt) cc_final: 0.7068 (tpt) REVERT: F 74 MET cc_start: 0.7544 (mtm) cc_final: 0.7081 (mtm) REVERT: F 75 SER cc_start: 0.8163 (p) cc_final: 0.7880 (p) REVERT: F 90 TRP cc_start: 0.7933 (m100) cc_final: 0.7189 (m100) REVERT: F 102 ASP cc_start: 0.8009 (m-30) cc_final: 0.7734 (m-30) REVERT: F 104 LYS cc_start: 0.8360 (tttt) cc_final: 0.8001 (ttmt) REVERT: F 112 LYS cc_start: 0.7951 (mttt) cc_final: 0.7705 (mttt) REVERT: F 131 LEU cc_start: 0.8402 (mp) cc_final: 0.8099 (mt) REVERT: F 132 TYR cc_start: 0.7710 (p90) cc_final: 0.7461 (p90) REVERT: F 139 LYS cc_start: 0.7767 (mtmm) cc_final: 0.6928 (mtmm) REVERT: F 149 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6871 (mm-30) REVERT: F 183 LYS cc_start: 0.8461 (mptt) cc_final: 0.8073 (mptt) REVERT: F 211 MET cc_start: 0.7259 (mmp) cc_final: 0.6949 (mmp) REVERT: F 212 MET cc_start: 0.7986 (mmp) cc_final: 0.7647 (mmp) REVERT: F 217 MET cc_start: 0.7001 (mpp) cc_final: 0.5841 (mpp) REVERT: F 241 GLN cc_start: 0.7878 (mm110) cc_final: 0.7419 (mm110) REVERT: F 250 ARG cc_start: 0.7866 (ptp-170) cc_final: 0.7231 (mtm180) REVERT: F 270 LYS cc_start: 0.8302 (pttp) cc_final: 0.7934 (ptmm) REVERT: F 291 THR cc_start: 0.7215 (p) cc_final: 0.6788 (t) REVERT: F 300 LYS cc_start: 0.8418 (tptm) cc_final: 0.7947 (tptm) REVERT: F 302 MET cc_start: 0.7777 (tmm) cc_final: 0.7448 (tmm) REVERT: F 337 HIS cc_start: 0.7684 (m170) cc_final: 0.7425 (m170) outliers start: 3 outliers final: 1 residues processed: 621 average time/residue: 0.1251 time to fit residues: 110.8759 Evaluate side-chains 589 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 141 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** 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 = 0.4084 r_free = 0.4084 target = 0.153494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126247 restraints weight = 29998.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130892 restraints weight = 17824.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.134274 restraints weight = 12089.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136512 restraints weight = 8779.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138211 restraints weight = 6881.762| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14142 Z= 0.116 Angle : 0.564 14.696 19146 Z= 0.289 Chirality : 0.042 0.273 2178 Planarity : 0.004 0.064 2448 Dihedral : 8.985 54.454 2070 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.13 % Allowed : 2.03 % Favored : 97.84 % 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 are not related in a simple way. whole: 1.46 (0.21), residues: 1728 helix: 1.29 (0.16), residues: 984 sheet: 1.25 (0.40), residues: 180 loop : 0.49 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 304 TYR 0.014 0.001 TYR A 72 PHE 0.022 0.002 PHE C 216 TRP 0.018 0.002 TRP A 220 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14142) covalent geometry : angle 0.56443 / 0.29 (19146) hydrogen bonds : bond 0.03632 / 2.38 ( 738) hydrogen bonds : angle 4.11631 / 2.94 ( 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 617 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 615 time to evaluate : 0.539 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: A 74 MET cc_start: 0.7969 (mtm) cc_final: 0.7487 (mtm) REVERT: A 96 LEU cc_start: 0.7550 (mt) cc_final: 0.7149 (tp) REVERT: A 104 LYS cc_start: 0.8686 (tttt) cc_final: 0.8262 (tttt) REVERT: A 109 LEU cc_start: 0.8466 (mt) cc_final: 0.8264 (mm) REVERT: A 114 LYS cc_start: 0.7677 (tptm) cc_final: 0.7104 (tptm) REVERT: A 124 GLN cc_start: 0.8246 (pp30) cc_final: 0.8031 (pp30) REVERT: A 125 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8142 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8298 (tttt) cc_final: 0.7961 (ttmt) REVERT: A 149 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 157 LEU cc_start: 0.7962 (tp) cc_final: 0.7538 (tt) REVERT: A 169 GLU cc_start: 0.7308 (tt0) cc_final: 0.7031 (tt0) REVERT: A 178 PHE cc_start: 0.9021 (m-80) cc_final: 0.8739 (m-10) REVERT: A 179 SER cc_start: 0.8860 (t) cc_final: 0.8516 (p) REVERT: A 206 HIS cc_start: 0.8045 (p90) cc_final: 0.7340 (p90) REVERT: A 211 MET cc_start: 0.7957 (mmp) cc_final: 0.7322 (mmp) REVERT: A 213 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7781 (mtmt) REVERT: A 215 GLN cc_start: 0.7654 (tp-100) cc_final: 0.6424 (tp-100) REVERT: A 217 MET cc_start: 0.8081 (mpp) cc_final: 0.7470 (mpp) REVERT: A 219 LEU cc_start: 0.8774 (mt) cc_final: 0.7765 (mt) REVERT: A 220 TRP cc_start: 0.8081 (m-10) cc_final: 0.7270 (m-10) REVERT: A 250 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7105 (mtt180) REVERT: A 251 MET cc_start: 0.7609 (mmm) cc_final: 0.7037 (mmm) REVERT: A 259 GLN cc_start: 0.7615 (mt0) cc_final: 0.7246 (mt0) REVERT: A 262 LEU cc_start: 0.8184 (tp) cc_final: 0.7850 (mm) REVERT: A 268 ILE cc_start: 0.8144 (mm) cc_final: 0.7752 (mm) REVERT: A 270 LYS cc_start: 0.8596 (mmpt) cc_final: 0.8339 (mmtt) REVERT: A 271 LEU cc_start: 0.8852 (tp) cc_final: 0.8476 (pp) REVERT: A 272 ILE cc_start: 0.8532 (mt) cc_final: 0.8173 (mt) REVERT: A 301 GLU cc_start: 0.7883 (tt0) cc_final: 0.6730 (tt0) REVERT: A 305 ASP cc_start: 0.8307 (m-30) cc_final: 0.7994 (m-30) REVERT: A 341 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 342 LYS cc_start: 0.8764 (mptt) cc_final: 0.8135 (mptt) REVERT: A 343 MET cc_start: 0.8293 (tpt) cc_final: 0.7900 (tpt) REVERT: A 345 LYS cc_start: 0.8739 (pptt) cc_final: 0.8500 (pptt) REVERT: B 74 MET cc_start: 0.8022 (mtm) cc_final: 0.7274 (mtm) REVERT: B 86 MET cc_start: 0.7839 (mtm) cc_final: 0.7475 (mtm) REVERT: B 90 TRP cc_start: 0.8187 (m100) cc_final: 0.7034 (m100) REVERT: B 102 ASP cc_start: 0.7900 (m-30) cc_final: 0.7664 (m-30) REVERT: B 104 LYS cc_start: 0.8545 (tttt) cc_final: 0.8197 (tttt) REVERT: B 114 LYS cc_start: 0.7552 (tptm) cc_final: 0.7197 (tptm) REVERT: B 123 LEU cc_start: 0.8350 (tp) cc_final: 0.8109 (tp) REVERT: B 124 GLN cc_start: 0.8232 (pp30) cc_final: 0.7927 (pp30) REVERT: B 144 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8293 (mtpt) REVERT: B 148 LYS cc_start: 0.8300 (tttt) cc_final: 0.7942 (ttmt) REVERT: B 157 LEU cc_start: 0.8169 (tp) cc_final: 0.7769 (tp) REVERT: B 158 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6600 (tm-30) REVERT: B 211 MET cc_start: 0.7994 (mmp) cc_final: 0.7733 (mmp) REVERT: B 213 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7664 (mtmt) REVERT: B 215 GLN cc_start: 0.7565 (tp-100) cc_final: 0.6240 (tp-100) REVERT: B 217 MET cc_start: 0.8122 (mpp) cc_final: 0.7619 (mpp) REVERT: B 219 LEU cc_start: 0.8779 (mt) cc_final: 0.7764 (mt) REVERT: B 243 LEU cc_start: 0.8582 (mt) cc_final: 0.8280 (mt) REVERT: B 259 GLN cc_start: 0.7901 (mt0) cc_final: 0.7479 (mt0) REVERT: B 266 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 268 ILE cc_start: 0.8142 (mm) cc_final: 0.7759 (mm) REVERT: B 271 LEU cc_start: 0.8703 (tp) cc_final: 0.8393 (pp) REVERT: B 272 ILE cc_start: 0.8388 (mt) cc_final: 0.8087 (mt) REVERT: B 299 LEU cc_start: 0.8825 (mt) cc_final: 0.8413 (mp) REVERT: B 338 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8066 (mtp-110) REVERT: B 341 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 342 LYS cc_start: 0.8603 (mptt) cc_final: 0.7754 (mptt) REVERT: B 345 LYS cc_start: 0.8677 (pptt) cc_final: 0.8322 (pptt) REVERT: C 74 MET cc_start: 0.5705 (mtm) cc_final: 0.5426 (mtm) REVERT: C 86 MET cc_start: 0.5603 (pmm) cc_final: 0.5361 (pmm) REVERT: C 158 GLN cc_start: 0.7958 (pm20) cc_final: 0.7523 (pm20) REVERT: C 170 SER cc_start: 0.7870 (p) cc_final: 0.7389 (p) REVERT: C 171 GLN cc_start: 0.8147 (mp10) cc_final: 0.7744 (mp10) REVERT: C 199 ARG cc_start: 0.5694 (tpp80) cc_final: 0.5279 (tpp80) REVERT: C 212 MET cc_start: 0.7741 (mmp) cc_final: 0.7423 (mmp) REVERT: C 215 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7751 (tm-30) REVERT: C 239 ARG cc_start: 0.7791 (mtt90) cc_final: 0.6868 (ttm110) REVERT: C 248 MET cc_start: 0.7613 (mtp) cc_final: 0.7064 (mtp) REVERT: C 251 MET cc_start: 0.6748 (mpp) cc_final: 0.6424 (mpp) REVERT: C 264 GLN cc_start: 0.8355 (mp10) cc_final: 0.8071 (mp10) REVERT: C 270 LYS cc_start: 0.8616 (mmmt) cc_final: 0.7781 (mmmt) REVERT: C 289 GLN cc_start: 0.8067 (mt0) cc_final: 0.7631 (mt0) REVERT: C 299 LEU cc_start: 0.8639 (mt) cc_final: 0.8347 (mt) REVERT: C 300 LYS cc_start: 0.8776 (tttt) cc_final: 0.8505 (tttt) REVERT: C 302 MET cc_start: 0.8266 (tmm) cc_final: 0.7974 (tmm) REVERT: C 313 GLU cc_start: 0.8258 (pt0) cc_final: 0.7925 (pt0) REVERT: C 335 ASP cc_start: 0.8089 (m-30) cc_final: 0.7826 (m-30) REVERT: C 343 MET cc_start: 0.8215 (tpt) cc_final: 0.7538 (tpt) REVERT: C 344 LYS cc_start: 0.9033 (mttm) cc_final: 0.8665 (mttm) REVERT: D 82 ASP cc_start: 0.8304 (t0) cc_final: 0.7957 (t70) REVERT: D 104 LYS cc_start: 0.8255 (tttt) cc_final: 0.7931 (ttmt) REVERT: D 139 LYS cc_start: 0.7671 (mtmm) cc_final: 0.6860 (mtmm) REVERT: D 179 SER cc_start: 0.8313 (p) cc_final: 0.8112 (p) REVERT: D 183 LYS cc_start: 0.8447 (mptt) cc_final: 0.8079 (mptt) REVERT: D 217 MET cc_start: 0.6636 (mmp) cc_final: 0.6408 (mmp) REVERT: D 248 MET cc_start: 0.7311 (mtp) cc_final: 0.6845 (mtp) REVERT: D 291 THR cc_start: 0.7364 (p) cc_final: 0.7058 (t) REVERT: D 300 LYS cc_start: 0.8681 (tptm) cc_final: 0.8340 (tptm) REVERT: D 305 ASP cc_start: 0.7664 (t0) cc_final: 0.7209 (t0) REVERT: D 312 ARG cc_start: 0.8088 (ptm-80) cc_final: 0.7767 (ptm-80) REVERT: D 337 HIS cc_start: 0.7783 (m170) cc_final: 0.7520 (m90) REVERT: E 86 MET cc_start: 0.7185 (tpt) cc_final: 0.6922 (ptp) REVERT: E 139 LYS cc_start: 0.8462 (ptpp) cc_final: 0.8133 (pttm) REVERT: E 158 GLN cc_start: 0.7828 (pm20) cc_final: 0.7525 (pm20) REVERT: E 167 TYR cc_start: 0.7264 (m-10) cc_final: 0.6907 (m-10) REVERT: E 170 SER cc_start: 0.7632 (p) cc_final: 0.7077 (p) REVERT: E 171 GLN cc_start: 0.8502 (mm110) cc_final: 0.8126 (mp10) REVERT: E 193 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7383 (mt-10) REVERT: E 212 MET cc_start: 0.7986 (mmp) cc_final: 0.7451 (mmp) REVERT: E 213 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7746 (mtmt) REVERT: E 215 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7316 (tm-30) REVERT: E 239 ARG cc_start: 0.7845 (mtt90) cc_final: 0.6989 (ttp-110) REVERT: E 248 MET cc_start: 0.7734 (mtp) cc_final: 0.7235 (mtp) REVERT: E 251 MET cc_start: 0.7004 (mmm) cc_final: 0.6576 (mmm) REVERT: E 264 GLN cc_start: 0.8541 (mp10) cc_final: 0.8341 (mp10) REVERT: E 266 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7683 (tm-30) REVERT: E 270 LYS cc_start: 0.8479 (mmmt) cc_final: 0.7501 (mmmt) REVERT: E 290 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7760 (mm-30) REVERT: E 295 SER cc_start: 0.7241 (p) cc_final: 0.7026 (p) REVERT: E 298 ASP cc_start: 0.7165 (m-30) cc_final: 0.6841 (m-30) REVERT: E 299 LEU cc_start: 0.8620 (mt) cc_final: 0.8337 (mt) REVERT: E 300 LYS cc_start: 0.8663 (tttt) cc_final: 0.8406 (tttt) REVERT: E 301 GLU cc_start: 0.8312 (tt0) cc_final: 0.7761 (tt0) REVERT: E 302 MET cc_start: 0.8200 (tmm) cc_final: 0.7917 (tmm) REVERT: E 304 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8377 (mmm-85) REVERT: E 312 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7851 (mtp-110) REVERT: E 313 GLU cc_start: 0.8492 (pt0) cc_final: 0.8231 (pt0) REVERT: E 335 ASP cc_start: 0.8333 (m-30) cc_final: 0.7972 (m-30) REVERT: E 340 ILE cc_start: 0.8479 (mt) cc_final: 0.8229 (mt) REVERT: E 341 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7580 (mm-30) REVERT: F 74 MET cc_start: 0.7565 (mtm) cc_final: 0.7101 (mtm) REVERT: F 75 SER cc_start: 0.8137 (p) cc_final: 0.7872 (p) REVERT: F 82 ASP cc_start: 0.8356 (t0) cc_final: 0.8046 (t0) REVERT: F 90 TRP cc_start: 0.7978 (m100) cc_final: 0.7127 (m100) REVERT: F 102 ASP cc_start: 0.8034 (m-30) cc_final: 0.7672 (m-30) REVERT: F 104 LYS cc_start: 0.8325 (tttt) cc_final: 0.8001 (ttmt) REVERT: F 112 LYS cc_start: 0.7956 (mttt) cc_final: 0.7744 (mttt) REVERT: F 149 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6724 (mm-30) REVERT: F 183 LYS cc_start: 0.8497 (mptt) cc_final: 0.8201 (mptt) REVERT: F 211 MET cc_start: 0.7432 (mmp) cc_final: 0.7022 (mmp) REVERT: F 212 MET cc_start: 0.8073 (mmp) cc_final: 0.7838 (mmp) REVERT: F 250 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7588 (mtm180) REVERT: F 270 LYS cc_start: 0.8293 (pttp) cc_final: 0.7904 (ptmm) REVERT: F 291 THR cc_start: 0.7645 (p) cc_final: 0.7340 (t) REVERT: F 300 LYS cc_start: 0.8373 (tptm) cc_final: 0.7934 (tptm) REVERT: F 302 MET cc_start: 0.7831 (tmm) cc_final: 0.7623 (tmm) REVERT: F 332 GLN cc_start: 0.8090 (mm110) cc_final: 0.7631 (mp10) REVERT: F 337 HIS cc_start: 0.7817 (m170) cc_final: 0.7441 (m90) outliers start: 2 outliers final: 0 residues processed: 616 average time/residue: 0.1245 time to fit residues: 109.0576 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 : 0.497 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 0.0070 chunk 165 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 256 HIS A 275 ASN B 241 GLN B 275 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.152721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125409 restraints weight = 29486.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130129 restraints weight = 17515.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133399 restraints weight = 11777.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135753 restraints weight = 8610.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137457 restraints weight = 6687.560| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14142 Z= 0.124 Angle : 0.569 12.185 19146 Z= 0.292 Chirality : 0.042 0.291 2178 Planarity : 0.004 0.052 2448 Dihedral : 8.877 57.132 2070 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.13 % Allowed : 1.44 % 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 are not related in a simple way. whole: 1.65 (0.21), residues: 1728 helix: 1.51 (0.16), residues: 948 sheet: 0.97 (0.40), residues: 186 loop : 0.65 (0.30), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 338 TYR 0.015 0.002 TYR E 72 PHE 0.028 0.002 PHE E 216 TRP 0.019 0.002 TRP B 220 HIS 0.009 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14142) covalent geometry : angle 0.56905 / 0.29 (19146) hydrogen bonds : bond 0.03564 / 2.36 ( 738) hydrogen bonds : angle 4.09022 / 2.93 ( 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 604 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 602 time to evaluate : 0.548 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: A 74 MET cc_start: 0.8102 (mtm) cc_final: 0.7570 (mtm) REVERT: A 96 LEU cc_start: 0.7462 (mt) cc_final: 0.7108 (mm) REVERT: A 104 LYS cc_start: 0.8691 (tttt) cc_final: 0.8227 (tttt) REVERT: A 114 LYS cc_start: 0.7596 (tptm) cc_final: 0.7008 (tptm) REVERT: A 125 PRO cc_start: 0.8612 (Cg_endo) cc_final: 0.8158 (Cg_exo) REVERT: A 149 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 157 LEU cc_start: 0.8040 (tp) cc_final: 0.7446 (tt) REVERT: A 169 GLU cc_start: 0.7207 (tt0) cc_final: 0.6849 (tt0) REVERT: A 178 PHE cc_start: 0.8996 (m-80) cc_final: 0.8749 (m-10) REVERT: A 179 SER cc_start: 0.8876 (t) cc_final: 0.8528 (p) REVERT: A 199 ARG cc_start: 0.7424 (tpp80) cc_final: 0.6408 (tpp80) REVERT: A 206 HIS cc_start: 0.8011 (p90) cc_final: 0.7342 (p90) REVERT: A 211 MET cc_start: 0.7970 (mmp) cc_final: 0.7317 (mmp) REVERT: A 213 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7734 (mtmt) REVERT: A 215 GLN cc_start: 0.7774 (tp-100) cc_final: 0.6668 (tp-100) REVERT: A 217 MET cc_start: 0.8211 (mpp) cc_final: 0.7620 (mpp) REVERT: A 219 LEU cc_start: 0.8823 (mt) cc_final: 0.8034 (mt) REVERT: A 220 TRP cc_start: 0.8266 (m-10) cc_final: 0.7439 (m-10) REVERT: A 250 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7572 (mmt90) REVERT: A 251 MET cc_start: 0.7338 (mmm) cc_final: 0.7061 (mmm) REVERT: A 258 ASN cc_start: 0.8293 (p0) cc_final: 0.8047 (p0) REVERT: A 259 GLN cc_start: 0.7640 (mt0) cc_final: 0.7005 (mt0) REVERT: A 262 LEU cc_start: 0.8186 (tp) cc_final: 0.7854 (mm) REVERT: A 263 LYS cc_start: 0.7860 (mttp) cc_final: 0.7652 (mttp) REVERT: A 266 GLU cc_start: 0.7956 (tp30) cc_final: 0.7415 (tp30) REVERT: A 301 GLU cc_start: 0.7994 (tt0) cc_final: 0.6856 (tt0) REVERT: A 305 ASP cc_start: 0.8290 (m-30) cc_final: 0.8013 (m-30) REVERT: A 341 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 342 LYS cc_start: 0.8784 (mptt) cc_final: 0.8222 (mptt) REVERT: A 343 MET cc_start: 0.8278 (tpt) cc_final: 0.7807 (tpt) REVERT: A 345 LYS cc_start: 0.8696 (pptt) cc_final: 0.8480 (pptt) REVERT: B 74 MET cc_start: 0.8044 (mtm) cc_final: 0.7291 (mtm) REVERT: B 86 MET cc_start: 0.7866 (mtm) cc_final: 0.7542 (mtm) REVERT: B 96 LEU cc_start: 0.7481 (mt) cc_final: 0.6818 (mm) REVERT: B 99 VAL cc_start: 0.8262 (t) cc_final: 0.7930 (m) REVERT: B 104 LYS cc_start: 0.8605 (tttt) cc_final: 0.8229 (tttt) REVERT: B 109 LEU cc_start: 0.8412 (mt) cc_final: 0.8212 (mm) REVERT: B 114 LYS cc_start: 0.7547 (tptm) cc_final: 0.7324 (tptm) REVERT: B 123 LEU cc_start: 0.8380 (tp) cc_final: 0.8052 (tp) REVERT: B 124 GLN cc_start: 0.8221 (pp30) cc_final: 0.7940 (pp30) REVERT: B 144 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8159 (mtpt) REVERT: B 148 LYS cc_start: 0.8266 (tttt) cc_final: 0.7988 (ttmt) REVERT: B 157 LEU cc_start: 0.8106 (tp) cc_final: 0.7656 (tp) REVERT: B 158 GLN cc_start: 0.7404 (tm-30) cc_final: 0.6513 (tm-30) REVERT: B 167 TYR cc_start: 0.6911 (m-10) cc_final: 0.6633 (m-10) REVERT: B 211 MET cc_start: 0.8006 (mmp) cc_final: 0.7717 (mmp) REVERT: B 213 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7673 (mtmt) REVERT: B 215 GLN cc_start: 0.7520 (tp-100) cc_final: 0.6114 (tp-100) REVERT: B 217 MET cc_start: 0.8136 (mpp) cc_final: 0.7437 (mpp) REVERT: B 219 LEU cc_start: 0.8784 (mt) cc_final: 0.7675 (mt) REVERT: B 250 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7348 (mtt90) REVERT: B 251 MET cc_start: 0.7506 (mmp) cc_final: 0.7073 (mmp) REVERT: B 259 GLN cc_start: 0.7910 (mt0) cc_final: 0.7467 (mt0) REVERT: B 266 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 268 ILE cc_start: 0.8189 (mm) cc_final: 0.7789 (mm) REVERT: B 270 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7849 (mptt) REVERT: B 271 LEU cc_start: 0.8719 (tp) cc_final: 0.8411 (pp) REVERT: B 272 ILE cc_start: 0.8404 (mt) cc_final: 0.8111 (mt) REVERT: B 286 GLU cc_start: 0.6816 (pm20) cc_final: 0.6552 (pm20) REVERT: B 299 LEU cc_start: 0.8851 (mt) cc_final: 0.8518 (mt) REVERT: B 338 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8086 (mmm-85) REVERT: B 341 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 342 LYS cc_start: 0.8700 (mptt) cc_final: 0.7948 (mptt) REVERT: B 345 LYS cc_start: 0.8651 (pptt) cc_final: 0.8331 (pptt) REVERT: C 74 MET cc_start: 0.5676 (mtm) cc_final: 0.5350 (mtm) REVERT: C 86 MET cc_start: 0.5570 (pmm) cc_final: 0.5353 (pmm) REVERT: C 158 GLN cc_start: 0.7809 (pm20) cc_final: 0.7406 (pm20) REVERT: C 171 GLN cc_start: 0.8406 (mp10) cc_final: 0.8027 (mp10) REVERT: C 199 ARG cc_start: 0.5707 (tpp80) cc_final: 0.5344 (tpp80) REVERT: C 212 MET cc_start: 0.7701 (mmp) cc_final: 0.7356 (mmp) REVERT: C 213 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7571 (mtmm) REVERT: C 215 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7773 (tm-30) REVERT: C 239 ARG cc_start: 0.7806 (mtt90) cc_final: 0.6974 (ttm110) REVERT: C 248 MET cc_start: 0.7596 (mtp) cc_final: 0.7052 (mtp) REVERT: C 251 MET cc_start: 0.6878 (mpp) cc_final: 0.6408 (tpp) REVERT: C 264 GLN cc_start: 0.8443 (mp10) cc_final: 0.8136 (mp10) REVERT: C 270 LYS cc_start: 0.8640 (mmmt) cc_final: 0.7781 (mmmt) REVERT: C 289 GLN cc_start: 0.8007 (mt0) cc_final: 0.7544 (mt0) REVERT: C 299 LEU cc_start: 0.8685 (mt) cc_final: 0.8261 (mt) REVERT: C 300 LYS cc_start: 0.8755 (tttt) cc_final: 0.8488 (tttt) REVERT: C 301 GLU cc_start: 0.8429 (tt0) cc_final: 0.8214 (tt0) REVERT: C 303 CYS cc_start: 0.8747 (m) cc_final: 0.8206 (m) REVERT: C 312 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7986 (mtp-110) REVERT: C 313 GLU cc_start: 0.8283 (pt0) cc_final: 0.7934 (pt0) REVERT: C 343 MET cc_start: 0.8298 (tpt) cc_final: 0.7644 (tpt) REVERT: C 344 LYS cc_start: 0.9037 (mttm) cc_final: 0.8683 (mttm) REVERT: C 347 LYS cc_start: 0.8089 (mppt) cc_final: 0.7864 (mmtt) REVERT: D 73 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 82 ASP cc_start: 0.8323 (t0) cc_final: 0.7978 (t70) REVERT: D 90 TRP cc_start: 0.7835 (m100) cc_final: 0.7625 (m-10) REVERT: D 99 VAL cc_start: 0.8257 (t) cc_final: 0.8022 (t) REVERT: D 112 LYS cc_start: 0.8092 (mttt) cc_final: 0.7857 (mttt) REVERT: D 131 LEU cc_start: 0.8415 (mp) cc_final: 0.8076 (mt) REVERT: D 139 LYS cc_start: 0.7609 (mtmm) cc_final: 0.6721 (mtmm) REVERT: D 183 LYS cc_start: 0.8358 (mptt) cc_final: 0.7933 (mptt) REVERT: D 213 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7617 (mtmm) REVERT: D 234 MET cc_start: 0.7435 (mtp) cc_final: 0.7179 (mtp) REVERT: D 250 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7999 (ptp-170) REVERT: D 251 MET cc_start: 0.7767 (mpp) cc_final: 0.6692 (mpp) REVERT: D 291 THR cc_start: 0.7664 (p) cc_final: 0.7161 (t) REVERT: D 294 PHE cc_start: 0.7244 (m-10) cc_final: 0.6908 (m-80) REVERT: D 300 LYS cc_start: 0.8685 (tptm) cc_final: 0.8342 (tptm) REVERT: D 305 ASP cc_start: 0.7622 (t0) cc_final: 0.7204 (t0) REVERT: D 337 HIS cc_start: 0.7788 (m-70) cc_final: 0.7474 (m90) REVERT: E 139 LYS cc_start: 0.8323 (ptpp) cc_final: 0.7980 (pttm) REVERT: E 158 GLN cc_start: 0.7563 (pm20) cc_final: 0.7202 (pm20) REVERT: E 167 TYR cc_start: 0.7315 (m-10) cc_final: 0.6941 (m-10) REVERT: E 170 SER cc_start: 0.7806 (p) cc_final: 0.7187 (p) REVERT: E 171 GLN cc_start: 0.8500 (mm110) cc_final: 0.8108 (mp10) REVERT: E 193 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7422 (mt-10) REVERT: E 212 MET cc_start: 0.7980 (mmp) cc_final: 0.7549 (mmp) REVERT: E 213 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7799 (mtmt) REVERT: E 215 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7628 (tm-30) REVERT: E 229 CYS cc_start: 0.7342 (t) cc_final: 0.7117 (t) REVERT: E 248 MET cc_start: 0.7747 (mtp) cc_final: 0.7229 (mtp) REVERT: E 251 MET cc_start: 0.7123 (mmm) cc_final: 0.6658 (mmm) REVERT: E 266 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7715 (tm-30) REVERT: E 270 LYS cc_start: 0.8487 (mmmt) cc_final: 0.7458 (mmmt) REVERT: E 279 ASP cc_start: 0.7518 (p0) cc_final: 0.7208 (t0) REVERT: E 290 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7897 (mm-30) REVERT: E 299 LEU cc_start: 0.8653 (mt) cc_final: 0.8352 (mt) REVERT: E 300 LYS cc_start: 0.8642 (tttt) cc_final: 0.8413 (tttt) REVERT: E 301 GLU cc_start: 0.8283 (tt0) cc_final: 0.7687 (tt0) REVERT: E 302 MET cc_start: 0.8243 (tmm) cc_final: 0.7988 (tmm) REVERT: E 304 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8355 (mmm-85) REVERT: E 312 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7829 (mtp-110) REVERT: E 313 GLU cc_start: 0.8536 (pt0) cc_final: 0.8260 (pt0) REVERT: E 335 ASP cc_start: 0.8365 (m-30) cc_final: 0.8085 (m-30) REVERT: E 340 ILE cc_start: 0.8444 (mt) cc_final: 0.8203 (mt) REVERT: E 341 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7696 (mm-30) REVERT: F 74 MET cc_start: 0.7668 (mtm) cc_final: 0.7146 (mtm) REVERT: F 75 SER cc_start: 0.8170 (p) cc_final: 0.7879 (p) REVERT: F 82 ASP cc_start: 0.8223 (t0) cc_final: 0.7947 (t70) REVERT: F 90 TRP cc_start: 0.7975 (m100) cc_final: 0.6971 (m100) REVERT: F 102 ASP cc_start: 0.8043 (m-30) cc_final: 0.7664 (m-30) REVERT: F 104 LYS cc_start: 0.8307 (tttt) cc_final: 0.7996 (ttmt) REVERT: F 112 LYS cc_start: 0.7951 (mttt) cc_final: 0.7728 (mttt) REVERT: F 124 GLN cc_start: 0.7706 (pp30) cc_final: 0.7434 (pp30) REVERT: F 131 LEU cc_start: 0.8340 (mp) cc_final: 0.8124 (mt) REVERT: F 149 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6619 (mm-30) REVERT: F 183 LYS cc_start: 0.8457 (mptt) cc_final: 0.8135 (mptt) REVERT: F 215 GLN cc_start: 0.7152 (tp-100) cc_final: 0.6691 (tp-100) REVERT: F 219 LEU cc_start: 0.7972 (mt) cc_final: 0.7116 (mt) REVERT: F 250 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.7570 (ttm-80) REVERT: F 263 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7752 (mmmm) REVERT: F 270 LYS cc_start: 0.8283 (pttp) cc_final: 0.7828 (ptmm) REVERT: F 291 THR cc_start: 0.7746 (p) cc_final: 0.7491 (t) REVERT: F 298 ASP cc_start: 0.8112 (m-30) cc_final: 0.7896 (m-30) REVERT: F 300 LYS cc_start: 0.8365 (tptm) cc_final: 0.7922 (tptm) REVERT: F 332 GLN cc_start: 0.7976 (mm110) cc_final: 0.7490 (mp10) REVERT: F 337 HIS cc_start: 0.7857 (m170) cc_final: 0.7470 (m90) outliers start: 2 outliers final: 2 residues processed: 604 average time/residue: 0.1257 time to fit residues: 107.5281 Evaluate side-chains 580 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 578 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN A 275 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 259 GLN C 275 ASN ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 337 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.143188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116334 restraints weight = 30099.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120888 restraints weight = 17565.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124089 restraints weight = 11761.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126340 restraints weight = 8566.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128006 restraints weight = 6681.656| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14142 Z= 0.210 Angle : 0.658 12.744 19146 Z= 0.345 Chirality : 0.045 0.329 2178 Planarity : 0.005 0.054 2448 Dihedral : 9.736 59.549 2070 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.26 % Allowed : 2.42 % Favored : 97.32 % 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 are not related in a simple way. whole: 1.54 (0.21), residues: 1728 helix: 1.44 (0.16), residues: 942 sheet: 0.44 (0.42), residues: 156 loop : 0.74 (0.29), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 250 TYR 0.014 0.002 TYR F 72 PHE 0.022 0.002 PHE C 216 TRP 0.027 0.004 TRP F 220 HIS 0.007 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (14142) covalent geometry : angle 0.65768 / 0.35 (19146) hydrogen bonds : bond 0.04512 / 3.01 ( 738) hydrogen bonds : angle 4.56863 / 3.30 ( 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 634 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 630 time to evaluate : 0.570 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: A 74 MET cc_start: 0.8315 (mtm) cc_final: 0.7722 (mtm) REVERT: A 90 TRP cc_start: 0.7994 (m100) cc_final: 0.7277 (m100) REVERT: A 92 ASP cc_start: 0.7572 (m-30) cc_final: 0.7276 (m-30) REVERT: A 96 LEU cc_start: 0.7446 (mt) cc_final: 0.6743 (tp) REVERT: A 100 ILE cc_start: 0.8298 (mm) cc_final: 0.7950 (mm) REVERT: A 102 ASP cc_start: 0.7825 (m-30) cc_final: 0.7457 (m-30) REVERT: A 104 LYS cc_start: 0.8676 (tttt) cc_final: 0.8324 (tttt) REVERT: A 106 THR cc_start: 0.8628 (m) cc_final: 0.8316 (p) REVERT: A 118 GLU cc_start: 0.7246 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 124 GLN cc_start: 0.8216 (pp30) cc_final: 0.7984 (pp30) REVERT: A 125 PRO cc_start: 0.8747 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: A 149 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 154 PHE cc_start: 0.7742 (t80) cc_final: 0.7280 (t80) REVERT: A 157 LEU cc_start: 0.7970 (tp) cc_final: 0.7511 (tp) REVERT: A 158 GLN cc_start: 0.7097 (tm130) cc_final: 0.6666 (tm130) REVERT: A 169 GLU cc_start: 0.7474 (tt0) cc_final: 0.7208 (tt0) REVERT: A 179 SER cc_start: 0.8944 (t) cc_final: 0.8652 (p) REVERT: A 193 GLU cc_start: 0.8005 (tt0) cc_final: 0.7716 (tt0) REVERT: A 199 ARG cc_start: 0.7485 (tpp80) cc_final: 0.6566 (tpp80) REVERT: A 206 HIS cc_start: 0.7925 (p90) cc_final: 0.7591 (p90) REVERT: A 211 MET cc_start: 0.8166 (mmp) cc_final: 0.7882 (mmp) REVERT: A 212 MET cc_start: 0.8229 (mmp) cc_final: 0.7989 (mmp) REVERT: A 213 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7818 (mtmt) REVERT: A 217 MET cc_start: 0.8135 (mpp) cc_final: 0.7606 (mpp) REVERT: A 219 LEU cc_start: 0.8891 (mt) cc_final: 0.8609 (mt) REVERT: A 230 GLN cc_start: 0.6260 (mm-40) cc_final: 0.5751 (mm110) REVERT: A 243 LEU cc_start: 0.8457 (mm) cc_final: 0.8238 (mm) REVERT: A 251 MET cc_start: 0.7517 (mmm) cc_final: 0.7254 (mmm) REVERT: A 258 ASN cc_start: 0.8286 (p0) cc_final: 0.7997 (p0) REVERT: A 259 GLN cc_start: 0.7779 (mt0) cc_final: 0.7196 (mt0) REVERT: A 263 LYS cc_start: 0.8022 (mttp) cc_final: 0.7785 (mttp) REVERT: A 266 GLU cc_start: 0.7996 (tp30) cc_final: 0.7520 (tp30) REVERT: A 286 GLU cc_start: 0.7569 (pm20) cc_final: 0.7288 (pm20) REVERT: A 301 GLU cc_start: 0.8085 (tt0) cc_final: 0.6882 (tt0) REVERT: A 305 ASP cc_start: 0.8415 (m-30) cc_final: 0.7840 (m-30) REVERT: A 341 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 342 LYS cc_start: 0.8831 (mptt) cc_final: 0.8455 (mptt) REVERT: A 343 MET cc_start: 0.8333 (tpt) cc_final: 0.7590 (tpt) REVERT: A 345 LYS cc_start: 0.8759 (pptt) cc_final: 0.8513 (pptt) REVERT: A 347 LYS cc_start: 0.9091 (mptt) cc_final: 0.8769 (mptt) REVERT: B 74 MET cc_start: 0.8266 (mtm) cc_final: 0.7484 (mtm) REVERT: B 86 MET cc_start: 0.7831 (mtm) cc_final: 0.7587 (mtm) REVERT: B 92 ASP cc_start: 0.7441 (m-30) cc_final: 0.7189 (m-30) REVERT: B 99 VAL cc_start: 0.8335 (t) cc_final: 0.8095 (m) REVERT: B 104 LYS cc_start: 0.8590 (tttt) cc_final: 0.8301 (tttt) REVERT: B 114 LYS cc_start: 0.7949 (tptm) cc_final: 0.7503 (tptm) REVERT: B 123 LEU cc_start: 0.8362 (tp) cc_final: 0.8032 (tp) REVERT: B 154 PHE cc_start: 0.7527 (t80) cc_final: 0.6855 (t80) REVERT: B 157 LEU cc_start: 0.8161 (tp) cc_final: 0.7776 (tp) REVERT: B 211 MET cc_start: 0.8076 (mmp) cc_final: 0.7846 (mmp) REVERT: B 213 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7595 (mtmt) REVERT: B 215 GLN cc_start: 0.7808 (tp-100) cc_final: 0.6523 (tp-100) REVERT: B 217 MET cc_start: 0.8174 (mpp) cc_final: 0.7516 (mpp) REVERT: B 219 LEU cc_start: 0.8800 (mt) cc_final: 0.7798 (mt) REVERT: B 243 LEU cc_start: 0.8616 (mm) cc_final: 0.8360 (mm) REVERT: B 258 ASN cc_start: 0.8345 (p0) cc_final: 0.8068 (p0) REVERT: B 259 GLN cc_start: 0.7872 (mt0) cc_final: 0.7180 (mt0) REVERT: B 266 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 286 GLU cc_start: 0.6920 (pm20) cc_final: 0.6533 (pm20) REVERT: B 299 LEU cc_start: 0.8811 (mt) cc_final: 0.8576 (mt) REVERT: B 301 GLU cc_start: 0.7771 (tt0) cc_final: 0.7049 (tt0) REVERT: B 305 ASP cc_start: 0.8271 (m-30) cc_final: 0.7910 (m-30) REVERT: B 338 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8128 (mtp85) REVERT: B 342 LYS cc_start: 0.8743 (mptt) cc_final: 0.8111 (mptt) REVERT: B 345 LYS cc_start: 0.8618 (pptt) cc_final: 0.8373 (pptt) REVERT: C 74 MET cc_start: 0.5656 (mtm) cc_final: 0.5274 (mtm) REVERT: C 86 MET cc_start: 0.5509 (pmm) cc_final: 0.5173 (pmm) REVERT: C 158 GLN cc_start: 0.7543 (pm20) cc_final: 0.7272 (pm20) REVERT: C 171 GLN cc_start: 0.8403 (mp10) cc_final: 0.8134 (mp10) REVERT: C 199 ARG cc_start: 0.6158 (tpp80) cc_final: 0.5776 (tpp80) REVERT: C 213 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7751 (mtmm) REVERT: C 215 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7831 (tm-30) REVERT: C 219 LEU cc_start: 0.7013 (mt) cc_final: 0.6360 (mt) REVERT: C 239 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7241 (ttm110) REVERT: C 248 MET cc_start: 0.7840 (mtp) cc_final: 0.7467 (mtp) REVERT: C 251 MET cc_start: 0.6679 (mpp) cc_final: 0.6261 (tpp) REVERT: C 264 GLN cc_start: 0.8501 (mp10) cc_final: 0.8189 (mp10) REVERT: C 289 GLN cc_start: 0.7940 (mt0) cc_final: 0.7584 (mt0) REVERT: C 299 LEU cc_start: 0.8710 (mt) cc_final: 0.8348 (mt) REVERT: C 300 LYS cc_start: 0.8809 (tttt) cc_final: 0.8566 (tttt) REVERT: C 304 ARG cc_start: 0.8515 (ttt90) cc_final: 0.8084 (ttt90) REVERT: C 312 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7926 (mtp-110) REVERT: C 313 GLU cc_start: 0.8389 (pt0) cc_final: 0.8041 (pt0) REVERT: C 335 ASP cc_start: 0.8359 (m-30) cc_final: 0.7954 (m-30) REVERT: C 344 LYS cc_start: 0.9057 (mttm) cc_final: 0.8552 (mttm) REVERT: D 73 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 82 ASP cc_start: 0.8364 (t0) cc_final: 0.8095 (t70) REVERT: D 90 TRP cc_start: 0.7985 (m100) cc_final: 0.7615 (m100) REVERT: D 99 VAL cc_start: 0.8396 (t) cc_final: 0.8129 (t) REVERT: D 102 ASP cc_start: 0.7968 (m-30) cc_final: 0.7635 (m-30) REVERT: D 104 LYS cc_start: 0.8328 (tttt) cc_final: 0.7939 (tttt) REVERT: D 112 LYS cc_start: 0.8242 (mttt) cc_final: 0.7960 (mttt) REVERT: D 124 GLN cc_start: 0.7690 (pp30) cc_final: 0.7364 (pp30) REVERT: D 131 LEU cc_start: 0.8444 (mp) cc_final: 0.8010 (mt) REVERT: D 139 LYS cc_start: 0.7599 (mtmm) cc_final: 0.6623 (mtmm) REVERT: D 142 ILE cc_start: 0.8983 (tp) cc_final: 0.8768 (tp) REVERT: D 183 LYS cc_start: 0.8289 (mptt) cc_final: 0.7918 (mptt) REVERT: D 211 MET cc_start: 0.7606 (mmp) cc_final: 0.7259 (mmt) REVERT: D 213 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7934 (mtmm) REVERT: D 248 MET cc_start: 0.7711 (mtp) cc_final: 0.7276 (mtp) REVERT: D 250 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7539 (mtt-85) REVERT: D 251 MET cc_start: 0.7436 (mpp) cc_final: 0.6692 (tpp) REVERT: D 265 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7500 (ptp-170) REVERT: D 291 THR cc_start: 0.7810 (p) cc_final: 0.7476 (t) REVERT: D 294 PHE cc_start: 0.7296 (m-10) cc_final: 0.6921 (m-80) REVERT: D 300 LYS cc_start: 0.8553 (tptm) cc_final: 0.8051 (tptm) REVERT: D 305 ASP cc_start: 0.7808 (t0) cc_final: 0.7419 (t0) REVERT: D 312 ARG cc_start: 0.8211 (ptm-80) cc_final: 0.7914 (ptm-80) REVERT: D 337 HIS cc_start: 0.7912 (m90) cc_final: 0.7098 (m90) REVERT: D 340 ILE cc_start: 0.8895 (mm) cc_final: 0.8693 (mm) REVERT: E 166 TRP cc_start: 0.5947 (m-10) cc_final: 0.5743 (m-10) REVERT: E 171 GLN cc_start: 0.8557 (mm110) cc_final: 0.8249 (mp10) REVERT: E 193 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7583 (mt-10) REVERT: E 199 ARG cc_start: 0.6823 (tpp80) cc_final: 0.6476 (tpp80) REVERT: E 205 ASP cc_start: 0.6203 (m-30) cc_final: 0.5813 (m-30) REVERT: E 212 MET cc_start: 0.7974 (mmp) cc_final: 0.7735 (mmp) REVERT: E 213 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8075 (mtmt) REVERT: E 215 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7878 (tm-30) REVERT: E 239 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7162 (ttp-110) REVERT: E 248 MET cc_start: 0.7775 (mtp) cc_final: 0.7310 (mtp) REVERT: E 251 MET cc_start: 0.6798 (mmm) cc_final: 0.6575 (mmm) REVERT: E 256 HIS cc_start: 0.7675 (t70) cc_final: 0.7448 (t70) REVERT: E 266 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7834 (tm-30) REVERT: E 270 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7604 (mmmt) REVERT: E 290 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7900 (mm-30) REVERT: E 299 LEU cc_start: 0.8675 (mt) cc_final: 0.8328 (mt) REVERT: E 300 LYS cc_start: 0.8697 (tttt) cc_final: 0.8398 (tttt) REVERT: E 301 GLU cc_start: 0.8378 (tt0) cc_final: 0.7993 (tt0) REVERT: E 302 MET cc_start: 0.8316 (tmm) cc_final: 0.8066 (tmm) REVERT: E 304 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8113 (mtp-110) REVERT: E 312 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7864 (mtp-110) REVERT: E 313 GLU cc_start: 0.8636 (pt0) cc_final: 0.8370 (pt0) REVERT: E 335 ASP cc_start: 0.8285 (m-30) cc_final: 0.7844 (m-30) REVERT: E 338 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8300 (mtp85) REVERT: E 341 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7657 (mm-30) REVERT: E 343 MET cc_start: 0.8315 (tpp) cc_final: 0.7945 (tpp) REVERT: F 74 MET cc_start: 0.8004 (mtm) cc_final: 0.7441 (mtm) REVERT: F 75 SER cc_start: 0.8158 (p) cc_final: 0.7816 (p) REVERT: F 82 ASP cc_start: 0.8240 (t0) cc_final: 0.8022 (t70) REVERT: F 90 TRP cc_start: 0.8147 (m100) cc_final: 0.7643 (m100) REVERT: F 102 ASP cc_start: 0.8086 (m-30) cc_final: 0.7619 (m-30) REVERT: F 104 LYS cc_start: 0.8350 (tttt) cc_final: 0.8062 (tttt) REVERT: F 112 LYS cc_start: 0.7979 (mttt) cc_final: 0.7764 (mttt) REVERT: F 124 GLN cc_start: 0.7739 (pp30) cc_final: 0.7409 (pp30) REVERT: F 183 LYS cc_start: 0.8364 (mptt) cc_final: 0.7998 (mptt) REVERT: F 190 PHE cc_start: 0.8122 (t80) cc_final: 0.7325 (t80) REVERT: F 212 MET cc_start: 0.8016 (mmp) cc_final: 0.7704 (mmp) REVERT: F 215 GLN cc_start: 0.7433 (tp-100) cc_final: 0.6745 (tp-100) REVERT: F 216 PHE cc_start: 0.8078 (t80) cc_final: 0.7802 (t80) REVERT: F 219 LEU cc_start: 0.8040 (mt) cc_final: 0.7169 (mt) REVERT: F 220 TRP cc_start: 0.8100 (t60) cc_final: 0.7794 (t60) REVERT: F 234 MET cc_start: 0.7125 (ptp) cc_final: 0.6882 (ptt) REVERT: F 242 ASP cc_start: 0.8254 (m-30) cc_final: 0.7992 (m-30) REVERT: F 263 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7986 (mmmm) REVERT: F 270 LYS cc_start: 0.8257 (pttp) cc_final: 0.7697 (tptm) REVERT: F 298 ASP cc_start: 0.8161 (m-30) cc_final: 0.7890 (m-30) REVERT: F 300 LYS cc_start: 0.8312 (tptm) cc_final: 0.7885 (tptm) outliers start: 4 outliers final: 0 residues processed: 634 average time/residue: 0.1285 time to fit residues: 114.9578 Evaluate side-chains 611 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.0270 chunk 147 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN B 256 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS C 171 GLN C 185 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.149377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122589 restraints weight = 29384.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127166 restraints weight = 17407.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130309 restraints weight = 11738.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.132593 restraints weight = 8649.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134201 restraints weight = 6763.139| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14142 Z= 0.122 Angle : 0.587 13.663 19146 Z= 0.301 Chirality : 0.042 0.277 2178 Planarity : 0.004 0.053 2448 Dihedral : 8.930 57.248 2070 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.07 % Allowed : 1.31 % Favored : 98.63 % 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 are not related in a simple way. whole: 1.66 (0.21), residues: 1728 helix: 1.69 (0.17), residues: 912 sheet: 0.35 (0.42), residues: 156 loop : 0.63 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.010 0.001 TYR F 72 PHE 0.023 0.002 PHE C 216 TRP 0.026 0.003 TRP D 220 HIS 0.010 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14142) covalent geometry : angle 0.58700 / 0.30 (19146) hydrogen bonds : bond 0.03711 / 2.46 ( 738) hydrogen bonds : angle 4.22869 / 3.04 ( 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 622 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 621 time to evaluate : 0.533 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: 0.8272 (mtm) cc_final: 0.7656 (mtm) REVERT: A 90 TRP cc_start: 0.7876 (m100) cc_final: 0.7513 (m100) REVERT: A 92 ASP cc_start: 0.7662 (m-30) cc_final: 0.7312 (m-30) REVERT: A 96 LEU cc_start: 0.7423 (mt) cc_final: 0.6802 (tp) REVERT: A 100 ILE cc_start: 0.8289 (mm) cc_final: 0.7917 (mm) REVERT: A 102 ASP cc_start: 0.7756 (m-30) cc_final: 0.7481 (m-30) REVERT: A 106 THR cc_start: 0.8577 (m) cc_final: 0.8255 (p) REVERT: A 124 GLN cc_start: 0.8261 (pp30) cc_final: 0.8029 (pp30) REVERT: A 125 PRO cc_start: 0.8654 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: A 146 THR cc_start: 0.8375 (p) cc_final: 0.7936 (p) REVERT: A 148 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8213 (ttpt) REVERT: A 157 LEU cc_start: 0.8006 (tp) cc_final: 0.7594 (tt) REVERT: A 162 LEU cc_start: 0.8552 (mm) cc_final: 0.8164 (mm) REVERT: A 178 PHE cc_start: 0.8898 (m-10) cc_final: 0.8508 (m-10) REVERT: A 179 SER cc_start: 0.8917 (t) cc_final: 0.8599 (p) REVERT: A 193 GLU cc_start: 0.7862 (tt0) cc_final: 0.7660 (tt0) REVERT: A 206 HIS cc_start: 0.8057 (p90) cc_final: 0.7683 (p90) REVERT: A 211 MET cc_start: 0.8055 (mmp) cc_final: 0.7844 (mmp) REVERT: A 212 MET cc_start: 0.8088 (mmp) cc_final: 0.7845 (mmp) REVERT: A 213 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7741 (mtmt) REVERT: A 217 MET cc_start: 0.7993 (mpp) cc_final: 0.7510 (mpp) REVERT: A 219 LEU cc_start: 0.8900 (mt) cc_final: 0.8629 (mt) REVERT: A 230 GLN cc_start: 0.6375 (mm-40) cc_final: 0.5933 (mm110) REVERT: A 243 LEU cc_start: 0.8488 (mm) cc_final: 0.8211 (mm) REVERT: A 248 MET cc_start: 0.7755 (mtm) cc_final: 0.7267 (mtm) REVERT: A 251 MET cc_start: 0.7469 (mmm) cc_final: 0.7079 (mmm) REVERT: A 258 ASN cc_start: 0.8312 (p0) cc_final: 0.8027 (p0) REVERT: A 259 GLN cc_start: 0.7769 (mt0) cc_final: 0.7182 (mt0) REVERT: A 262 LEU cc_start: 0.8223 (tp) cc_final: 0.7863 (mm) REVERT: A 263 LYS cc_start: 0.7870 (mttp) cc_final: 0.7630 (mttp) REVERT: A 266 GLU cc_start: 0.7969 (tp30) cc_final: 0.7543 (tp30) REVERT: A 270 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8281 (mmpt) REVERT: A 272 ILE cc_start: 0.8607 (mt) cc_final: 0.8387 (mt) REVERT: A 301 GLU cc_start: 0.8034 (tt0) cc_final: 0.7163 (tt0) REVERT: A 338 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7888 (mtp85) REVERT: A 341 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 342 LYS cc_start: 0.8785 (mptt) cc_final: 0.8339 (mptt) REVERT: A 343 MET cc_start: 0.8259 (tpt) cc_final: 0.7517 (tpt) REVERT: A 345 LYS cc_start: 0.8729 (pptt) cc_final: 0.8471 (pptt) REVERT: A 347 LYS cc_start: 0.9064 (mptt) cc_final: 0.8759 (mptt) REVERT: B 74 MET cc_start: 0.8128 (mtm) cc_final: 0.7367 (mtm) REVERT: B 90 TRP cc_start: 0.8119 (m100) cc_final: 0.7401 (m100) REVERT: B 92 ASP cc_start: 0.7315 (m-30) cc_final: 0.7045 (m-30) REVERT: B 96 LEU cc_start: 0.7609 (mt) cc_final: 0.7288 (mm) REVERT: B 104 LYS cc_start: 0.8590 (tttt) cc_final: 0.8290 (tttt) REVERT: B 114 LYS cc_start: 0.7775 (tptm) cc_final: 0.7434 (tptm) REVERT: B 118 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6444 (mt-10) REVERT: B 123 LEU cc_start: 0.8303 (tp) cc_final: 0.7986 (tp) REVERT: B 124 GLN cc_start: 0.8147 (pp30) cc_final: 0.7907 (pp30) REVERT: B 129 VAL cc_start: 0.6654 (t) cc_final: 0.6257 (t) REVERT: B 146 THR cc_start: 0.8406 (p) cc_final: 0.7892 (p) REVERT: B 154 PHE cc_start: 0.7638 (t80) cc_final: 0.7011 (t80) REVERT: B 157 LEU cc_start: 0.8149 (tp) cc_final: 0.7755 (tp) REVERT: B 178 PHE cc_start: 0.8828 (m-10) cc_final: 0.8463 (m-10) REVERT: B 211 MET cc_start: 0.7957 (mmp) cc_final: 0.7730 (mmp) REVERT: B 213 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7563 (mtmt) REVERT: B 215 GLN cc_start: 0.7683 (tp-100) cc_final: 0.6387 (tp-100) REVERT: B 217 MET cc_start: 0.8025 (mpp) cc_final: 0.7489 (mpp) REVERT: B 219 LEU cc_start: 0.8771 (mt) cc_final: 0.7721 (mt) REVERT: B 234 MET cc_start: 0.7133 (ttm) cc_final: 0.6649 (ttm) REVERT: B 237 THR cc_start: 0.8506 (t) cc_final: 0.8108 (m) REVERT: B 243 LEU cc_start: 0.8636 (mm) cc_final: 0.8395 (mm) REVERT: B 258 ASN cc_start: 0.8345 (p0) cc_final: 0.8074 (p0) REVERT: B 259 GLN cc_start: 0.7855 (mt0) cc_final: 0.7146 (mt0) REVERT: B 266 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 286 GLU cc_start: 0.6817 (pm20) cc_final: 0.6535 (pm20) REVERT: B 299 LEU cc_start: 0.8848 (mt) cc_final: 0.8569 (mt) REVERT: B 301 GLU cc_start: 0.7613 (tt0) cc_final: 0.7056 (tt0) REVERT: B 334 GLN cc_start: 0.7759 (mp10) cc_final: 0.7545 (mp10) REVERT: B 338 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8065 (mtp85) REVERT: B 342 LYS cc_start: 0.8672 (mptt) cc_final: 0.7956 (mptt) REVERT: B 345 LYS cc_start: 0.8530 (pptt) cc_final: 0.8230 (pptt) REVERT: C 74 MET cc_start: 0.5662 (mtm) cc_final: 0.5233 (mtm) REVERT: C 86 MET cc_start: 0.5296 (pmm) cc_final: 0.5051 (pmm) REVERT: C 158 GLN cc_start: 0.7539 (pm20) cc_final: 0.7277 (pm20) REVERT: C 171 GLN cc_start: 0.8314 (mp-120) cc_final: 0.8032 (mp10) REVERT: C 199 ARG cc_start: 0.5787 (tpp80) cc_final: 0.5502 (tpp80) REVERT: C 213 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7799 (mtmm) REVERT: C 239 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7211 (ttm110) REVERT: C 248 MET cc_start: 0.7603 (mtp) cc_final: 0.7226 (mtp) REVERT: C 251 MET cc_start: 0.6861 (mpp) cc_final: 0.6346 (tpp) REVERT: C 264 GLN cc_start: 0.8379 (mp10) cc_final: 0.8140 (mp10) REVERT: C 270 LYS cc_start: 0.8675 (mmmt) cc_final: 0.7828 (mmmt) REVERT: C 289 GLN cc_start: 0.7821 (mt0) cc_final: 0.7502 (mt0) REVERT: C 299 LEU cc_start: 0.8685 (mt) cc_final: 0.8174 (mt) REVERT: C 300 LYS cc_start: 0.8792 (tttt) cc_final: 0.8557 (tttt) REVERT: C 303 CYS cc_start: 0.8712 (m) cc_final: 0.8210 (m) REVERT: C 304 ARG cc_start: 0.8427 (ttt90) cc_final: 0.8028 (ttt90) REVERT: C 312 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7913 (mtp-110) REVERT: C 313 GLU cc_start: 0.8372 (pt0) cc_final: 0.8028 (pt0) REVERT: C 335 ASP cc_start: 0.8390 (m-30) cc_final: 0.7976 (m-30) REVERT: C 343 MET cc_start: 0.8180 (tpp) cc_final: 0.7863 (tpp) REVERT: C 344 LYS cc_start: 0.8933 (mttm) cc_final: 0.8479 (mttm) REVERT: D 73 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 82 ASP cc_start: 0.8319 (t0) cc_final: 0.8007 (t70) REVERT: D 97 ASP cc_start: 0.7565 (p0) cc_final: 0.7341 (p0) REVERT: D 99 VAL cc_start: 0.8351 (t) cc_final: 0.8110 (t) REVERT: D 102 ASP cc_start: 0.7900 (m-30) cc_final: 0.7582 (m-30) REVERT: D 104 LYS cc_start: 0.8383 (tttt) cc_final: 0.8046 (ttmt) REVERT: D 112 LYS cc_start: 0.8257 (mttt) cc_final: 0.7951 (mttt) REVERT: D 113 LYS cc_start: 0.7634 (tppt) cc_final: 0.7277 (tppt) REVERT: D 117 PHE cc_start: 0.8022 (m-10) cc_final: 0.7538 (m-10) REVERT: D 124 GLN cc_start: 0.7642 (pp30) cc_final: 0.7397 (pp30) REVERT: D 131 LEU cc_start: 0.8379 (mp) cc_final: 0.8082 (mp) REVERT: D 139 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6280 (mtmm) REVERT: D 183 LYS cc_start: 0.8267 (mptt) cc_final: 0.7864 (mptt) REVERT: D 211 MET cc_start: 0.7505 (mmp) cc_final: 0.7197 (mmp) REVERT: D 213 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7894 (mtmm) REVERT: D 237 THR cc_start: 0.7967 (t) cc_final: 0.7657 (t) REVERT: D 241 GLN cc_start: 0.8424 (pm20) cc_final: 0.7958 (mm110) REVERT: D 242 ASP cc_start: 0.8184 (m-30) cc_final: 0.7791 (m-30) REVERT: D 248 MET cc_start: 0.7522 (mtp) cc_final: 0.7154 (mtp) REVERT: D 265 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7507 (ptp-170) REVERT: D 300 LYS cc_start: 0.8506 (tptm) cc_final: 0.8029 (tptm) REVERT: D 305 ASP cc_start: 0.7743 (t0) cc_final: 0.7352 (t0) REVERT: D 312 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7833 (ptm-80) REVERT: D 337 HIS cc_start: 0.7893 (m90) cc_final: 0.7258 (m90) REVERT: E 158 GLN cc_start: 0.7186 (pm20) cc_final: 0.6917 (pm20) REVERT: E 166 TRP cc_start: 0.5959 (m-10) cc_final: 0.5285 (m-10) REVERT: E 170 SER cc_start: 0.7761 (p) cc_final: 0.7212 (p) REVERT: E 171 GLN cc_start: 0.8532 (mm110) cc_final: 0.8275 (mp10) REVERT: E 193 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7473 (mt-10) REVERT: E 199 ARG cc_start: 0.6712 (tpp80) cc_final: 0.6377 (tpp80) REVERT: E 205 ASP cc_start: 0.6298 (m-30) cc_final: 0.5888 (m-30) REVERT: E 212 MET cc_start: 0.7961 (mmp) cc_final: 0.7708 (mmp) REVERT: E 213 LYS cc_start: 0.8296 (mtmt) cc_final: 0.8015 (mtmt) REVERT: E 215 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7828 (tm-30) REVERT: E 239 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7195 (ttp-110) REVERT: E 248 MET cc_start: 0.7644 (mtp) cc_final: 0.7163 (mtp) REVERT: E 251 MET cc_start: 0.6898 (mmm) cc_final: 0.6624 (mmm) REVERT: E 264 GLN cc_start: 0.8541 (mp10) cc_final: 0.8286 (mp10) REVERT: E 266 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 270 LYS cc_start: 0.8498 (mmmt) cc_final: 0.7514 (mmmt) REVERT: E 290 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7916 (mm-30) REVERT: E 299 LEU cc_start: 0.8631 (mt) cc_final: 0.8222 (mt) REVERT: E 300 LYS cc_start: 0.8651 (tttt) cc_final: 0.8347 (tttt) REVERT: E 303 CYS cc_start: 0.8665 (m) cc_final: 0.8097 (m) REVERT: E 304 ARG cc_start: 0.8471 (mtp180) cc_final: 0.8164 (mmm-85) REVERT: E 312 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7851 (mtp-110) REVERT: E 313 GLU cc_start: 0.8646 (pt0) cc_final: 0.8352 (pt0) REVERT: E 335 ASP cc_start: 0.8144 (m-30) cc_final: 0.7768 (m-30) REVERT: E 338 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8192 (mtp85) REVERT: E 341 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7640 (mm-30) REVERT: E 343 MET cc_start: 0.8241 (tpp) cc_final: 0.7943 (tpp) REVERT: F 74 MET cc_start: 0.7860 (mtm) cc_final: 0.7305 (mtm) REVERT: F 75 SER cc_start: 0.8119 (p) cc_final: 0.7798 (p) REVERT: F 82 ASP cc_start: 0.8375 (t0) cc_final: 0.8067 (t70) REVERT: F 90 TRP cc_start: 0.8065 (m100) cc_final: 0.7575 (m100) REVERT: F 102 ASP cc_start: 0.8014 (m-30) cc_final: 0.7596 (m-30) REVERT: F 104 LYS cc_start: 0.8279 (tttt) cc_final: 0.7896 (tttm) REVERT: F 124 GLN cc_start: 0.7688 (pp30) cc_final: 0.7346 (pp30) REVERT: F 144 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7824 (mtpt) REVERT: F 183 LYS cc_start: 0.8362 (mptt) cc_final: 0.7961 (mptt) REVERT: F 213 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8123 (mtmt) REVERT: F 215 GLN cc_start: 0.7358 (tp-100) cc_final: 0.6641 (tp-100) REVERT: F 219 LEU cc_start: 0.7993 (mt) cc_final: 0.7072 (mt) REVERT: F 234 MET cc_start: 0.7129 (ptp) cc_final: 0.6923 (ptt) REVERT: F 242 ASP cc_start: 0.8245 (m-30) cc_final: 0.8029 (m-30) REVERT: F 263 LYS cc_start: 0.8257 (mmmm) cc_final: 0.7912 (mmmm) REVERT: F 265 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7132 (ptp-170) REVERT: F 270 LYS cc_start: 0.8319 (pttp) cc_final: 0.7747 (tptm) REVERT: F 298 ASP cc_start: 0.8172 (m-30) cc_final: 0.7953 (m-30) REVERT: F 300 LYS cc_start: 0.8270 (tptm) cc_final: 0.7851 (tptm) REVERT: F 302 MET cc_start: 0.7737 (tmm) cc_final: 0.7243 (tmm) REVERT: F 337 HIS cc_start: 0.8026 (m170) cc_final: 0.7541 (m90) outliers start: 1 outliers final: 0 residues processed: 622 average time/residue: 0.1262 time to fit residues: 110.1693 Evaluate side-chains 610 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.147142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120092 restraints weight = 29596.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124616 restraints weight = 17750.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127816 restraints weight = 12049.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130123 restraints weight = 8888.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131814 restraints weight = 6981.979| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.7201 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= 0.151 Angle : 0.616 13.741 19146 Z= 0.320 Chirality : 0.044 0.381 2178 Planarity : 0.004 0.054 2448 Dihedral : 9.056 58.658 2070 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.22 % 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 are not related in a simple way. whole: 1.54 (0.21), residues: 1728 helix: 1.59 (0.17), residues: 912 sheet: 0.24 (0.42), residues: 156 loop : 0.60 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 250 TYR 0.016 0.001 TYR B 132 PHE 0.035 0.002 PHE E 216 TRP 0.038 0.004 TRP F 220 HIS 0.003 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14142) covalent geometry : angle 0.61551 / 0.32 (19146) hydrogen bonds : bond 0.03906 / 2.62 ( 738) hydrogen bonds : angle 4.33095 / 3.12 ( 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 626 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 625 time to evaluate : 0.527 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: A 74 MET cc_start: 0.8276 (mtm) cc_final: 0.7645 (mtm) REVERT: A 92 ASP cc_start: 0.7683 (m-30) cc_final: 0.7365 (m-30) REVERT: A 96 LEU cc_start: 0.7520 (mt) cc_final: 0.7254 (mm) REVERT: A 100 ILE cc_start: 0.8185 (mm) cc_final: 0.7923 (mm) REVERT: A 102 ASP cc_start: 0.7723 (m-30) cc_final: 0.7453 (m-30) REVERT: A 106 THR cc_start: 0.8573 (m) cc_final: 0.8258 (p) REVERT: A 125 PRO cc_start: 0.8671 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: A 146 THR cc_start: 0.8256 (p) cc_final: 0.7981 (p) REVERT: A 148 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8176 (ttpt) REVERT: A 157 LEU cc_start: 0.8047 (tp) cc_final: 0.7759 (tt) REVERT: A 179 SER cc_start: 0.8942 (t) cc_final: 0.8619 (p) REVERT: A 191 ILE cc_start: 0.8169 (mt) cc_final: 0.7911 (mt) REVERT: A 193 GLU cc_start: 0.7907 (tt0) cc_final: 0.7675 (tt0) REVERT: A 206 HIS cc_start: 0.7869 (p90) cc_final: 0.7545 (p90) REVERT: A 211 MET cc_start: 0.8028 (mmp) cc_final: 0.7777 (mmp) REVERT: A 213 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7770 (mtmt) REVERT: A 217 MET cc_start: 0.7951 (mpp) cc_final: 0.7473 (mpp) REVERT: A 219 LEU cc_start: 0.8929 (mt) cc_final: 0.8691 (mt) REVERT: A 230 GLN cc_start: 0.6454 (mm-40) cc_final: 0.6092 (mm110) REVERT: A 248 MET cc_start: 0.7791 (mtm) cc_final: 0.7079 (mmm) REVERT: A 251 MET cc_start: 0.7488 (mmm) cc_final: 0.7147 (mmm) REVERT: A 258 ASN cc_start: 0.8294 (p0) cc_final: 0.8027 (p0) REVERT: A 259 GLN cc_start: 0.7781 (mt0) cc_final: 0.7232 (mt0) REVERT: A 262 LEU cc_start: 0.8165 (tp) cc_final: 0.7841 (mm) REVERT: A 263 LYS cc_start: 0.7850 (mttp) cc_final: 0.7636 (mttp) REVERT: A 266 GLU cc_start: 0.7863 (tp30) cc_final: 0.7487 (tp30) REVERT: A 270 LYS cc_start: 0.8584 (mmpt) cc_final: 0.8329 (mmpt) REVERT: A 272 ILE cc_start: 0.8600 (mt) cc_final: 0.8394 (mt) REVERT: A 286 GLU cc_start: 0.7455 (pm20) cc_final: 0.7128 (pm20) REVERT: A 301 GLU cc_start: 0.8043 (tt0) cc_final: 0.7039 (tt0) REVERT: A 338 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7772 (mtp85) REVERT: A 341 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 342 LYS cc_start: 0.8776 (mptt) cc_final: 0.8365 (mptt) REVERT: A 343 MET cc_start: 0.8196 (tpt) cc_final: 0.7393 (tpt) REVERT: A 345 LYS cc_start: 0.8708 (pptt) cc_final: 0.8459 (pptt) REVERT: A 347 LYS cc_start: 0.9091 (mptt) cc_final: 0.8737 (mptt) REVERT: B 74 MET cc_start: 0.8154 (mtm) cc_final: 0.7365 (mtm) REVERT: B 92 ASP cc_start: 0.7316 (m-30) cc_final: 0.7055 (m-30) REVERT: B 99 VAL cc_start: 0.8286 (t) cc_final: 0.8086 (m) REVERT: B 104 LYS cc_start: 0.8578 (tttt) cc_final: 0.8273 (tttt) REVERT: B 114 LYS cc_start: 0.7789 (tptm) cc_final: 0.7484 (tptm) REVERT: B 118 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6525 (mt-10) REVERT: B 123 LEU cc_start: 0.8306 (tp) cc_final: 0.8005 (tp) REVERT: B 129 VAL cc_start: 0.6839 (t) cc_final: 0.6459 (t) REVERT: B 132 TYR cc_start: 0.7364 (p90) cc_final: 0.6715 (p90) REVERT: B 144 LYS cc_start: 0.8434 (mtpt) cc_final: 0.8220 (mtpt) REVERT: B 146 THR cc_start: 0.8449 (p) cc_final: 0.7873 (p) REVERT: B 154 PHE cc_start: 0.7576 (t80) cc_final: 0.7016 (t80) REVERT: B 157 LEU cc_start: 0.8172 (tp) cc_final: 0.7811 (tp) REVERT: B 178 PHE cc_start: 0.8848 (m-10) cc_final: 0.8387 (m-10) REVERT: B 211 MET cc_start: 0.7958 (mmp) cc_final: 0.7715 (mmp) REVERT: B 213 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7672 (mtmt) REVERT: B 215 GLN cc_start: 0.7670 (tp-100) cc_final: 0.6280 (tp-100) REVERT: B 217 MET cc_start: 0.8006 (mpp) cc_final: 0.7455 (mpp) REVERT: B 219 LEU cc_start: 0.8822 (mt) cc_final: 0.7621 (mt) REVERT: B 230 GLN cc_start: 0.6013 (mm-40) cc_final: 0.5767 (mm-40) REVERT: B 231 VAL cc_start: 0.7943 (t) cc_final: 0.7728 (t) REVERT: B 234 MET cc_start: 0.7128 (ttm) cc_final: 0.6632 (ttm) REVERT: B 243 LEU cc_start: 0.8641 (mm) cc_final: 0.8391 (mm) REVERT: B 250 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7509 (ttm170) REVERT: B 251 MET cc_start: 0.7396 (mmp) cc_final: 0.7127 (mmp) REVERT: B 258 ASN cc_start: 0.8350 (p0) cc_final: 0.8098 (p0) REVERT: B 259 GLN cc_start: 0.7889 (mt0) cc_final: 0.7189 (mt0) REVERT: B 266 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 286 GLU cc_start: 0.6739 (pm20) cc_final: 0.6432 (pm20) REVERT: B 299 LEU cc_start: 0.8834 (mt) cc_final: 0.8598 (mt) REVERT: B 301 GLU cc_start: 0.7662 (tt0) cc_final: 0.7102 (tt0) REVERT: B 338 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8018 (mtp85) REVERT: B 342 LYS cc_start: 0.8632 (mptt) cc_final: 0.7943 (mptt) REVERT: B 345 LYS cc_start: 0.8519 (pptt) cc_final: 0.8230 (pptt) REVERT: C 74 MET cc_start: 0.5670 (mtm) cc_final: 0.5199 (mtm) REVERT: C 86 MET cc_start: 0.5352 (pmm) cc_final: 0.5113 (pmm) REVERT: C 158 GLN cc_start: 0.7559 (pm20) cc_final: 0.7316 (pm20) REVERT: C 171 GLN cc_start: 0.8302 (mp-120) cc_final: 0.8043 (mp10) REVERT: C 199 ARG cc_start: 0.5967 (tpp80) cc_final: 0.5607 (tpp80) REVERT: C 213 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7871 (mtmm) REVERT: C 239 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7198 (ttm110) REVERT: C 248 MET cc_start: 0.7705 (mtp) cc_final: 0.7339 (mtp) REVERT: C 251 MET cc_start: 0.6722 (mpp) cc_final: 0.6264 (tpp) REVERT: C 264 GLN cc_start: 0.8389 (mp10) cc_final: 0.8126 (mp10) REVERT: C 289 GLN cc_start: 0.7824 (mt0) cc_final: 0.7525 (mt0) REVERT: C 290 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 299 LEU cc_start: 0.8704 (mt) cc_final: 0.8251 (mt) REVERT: C 300 LYS cc_start: 0.8797 (tttt) cc_final: 0.8561 (tttt) REVERT: C 303 CYS cc_start: 0.8678 (m) cc_final: 0.8218 (m) REVERT: C 304 ARG cc_start: 0.8417 (ttt90) cc_final: 0.8022 (ttt90) REVERT: C 312 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7884 (mtp-110) REVERT: C 313 GLU cc_start: 0.8379 (pt0) cc_final: 0.8019 (pt0) REVERT: C 335 ASP cc_start: 0.8339 (m-30) cc_final: 0.7986 (m-30) REVERT: C 343 MET cc_start: 0.8155 (tpp) cc_final: 0.7896 (tpp) REVERT: C 344 LYS cc_start: 0.8894 (mttm) cc_final: 0.8605 (mttm) REVERT: D 82 ASP cc_start: 0.8237 (t0) cc_final: 0.7949 (t70) REVERT: D 97 ASP cc_start: 0.7607 (p0) cc_final: 0.7383 (p0) REVERT: D 102 ASP cc_start: 0.7817 (m-30) cc_final: 0.7519 (m-30) REVERT: D 104 LYS cc_start: 0.8398 (tttt) cc_final: 0.8115 (tttt) REVERT: D 112 LYS cc_start: 0.8286 (mttt) cc_final: 0.7988 (mttt) REVERT: D 117 PHE cc_start: 0.7925 (m-10) cc_final: 0.7572 (m-10) REVERT: D 124 GLN cc_start: 0.7613 (pp30) cc_final: 0.7219 (pp30) REVERT: D 131 LEU cc_start: 0.8420 (mp) cc_final: 0.8092 (mp) REVERT: D 139 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6346 (mtmm) REVERT: D 183 LYS cc_start: 0.8193 (mptt) cc_final: 0.7797 (mptt) REVERT: D 211 MET cc_start: 0.7400 (mmp) cc_final: 0.7114 (mmt) REVERT: D 213 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7872 (mtmm) REVERT: D 241 GLN cc_start: 0.8476 (pm20) cc_final: 0.7947 (mm110) REVERT: D 242 ASP cc_start: 0.8196 (m-30) cc_final: 0.7848 (m-30) REVERT: D 248 MET cc_start: 0.7522 (mtp) cc_final: 0.7182 (mtp) REVERT: D 251 MET cc_start: 0.7436 (mpp) cc_final: 0.6730 (tpp) REVERT: D 300 LYS cc_start: 0.8480 (tptm) cc_final: 0.8014 (tptm) REVERT: D 305 ASP cc_start: 0.7739 (t0) cc_final: 0.7368 (t0) REVERT: D 312 ARG cc_start: 0.8143 (ptm-80) cc_final: 0.7816 (ptm-80) REVERT: D 337 HIS cc_start: 0.7898 (m90) cc_final: 0.7221 (m90) REVERT: D 347 LYS cc_start: 0.7705 (pttm) cc_final: 0.7502 (pttp) REVERT: E 166 TRP cc_start: 0.6018 (m-10) cc_final: 0.4694 (m-10) REVERT: E 193 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7535 (mt-10) REVERT: E 199 ARG cc_start: 0.6806 (tpp80) cc_final: 0.6541 (tpp80) REVERT: E 205 ASP cc_start: 0.6416 (m-30) cc_final: 0.5984 (m-30) REVERT: E 212 MET cc_start: 0.7926 (mmp) cc_final: 0.7574 (mmp) REVERT: E 213 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7992 (mtmt) REVERT: E 239 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7240 (ttp-110) REVERT: E 248 MET cc_start: 0.7608 (mtp) cc_final: 0.7115 (mtp) REVERT: E 251 MET cc_start: 0.6900 (mmm) cc_final: 0.6682 (mmm) REVERT: E 264 GLN cc_start: 0.8579 (mp10) cc_final: 0.8357 (mp10) REVERT: E 266 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 270 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7536 (mmmt) REVERT: E 290 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 299 LEU cc_start: 0.8643 (mt) cc_final: 0.8227 (mt) REVERT: E 300 LYS cc_start: 0.8646 (tttt) cc_final: 0.8437 (tttt) REVERT: E 301 GLU cc_start: 0.8336 (tt0) cc_final: 0.7897 (tt0) REVERT: E 303 CYS cc_start: 0.8649 (m) cc_final: 0.8159 (m) REVERT: E 304 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8154 (mmm-85) REVERT: E 312 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7842 (mtp-110) REVERT: E 313 GLU cc_start: 0.8683 (pt0) cc_final: 0.8360 (pt0) REVERT: E 327 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6212 (mm-30) REVERT: E 335 ASP cc_start: 0.8191 (m-30) cc_final: 0.7844 (m-30) REVERT: E 338 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8157 (mtp85) REVERT: E 341 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7641 (mm-30) REVERT: E 343 MET cc_start: 0.8228 (tpp) cc_final: 0.7834 (tpp) REVERT: F 74 MET cc_start: 0.7867 (mtm) cc_final: 0.7248 (mtm) REVERT: F 75 SER cc_start: 0.8125 (p) cc_final: 0.7810 (p) REVERT: F 82 ASP cc_start: 0.8339 (t0) cc_final: 0.8085 (t70) REVERT: F 90 TRP cc_start: 0.8137 (m100) cc_final: 0.7907 (m100) REVERT: F 102 ASP cc_start: 0.7970 (m-30) cc_final: 0.7482 (m-30) REVERT: F 104 LYS cc_start: 0.8301 (tttt) cc_final: 0.7954 (mttm) REVERT: F 119 ASN cc_start: 0.7993 (p0) cc_final: 0.7542 (t0) REVERT: F 124 GLN cc_start: 0.7724 (pp30) cc_final: 0.7407 (pp30) REVERT: F 131 LEU cc_start: 0.8309 (mt) cc_final: 0.8035 (mt) REVERT: F 144 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7908 (mtpt) REVERT: F 183 LYS cc_start: 0.8279 (mptt) cc_final: 0.7924 (mptt) REVERT: F 213 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8161 (mtmt) REVERT: F 215 GLN cc_start: 0.7358 (tp-100) cc_final: 0.6617 (tp-100) REVERT: F 216 PHE cc_start: 0.7967 (t80) cc_final: 0.7696 (t80) REVERT: F 217 MET cc_start: 0.7451 (mmp) cc_final: 0.7221 (mmt) REVERT: F 219 LEU cc_start: 0.8005 (mt) cc_final: 0.7075 (mt) REVERT: F 234 MET cc_start: 0.7165 (ptp) cc_final: 0.6964 (ptp) REVERT: F 242 ASP cc_start: 0.8243 (m-30) cc_final: 0.8013 (m-30) REVERT: F 248 MET cc_start: 0.7028 (mtp) cc_final: 0.6669 (mtp) REVERT: F 250 ARG cc_start: 0.7488 (ptp-110) cc_final: 0.7210 (ttm170) REVERT: F 251 MET cc_start: 0.7825 (mmt) cc_final: 0.7527 (mpp) REVERT: F 263 LYS cc_start: 0.8296 (mmmm) cc_final: 0.7977 (mmmm) REVERT: F 265 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.6961 (ptp-170) REVERT: F 270 LYS cc_start: 0.8249 (pttp) cc_final: 0.7650 (tptp) REVERT: F 292 ASP cc_start: 0.7873 (p0) cc_final: 0.7673 (p0) REVERT: F 300 LYS cc_start: 0.8082 (tptm) cc_final: 0.7630 (tptm) REVERT: F 301 GLU cc_start: 0.8375 (tt0) cc_final: 0.8052 (tp30) REVERT: F 302 MET cc_start: 0.7873 (tmm) cc_final: 0.7540 (tmm) REVERT: F 337 HIS cc_start: 0.7996 (m170) cc_final: 0.7550 (m90) outliers start: 1 outliers final: 0 residues processed: 626 average time/residue: 0.1325 time to fit residues: 116.0712 Evaluate side-chains 601 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 0.9980 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120302 restraints weight = 29675.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124827 restraints weight = 17781.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128010 restraints weight = 12110.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130345 restraints weight = 8956.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132025 restraints weight = 7012.657| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14142 Z= 0.140 Angle : 0.623 13.453 19146 Z= 0.320 Chirality : 0.044 0.377 2178 Planarity : 0.004 0.074 2448 Dihedral : 8.817 56.734 2070 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 are not related in a simple way. whole: 1.52 (0.21), residues: 1728 helix: 1.56 (0.17), residues: 912 sheet: 0.47 (0.42), residues: 150 loop : 0.53 (0.28), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 280 TYR 0.016 0.001 TYR B 132 PHE 0.028 0.002 PHE E 216 TRP 0.023 0.003 TRP B 220 HIS 0.008 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (14142) covalent geometry : angle 0.62317 / 0.32 (19146) hydrogen bonds : bond 0.03754 / 2.52 ( 738) hydrogen bonds : angle 4.30256 / 3.10 ( 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 624 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.496 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: 0.8279 (mtm) cc_final: 0.7669 (mtm) REVERT: A 92 ASP cc_start: 0.7661 (m-30) cc_final: 0.7318 (m-30) REVERT: A 100 ILE cc_start: 0.8229 (mm) cc_final: 0.7885 (mm) REVERT: A 102 ASP cc_start: 0.7758 (m-30) cc_final: 0.7495 (m-30) REVERT: A 106 THR cc_start: 0.8552 (m) cc_final: 0.8223 (p) REVERT: A 124 GLN cc_start: 0.8222 (pp30) cc_final: 0.7984 (pp30) REVERT: A 125 PRO cc_start: 0.8667 (Cg_endo) cc_final: 0.8136 (Cg_exo) REVERT: A 146 THR cc_start: 0.8326 (p) cc_final: 0.8069 (p) REVERT: A 157 LEU cc_start: 0.8017 (tp) cc_final: 0.7644 (tt) REVERT: A 179 SER cc_start: 0.8935 (t) cc_final: 0.8615 (p) REVERT: A 191 ILE cc_start: 0.8111 (mt) cc_final: 0.7870 (mt) REVERT: A 206 HIS cc_start: 0.7891 (p90) cc_final: 0.7569 (p90) REVERT: A 211 MET cc_start: 0.8055 (mmp) cc_final: 0.7844 (mmp) REVERT: A 213 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7505 (mtmt) REVERT: A 217 MET cc_start: 0.7964 (mpp) cc_final: 0.7512 (mpp) REVERT: A 230 GLN cc_start: 0.6488 (mm-40) cc_final: 0.6148 (mm110) REVERT: A 248 MET cc_start: 0.7811 (mtm) cc_final: 0.7079 (mmm) REVERT: A 258 ASN cc_start: 0.8300 (p0) cc_final: 0.8028 (p0) REVERT: A 259 GLN cc_start: 0.7785 (mt0) cc_final: 0.7231 (mt0) REVERT: A 262 LEU cc_start: 0.8152 (tp) cc_final: 0.7837 (mm) REVERT: A 263 LYS cc_start: 0.7844 (mttp) cc_final: 0.7624 (mttp) REVERT: A 266 GLU cc_start: 0.7967 (tp30) cc_final: 0.7150 (tp30) REVERT: A 270 LYS cc_start: 0.8553 (mmpt) cc_final: 0.7793 (mmtt) REVERT: A 272 ILE cc_start: 0.8604 (mt) cc_final: 0.8325 (mt) REVERT: A 286 GLU cc_start: 0.7529 (pm20) cc_final: 0.7163 (pm20) REVERT: A 301 GLU cc_start: 0.7899 (tt0) cc_final: 0.7058 (tt0) REVERT: A 338 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7860 (mtp85) REVERT: A 341 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 342 LYS cc_start: 0.8789 (mptt) cc_final: 0.8352 (mptt) REVERT: A 343 MET cc_start: 0.8259 (tpt) cc_final: 0.7459 (tpt) REVERT: A 345 LYS cc_start: 0.8691 (pptt) cc_final: 0.8451 (pptt) REVERT: A 347 LYS cc_start: 0.9081 (mptt) cc_final: 0.8778 (mptt) REVERT: B 74 MET cc_start: 0.8199 (mtm) cc_final: 0.7385 (mtm) REVERT: B 92 ASP cc_start: 0.7301 (m-30) cc_final: 0.6948 (m-30) REVERT: B 104 LYS cc_start: 0.8581 (tttt) cc_final: 0.8277 (tttt) REVERT: B 114 LYS cc_start: 0.7726 (tptm) cc_final: 0.7397 (tptm) REVERT: B 118 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6622 (mt-10) REVERT: B 123 LEU cc_start: 0.8315 (tp) cc_final: 0.8022 (tp) REVERT: B 129 VAL cc_start: 0.6525 (t) cc_final: 0.6199 (t) REVERT: B 132 TYR cc_start: 0.7342 (p90) cc_final: 0.6577 (p90) REVERT: B 144 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8211 (mtpt) REVERT: B 146 THR cc_start: 0.8380 (p) cc_final: 0.7763 (p) REVERT: B 154 PHE cc_start: 0.7554 (t80) cc_final: 0.7058 (t80) REVERT: B 157 LEU cc_start: 0.8144 (tp) cc_final: 0.7722 (tp) REVERT: B 178 PHE cc_start: 0.8786 (m-10) cc_final: 0.8378 (m-10) REVERT: B 211 MET cc_start: 0.7978 (mmp) cc_final: 0.7727 (mmp) REVERT: B 213 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7576 (mtmt) REVERT: B 215 GLN cc_start: 0.7732 (tp-100) cc_final: 0.6426 (tp-100) REVERT: B 217 MET cc_start: 0.8018 (mpp) cc_final: 0.7473 (mpp) REVERT: B 219 LEU cc_start: 0.8805 (mt) cc_final: 0.7685 (mt) REVERT: B 231 VAL cc_start: 0.7905 (t) cc_final: 0.7679 (t) REVERT: B 234 MET cc_start: 0.7054 (ttm) cc_final: 0.6535 (ttm) REVERT: B 237 THR cc_start: 0.8520 (t) cc_final: 0.8082 (m) REVERT: B 243 LEU cc_start: 0.8654 (mm) cc_final: 0.8382 (mm) REVERT: B 250 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7205 (ttm-80) REVERT: B 251 MET cc_start: 0.7425 (mmp) cc_final: 0.7062 (mmp) REVERT: B 258 ASN cc_start: 0.8316 (p0) cc_final: 0.8036 (p0) REVERT: B 259 GLN cc_start: 0.7880 (mt0) cc_final: 0.7179 (mt0) REVERT: B 266 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 286 GLU cc_start: 0.6810 (pm20) cc_final: 0.6486 (pm20) REVERT: B 299 LEU cc_start: 0.8848 (mt) cc_final: 0.8505 (mt) REVERT: B 301 GLU cc_start: 0.7656 (tt0) cc_final: 0.6924 (tt0) REVERT: B 305 ASP cc_start: 0.8167 (m-30) cc_final: 0.7730 (m-30) REVERT: B 334 GLN cc_start: 0.7691 (mp10) cc_final: 0.7489 (mp10) REVERT: B 338 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8047 (mtp85) REVERT: B 342 LYS cc_start: 0.8637 (mptt) cc_final: 0.7984 (mptt) REVERT: B 345 LYS cc_start: 0.8495 (pptt) cc_final: 0.8189 (pptt) REVERT: C 74 MET cc_start: 0.5649 (mtm) cc_final: 0.5136 (mtm) REVERT: C 158 GLN cc_start: 0.7415 (pm20) cc_final: 0.7204 (pm20) REVERT: C 171 GLN cc_start: 0.8314 (mp-120) cc_final: 0.8053 (mp10) REVERT: C 191 ILE cc_start: 0.7556 (tt) cc_final: 0.7227 (tt) REVERT: C 199 ARG cc_start: 0.5978 (tpp80) cc_final: 0.5609 (tpp80) REVERT: C 229 CYS cc_start: 0.7824 (t) cc_final: 0.7446 (p) REVERT: C 237 THR cc_start: 0.7094 (t) cc_final: 0.6886 (t) REVERT: C 239 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7236 (ttm110) REVERT: C 248 MET cc_start: 0.7813 (mtp) cc_final: 0.7441 (mtp) REVERT: C 251 MET cc_start: 0.6718 (mpp) cc_final: 0.6256 (tpp) REVERT: C 264 GLN cc_start: 0.8448 (mp10) cc_final: 0.8156 (mp10) REVERT: C 289 GLN cc_start: 0.7858 (mt0) cc_final: 0.7569 (mt0) REVERT: C 290 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 299 LEU cc_start: 0.8700 (mt) cc_final: 0.8218 (mt) REVERT: C 300 LYS cc_start: 0.8807 (tttt) cc_final: 0.8567 (tttt) REVERT: C 303 CYS cc_start: 0.8679 (m) cc_final: 0.8260 (m) REVERT: C 304 ARG cc_start: 0.8408 (ttt90) cc_final: 0.8018 (ttt90) REVERT: C 312 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7954 (mtp-110) REVERT: C 313 GLU cc_start: 0.8461 (pt0) cc_final: 0.8056 (pt0) REVERT: C 332 GLN cc_start: 0.7007 (mt0) cc_final: 0.6748 (mt0) REVERT: C 335 ASP cc_start: 0.8259 (m-30) cc_final: 0.7915 (m-30) REVERT: C 343 MET cc_start: 0.8399 (tpp) cc_final: 0.8040 (tpt) REVERT: C 344 LYS cc_start: 0.8920 (mttm) cc_final: 0.8409 (mttm) REVERT: D 82 ASP cc_start: 0.8101 (t0) cc_final: 0.7894 (t70) REVERT: D 97 ASP cc_start: 0.7651 (p0) cc_final: 0.7442 (p0) REVERT: D 102 ASP cc_start: 0.7869 (m-30) cc_final: 0.7431 (m-30) REVERT: D 117 PHE cc_start: 0.7998 (m-10) cc_final: 0.7644 (m-10) REVERT: D 124 GLN cc_start: 0.7570 (pp30) cc_final: 0.7153 (pp30) REVERT: D 131 LEU cc_start: 0.8370 (mp) cc_final: 0.8091 (mp) REVERT: D 139 LYS cc_start: 0.7489 (mtmm) cc_final: 0.6503 (mtmm) REVERT: D 183 LYS cc_start: 0.8220 (mptt) cc_final: 0.7814 (mptt) REVERT: D 211 MET cc_start: 0.7458 (mmp) cc_final: 0.7229 (mmt) REVERT: D 237 THR cc_start: 0.8018 (t) cc_final: 0.7672 (t) REVERT: D 241 GLN cc_start: 0.8441 (pm20) cc_final: 0.7912 (mm110) REVERT: D 242 ASP cc_start: 0.8226 (m-30) cc_final: 0.7866 (m-30) REVERT: D 248 MET cc_start: 0.7655 (mtp) cc_final: 0.7286 (mtp) REVERT: D 250 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7294 (mtt-85) REVERT: D 251 MET cc_start: 0.7429 (mpp) cc_final: 0.6706 (tpp) REVERT: D 300 LYS cc_start: 0.8475 (tptm) cc_final: 0.8000 (tptm) REVERT: D 305 ASP cc_start: 0.7841 (t0) cc_final: 0.7455 (t0) REVERT: D 312 ARG cc_start: 0.8183 (ptm-80) cc_final: 0.7821 (ptm-80) REVERT: D 347 LYS cc_start: 0.7729 (pttm) cc_final: 0.7426 (pttp) REVERT: E 144 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7679 (tptp) REVERT: E 166 TRP cc_start: 0.5971 (m-10) cc_final: 0.4584 (m-10) REVERT: E 170 SER cc_start: 0.7720 (p) cc_final: 0.7195 (p) REVERT: E 171 GLN cc_start: 0.8545 (mm110) cc_final: 0.8341 (mp10) REVERT: E 193 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7505 (mt-10) REVERT: E 199 ARG cc_start: 0.6830 (tpp80) cc_final: 0.6539 (tpp80) REVERT: E 205 ASP cc_start: 0.6605 (m-30) cc_final: 0.6139 (m-30) REVERT: E 207 GLU cc_start: 0.7878 (tp30) cc_final: 0.7551 (tp30) REVERT: E 213 LYS cc_start: 0.8386 (mtmt) cc_final: 0.8059 (mtmt) REVERT: E 239 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7202 (ttp-110) REVERT: E 248 MET cc_start: 0.7591 (mtp) cc_final: 0.7094 (mtp) REVERT: E 251 MET cc_start: 0.6865 (mmm) cc_final: 0.6635 (mmm) REVERT: E 264 GLN cc_start: 0.8606 (mp10) cc_final: 0.8361 (mp10) REVERT: E 266 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 270 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7585 (mmmt) REVERT: E 289 GLN cc_start: 0.8490 (mp10) cc_final: 0.8242 (mp10) REVERT: E 290 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7838 (mm-30) REVERT: E 299 LEU cc_start: 0.8638 (mt) cc_final: 0.8227 (mt) REVERT: E 300 LYS cc_start: 0.8643 (tttt) cc_final: 0.8428 (tttt) REVERT: E 303 CYS cc_start: 0.8706 (m) cc_final: 0.8213 (m) REVERT: E 304 ARG cc_start: 0.8495 (mtp180) cc_final: 0.8166 (mmm-85) REVERT: E 312 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: E 313 GLU cc_start: 0.8678 (pt0) cc_final: 0.8385 (pt0) REVERT: E 327 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6309 (mm-30) REVERT: E 335 ASP cc_start: 0.8195 (m-30) cc_final: 0.7695 (m-30) REVERT: E 336 LEU cc_start: 0.8978 (mp) cc_final: 0.8749 (mp) REVERT: E 338 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8179 (mtp85) REVERT: E 340 ILE cc_start: 0.8424 (mt) cc_final: 0.8178 (mt) REVERT: E 341 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7682 (mm-30) REVERT: E 343 MET cc_start: 0.8340 (tpp) cc_final: 0.8024 (tpp) REVERT: F 73 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8153 (mt-10) REVERT: F 74 MET cc_start: 0.7970 (mtm) cc_final: 0.7345 (mtm) REVERT: F 75 SER cc_start: 0.8152 (p) cc_final: 0.7832 (p) REVERT: F 82 ASP cc_start: 0.8265 (t0) cc_final: 0.8004 (t70) REVERT: F 102 ASP cc_start: 0.7895 (m-30) cc_final: 0.7670 (m-30) REVERT: F 104 LYS cc_start: 0.8298 (tttt) cc_final: 0.7957 (tttm) REVERT: F 119 ASN cc_start: 0.8137 (p0) cc_final: 0.7597 (t0) REVERT: F 124 GLN cc_start: 0.7663 (pp30) cc_final: 0.7343 (pp30) REVERT: F 131 LEU cc_start: 0.8346 (mt) cc_final: 0.8023 (mt) REVERT: F 144 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7899 (mtpt) REVERT: F 183 LYS cc_start: 0.8330 (mptt) cc_final: 0.7951 (mptt) REVERT: F 213 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8120 (mtmt) REVERT: F 215 GLN cc_start: 0.7494 (tp-100) cc_final: 0.6796 (tp-100) REVERT: F 216 PHE cc_start: 0.7987 (t80) cc_final: 0.7767 (t80) REVERT: F 219 LEU cc_start: 0.7976 (mt) cc_final: 0.7004 (mt) REVERT: F 242 ASP cc_start: 0.8283 (m-30) cc_final: 0.8056 (m-30) REVERT: F 250 ARG cc_start: 0.7783 (ptp-110) cc_final: 0.7387 (ttm-80) REVERT: F 263 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7944 (mmmm) REVERT: F 270 LYS cc_start: 0.8183 (pttp) cc_final: 0.7491 (tptp) REVERT: F 285 LEU cc_start: 0.8614 (mm) cc_final: 0.8382 (mt) REVERT: F 300 LYS cc_start: 0.8146 (tptm) cc_final: 0.7712 (tptm) REVERT: F 301 GLU cc_start: 0.8430 (tt0) cc_final: 0.8222 (tt0) REVERT: F 302 MET cc_start: 0.7915 (tmm) cc_final: 0.7539 (tmm) REVERT: F 316 ASN cc_start: 0.8184 (m110) cc_final: 0.6899 (t0) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.1342 time to fit residues: 117.6438 Evaluate side-chains 610 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 0.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 0.0020 chunk 78 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 170 optimal weight: 0.0980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122535 restraints weight = 29403.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127159 restraints weight = 17684.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130409 restraints weight = 12053.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.132687 restraints weight = 8924.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134413 restraints weight = 7035.619| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14142 Z= 0.111 Angle : 0.606 14.806 19146 Z= 0.305 Chirality : 0.043 0.362 2178 Planarity : 0.004 0.053 2448 Dihedral : 8.137 53.791 2070 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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 are not related in a simple way. whole: 1.81 (0.21), residues: 1728 helix: 1.65 (0.17), residues: 948 sheet: 0.27 (0.42), residues: 156 loop : 0.98 (0.30), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 265 TYR 0.013 0.001 TYR B 132 PHE 0.023 0.001 PHE E 216 TRP 0.024 0.003 TRP B 220 HIS 0.011 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14142) covalent geometry : angle 0.60619 / 0.30 (19146) hydrogen bonds : bond 0.03386 / 2.26 ( 738) hydrogen bonds : angle 4.14255 / 2.98 ( 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 620 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.507 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: 0.8194 (mtm) cc_final: 0.7539 (mtm) REVERT: A 92 ASP cc_start: 0.7681 (m-30) cc_final: 0.7337 (m-30) REVERT: A 102 ASP cc_start: 0.7691 (m-30) cc_final: 0.7424 (m-30) REVERT: A 106 THR cc_start: 0.8546 (m) cc_final: 0.8223 (p) REVERT: A 124 GLN cc_start: 0.8245 (pp30) cc_final: 0.8002 (pp30) REVERT: A 125 PRO cc_start: 0.8618 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: A 157 LEU cc_start: 0.8002 (tp) cc_final: 0.7667 (tt) REVERT: A 158 GLN cc_start: 0.7119 (tm130) cc_final: 0.6816 (tm130) REVERT: A 178 PHE cc_start: 0.8711 (m-10) cc_final: 0.8031 (m-10) REVERT: A 179 SER cc_start: 0.8959 (t) cc_final: 0.8627 (p) REVERT: A 191 ILE cc_start: 0.8184 (mt) cc_final: 0.7947 (mt) REVERT: A 193 GLU cc_start: 0.7789 (tt0) cc_final: 0.7564 (tt0) REVERT: A 206 HIS cc_start: 0.7864 (p90) cc_final: 0.7540 (p90) REVERT: A 213 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7514 (mtmt) REVERT: A 217 MET cc_start: 0.7854 (mpp) cc_final: 0.7360 (mpp) REVERT: A 219 LEU cc_start: 0.8893 (mt) cc_final: 0.8466 (mt) REVERT: A 230 GLN cc_start: 0.6462 (mm-40) cc_final: 0.6113 (mm110) REVERT: A 248 MET cc_start: 0.7773 (mtm) cc_final: 0.7067 (mmm) REVERT: A 251 MET cc_start: 0.7884 (mmm) cc_final: 0.7463 (mmm) REVERT: A 259 GLN cc_start: 0.7715 (mt0) cc_final: 0.7286 (mt0) REVERT: A 262 LEU cc_start: 0.8121 (tp) cc_final: 0.7808 (mm) REVERT: A 263 LYS cc_start: 0.7792 (mttp) cc_final: 0.7586 (mttp) REVERT: A 266 GLU cc_start: 0.7983 (tp30) cc_final: 0.7099 (tp30) REVERT: A 270 LYS cc_start: 0.8495 (mmpt) cc_final: 0.7753 (mmtt) REVERT: A 286 GLU cc_start: 0.7531 (pm20) cc_final: 0.7177 (pm20) REVERT: A 301 GLU cc_start: 0.7863 (tt0) cc_final: 0.6994 (tt0) REVERT: A 338 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7897 (mtp85) REVERT: A 341 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7156 (mm-30) REVERT: A 342 LYS cc_start: 0.8765 (mptt) cc_final: 0.8311 (mptt) REVERT: A 343 MET cc_start: 0.8244 (tpt) cc_final: 0.7775 (tpt) REVERT: A 345 LYS cc_start: 0.8622 (pptt) cc_final: 0.8390 (pptt) REVERT: B 74 MET cc_start: 0.8187 (mtm) cc_final: 0.7364 (mtm) REVERT: B 92 ASP cc_start: 0.7256 (m-30) cc_final: 0.6905 (m-30) REVERT: B 96 LEU cc_start: 0.7601 (mt) cc_final: 0.7399 (mt) REVERT: B 104 LYS cc_start: 0.8570 (tttt) cc_final: 0.8277 (tttt) REVERT: B 114 LYS cc_start: 0.7542 (tptm) cc_final: 0.7250 (tptm) REVERT: B 118 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6555 (mt-10) REVERT: B 123 LEU cc_start: 0.8367 (tp) cc_final: 0.8096 (tp) REVERT: B 129 VAL cc_start: 0.6545 (t) cc_final: 0.6135 (t) REVERT: B 132 TYR cc_start: 0.7333 (p90) cc_final: 0.6554 (p90) REVERT: B 139 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7960 (pttm) REVERT: B 144 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8171 (mtpt) REVERT: B 146 THR cc_start: 0.8349 (p) cc_final: 0.7751 (p) REVERT: B 154 PHE cc_start: 0.7505 (t80) cc_final: 0.7090 (t80) REVERT: B 157 LEU cc_start: 0.8142 (tp) cc_final: 0.7721 (tp) REVERT: B 178 PHE cc_start: 0.8774 (m-10) cc_final: 0.8314 (m-10) REVERT: B 211 MET cc_start: 0.7960 (mmp) cc_final: 0.7729 (mmp) REVERT: B 213 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7549 (mtmt) REVERT: B 215 GLN cc_start: 0.7732 (tp-100) cc_final: 0.6408 (tp-100) REVERT: B 217 MET cc_start: 0.7984 (mpp) cc_final: 0.7490 (mpp) REVERT: B 219 LEU cc_start: 0.8843 (mt) cc_final: 0.7664 (mt) REVERT: B 231 VAL cc_start: 0.7987 (t) cc_final: 0.7758 (t) REVERT: B 234 MET cc_start: 0.7112 (ttm) cc_final: 0.6604 (ttm) REVERT: B 237 THR cc_start: 0.8447 (t) cc_final: 0.7984 (m) REVERT: B 243 LEU cc_start: 0.8633 (mm) cc_final: 0.8408 (mm) REVERT: B 250 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7382 (ttm170) REVERT: B 258 ASN cc_start: 0.8248 (p0) cc_final: 0.7973 (p0) REVERT: B 259 GLN cc_start: 0.7825 (mt0) cc_final: 0.7175 (mt0) REVERT: B 266 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 286 GLU cc_start: 0.6783 (pm20) cc_final: 0.6460 (pm20) REVERT: B 299 LEU cc_start: 0.8849 (mt) cc_final: 0.8356 (mt) REVERT: B 301 GLU cc_start: 0.7590 (tt0) cc_final: 0.6871 (tt0) REVERT: B 305 ASP cc_start: 0.8162 (m-30) cc_final: 0.7711 (m-30) REVERT: B 334 GLN cc_start: 0.7681 (mp10) cc_final: 0.7435 (mp10) REVERT: B 338 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7950 (mtp85) REVERT: B 342 LYS cc_start: 0.8635 (mptt) cc_final: 0.7960 (mptt) REVERT: B 345 LYS cc_start: 0.8427 (pptt) cc_final: 0.8137 (pptt) REVERT: C 74 MET cc_start: 0.5632 (mtm) cc_final: 0.5131 (mtm) REVERT: C 158 GLN cc_start: 0.7436 (pm20) cc_final: 0.7229 (pm20) REVERT: C 171 GLN cc_start: 0.8308 (mp-120) cc_final: 0.8053 (mp10) REVERT: C 190 PHE cc_start: 0.7025 (t80) cc_final: 0.6738 (t80) REVERT: C 199 ARG cc_start: 0.5725 (tpp80) cc_final: 0.5443 (tpp80) REVERT: C 205 ASP cc_start: 0.6425 (m-30) cc_final: 0.6020 (m-30) REVERT: C 226 ASP cc_start: 0.6314 (t0) cc_final: 0.5824 (t0) REVERT: C 229 CYS cc_start: 0.7845 (t) cc_final: 0.7112 (p) REVERT: C 237 THR cc_start: 0.7056 (t) cc_final: 0.6817 (t) REVERT: C 239 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7267 (ttm110) REVERT: C 248 MET cc_start: 0.7580 (mtp) cc_final: 0.7201 (mtp) REVERT: C 251 MET cc_start: 0.6812 (mpp) cc_final: 0.6414 (tpp) REVERT: C 264 GLN cc_start: 0.8406 (mp10) cc_final: 0.8150 (mp10) REVERT: C 273 LEU cc_start: 0.8254 (mm) cc_final: 0.8034 (mm) REVERT: C 289 GLN cc_start: 0.7831 (mt0) cc_final: 0.7535 (mt0) REVERT: C 290 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7925 (mm-30) REVERT: C 299 LEU cc_start: 0.8712 (mt) cc_final: 0.8182 (mt) REVERT: C 300 LYS cc_start: 0.8820 (tttt) cc_final: 0.8586 (tttt) REVERT: C 303 CYS cc_start: 0.8688 (m) cc_final: 0.8225 (m) REVERT: C 304 ARG cc_start: 0.8300 (ttt90) cc_final: 0.7908 (ttt90) REVERT: C 312 ARG cc_start: 0.8092 (mtp-110) cc_final: 0.7874 (mtp-110) REVERT: C 313 GLU cc_start: 0.8499 (pt0) cc_final: 0.8133 (pt0) REVERT: C 332 GLN cc_start: 0.6974 (mt0) cc_final: 0.6461 (mp10) REVERT: C 335 ASP cc_start: 0.8258 (m-30) cc_final: 0.7613 (m-30) REVERT: C 343 MET cc_start: 0.8386 (tpp) cc_final: 0.7435 (tpp) REVERT: C 344 LYS cc_start: 0.8891 (mttm) cc_final: 0.8487 (mttm) REVERT: D 73 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8276 (mt-10) REVERT: D 90 TRP cc_start: 0.8075 (m100) cc_final: 0.7626 (m100) REVERT: D 97 ASP cc_start: 0.7571 (p0) cc_final: 0.7321 (p0) REVERT: D 102 ASP cc_start: 0.7848 (m-30) cc_final: 0.7431 (m-30) REVERT: D 104 LYS cc_start: 0.8284 (tttt) cc_final: 0.7935 (ttmt) REVERT: D 117 PHE cc_start: 0.7946 (m-10) cc_final: 0.7644 (m-10) REVERT: D 124 GLN cc_start: 0.7571 (pp30) cc_final: 0.7164 (pp30) REVERT: D 131 LEU cc_start: 0.8463 (mp) cc_final: 0.8223 (mp) REVERT: D 139 LYS cc_start: 0.7312 (mtmm) cc_final: 0.6272 (mtmm) REVERT: D 140 THR cc_start: 0.8126 (p) cc_final: 0.7859 (p) REVERT: D 141 LEU cc_start: 0.8177 (tp) cc_final: 0.7897 (tp) REVERT: D 144 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7418 (mtpt) REVERT: D 183 LYS cc_start: 0.8220 (mptt) cc_final: 0.7836 (mptt) REVERT: D 211 MET cc_start: 0.7425 (mmp) cc_final: 0.7195 (mmt) REVERT: D 237 THR cc_start: 0.7945 (t) cc_final: 0.7601 (t) REVERT: D 241 GLN cc_start: 0.8431 (pm20) cc_final: 0.7682 (mm110) REVERT: D 248 MET cc_start: 0.7495 (mtp) cc_final: 0.7040 (mtp) REVERT: D 251 MET cc_start: 0.7545 (mpp) cc_final: 0.6601 (tpp) REVERT: D 265 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7161 (mtm180) REVERT: D 300 LYS cc_start: 0.8519 (tptm) cc_final: 0.8052 (tptm) REVERT: D 305 ASP cc_start: 0.7770 (t0) cc_final: 0.7511 (t0) REVERT: D 309 LEU cc_start: 0.8260 (tp) cc_final: 0.8032 (tp) REVERT: D 312 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7744 (ptm-80) REVERT: D 337 HIS cc_start: 0.7917 (m90) cc_final: 0.7252 (m90) REVERT: D 343 MET cc_start: 0.7821 (ppp) cc_final: 0.7589 (ppp) REVERT: D 347 LYS cc_start: 0.7783 (pttm) cc_final: 0.7395 (pttp) REVERT: E 86 MET cc_start: 0.5967 (ptt) cc_final: 0.5166 (pmm) REVERT: E 144 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7643 (tptp) REVERT: E 171 GLN cc_start: 0.8569 (mm110) cc_final: 0.8306 (mp10) REVERT: E 193 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7469 (mt-10) REVERT: E 199 ARG cc_start: 0.6729 (tpp80) cc_final: 0.6390 (tpp80) REVERT: E 205 ASP cc_start: 0.6678 (m-30) cc_final: 0.6175 (m-30) REVERT: E 207 GLU cc_start: 0.7864 (tp30) cc_final: 0.7423 (tp30) REVERT: E 213 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8054 (mtmt) REVERT: E 239 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7133 (ttp-110) REVERT: E 248 MET cc_start: 0.7602 (mtp) cc_final: 0.7093 (mtp) REVERT: E 250 ARG cc_start: 0.6662 (tpt90) cc_final: 0.6117 (tmt-80) REVERT: E 251 MET cc_start: 0.6967 (mmm) cc_final: 0.5999 (mmm) REVERT: E 264 GLN cc_start: 0.8534 (mp10) cc_final: 0.8057 (mp10) REVERT: E 266 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 270 LYS cc_start: 0.8545 (mmmt) cc_final: 0.7635 (mmmt) REVERT: E 290 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 299 LEU cc_start: 0.8666 (mt) cc_final: 0.8282 (mt) REVERT: E 300 LYS cc_start: 0.8613 (tttt) cc_final: 0.8406 (tttt) REVERT: E 303 CYS cc_start: 0.8665 (m) cc_final: 0.8185 (m) REVERT: E 304 ARG cc_start: 0.8461 (mtp180) cc_final: 0.8111 (mmm-85) REVERT: E 312 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7913 (mtp-110) REVERT: E 313 GLU cc_start: 0.8661 (pt0) cc_final: 0.8389 (pt0) REVERT: E 327 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6324 (mm-30) REVERT: E 335 ASP cc_start: 0.8059 (m-30) cc_final: 0.7612 (m-30) REVERT: E 336 LEU cc_start: 0.9007 (mp) cc_final: 0.8781 (mp) REVERT: E 338 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8161 (mtp85) REVERT: E 340 ILE cc_start: 0.8441 (mt) cc_final: 0.8208 (mt) REVERT: E 341 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 343 MET cc_start: 0.8339 (tpp) cc_final: 0.8057 (tpp) REVERT: F 68 LYS cc_start: 0.7886 (mppt) cc_final: 0.7561 (mppt) REVERT: F 73 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 74 MET cc_start: 0.7936 (mtm) cc_final: 0.7286 (mtm) REVERT: F 90 TRP cc_start: 0.8158 (m100) cc_final: 0.7424 (m100) REVERT: F 99 VAL cc_start: 0.8408 (t) cc_final: 0.8206 (t) REVERT: F 102 ASP cc_start: 0.7848 (m-30) cc_final: 0.7630 (m-30) REVERT: F 104 LYS cc_start: 0.8295 (tttt) cc_final: 0.7964 (tttm) REVERT: F 119 ASN cc_start: 0.8174 (p0) cc_final: 0.7593 (t0) REVERT: F 124 GLN cc_start: 0.7681 (pp30) cc_final: 0.7390 (pp30) REVERT: F 131 LEU cc_start: 0.8329 (mt) cc_final: 0.7994 (mt) REVERT: F 144 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7788 (mtpt) REVERT: F 183 LYS cc_start: 0.8298 (mptt) cc_final: 0.7914 (mptt) REVERT: F 198 LEU cc_start: 0.7456 (mt) cc_final: 0.7167 (mt) REVERT: F 213 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7937 (mtmt) REVERT: F 215 GLN cc_start: 0.7421 (tp-100) cc_final: 0.6688 (tp-100) REVERT: F 216 PHE cc_start: 0.7961 (t80) cc_final: 0.7711 (t80) REVERT: F 217 MET cc_start: 0.7400 (mmp) cc_final: 0.7155 (mmt) REVERT: F 219 LEU cc_start: 0.7962 (mt) cc_final: 0.6961 (mt) REVERT: F 220 TRP cc_start: 0.8309 (t60) cc_final: 0.8072 (t60) REVERT: F 250 ARG cc_start: 0.7655 (ptp-110) cc_final: 0.6700 (ttm-80) REVERT: F 263 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7891 (mmmm) REVERT: F 265 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.6900 (ptp-170) REVERT: F 270 LYS cc_start: 0.8160 (pttp) cc_final: 0.7466 (tptp) REVERT: F 285 LEU cc_start: 0.8582 (mm) cc_final: 0.8372 (mt) REVERT: F 292 ASP cc_start: 0.7840 (p0) cc_final: 0.7578 (p0) REVERT: F 300 LYS cc_start: 0.8123 (tptm) cc_final: 0.7732 (tptm) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.1330 time to fit residues: 115.3796 Evaluate side-chains 611 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 0.7980 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS C 256 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 GLN ** 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 = 0.4021 r_free = 0.4021 target = 0.148557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120857 restraints weight = 29209.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125422 restraints weight = 17589.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128641 restraints weight = 12022.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130933 restraints weight = 8913.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132530 restraints weight = 7040.850| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.7826 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= 0.129 Angle : 0.625 14.473 19146 Z= 0.320 Chirality : 0.044 0.385 2178 Planarity : 0.004 0.052 2448 Dihedral : 8.431 55.414 2070 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 are not related in a simple way. whole: 1.55 (0.21), residues: 1728 helix: 1.41 (0.16), residues: 978 sheet: 0.27 (0.42), residues: 156 loop : 0.84 (0.31), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 265 TYR 0.014 0.001 TYR B 132 PHE 0.021 0.002 PHE E 216 TRP 0.026 0.003 TRP A 90 HIS 0.011 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14142) covalent geometry : angle 0.62529 / 0.32 (19146) hydrogen bonds : bond 0.03629 / 2.42 ( 738) hydrogen bonds : angle 4.25726 / 3.06 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.40 seconds wall clock time: 49 minutes 8.42 seconds (2948.42 seconds total)