Starting phenix.real_space_refine on Thu Jun 12 14:20:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxt_43639/06_2025/8vxt_43639.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 5.90, per 1000 atoms: 0.42 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: 3.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE A 93 " --> pdb=" O TRP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 113 removed outlier: 3.956A pdb=" N LEU A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.582A pdb=" N GLU A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 205 through 226 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 261 through 274 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 355 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE B 93 " --> pdb=" O TRP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU B 118 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 168 through 184 removed outlier: 4.356A pdb=" N LYS B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 205 through 226 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 261 through 274 Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 355 Processing helix chain 'C' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE C 93 " --> pdb=" O TRP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.956A pdb=" N LEU C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU C 118 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 205 through 226 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 355 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.839A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE D 93 " --> pdb=" O TRP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 114 through 118 removed outlier: 3.584A pdb=" N GLU D 118 " --> pdb=" O HIS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.798A pdb=" N GLY D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 205 through 226 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 261 through 274 Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 355 Processing helix chain 'E' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS E 79 " --> pdb=" O SER E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE E 93 " --> pdb=" O TRP E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLU E 118 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.799A pdb=" N GLY E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 168 through 184 removed outlier: 4.355A pdb=" N LYS E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 205 through 226 Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 295 through 320 removed outlier: 4.178A pdb=" N GLU E 320 " --> pdb=" O ASN E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 355 Processing helix chain 'F' and resid 70 through 80 removed outlier: 3.840A pdb=" N HIS F 79 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.669A pdb=" N ILE F 93 " --> pdb=" O TRP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.955A pdb=" N LEU F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.582A pdb=" N GLU F 118 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.798A pdb=" N GLY F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 168 through 184 removed outlier: 4.356A pdb=" N LYS F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 205 through 226 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 261 through 274 Processing helix chain 'F' and resid 284 through 291 Processing helix chain 'F' and resid 295 through 320 removed outlier: 4.177A pdb=" N GLU F 320 " --> pdb=" O ASN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE A 190 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER A 187 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET A 234 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 189 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 236 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 191 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 237 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 130 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE B 190 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 187 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET B 234 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 189 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA B 236 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 191 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 237 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 130 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE C 190 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 187 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET C 234 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE C 189 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA C 236 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 191 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 237 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 130 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE D 190 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER D 187 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET D 234 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE D 189 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA D 236 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 191 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 237 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 130 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.362A pdb=" N ARG E 153 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE E 190 " --> pdb=" O ARG E 153 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 155 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER E 187 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET E 234 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE E 189 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA E 236 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 191 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 237 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 130 " --> pdb=" O PHE E 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 156 removed outlier: 6.363A pdb=" N ARG F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE F 190 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER F 187 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET F 234 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE F 189 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA F 236 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 191 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 237 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU F 130 " --> pdb=" O PHE F 255 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 4806 1.37 - 1.52: 3716 1.52 - 1.66: 5464 1.66 - 1.80: 101 1.80 - 1.95: 55 Bond restraints: 14142 Sorted by residual: bond pdb=" CZ ARG E 304 " pdb=" NH2 ARG E 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.87e+00 bond pdb=" CZ ARG F 304 " pdb=" NH2 ARG F 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.84e+00 bond pdb=" CZ ARG C 304 " pdb=" NH2 ARG C 304 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.30e-02 5.92e+03 1.83e+00 bond pdb=" CZ ARG A 304 " pdb=" NH2 ARG A 304 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.30e-02 5.92e+03 1.80e+00 bond pdb=" CZ ARG D 304 " pdb=" NH2 ARG D 304 " ideal model delta sigma weight residual 1.330 1.313 0.017 1.30e-02 5.92e+03 1.73e+00 ... (remaining 14137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 18836 2.24 - 4.48: 262 4.48 - 6.72: 30 6.72 - 8.96: 12 8.96 - 11.20: 6 Bond angle restraints: 19146 Sorted by residual: angle pdb=" C3' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" C5' AGS D 401 " ideal model delta sigma weight residual 115.29 126.49 -11.20 1.82e+00 3.02e-01 3.79e+01 angle pdb=" C3' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" C5' AGS B 401 " ideal model delta sigma weight residual 115.29 126.48 -11.19 1.82e+00 3.02e-01 3.78e+01 angle pdb=" C3' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" C5' AGS F 401 " ideal model delta sigma weight residual 115.29 126.46 -11.17 1.82e+00 3.02e-01 3.77e+01 angle pdb=" C3' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" C5' AGS E 401 " ideal model delta sigma weight residual 115.29 126.45 -11.16 1.82e+00 3.02e-01 3.76e+01 angle pdb=" C3' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" C5' AGS C 401 " ideal model delta sigma weight residual 115.29 126.45 -11.16 1.82e+00 3.02e-01 3.76e+01 ... (remaining 19141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 7752 15.59 - 31.17: 816 31.17 - 46.76: 138 46.76 - 62.35: 42 62.35 - 77.94: 36 Dihedral angle restraints: 8784 sinusoidal: 3678 harmonic: 5106 Sorted by residual: dihedral pdb=" CA ARG E 121 " pdb=" C ARG E 121 " pdb=" N LEU E 122 " pdb=" CA LEU E 122 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG A 121 " pdb=" C ARG A 121 " pdb=" N LEU A 122 " pdb=" CA LEU A 122 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N LEU B 122 " pdb=" CA LEU B 122 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 8781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2184 0.246 - 0.492: 0 0.492 - 0.739: 0 0.739 - 0.985: 0 0.985 - 1.231: 6 Chirality restraints: 2190 Sorted by residual: chirality pdb=" C4' AGS B 401 " pdb=" C3' AGS B 401 " pdb=" C5' AGS B 401 " pdb=" O4' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" C4' AGS A 401 " pdb=" C3' AGS A 401 " pdb=" C5' AGS A 401 " pdb=" O4' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" C4' AGS E 401 " pdb=" C3' AGS E 401 " pdb=" C5' AGS E 401 " pdb=" O4' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.49 -1.26 -1.23 2.00e-01 2.50e+01 3.78e+01 ... (remaining 2187 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 239 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO E 240 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 239 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 240 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 239 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 240 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2358 2.76 - 3.29: 15121 3.29 - 3.83: 22334 3.83 - 4.36: 26719 4.36 - 4.90: 42491 Nonbonded interactions: 109023 Sorted by model distance: nonbonded pdb=" NZ LYS A 139 " pdb=" O1B AGS A 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS C 139 " pdb=" O1B AGS C 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS D 139 " pdb=" O1B AGS D 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS B 139 " pdb=" O1B AGS B 401 " model vdw 2.224 3.120 nonbonded pdb=" NZ LYS F 139 " pdb=" O1B AGS F 401 " model vdw 2.224 3.120 ... (remaining 109018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14142 Z= 0.156 Angle : 0.708 11.204 19146 Z= 0.412 Chirality : 0.076 1.231 2190 Planarity : 0.005 0.060 2448 Dihedral : 14.079 77.936 5436 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.019 0.003 TRP D 166 HIS 0.006 0.001 HIS F 115 PHE 0.009 0.001 PHE D 178 TYR 0.009 0.002 TYR C 314 ARG 0.015 0.001 ARG F 304 Details of bonding type rmsd hydrogen bonds : bond 0.14727 ( 738) hydrogen bonds : angle 5.66385 ( 2052) covalent geometry : bond 0.00303 (14142) covalent geometry : angle 0.70848 (19146) *********************** 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 : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7802 (t70) cc_final: 0.7391 (t0) REVERT: A 85 ASN cc_start: 0.8106 (p0) cc_final: 0.7692 (p0) REVERT: A 90 TRP cc_start: 0.7886 (m100) cc_final: 0.7575 (m100) REVERT: A 109 LEU cc_start: 0.8672 (mt) cc_final: 0.8264 (mt) REVERT: A 114 LYS cc_start: 0.8106 (tptm) cc_final: 0.7905 (tptm) REVERT: A 117 PHE cc_start: 0.7726 (m-10) cc_final: 0.7433 (m-10) REVERT: A 118 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6755 (mt-10) REVERT: A 125 PRO cc_start: 0.8015 (Cg_endo) cc_final: 0.7721 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8226 (tttt) cc_final: 0.7640 (ttmt) REVERT: A 154 PHE cc_start: 0.7644 (t80) cc_final: 0.6906 (t80) REVERT: A 157 LEU cc_start: 0.7960 (tp) cc_final: 0.7549 (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: 0.7603 (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: 0.7815 (mtmt) REVERT: A 215 GLN cc_start: 0.7579 (tp-100) cc_final: 0.6869 (tp-100) REVERT: A 217 MET cc_start: 0.8014 (mpp) cc_final: 0.7644 (mpp) REVERT: A 232 ILE cc_start: 0.8142 (mt) cc_final: 0.7733 (pt) REVERT: A 240 PRO cc_start: 0.7974 (Cg_endo) cc_final: 0.7640 (Cg_exo) REVERT: A 248 MET cc_start: 0.7476 (mtp) cc_final: 0.7259 (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: 0.7401 (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: 0.7439 (mtm) REVERT: B 82 ASP cc_start: 0.7935 (t70) cc_final: 0.7706 (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: 0.7749 (mtp) REVERT: B 102 ASP cc_start: 0.8110 (m-30) cc_final: 0.7782 (m-30) REVERT: B 109 LEU cc_start: 0.8629 (mt) cc_final: 0.8216 (mt) REVERT: B 113 LYS cc_start: 0.8017 (tppp) cc_final: 0.7733 (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: 0.6957 (mm-30) REVERT: B 154 PHE cc_start: 0.7653 (t80) cc_final: 0.7187 (t80) REVERT: B 157 LEU cc_start: 0.7835 (tp) cc_final: 0.7397 (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: 0.7735 (mmp) REVERT: B 213 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7664 (mtmt) REVERT: B 215 GLN cc_start: 0.7529 (tp-100) cc_final: 0.6743 (tp-100) REVERT: B 232 ILE cc_start: 0.8129 (mt) cc_final: 0.7845 (mt) REVERT: B 240 PRO cc_start: 0.8343 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: B 243 LEU cc_start: 0.8406 (mt) cc_final: 0.8162 (mt) REVERT: B 259 GLN cc_start: 0.7585 (mt0) cc_final: 0.7206 (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: 0.6927 (mm-30) REVERT: B 299 LEU cc_start: 0.8657 (mt) cc_final: 0.8420 (mt) REVERT: B 331 VAL cc_start: 0.7609 (t) cc_final: 0.7369 (t) REVERT: B 341 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 342 LYS cc_start: 0.8703 (mptt) cc_final: 0.7969 (mptt) REVERT: B 343 MET cc_start: 0.8260 (tpt) cc_final: 0.8031 (tpt) REVERT: C 74 MET cc_start: 0.5899 (mtm) cc_final: 0.5257 (mtm) REVERT: C 132 TYR cc_start: 0.6485 (p90) cc_final: 0.6250 (p90) REVERT: C 211 MET cc_start: 0.6721 (mmp) cc_final: 0.6434 (mmp) REVERT: C 212 MET cc_start: 0.6911 (mmp) cc_final: 0.6356 (mmp) REVERT: C 239 ARG cc_start: 0.7435 (mtt90) cc_final: 0.7051 (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: 0.8337 (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: 0.7858 (mmm-85) REVERT: C 336 LEU cc_start: 0.8585 (mp) cc_final: 0.8302 (mp) REVERT: C 343 MET cc_start: 0.8441 (tpt) cc_final: 0.8111 (tpt) REVERT: C 344 LYS cc_start: 0.8784 (mttm) cc_final: 0.8522 (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: 0.7587 (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: 0.6750 (mtp) REVERT: D 250 ARG cc_start: 0.6713 (mtt-85) cc_final: 0.6490 (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: 0.7264 (m90) REVERT: E 191 ILE cc_start: 0.6401 (mt) cc_final: 0.6177 (mt) REVERT: E 211 MET cc_start: 0.6846 (mmp) cc_final: 0.6459 (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: 0.7493 (mtmt) REVERT: E 248 MET cc_start: 0.7603 (mtp) cc_final: 0.7059 (mtp) REVERT: E 285 LEU cc_start: 0.8558 (mt) cc_final: 0.8317 (mt) REVERT: E 290 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 298 ASP cc_start: 0.7631 (m-30) cc_final: 0.7282 (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: 0.8034 (mt) REVERT: E 341 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7951 (mm-30) REVERT: E 343 MET cc_start: 0.8479 (tpt) cc_final: 0.8173 (tpt) REVERT: F 74 MET cc_start: 0.7680 (mtm) cc_final: 0.7391 (mtm) REVERT: F 82 ASP cc_start: 0.6771 (t70) cc_final: 0.6229 (t0) REVERT: F 85 ASN cc_start: 0.8163 (p0) cc_final: 0.7646 (p0) REVERT: F 104 LYS cc_start: 0.8311 (tttt) cc_final: 0.8079 (ttmm) REVERT: F 139 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7608 (mtmm) REVERT: F 149 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6827 (mm-30) REVERT: F 199 ARG cc_start: 0.6181 (tpp80) cc_final: 0.4963 (tpp80) REVERT: F 211 MET cc_start: 0.7309 (mmp) cc_final: 0.6775 (mmp) REVERT: F 212 MET cc_start: 0.8011 (mmp) cc_final: 0.7573 (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: 0.7898 (tptm) REVERT: F 302 MET cc_start: 0.7292 (tmm) cc_final: 0.6951 (tmm) REVERT: F 337 HIS cc_start: 0.7500 (m170) cc_final: 0.7295 (m90) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.2892 time to fit residues: 237.4553 Evaluate side-chains 554 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 264 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 230 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134094 restraints weight = 30039.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138740 restraints weight = 18585.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141981 restraints weight = 12759.393| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14142 Z= 0.156 Angle : 0.666 9.372 19146 Z= 0.349 Chirality : 0.044 0.151 2190 Planarity : 0.005 0.052 2448 Dihedral : 11.041 96.031 1962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1728 helix: 0.99 (0.16), residues: 906 sheet: 0.74 (0.38), residues: 192 loop : 0.13 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 220 HIS 0.012 0.001 HIS C 337 PHE 0.034 0.002 PHE D 294 TYR 0.015 0.003 TYR E 314 ARG 0.008 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 738) hydrogen bonds : angle 4.63515 ( 2052) covalent geometry : bond 0.00329 (14142) covalent geometry : angle 0.66572 (19146) *********************** 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 560 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 559 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8143 (mtm) cc_final: 0.7788 (mtm) REVERT: A 101 THR cc_start: 0.8397 (p) cc_final: 0.8042 (t) REVERT: A 114 LYS cc_start: 0.7777 (tptm) cc_final: 0.7461 (tptm) REVERT: A 117 PHE cc_start: 0.7836 (m-10) cc_final: 0.7488 (m-10) REVERT: A 118 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6263 (mt-10) REVERT: A 122 LEU cc_start: 0.7514 (pt) cc_final: 0.6993 (tt) REVERT: A 124 GLN cc_start: 0.7929 (pp30) cc_final: 0.7704 (pp30) REVERT: A 125 PRO cc_start: 0.8122 (Cg_endo) cc_final: 0.7782 (Cg_exo) REVERT: A 141 LEU cc_start: 0.8464 (tp) cc_final: 0.8228 (tp) REVERT: A 148 LYS cc_start: 0.8235 (tttt) cc_final: 0.7911 (ttmt) REVERT: A 149 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 154 PHE cc_start: 0.7702 (t80) cc_final: 0.7086 (t80) REVERT: A 157 LEU cc_start: 0.8055 (tp) cc_final: 0.7731 (tp) REVERT: A 193 GLU cc_start: 0.7697 (tt0) cc_final: 0.7459 (tt0) REVERT: A 206 HIS cc_start: 0.7960 (p90) cc_final: 0.7303 (p90) REVERT: A 211 MET cc_start: 0.8047 (mmp) cc_final: 0.7325 (mmt) REVERT: A 212 MET cc_start: 0.7846 (mmp) cc_final: 0.7548 (mmp) REVERT: A 213 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7623 (mtmt) REVERT: A 215 GLN cc_start: 0.7546 (tp-100) cc_final: 0.6307 (tp-100) REVERT: A 217 MET cc_start: 0.8026 (mpp) cc_final: 0.7562 (mpp) REVERT: A 219 LEU cc_start: 0.8668 (mt) cc_final: 0.7489 (mt) REVERT: A 232 ILE cc_start: 0.8330 (mt) cc_final: 0.8051 (mt) REVERT: A 237 THR cc_start: 0.7730 (t) cc_final: 0.6951 (m) REVERT: A 259 GLN cc_start: 0.7343 (mt0) cc_final: 0.6992 (mt0) REVERT: A 273 LEU cc_start: 0.8111 (mm) cc_final: 0.7892 (mm) REVERT: A 305 ASP cc_start: 0.8165 (t0) cc_final: 0.7870 (m-30) REVERT: A 341 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 342 LYS cc_start: 0.8566 (mptt) cc_final: 0.8024 (mptt) REVERT: A 343 MET cc_start: 0.8220 (tpt) cc_final: 0.7937 (tpt) REVERT: B 74 MET cc_start: 0.8024 (mtm) cc_final: 0.7363 (mtm) REVERT: B 85 ASN cc_start: 0.8021 (p0) cc_final: 0.7812 (p0) REVERT: B 113 LYS cc_start: 0.7945 (tppp) cc_final: 0.7697 (tttp) REVERT: B 117 PHE cc_start: 0.7731 (m-10) cc_final: 0.7422 (m-10) REVERT: B 148 LYS cc_start: 0.8426 (tttt) cc_final: 0.7877 (ttmt) REVERT: B 149 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7221 (mm-30) REVERT: B 157 LEU cc_start: 0.8120 (tp) cc_final: 0.7744 (tp) REVERT: B 158 GLN cc_start: 0.6980 (pm20) cc_final: 0.6158 (pm20) REVERT: B 193 GLU cc_start: 0.7577 (tt0) cc_final: 0.7254 (tt0) REVERT: B 199 ARG cc_start: 0.7397 (tpp80) cc_final: 0.6600 (tpp80) REVERT: B 211 MET cc_start: 0.8026 (mmp) cc_final: 0.7609 (mmp) REVERT: B 212 MET cc_start: 0.7905 (mmp) cc_final: 0.7641 (mmp) REVERT: B 213 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7561 (mtmt) REVERT: B 215 GLN cc_start: 0.7500 (tp-100) cc_final: 0.6577 (tp-100) REVERT: B 217 MET cc_start: 0.8071 (mpp) cc_final: 0.7267 (mpp) REVERT: B 221 ASP cc_start: 0.7152 (m-30) cc_final: 0.6913 (m-30) REVERT: B 231 VAL cc_start: 0.7884 (t) cc_final: 0.7596 (p) REVERT: B 232 ILE cc_start: 0.8318 (mt) cc_final: 0.8055 (mt) REVERT: B 243 LEU cc_start: 0.8419 (mt) cc_final: 0.8133 (mt) REVERT: B 259 GLN cc_start: 0.7586 (mt0) cc_final: 0.7241 (mt0) REVERT: B 266 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 286 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 295 SER cc_start: 0.6793 (p) cc_final: 0.6497 (p) REVERT: B 299 LEU cc_start: 0.8625 (mt) cc_final: 0.8248 (mt) REVERT: B 311 VAL cc_start: 0.8203 (t) cc_final: 0.7989 (t) REVERT: B 338 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8110 (mtp85) REVERT: B 341 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7345 (mm-30) REVERT: B 342 LYS cc_start: 0.8518 (mptt) cc_final: 0.7681 (mptt) REVERT: B 345 LYS cc_start: 0.8777 (pptt) cc_final: 0.8477 (pptt) REVERT: C 74 MET cc_start: 0.5648 (mtm) cc_final: 0.5214 (mtm) REVERT: C 184 LEU cc_start: 0.6236 (mm) cc_final: 0.5860 (mt) REVERT: C 190 PHE cc_start: 0.6485 (t80) cc_final: 0.6207 (t80) REVERT: C 199 ARG cc_start: 0.5958 (tpp80) cc_final: 0.5713 (tpp80) REVERT: C 211 MET cc_start: 0.7166 (mmp) cc_final: 0.6933 (mmp) REVERT: C 212 MET cc_start: 0.7521 (mmp) cc_final: 0.6716 (mmp) REVERT: C 239 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7246 (mtt90) REVERT: C 248 MET cc_start: 0.7613 (mtp) cc_final: 0.7047 (mtp) REVERT: C 251 MET cc_start: 0.6355 (mmt) cc_final: 0.5809 (mmt) REVERT: C 289 GLN cc_start: 0.8283 (mt0) cc_final: 0.8063 (mt0) REVERT: C 308 LEU cc_start: 0.8582 (tp) cc_final: 0.8357 (tp) REVERT: C 335 ASP cc_start: 0.7868 (m-30) cc_final: 0.7602 (m-30) REVERT: C 336 LEU cc_start: 0.8639 (mp) cc_final: 0.8370 (mp) REVERT: C 343 MET cc_start: 0.8233 (tpt) cc_final: 0.7387 (tpt) REVERT: C 344 LYS cc_start: 0.8921 (mttm) cc_final: 0.8557 (mttm) REVERT: C 347 LYS cc_start: 0.8144 (mptt) cc_final: 0.7881 (mptt) REVERT: D 82 ASP cc_start: 0.7589 (t0) cc_final: 0.6953 (t70) REVERT: D 89 THR cc_start: 0.7743 (p) cc_final: 0.7476 (p) REVERT: D 104 LYS cc_start: 0.8305 (tttt) cc_final: 0.7990 (tttm) REVERT: D 132 TYR cc_start: 0.7252 (p90) cc_final: 0.6978 (p90) REVERT: D 139 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7208 (mtmm) REVERT: D 173 LEU cc_start: 0.8233 (tp) cc_final: 0.8025 (tp) REVERT: D 196 SER cc_start: 0.7140 (t) cc_final: 0.6825 (p) REVERT: D 212 MET cc_start: 0.7871 (mmp) cc_final: 0.7032 (mmp) REVERT: D 217 MET cc_start: 0.7075 (mmp) cc_final: 0.6633 (mmt) REVERT: D 237 THR cc_start: 0.7056 (t) cc_final: 0.6415 (m) REVERT: D 241 GLN cc_start: 0.8229 (mp-120) cc_final: 0.7369 (mm110) REVERT: D 248 MET cc_start: 0.7035 (mtp) cc_final: 0.6507 (mtp) REVERT: D 259 GLN cc_start: 0.7984 (mp10) cc_final: 0.7777 (mp10) REVERT: D 300 LYS cc_start: 0.8464 (tptm) cc_final: 0.8130 (tptm) REVERT: D 305 ASP cc_start: 0.7464 (t0) cc_final: 0.7086 (t0) REVERT: D 337 HIS cc_start: 0.7571 (m170) cc_final: 0.7270 (m90) REVERT: E 155 ILE cc_start: 0.7192 (pt) cc_final: 0.6378 (tp) REVERT: E 171 GLN cc_start: 0.8550 (mm110) cc_final: 0.8161 (mm-40) REVERT: E 205 ASP cc_start: 0.4656 (m-30) cc_final: 0.4353 (m-30) REVERT: E 212 MET cc_start: 0.7638 (mmp) cc_final: 0.6730 (mmp) REVERT: E 248 MET cc_start: 0.7709 (mtp) cc_final: 0.7196 (mtp) REVERT: E 251 MET cc_start: 0.5691 (mmt) cc_final: 0.5321 (mmt) REVERT: E 286 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 290 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7624 (mm-30) REVERT: E 298 ASP cc_start: 0.7693 (m-30) cc_final: 0.7329 (m-30) REVERT: E 304 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8213 (mtp-110) REVERT: E 336 LEU cc_start: 0.8603 (mp) cc_final: 0.8386 (mp) REVERT: E 341 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 343 MET cc_start: 0.8266 (tpt) cc_final: 0.7405 (tpt) REVERT: E 347 LYS cc_start: 0.8228 (mptt) cc_final: 0.7997 (mmtt) REVERT: F 74 MET cc_start: 0.7390 (mtm) cc_final: 0.7064 (mtm) REVERT: F 82 ASP cc_start: 0.7156 (t70) cc_final: 0.6945 (t0) REVERT: F 87 HIS cc_start: 0.7593 (m-70) cc_final: 0.6927 (m-70) REVERT: F 102 ASP cc_start: 0.8002 (m-30) cc_final: 0.7696 (m-30) REVERT: F 104 LYS cc_start: 0.8336 (tttt) cc_final: 0.8008 (tttm) REVERT: F 115 HIS cc_start: 0.5808 (OUTLIER) cc_final: 0.5523 (p90) REVERT: F 139 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7386 (mtmm) REVERT: F 183 LYS cc_start: 0.8596 (mptt) cc_final: 0.8311 (mptt) REVERT: F 199 ARG cc_start: 0.5983 (tpp80) cc_final: 0.4852 (tpp80) REVERT: F 211 MET cc_start: 0.7300 (mmp) cc_final: 0.6947 (mmp) REVERT: F 212 MET cc_start: 0.7941 (mmp) cc_final: 0.7497 (mmp) REVERT: F 215 GLN cc_start: 0.6972 (tp-100) cc_final: 0.6725 (tp-100) REVERT: F 219 LEU cc_start: 0.7592 (mt) cc_final: 0.6793 (mt) REVERT: F 237 THR cc_start: 0.6983 (t) cc_final: 0.6318 (m) REVERT: F 241 GLN cc_start: 0.8003 (mm110) cc_final: 0.7559 (mm-40) REVERT: F 248 MET cc_start: 0.7133 (mtp) cc_final: 0.6638 (mtp) REVERT: F 270 LYS cc_start: 0.8284 (pttp) cc_final: 0.7862 (ptmm) REVERT: F 300 LYS cc_start: 0.8238 (tptm) cc_final: 0.7924 (tptm) REVERT: F 302 MET cc_start: 0.7691 (tmm) cc_final: 0.7357 (tmm) REVERT: F 337 HIS cc_start: 0.7702 (m170) cc_final: 0.7356 (m170) outliers start: 1 outliers final: 0 residues processed: 560 average time/residue: 0.2910 time to fit residues: 225.4141 Evaluate side-chains 540 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 129 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 171 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN D 215 GLN E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118595 restraints weight = 30896.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123146 restraints weight = 18498.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126300 restraints weight = 12470.075| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14142 Z= 0.326 Angle : 0.829 10.720 19146 Z= 0.445 Chirality : 0.051 0.269 2190 Planarity : 0.006 0.063 2448 Dihedral : 11.603 107.577 1962 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 0.20 % Allowed : 4.64 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1728 helix: 0.21 (0.15), residues: 978 sheet: 0.92 (0.41), residues: 186 loop : -0.06 (0.29), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP C 220 HIS 0.012 0.002 HIS C 281 PHE 0.050 0.004 PHE D 216 TYR 0.023 0.003 TYR B 314 ARG 0.012 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.05928 ( 738) hydrogen bonds : angle 5.25674 ( 2052) covalent geometry : bond 0.00632 (14142) covalent geometry : angle 0.82877 (19146) *********************** 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 621 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 618 time to evaluate : 1.445 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: A 74 MET cc_start: 0.8268 (mtm) cc_final: 0.7893 (mtm) REVERT: A 96 LEU cc_start: 0.7635 (mt) cc_final: 0.7214 (mt) REVERT: A 99 VAL cc_start: 0.8337 (t) cc_final: 0.8021 (m) REVERT: A 100 ILE cc_start: 0.8144 (mm) cc_final: 0.7828 (mm) REVERT: A 104 LYS cc_start: 0.8617 (tttt) cc_final: 0.8234 (tttt) REVERT: A 114 LYS cc_start: 0.7696 (tptm) cc_final: 0.7394 (tptm) REVERT: A 117 PHE cc_start: 0.7936 (m-10) cc_final: 0.7664 (m-10) REVERT: A 124 GLN cc_start: 0.8156 (pp30) cc_final: 0.7844 (pp30) REVERT: A 125 PRO cc_start: 0.8585 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: A 130 LEU cc_start: 0.7834 (tp) cc_final: 0.7547 (tp) REVERT: A 131 LEU cc_start: 0.8021 (mp) cc_final: 0.7694 (mt) REVERT: A 148 LYS cc_start: 0.8396 (tttt) cc_final: 0.8122 (ttmt) REVERT: A 149 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 154 PHE cc_start: 0.7698 (t80) cc_final: 0.7011 (t80) REVERT: A 157 LEU cc_start: 0.8061 (tp) cc_final: 0.7786 (tp) REVERT: A 169 GLU cc_start: 0.8065 (tt0) cc_final: 0.7780 (tt0) REVERT: A 179 SER cc_start: 0.8795 (t) cc_final: 0.8530 (p) REVERT: A 206 HIS cc_start: 0.8170 (p90) cc_final: 0.7578 (p90) REVERT: A 211 MET cc_start: 0.8070 (mmp) cc_final: 0.7547 (mmp) REVERT: A 212 MET cc_start: 0.8038 (mmp) cc_final: 0.7758 (mmp) REVERT: A 213 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7794 (mtmt) REVERT: A 217 MET cc_start: 0.8107 (mpp) cc_final: 0.7666 (mpp) REVERT: A 218 SER cc_start: 0.8665 (p) cc_final: 0.8411 (p) REVERT: A 219 LEU cc_start: 0.8742 (mt) cc_final: 0.8460 (mt) REVERT: A 241 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8276 (mm-40) REVERT: A 251 MET cc_start: 0.7924 (mmm) cc_final: 0.7660 (mmm) REVERT: A 259 GLN cc_start: 0.7532 (mt0) cc_final: 0.7276 (mt0) REVERT: A 305 ASP cc_start: 0.8298 (t0) cc_final: 0.7995 (m-30) REVERT: A 341 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7204 (mm-30) REVERT: A 342 LYS cc_start: 0.8806 (mptt) cc_final: 0.8500 (mptt) REVERT: A 344 LYS cc_start: 0.8507 (mttm) cc_final: 0.8029 (mttm) REVERT: B 74 MET cc_start: 0.8146 (mtm) cc_final: 0.7390 (mtm) REVERT: B 85 ASN cc_start: 0.8175 (p0) cc_final: 0.7908 (p0) REVERT: B 86 MET cc_start: 0.7850 (mtm) cc_final: 0.7496 (mtm) REVERT: B 90 TRP cc_start: 0.8128 (m100) cc_final: 0.7548 (m100) REVERT: B 101 THR cc_start: 0.8426 (p) cc_final: 0.8036 (p) REVERT: B 104 LYS cc_start: 0.8546 (tttt) cc_final: 0.8135 (tttt) REVERT: B 105 ASP cc_start: 0.7448 (p0) cc_final: 0.7237 (p0) REVERT: B 122 LEU cc_start: 0.8129 (tt) cc_final: 0.7763 (tp) REVERT: B 131 LEU cc_start: 0.8059 (mp) cc_final: 0.7724 (tp) REVERT: B 148 LYS cc_start: 0.8464 (tttt) cc_final: 0.8130 (ttmt) REVERT: B 154 PHE cc_start: 0.7727 (t80) cc_final: 0.6991 (t80) REVERT: B 157 LEU cc_start: 0.8176 (tp) cc_final: 0.7825 (tp) REVERT: B 158 GLN cc_start: 0.7215 (pm20) cc_final: 0.6406 (pm20) REVERT: B 211 MET cc_start: 0.8018 (mmp) cc_final: 0.7647 (mmp) REVERT: B 213 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7554 (mtmt) REVERT: B 215 GLN cc_start: 0.7548 (tp-100) cc_final: 0.6366 (tp-100) REVERT: B 217 MET cc_start: 0.8111 (mpp) cc_final: 0.7574 (mpp) REVERT: B 218 SER cc_start: 0.8574 (p) cc_final: 0.8028 (p) REVERT: B 219 LEU cc_start: 0.8719 (mt) cc_final: 0.7736 (mt) REVERT: B 243 LEU cc_start: 0.8532 (mt) cc_final: 0.8251 (mt) REVERT: B 259 GLN cc_start: 0.7757 (mt0) cc_final: 0.7467 (mt0) REVERT: B 266 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7315 (tm-30) REVERT: B 286 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 295 SER cc_start: 0.7090 (p) cc_final: 0.6819 (p) REVERT: B 299 LEU cc_start: 0.8809 (mt) cc_final: 0.8571 (mt) REVERT: B 341 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 342 LYS cc_start: 0.8617 (mptt) cc_final: 0.7808 (mptt) REVERT: B 343 MET cc_start: 0.8265 (tpt) cc_final: 0.6933 (tpt) REVERT: B 344 LYS cc_start: 0.8255 (ptpp) cc_final: 0.7764 (ptpp) REVERT: B 345 LYS cc_start: 0.8826 (pptt) cc_final: 0.8518 (pptt) REVERT: B 346 SER cc_start: 0.8678 (p) cc_final: 0.8465 (p) REVERT: B 347 LYS cc_start: 0.8866 (mptt) cc_final: 0.8355 (mptt) REVERT: C 86 MET cc_start: 0.5616 (pmm) cc_final: 0.5223 (pmm) REVERT: C 158 GLN cc_start: 0.8180 (pm20) cc_final: 0.7801 (pm20) REVERT: C 170 SER cc_start: 0.8026 (p) cc_final: 0.7714 (p) REVERT: C 171 GLN cc_start: 0.8478 (mm110) cc_final: 0.8105 (mm-40) REVERT: C 212 MET cc_start: 0.7683 (mmp) cc_final: 0.7225 (mmp) REVERT: C 239 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7640 (mtt90) REVERT: C 248 MET cc_start: 0.7971 (mtp) cc_final: 0.7485 (mtp) REVERT: C 251 MET cc_start: 0.6494 (mmt) cc_final: 0.5862 (mmt) REVERT: C 289 GLN cc_start: 0.8189 (mt0) cc_final: 0.7867 (mt0) REVERT: C 295 SER cc_start: 0.8101 (p) cc_final: 0.7633 (p) REVERT: C 298 ASP cc_start: 0.7544 (m-30) cc_final: 0.7149 (m-30) REVERT: C 299 LEU cc_start: 0.8721 (mt) cc_final: 0.8386 (mt) REVERT: C 300 LYS cc_start: 0.9016 (tttt) cc_final: 0.8768 (tttt) REVERT: C 302 MET cc_start: 0.8224 (tmm) cc_final: 0.7925 (tmm) REVERT: C 304 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8366 (mmm160) REVERT: C 308 LEU cc_start: 0.8719 (tp) cc_final: 0.8444 (tp) REVERT: C 313 GLU cc_start: 0.8166 (pt0) cc_final: 0.7921 (pt0) REVERT: C 343 MET cc_start: 0.8370 (tpt) cc_final: 0.7533 (tpt) REVERT: C 344 LYS cc_start: 0.9051 (mttm) cc_final: 0.8675 (mttm) REVERT: C 347 LYS cc_start: 0.8406 (mptt) cc_final: 0.8093 (mptt) REVERT: D 82 ASP cc_start: 0.8223 (t0) cc_final: 0.7824 (t70) REVERT: D 104 LYS cc_start: 0.8475 (tttt) cc_final: 0.8205 (tttm) REVERT: D 139 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7665 (mtmm) REVERT: D 178 PHE cc_start: 0.7909 (m-10) cc_final: 0.7690 (m-10) REVERT: D 183 LYS cc_start: 0.8491 (mptt) cc_final: 0.8083 (mptt) REVERT: D 211 MET cc_start: 0.7580 (mmp) cc_final: 0.7130 (mmp) REVERT: D 212 MET cc_start: 0.7748 (mmp) cc_final: 0.7249 (mmp) REVERT: D 241 GLN cc_start: 0.8192 (mp-120) cc_final: 0.7925 (mm-40) REVERT: D 248 MET cc_start: 0.7135 (mtp) cc_final: 0.6626 (mtp) REVERT: D 250 ARG cc_start: 0.7660 (ttt180) cc_final: 0.6117 (ptm160) REVERT: D 251 MET cc_start: 0.7858 (mmt) cc_final: 0.7314 (mmt) REVERT: D 259 GLN cc_start: 0.8300 (mp10) cc_final: 0.8030 (mp10) REVERT: D 300 LYS cc_start: 0.8575 (tptm) cc_final: 0.8125 (tptm) REVERT: D 302 MET cc_start: 0.7863 (tmm) cc_final: 0.7641 (tmm) REVERT: D 305 ASP cc_start: 0.7642 (t0) cc_final: 0.7316 (t0) REVERT: D 309 LEU cc_start: 0.8520 (tp) cc_final: 0.8201 (tp) REVERT: D 312 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7987 (mtp-110) REVERT: D 337 HIS cc_start: 0.7825 (m170) cc_final: 0.7531 (m-70) REVERT: E 117 PHE cc_start: 0.6315 (m-80) cc_final: 0.5968 (m-80) REVERT: E 158 GLN cc_start: 0.8189 (pm20) cc_final: 0.7800 (pm20) REVERT: E 171 GLN cc_start: 0.8634 (mm110) cc_final: 0.8177 (mp10) REVERT: E 193 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7514 (mt-10) REVERT: E 205 ASP cc_start: 0.5471 (m-30) cc_final: 0.5190 (m-30) REVERT: E 212 MET cc_start: 0.7817 (mmp) cc_final: 0.7113 (mmp) REVERT: E 239 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7857 (mtt90) REVERT: E 248 MET cc_start: 0.7958 (mtp) cc_final: 0.7459 (mtp) REVERT: E 266 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7749 (tm-30) REVERT: E 290 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7677 (mm-30) REVERT: E 298 ASP cc_start: 0.7522 (m-30) cc_final: 0.7111 (m-30) REVERT: E 299 LEU cc_start: 0.8787 (mt) cc_final: 0.8332 (mt) REVERT: E 300 LYS cc_start: 0.8847 (tttt) cc_final: 0.8567 (tttt) REVERT: E 301 GLU cc_start: 0.8152 (tt0) cc_final: 0.7727 (tt0) REVERT: E 302 MET cc_start: 0.8273 (tmm) cc_final: 0.7923 (tmm) REVERT: E 304 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8249 (mmm-85) REVERT: E 309 LEU cc_start: 0.8807 (tp) cc_final: 0.8591 (tp) REVERT: E 313 GLU cc_start: 0.8366 (pt0) cc_final: 0.8158 (pt0) REVERT: E 335 ASP cc_start: 0.7980 (m-30) cc_final: 0.7713 (m-30) REVERT: E 341 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7689 (mm-30) REVERT: F 74 MET cc_start: 0.7731 (mtm) cc_final: 0.7053 (mtm) REVERT: F 90 TRP cc_start: 0.8221 (m100) cc_final: 0.7789 (m100) REVERT: F 102 ASP cc_start: 0.8125 (m-30) cc_final: 0.7809 (m-30) REVERT: F 104 LYS cc_start: 0.8434 (tttt) cc_final: 0.8060 (ttmt) REVERT: F 112 LYS cc_start: 0.7918 (mttt) cc_final: 0.7684 (mttt) REVERT: F 131 LEU cc_start: 0.8348 (mp) cc_final: 0.7876 (mt) REVERT: F 139 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7882 (mtmm) REVERT: F 178 PHE cc_start: 0.7875 (m-10) cc_final: 0.7406 (m-10) REVERT: F 183 LYS cc_start: 0.8554 (mptt) cc_final: 0.8223 (mptt) REVERT: F 211 MET cc_start: 0.7433 (mmp) cc_final: 0.7004 (mmp) REVERT: F 212 MET cc_start: 0.8093 (mmp) cc_final: 0.7647 (mmp) REVERT: F 217 MET cc_start: 0.7609 (mmt) cc_final: 0.6996 (mmt) REVERT: F 223 LEU cc_start: 0.7862 (mt) cc_final: 0.7383 (mt) REVERT: F 248 MET cc_start: 0.7002 (mtp) cc_final: 0.6445 (mtp) REVERT: F 251 MET cc_start: 0.7651 (mmt) cc_final: 0.7347 (mmt) REVERT: F 259 GLN cc_start: 0.7942 (mp10) cc_final: 0.7713 (mp10) REVERT: F 270 LYS cc_start: 0.8454 (pttp) cc_final: 0.8023 (ptmm) REVERT: F 300 LYS cc_start: 0.8390 (tptm) cc_final: 0.7950 (tptm) REVERT: F 302 MET cc_start: 0.7923 (tmm) cc_final: 0.7599 (tmm) REVERT: F 304 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.7163 (tpp-160) REVERT: F 332 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7978 (mm-40) REVERT: F 337 HIS cc_start: 0.7865 (m170) cc_final: 0.7500 (m170) outliers start: 3 outliers final: 0 residues processed: 619 average time/residue: 0.2791 time to fit residues: 243.3923 Evaluate side-chains 592 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 256 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.152834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.125927 restraints weight = 29939.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130493 restraints weight = 18077.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.133726 restraints weight = 12298.604| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4044 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= 0.156 Angle : 0.636 11.370 19146 Z= 0.338 Chirality : 0.045 0.188 2190 Planarity : 0.005 0.071 2448 Dihedral : 11.500 107.649 1962 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1728 helix: 0.82 (0.16), residues: 972 sheet: 0.57 (0.40), residues: 192 loop : 0.32 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 220 HIS 0.013 0.001 HIS B 337 PHE 0.036 0.003 PHE B 216 TYR 0.014 0.002 TYR B 314 ARG 0.008 0.001 ARG E 250 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 738) hydrogen bonds : angle 4.64582 ( 2052) covalent geometry : bond 0.00329 (14142) covalent geometry : angle 0.63596 (19146) *********************** 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 621 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8164 (mtm) cc_final: 0.7786 (mtm) REVERT: A 90 TRP cc_start: 0.8051 (m100) cc_final: 0.7398 (m100) REVERT: A 96 LEU cc_start: 0.7633 (mt) cc_final: 0.7330 (mt) REVERT: A 99 VAL cc_start: 0.8218 (t) cc_final: 0.8011 (m) REVERT: A 104 LYS cc_start: 0.8678 (tttt) cc_final: 0.8251 (tttt) REVERT: A 117 PHE cc_start: 0.7838 (m-10) cc_final: 0.7608 (m-10) REVERT: A 118 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6891 (mt-10) REVERT: A 124 GLN cc_start: 0.8179 (pp30) cc_final: 0.7923 (pp30) REVERT: A 125 PRO cc_start: 0.8619 (Cg_endo) cc_final: 0.8048 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8301 (tttt) cc_final: 0.7862 (ttmt) REVERT: A 154 PHE cc_start: 0.7734 (t80) cc_final: 0.7182 (t80) REVERT: A 157 LEU cc_start: 0.8003 (tp) cc_final: 0.7598 (tp) REVERT: A 158 GLN cc_start: 0.7280 (pm20) cc_final: 0.6434 (pm20) REVERT: A 169 GLU cc_start: 0.7816 (tt0) cc_final: 0.7258 (tt0) REVERT: A 177 VAL cc_start: 0.8697 (t) cc_final: 0.8487 (t) REVERT: A 179 SER cc_start: 0.8798 (t) cc_final: 0.8507 (p) REVERT: A 193 GLU cc_start: 0.7839 (tt0) cc_final: 0.7629 (tt0) REVERT: A 206 HIS cc_start: 0.8082 (p90) cc_final: 0.7324 (p90) REVERT: A 211 MET cc_start: 0.7869 (mmp) cc_final: 0.7311 (mmp) REVERT: A 212 MET cc_start: 0.7759 (mmp) cc_final: 0.7535 (mmp) REVERT: A 213 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7743 (mtmt) REVERT: A 215 GLN cc_start: 0.7645 (tp-100) cc_final: 0.6475 (tp-100) REVERT: A 217 MET cc_start: 0.7984 (mpp) cc_final: 0.7317 (mpp) REVERT: A 218 SER cc_start: 0.8752 (p) cc_final: 0.8325 (p) REVERT: A 219 LEU cc_start: 0.8787 (mt) cc_final: 0.7672 (mt) REVERT: A 220 TRP cc_start: 0.8128 (m-10) cc_final: 0.7009 (m-10) REVERT: A 241 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8282 (mm-40) REVERT: A 243 LEU cc_start: 0.8291 (mt) cc_final: 0.8049 (mt) REVERT: A 251 MET cc_start: 0.7433 (mmm) cc_final: 0.7093 (mmm) REVERT: A 259 GLN cc_start: 0.7603 (mt0) cc_final: 0.7305 (mt0) REVERT: A 263 LYS cc_start: 0.7800 (mttp) cc_final: 0.7554 (mttp) REVERT: A 266 GLU cc_start: 0.7857 (tp30) cc_final: 0.7237 (tp30) REVERT: A 305 ASP cc_start: 0.8310 (t0) cc_final: 0.7958 (m-30) REVERT: A 338 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7889 (mtp85) REVERT: A 341 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 342 LYS cc_start: 0.8738 (mptt) cc_final: 0.8377 (mptt) REVERT: B 74 MET cc_start: 0.8039 (mtm) cc_final: 0.7309 (mtm) REVERT: B 86 MET cc_start: 0.7782 (mtm) cc_final: 0.7554 (mtm) REVERT: B 101 THR cc_start: 0.8475 (p) cc_final: 0.8128 (p) REVERT: B 131 LEU cc_start: 0.8128 (mp) cc_final: 0.7910 (tp) REVERT: B 146 THR cc_start: 0.8261 (p) cc_final: 0.7922 (p) REVERT: B 152 CYS cc_start: 0.7068 (m) cc_final: 0.6832 (m) REVERT: B 154 PHE cc_start: 0.7700 (t80) cc_final: 0.7050 (t80) REVERT: B 157 LEU cc_start: 0.8090 (tp) cc_final: 0.7753 (tp) REVERT: B 158 GLN cc_start: 0.7294 (pm20) cc_final: 0.6437 (pm20) REVERT: B 211 MET cc_start: 0.7931 (mmp) cc_final: 0.7566 (mmp) REVERT: B 213 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7604 (mtmt) REVERT: B 215 GLN cc_start: 0.7547 (tp-100) cc_final: 0.6690 (tp-100) REVERT: B 217 MET cc_start: 0.8021 (mpp) cc_final: 0.7519 (mpp) REVERT: B 218 SER cc_start: 0.8667 (p) cc_final: 0.8397 (p) REVERT: B 243 LEU cc_start: 0.8532 (mt) cc_final: 0.8297 (mt) REVERT: B 259 GLN cc_start: 0.7867 (mt0) cc_final: 0.7484 (mt0) REVERT: B 266 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7009 (tm-30) REVERT: B 270 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7904 (mptt) REVERT: B 273 LEU cc_start: 0.8163 (mm) cc_final: 0.7960 (mm) REVERT: B 342 LYS cc_start: 0.8558 (mptt) cc_final: 0.7714 (mptt) REVERT: B 343 MET cc_start: 0.8179 (tpt) cc_final: 0.6747 (tpt) REVERT: B 345 LYS cc_start: 0.8774 (pptt) cc_final: 0.8432 (pptt) REVERT: B 347 LYS cc_start: 0.8873 (mptt) cc_final: 0.8334 (mptt) REVERT: C 86 MET cc_start: 0.5530 (pmm) cc_final: 0.5191 (pmm) REVERT: C 158 GLN cc_start: 0.8115 (pm20) cc_final: 0.7637 (pm20) REVERT: C 167 TYR cc_start: 0.7506 (m-10) cc_final: 0.7102 (m-10) REVERT: C 170 SER cc_start: 0.8057 (p) cc_final: 0.7647 (p) REVERT: C 171 GLN cc_start: 0.8412 (mm110) cc_final: 0.7944 (mm-40) REVERT: C 212 MET cc_start: 0.7590 (mmp) cc_final: 0.7156 (mmp) REVERT: C 215 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7435 (tm-30) REVERT: C 226 ASP cc_start: 0.5720 (t0) cc_final: 0.5507 (t0) REVERT: C 239 ARG cc_start: 0.7869 (mtt90) cc_final: 0.7115 (mtt90) REVERT: C 248 MET cc_start: 0.7909 (mtp) cc_final: 0.7318 (mtp) REVERT: C 270 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7479 (mmmt) REVERT: C 289 GLN cc_start: 0.8036 (mt0) cc_final: 0.7737 (mt0) REVERT: C 295 SER cc_start: 0.7952 (p) cc_final: 0.7711 (p) REVERT: C 298 ASP cc_start: 0.7313 (m-30) cc_final: 0.6987 (m-30) REVERT: C 299 LEU cc_start: 0.8652 (mt) cc_final: 0.8283 (mt) REVERT: C 300 LYS cc_start: 0.8938 (tttt) cc_final: 0.8649 (tttt) REVERT: C 302 MET cc_start: 0.8045 (tmm) cc_final: 0.7703 (tmm) REVERT: C 304 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8258 (mmm160) REVERT: C 308 LEU cc_start: 0.8578 (tp) cc_final: 0.8280 (tp) REVERT: C 313 GLU cc_start: 0.8123 (pt0) cc_final: 0.7885 (pt0) REVERT: C 343 MET cc_start: 0.8180 (tpt) cc_final: 0.7326 (tpt) REVERT: C 344 LYS cc_start: 0.9005 (mttm) cc_final: 0.8603 (mttm) REVERT: C 347 LYS cc_start: 0.8293 (mptt) cc_final: 0.8069 (mptt) REVERT: D 82 ASP cc_start: 0.8300 (t0) cc_final: 0.7899 (t70) REVERT: D 90 TRP cc_start: 0.8223 (m100) cc_final: 0.7788 (m100) REVERT: D 104 LYS cc_start: 0.8377 (tttt) cc_final: 0.8026 (tttm) REVERT: D 113 LYS cc_start: 0.7196 (tppt) cc_final: 0.6954 (tppt) REVERT: D 139 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7220 (mtmm) REVERT: D 179 SER cc_start: 0.8074 (p) cc_final: 0.7756 (p) REVERT: D 183 LYS cc_start: 0.8506 (mptt) cc_final: 0.8042 (mptt) REVERT: D 211 MET cc_start: 0.7523 (mmp) cc_final: 0.7093 (mmp) REVERT: D 212 MET cc_start: 0.7735 (mmp) cc_final: 0.7413 (mmp) REVERT: D 241 GLN cc_start: 0.8128 (mp-120) cc_final: 0.7327 (mm-40) REVERT: D 251 MET cc_start: 0.7737 (mmt) cc_final: 0.7089 (mmt) REVERT: D 291 THR cc_start: 0.6746 (p) cc_final: 0.6162 (t) REVERT: D 300 LYS cc_start: 0.8589 (tptm) cc_final: 0.8275 (tptm) REVERT: D 302 MET cc_start: 0.7782 (tmm) cc_final: 0.7560 (tmm) REVERT: D 305 ASP cc_start: 0.7487 (t0) cc_final: 0.7117 (t0) REVERT: D 337 HIS cc_start: 0.7604 (m170) cc_final: 0.7270 (m-70) REVERT: E 117 PHE cc_start: 0.6132 (m-80) cc_final: 0.5821 (m-80) REVERT: E 139 LYS cc_start: 0.8124 (ptpp) cc_final: 0.7832 (pttm) REVERT: E 158 GLN cc_start: 0.8135 (pm20) cc_final: 0.7810 (pm20) REVERT: E 167 TYR cc_start: 0.7283 (m-10) cc_final: 0.6880 (m-10) REVERT: E 171 GLN cc_start: 0.8580 (mm110) cc_final: 0.8160 (mp10) REVERT: E 193 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7295 (mt-10) REVERT: E 205 ASP cc_start: 0.5421 (m-30) cc_final: 0.5170 (m-30) REVERT: E 212 MET cc_start: 0.7718 (mmp) cc_final: 0.7109 (mmp) REVERT: E 215 GLN cc_start: 0.7882 (tp-100) cc_final: 0.6773 (tm-30) REVERT: E 217 MET cc_start: 0.8594 (ptp) cc_final: 0.7920 (tpp) REVERT: E 219 LEU cc_start: 0.7442 (mt) cc_final: 0.6821 (mt) REVERT: E 248 MET cc_start: 0.7908 (mtp) cc_final: 0.7355 (mtp) REVERT: E 250 ARG cc_start: 0.6027 (mmm160) cc_final: 0.5574 (mmm160) REVERT: E 264 GLN cc_start: 0.8501 (mp10) cc_final: 0.8183 (mp10) REVERT: E 266 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 270 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7372 (mmmt) REVERT: E 290 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7436 (mm-30) REVERT: E 298 ASP cc_start: 0.7422 (m-30) cc_final: 0.6986 (m-30) REVERT: E 299 LEU cc_start: 0.8771 (mt) cc_final: 0.8298 (mt) REVERT: E 300 LYS cc_start: 0.8757 (tttt) cc_final: 0.8427 (tttt) REVERT: E 301 GLU cc_start: 0.8089 (tt0) cc_final: 0.7582 (tt0) REVERT: E 302 MET cc_start: 0.8079 (tmm) cc_final: 0.7757 (tmm) REVERT: E 304 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.8213 (mmm-85) REVERT: E 313 GLU cc_start: 0.8379 (pt0) cc_final: 0.8132 (pt0) REVERT: E 341 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7665 (mm-30) REVERT: E 343 MET cc_start: 0.8247 (tpt) cc_final: 0.7627 (tpt) REVERT: F 74 MET cc_start: 0.7596 (mtm) cc_final: 0.7235 (mtm) REVERT: F 82 ASP cc_start: 0.8359 (t0) cc_final: 0.8134 (t0) REVERT: F 90 TRP cc_start: 0.8217 (m100) cc_final: 0.7667 (m100) REVERT: F 100 ILE cc_start: 0.8456 (mm) cc_final: 0.8252 (mm) REVERT: F 102 ASP cc_start: 0.8014 (m-30) cc_final: 0.7710 (m-30) REVERT: F 104 LYS cc_start: 0.8426 (tttt) cc_final: 0.8033 (ttmt) REVERT: F 131 LEU cc_start: 0.8503 (mp) cc_final: 0.8297 (mt) REVERT: F 180 LEU cc_start: 0.8100 (tt) cc_final: 0.7824 (tt) REVERT: F 183 LYS cc_start: 0.8476 (mptt) cc_final: 0.8047 (mptt) REVERT: F 211 MET cc_start: 0.7398 (mmp) cc_final: 0.7183 (mmt) REVERT: F 212 MET cc_start: 0.8008 (mmp) cc_final: 0.7630 (mmp) REVERT: F 215 GLN cc_start: 0.7020 (tp-100) cc_final: 0.6688 (tp-100) REVERT: F 217 MET cc_start: 0.7439 (mmt) cc_final: 0.6745 (mmt) REVERT: F 219 LEU cc_start: 0.7907 (mt) cc_final: 0.7248 (mt) REVERT: F 241 GLN cc_start: 0.7880 (mm110) cc_final: 0.7410 (mm110) REVERT: F 248 MET cc_start: 0.7029 (mtp) cc_final: 0.6520 (mtp) REVERT: F 270 LYS cc_start: 0.8420 (pttp) cc_final: 0.7971 (ptmm) REVERT: F 298 ASP cc_start: 0.8084 (m-30) cc_final: 0.7876 (m-30) REVERT: F 300 LYS cc_start: 0.8320 (tptm) cc_final: 0.7959 (tptm) REVERT: F 302 MET cc_start: 0.7756 (tmm) cc_final: 0.7388 (tmm) REVERT: F 304 ARG cc_start: 0.7160 (tpp-160) cc_final: 0.6772 (tpp-160) REVERT: F 332 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7832 (tp-100) REVERT: F 337 HIS cc_start: 0.7607 (m170) cc_final: 0.7237 (m170) outliers start: 1 outliers final: 0 residues processed: 620 average time/residue: 0.2903 time to fit residues: 253.7600 Evaluate side-chains 592 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 241 GLN A 275 ASN B 79 HIS B 275 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** 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 337 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125492 restraints weight = 30189.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.130086 restraints weight = 18202.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.133276 restraints weight = 12354.672| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4411 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= 0.153 Angle : 0.620 11.791 19146 Z= 0.327 Chirality : 0.045 0.310 2190 Planarity : 0.005 0.057 2448 Dihedral : 11.491 105.821 1962 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.13 % Allowed : 2.22 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1728 helix: 0.95 (0.16), residues: 984 sheet: 0.57 (0.41), residues: 192 loop : 0.55 (0.31), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 220 HIS 0.010 0.001 HIS A 337 PHE 0.041 0.002 PHE F 216 TYR 0.012 0.002 TYR D 132 ARG 0.008 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 738) hydrogen bonds : angle 4.47951 ( 2052) covalent geometry : bond 0.00317 (14142) covalent geometry : angle 0.62001 (19146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 616 time to evaluate : 1.453 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: 0.8213 (mtm) cc_final: 0.7789 (mtm) REVERT: A 90 TRP cc_start: 0.8070 (m100) cc_final: 0.7146 (m100) REVERT: A 96 LEU cc_start: 0.7615 (mt) cc_final: 0.7304 (mt) REVERT: A 101 THR cc_start: 0.8334 (p) cc_final: 0.7944 (p) REVERT: A 104 LYS cc_start: 0.8673 (tttt) cc_final: 0.8210 (tttt) REVERT: A 117 PHE cc_start: 0.7866 (m-10) cc_final: 0.7663 (m-10) REVERT: A 118 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 124 GLN cc_start: 0.8169 (pp30) cc_final: 0.7947 (pp30) REVERT: A 125 PRO cc_start: 0.8504 (Cg_endo) cc_final: 0.8048 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8293 (mp) cc_final: 0.8012 (tp) REVERT: A 146 THR cc_start: 0.8284 (p) cc_final: 0.7864 (p) REVERT: A 148 LYS cc_start: 0.8299 (tttt) cc_final: 0.7906 (ttmt) REVERT: A 157 LEU cc_start: 0.7958 (tp) cc_final: 0.7629 (tp) REVERT: A 158 GLN cc_start: 0.7281 (pm20) cc_final: 0.6888 (pm20) REVERT: A 179 SER cc_start: 0.8844 (t) cc_final: 0.8574 (p) REVERT: A 206 HIS cc_start: 0.8092 (p90) cc_final: 0.7408 (p90) REVERT: A 211 MET cc_start: 0.7937 (mmp) cc_final: 0.7365 (mmp) REVERT: A 212 MET cc_start: 0.7915 (mmp) cc_final: 0.7594 (mmp) REVERT: A 213 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7768 (mtmt) REVERT: A 215 GLN cc_start: 0.7656 (tp-100) cc_final: 0.6494 (tp-100) REVERT: A 217 MET cc_start: 0.8064 (mpp) cc_final: 0.7604 (mpp) REVERT: A 218 SER cc_start: 0.8624 (p) cc_final: 0.8133 (p) REVERT: A 219 LEU cc_start: 0.8721 (mt) cc_final: 0.7649 (mt) REVERT: A 243 LEU cc_start: 0.8350 (mt) cc_final: 0.8106 (mt) REVERT: A 250 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7841 (ttp-170) REVERT: A 251 MET cc_start: 0.7639 (mmm) cc_final: 0.7185 (mmm) REVERT: A 259 GLN cc_start: 0.7659 (mt0) cc_final: 0.7317 (mt0) REVERT: A 263 LYS cc_start: 0.7810 (mttp) cc_final: 0.7587 (mttp) REVERT: A 301 GLU cc_start: 0.8103 (tt0) cc_final: 0.7070 (tt0) REVERT: A 305 ASP cc_start: 0.8311 (t0) cc_final: 0.7977 (m-30) REVERT: A 338 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7970 (mtp85) REVERT: A 341 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 342 LYS cc_start: 0.8726 (mptt) cc_final: 0.8350 (mptt) REVERT: A 343 MET cc_start: 0.8088 (mmm) cc_final: 0.7768 (mmm) REVERT: B 74 MET cc_start: 0.8070 (mtm) cc_final: 0.7375 (mtm) REVERT: B 90 TRP cc_start: 0.8056 (m100) cc_final: 0.7112 (m100) REVERT: B 104 LYS cc_start: 0.8537 (tttt) cc_final: 0.8201 (tttt) REVERT: B 131 LEU cc_start: 0.8100 (mp) cc_final: 0.7759 (tp) REVERT: B 144 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8300 (mtmt) REVERT: B 148 LYS cc_start: 0.8355 (tttt) cc_final: 0.7984 (ttmt) REVERT: B 152 CYS cc_start: 0.7223 (m) cc_final: 0.6935 (m) REVERT: B 154 PHE cc_start: 0.7656 (t80) cc_final: 0.7009 (t80) REVERT: B 157 LEU cc_start: 0.8065 (tp) cc_final: 0.7715 (tp) REVERT: B 158 GLN cc_start: 0.7240 (pm20) cc_final: 0.6395 (pm20) REVERT: B 211 MET cc_start: 0.8001 (mmp) cc_final: 0.7615 (mmp) REVERT: B 213 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7645 (mtmt) REVERT: B 215 GLN cc_start: 0.7493 (tp-100) cc_final: 0.6542 (tp-100) REVERT: B 217 MET cc_start: 0.8090 (mpp) cc_final: 0.7473 (mpp) REVERT: B 243 LEU cc_start: 0.8580 (mt) cc_final: 0.8293 (mt) REVERT: B 250 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.6848 (mtt-85) REVERT: B 259 GLN cc_start: 0.7891 (mt0) cc_final: 0.7479 (mt0) REVERT: B 266 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 270 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7889 (mptt) REVERT: B 273 LEU cc_start: 0.8140 (mm) cc_final: 0.7901 (mm) REVERT: B 283 ASP cc_start: 0.5967 (p0) cc_final: 0.5737 (p0) REVERT: B 305 ASP cc_start: 0.8423 (m-30) cc_final: 0.7930 (m-30) REVERT: B 338 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8133 (mtp85) REVERT: B 341 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 342 LYS cc_start: 0.8558 (mptt) cc_final: 0.7858 (mptt) REVERT: B 343 MET cc_start: 0.8227 (tpt) cc_final: 0.6810 (tpt) REVERT: B 345 LYS cc_start: 0.8732 (pptt) cc_final: 0.8524 (pptt) REVERT: B 347 LYS cc_start: 0.8897 (mptt) cc_final: 0.8360 (mptt) REVERT: C 86 MET cc_start: 0.5558 (pmm) cc_final: 0.5200 (pmm) REVERT: C 158 GLN cc_start: 0.8081 (pm20) cc_final: 0.7607 (pm20) REVERT: C 167 TYR cc_start: 0.7556 (m-10) cc_final: 0.7115 (m-10) REVERT: C 171 GLN cc_start: 0.8428 (mm110) cc_final: 0.7894 (mp10) REVERT: C 212 MET cc_start: 0.7736 (mmp) cc_final: 0.7407 (mmp) REVERT: C 215 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7460 (tm-30) REVERT: C 239 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7714 (mtt90) REVERT: C 245 SER cc_start: 0.8257 (t) cc_final: 0.7840 (t) REVERT: C 248 MET cc_start: 0.7883 (mtp) cc_final: 0.7270 (mtp) REVERT: C 264 GLN cc_start: 0.8360 (mp10) cc_final: 0.7950 (mp10) REVERT: C 270 LYS cc_start: 0.8510 (mmmt) cc_final: 0.7653 (mmmt) REVERT: C 289 GLN cc_start: 0.8046 (mt0) cc_final: 0.7670 (mt0) REVERT: C 299 LEU cc_start: 0.8658 (mt) cc_final: 0.8309 (mt) REVERT: C 300 LYS cc_start: 0.8911 (tttt) cc_final: 0.8575 (tttt) REVERT: C 302 MET cc_start: 0.8088 (tmm) cc_final: 0.7746 (tmm) REVERT: C 304 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8006 (mtp85) REVERT: C 308 LEU cc_start: 0.8576 (tp) cc_final: 0.8306 (tp) REVERT: C 309 LEU cc_start: 0.8751 (tp) cc_final: 0.8403 (tp) REVERT: C 312 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.8010 (mtp-110) REVERT: C 313 GLU cc_start: 0.8160 (pt0) cc_final: 0.7902 (pt0) REVERT: C 335 ASP cc_start: 0.8079 (m-30) cc_final: 0.7819 (m-30) REVERT: C 343 MET cc_start: 0.8265 (tpt) cc_final: 0.7423 (tpt) REVERT: C 344 LYS cc_start: 0.9036 (mttm) cc_final: 0.8629 (mttm) REVERT: D 82 ASP cc_start: 0.8268 (t0) cc_final: 0.7920 (t70) REVERT: D 90 TRP cc_start: 0.8326 (m100) cc_final: 0.7727 (m100) REVERT: D 102 ASP cc_start: 0.8012 (m-30) cc_final: 0.7649 (m-30) REVERT: D 104 LYS cc_start: 0.8393 (tttt) cc_final: 0.8017 (ttmt) REVERT: D 139 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7336 (mtmm) REVERT: D 179 SER cc_start: 0.8068 (p) cc_final: 0.7794 (p) REVERT: D 183 LYS cc_start: 0.8523 (mptt) cc_final: 0.8122 (mptt) REVERT: D 212 MET cc_start: 0.7781 (mmp) cc_final: 0.7478 (mmp) REVERT: D 241 GLN cc_start: 0.8193 (mp-120) cc_final: 0.7206 (mm-40) REVERT: D 250 ARG cc_start: 0.7578 (ttt-90) cc_final: 0.7165 (ttt180) REVERT: D 251 MET cc_start: 0.7909 (mmt) cc_final: 0.7585 (mmt) REVERT: D 265 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7306 (ptp-170) REVERT: D 291 THR cc_start: 0.6665 (p) cc_final: 0.6295 (t) REVERT: D 300 LYS cc_start: 0.8565 (tptm) cc_final: 0.8247 (tptm) REVERT: D 302 MET cc_start: 0.7835 (tmm) cc_final: 0.7608 (tmm) REVERT: D 305 ASP cc_start: 0.7576 (t0) cc_final: 0.7189 (t0) REVERT: D 337 HIS cc_start: 0.7606 (m170) cc_final: 0.7340 (m90) REVERT: E 117 PHE cc_start: 0.6230 (m-80) cc_final: 0.5883 (m-80) REVERT: E 139 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7915 (pttm) REVERT: E 158 GLN cc_start: 0.8090 (pm20) cc_final: 0.7752 (pm20) REVERT: E 167 TYR cc_start: 0.7392 (m-10) cc_final: 0.6935 (m-10) REVERT: E 171 GLN cc_start: 0.8521 (mm110) cc_final: 0.8073 (mp10) REVERT: E 193 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7282 (mt-10) REVERT: E 205 ASP cc_start: 0.5515 (m-30) cc_final: 0.5272 (m-30) REVERT: E 212 MET cc_start: 0.7803 (mmp) cc_final: 0.7164 (mmp) REVERT: E 215 GLN cc_start: 0.7918 (tp-100) cc_final: 0.6958 (tm-30) REVERT: E 217 MET cc_start: 0.8566 (ptp) cc_final: 0.8205 (tpt) REVERT: E 248 MET cc_start: 0.7805 (mtp) cc_final: 0.7267 (mtp) REVERT: E 251 MET cc_start: 0.6935 (mpp) cc_final: 0.6217 (mpp) REVERT: E 256 HIS cc_start: 0.7772 (t70) cc_final: 0.7451 (t70) REVERT: E 264 GLN cc_start: 0.8535 (mp10) cc_final: 0.8214 (mp10) REVERT: E 266 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7551 (tm-30) REVERT: E 270 LYS cc_start: 0.8468 (mmmt) cc_final: 0.7388 (mmmt) REVERT: E 290 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 298 ASP cc_start: 0.7296 (m-30) cc_final: 0.6912 (m-30) REVERT: E 299 LEU cc_start: 0.8696 (mt) cc_final: 0.8309 (mt) REVERT: E 300 LYS cc_start: 0.8746 (tttt) cc_final: 0.8440 (tttt) REVERT: E 302 MET cc_start: 0.8137 (tmm) cc_final: 0.7818 (tmm) REVERT: E 304 ARG cc_start: 0.8559 (mtp-110) cc_final: 0.8276 (mmm-85) REVERT: E 313 GLU cc_start: 0.8400 (pt0) cc_final: 0.8152 (pt0) REVERT: E 335 ASP cc_start: 0.8369 (m-30) cc_final: 0.8047 (m-30) REVERT: E 336 LEU cc_start: 0.8854 (mp) cc_final: 0.8642 (mp) REVERT: E 341 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7704 (mm-30) REVERT: F 74 MET cc_start: 0.7655 (mtm) cc_final: 0.7263 (mtm) REVERT: F 82 ASP cc_start: 0.8372 (t0) cc_final: 0.8130 (t0) REVERT: F 90 TRP cc_start: 0.8272 (m100) cc_final: 0.7655 (m100) REVERT: F 102 ASP cc_start: 0.8042 (m-30) cc_final: 0.7740 (m-30) REVERT: F 104 LYS cc_start: 0.8396 (tttt) cc_final: 0.8002 (ttmt) REVERT: F 112 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7612 (mtmt) REVERT: F 124 GLN cc_start: 0.7580 (pp30) cc_final: 0.7258 (pp30) REVERT: F 131 LEU cc_start: 0.8501 (mp) cc_final: 0.8242 (mt) REVERT: F 180 LEU cc_start: 0.8152 (tt) cc_final: 0.7896 (tt) REVERT: F 183 LYS cc_start: 0.8564 (mptt) cc_final: 0.8091 (mptt) REVERT: F 211 MET cc_start: 0.7416 (mmp) cc_final: 0.7024 (mmp) REVERT: F 212 MET cc_start: 0.7992 (mmp) cc_final: 0.7656 (mmp) REVERT: F 215 GLN cc_start: 0.6977 (tp-100) cc_final: 0.6688 (tp-100) REVERT: F 217 MET cc_start: 0.7537 (mmt) cc_final: 0.6810 (mmt) REVERT: F 219 LEU cc_start: 0.7935 (mt) cc_final: 0.7331 (mt) REVERT: F 248 MET cc_start: 0.7141 (mtp) cc_final: 0.6641 (mtp) REVERT: F 270 LYS cc_start: 0.8414 (pttp) cc_final: 0.7978 (ptmm) REVERT: F 300 LYS cc_start: 0.8385 (tptm) cc_final: 0.7898 (tptm) REVERT: F 302 MET cc_start: 0.7819 (tmm) cc_final: 0.7506 (tmm) REVERT: F 304 ARG cc_start: 0.7300 (tpp-160) cc_final: 0.6907 (tpp-160) REVERT: F 308 LEU cc_start: 0.8264 (pp) cc_final: 0.7953 (pp) REVERT: F 332 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7810 (tp-100) REVERT: F 337 HIS cc_start: 0.7779 (m170) cc_final: 0.7446 (m170) outliers start: 2 outliers final: 2 residues processed: 618 average time/residue: 0.2751 time to fit residues: 237.6367 Evaluate side-chains 589 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 587 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 115 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124173 restraints weight = 30532.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128793 restraints weight = 18246.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132013 restraints weight = 12346.750| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14142 Z= 0.161 Angle : 0.628 12.467 19146 Z= 0.330 Chirality : 0.045 0.254 2190 Planarity : 0.005 0.053 2448 Dihedral : 11.395 107.411 1962 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1728 helix: 1.02 (0.16), residues: 966 sheet: 0.53 (0.40), residues: 192 loop : 0.39 (0.30), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 220 HIS 0.015 0.001 HIS B 337 PHE 0.027 0.002 PHE C 216 TYR 0.017 0.002 TYR A 72 ARG 0.009 0.001 ARG E 250 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 738) hydrogen bonds : angle 4.44403 ( 2052) covalent geometry : bond 0.00329 (14142) covalent geometry : angle 0.62789 (19146) *********************** 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 614 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 1.437 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: 0.8147 (mtm) cc_final: 0.7738 (mtm) REVERT: A 104 LYS cc_start: 0.8640 (tttt) cc_final: 0.8297 (tttt) REVERT: A 118 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 125 PRO cc_start: 0.8576 (Cg_endo) cc_final: 0.8111 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8303 (mp) cc_final: 0.7993 (tp) REVERT: A 146 THR cc_start: 0.8385 (p) cc_final: 0.8029 (p) REVERT: A 148 LYS cc_start: 0.8320 (tttt) cc_final: 0.7973 (ttmt) REVERT: A 157 LEU cc_start: 0.7997 (tp) cc_final: 0.7621 (tp) REVERT: A 158 GLN cc_start: 0.7272 (pm20) cc_final: 0.6858 (pm20) REVERT: A 179 SER cc_start: 0.8816 (t) cc_final: 0.8517 (p) REVERT: A 193 GLU cc_start: 0.7835 (tt0) cc_final: 0.7628 (tt0) REVERT: A 206 HIS cc_start: 0.8125 (p90) cc_final: 0.7482 (p90) REVERT: A 211 MET cc_start: 0.7928 (mmp) cc_final: 0.7343 (mmp) REVERT: A 212 MET cc_start: 0.7894 (mmp) cc_final: 0.7598 (mmp) REVERT: A 213 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7804 (mtmt) REVERT: A 215 GLN cc_start: 0.7679 (tp-100) cc_final: 0.6543 (tp-100) REVERT: A 217 MET cc_start: 0.7998 (mpp) cc_final: 0.7674 (mpp) REVERT: A 218 SER cc_start: 0.8663 (p) cc_final: 0.8208 (p) REVERT: A 219 LEU cc_start: 0.8783 (mt) cc_final: 0.7699 (mt) REVERT: A 243 LEU cc_start: 0.8373 (mt) cc_final: 0.8129 (mt) REVERT: A 250 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7769 (ttm170) REVERT: A 259 GLN cc_start: 0.7734 (mt0) cc_final: 0.7410 (mt0) REVERT: A 263 LYS cc_start: 0.7802 (mttp) cc_final: 0.7588 (mttp) REVERT: A 301 GLU cc_start: 0.8137 (tt0) cc_final: 0.7175 (tt0) REVERT: A 305 ASP cc_start: 0.8348 (t0) cc_final: 0.8090 (m-30) REVERT: A 338 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7767 (mtp85) REVERT: A 341 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 342 LYS cc_start: 0.8743 (mptt) cc_final: 0.8374 (mptt) REVERT: A 343 MET cc_start: 0.8106 (mmm) cc_final: 0.7724 (mmm) REVERT: B 74 MET cc_start: 0.8087 (mtm) cc_final: 0.7323 (mtm) REVERT: B 90 TRP cc_start: 0.8096 (m100) cc_final: 0.7228 (m100) REVERT: B 104 LYS cc_start: 0.8555 (tttt) cc_final: 0.8266 (tttt) REVERT: B 122 LEU cc_start: 0.8153 (tt) cc_final: 0.7927 (tp) REVERT: B 146 THR cc_start: 0.8306 (p) cc_final: 0.7754 (p) REVERT: B 154 PHE cc_start: 0.7676 (t80) cc_final: 0.7021 (t80) REVERT: B 157 LEU cc_start: 0.8080 (tp) cc_final: 0.7811 (tp) REVERT: B 158 GLN cc_start: 0.7267 (pm20) cc_final: 0.6884 (pm20) REVERT: B 167 TYR cc_start: 0.6843 (m-10) cc_final: 0.6616 (m-10) REVERT: B 211 MET cc_start: 0.8009 (mmp) cc_final: 0.7637 (mmp) REVERT: B 213 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7681 (mtmt) REVERT: B 215 GLN cc_start: 0.7518 (tp-100) cc_final: 0.6600 (tp-100) REVERT: B 217 MET cc_start: 0.8106 (mpp) cc_final: 0.7675 (mpp) REVERT: B 243 LEU cc_start: 0.8603 (mt) cc_final: 0.8298 (mt) REVERT: B 259 GLN cc_start: 0.7898 (mt0) cc_final: 0.7480 (mt0) REVERT: B 266 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7303 (tm-30) REVERT: B 273 LEU cc_start: 0.8087 (mm) cc_final: 0.7852 (mm) REVERT: B 283 ASP cc_start: 0.5985 (p0) cc_final: 0.5761 (p0) REVERT: B 338 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8123 (mtp85) REVERT: B 341 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 342 LYS cc_start: 0.8594 (mptt) cc_final: 0.7855 (mptt) REVERT: B 343 MET cc_start: 0.8258 (tpt) cc_final: 0.6828 (tpt) REVERT: B 344 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7308 (pttt) REVERT: B 345 LYS cc_start: 0.8744 (pptt) cc_final: 0.8523 (pptt) REVERT: B 347 LYS cc_start: 0.8909 (mptt) cc_final: 0.8368 (mptt) REVERT: C 86 MET cc_start: 0.5607 (pmm) cc_final: 0.5190 (pmm) REVERT: C 158 GLN cc_start: 0.7964 (pm20) cc_final: 0.7563 (pm20) REVERT: C 167 TYR cc_start: 0.7597 (m-10) cc_final: 0.7126 (m-10) REVERT: C 170 SER cc_start: 0.8044 (p) cc_final: 0.7419 (p) REVERT: C 171 GLN cc_start: 0.8444 (mm110) cc_final: 0.7938 (mp10) REVERT: C 212 MET cc_start: 0.7780 (mmp) cc_final: 0.7475 (mmp) REVERT: C 215 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7609 (tm-30) REVERT: C 219 LEU cc_start: 0.7296 (mt) cc_final: 0.7065 (mt) REVERT: C 245 SER cc_start: 0.8251 (t) cc_final: 0.7804 (t) REVERT: C 248 MET cc_start: 0.7897 (mtp) cc_final: 0.7289 (mtp) REVERT: C 262 LEU cc_start: 0.8785 (mm) cc_final: 0.8288 (mm) REVERT: C 264 GLN cc_start: 0.8380 (mp10) cc_final: 0.7943 (mp10) REVERT: C 265 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7576 (mtt180) REVERT: C 270 LYS cc_start: 0.8611 (mmmt) cc_final: 0.7733 (mmmt) REVERT: C 289 GLN cc_start: 0.8059 (mt0) cc_final: 0.7664 (mt0) REVERT: C 299 LEU cc_start: 0.8673 (mt) cc_final: 0.8315 (mt) REVERT: C 300 LYS cc_start: 0.8912 (tttt) cc_final: 0.8560 (tttt) REVERT: C 302 MET cc_start: 0.8217 (tmm) cc_final: 0.7881 (tmm) REVERT: C 304 ARG cc_start: 0.8525 (mtp85) cc_final: 0.7979 (mtp85) REVERT: C 309 LEU cc_start: 0.8712 (tp) cc_final: 0.8423 (tp) REVERT: C 313 GLU cc_start: 0.8245 (pt0) cc_final: 0.7897 (pt0) REVERT: C 343 MET cc_start: 0.8235 (tpt) cc_final: 0.7469 (tpt) REVERT: C 344 LYS cc_start: 0.9008 (mttm) cc_final: 0.8667 (mttm) REVERT: D 82 ASP cc_start: 0.8312 (t0) cc_final: 0.8063 (t70) REVERT: D 90 TRP cc_start: 0.8375 (m100) cc_final: 0.7792 (m100) REVERT: D 102 ASP cc_start: 0.8003 (m-30) cc_final: 0.7670 (m-30) REVERT: D 104 LYS cc_start: 0.8410 (tttt) cc_final: 0.8047 (ttmt) REVERT: D 139 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7329 (mtmm) REVERT: D 179 SER cc_start: 0.8120 (p) cc_final: 0.7877 (p) REVERT: D 183 LYS cc_start: 0.8497 (mptt) cc_final: 0.8121 (mptt) REVERT: D 211 MET cc_start: 0.7640 (mmp) cc_final: 0.7234 (mmp) REVERT: D 291 THR cc_start: 0.7035 (p) cc_final: 0.6788 (t) REVERT: D 300 LYS cc_start: 0.8580 (tptm) cc_final: 0.8257 (tptm) REVERT: D 302 MET cc_start: 0.7854 (tmm) cc_final: 0.7645 (tmm) REVERT: D 305 ASP cc_start: 0.7617 (t0) cc_final: 0.7295 (t0) REVERT: D 309 LEU cc_start: 0.8305 (tp) cc_final: 0.7951 (tp) REVERT: D 312 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7907 (ptp-170) REVERT: D 337 HIS cc_start: 0.7657 (m170) cc_final: 0.7310 (m90) REVERT: E 117 PHE cc_start: 0.6381 (m-80) cc_final: 0.5996 (m-80) REVERT: E 139 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7789 (ptpt) REVERT: E 158 GLN cc_start: 0.7928 (pm20) cc_final: 0.7577 (pm20) REVERT: E 171 GLN cc_start: 0.8538 (mm110) cc_final: 0.8116 (mp10) REVERT: E 193 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7306 (mt-10) REVERT: E 212 MET cc_start: 0.7844 (mmp) cc_final: 0.7256 (mmp) REVERT: E 215 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7117 (tm-30) REVERT: E 217 MET cc_start: 0.8558 (ptp) cc_final: 0.8202 (tpp) REVERT: E 248 MET cc_start: 0.7745 (mtp) cc_final: 0.7204 (mtp) REVERT: E 251 MET cc_start: 0.6837 (mpp) cc_final: 0.6212 (tpp) REVERT: E 256 HIS cc_start: 0.7706 (t70) cc_final: 0.7446 (t70) REVERT: E 264 GLN cc_start: 0.8524 (mp10) cc_final: 0.8208 (mp10) REVERT: E 266 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7541 (tm-30) REVERT: E 270 LYS cc_start: 0.8518 (mmmt) cc_final: 0.7438 (mmmt) REVERT: E 290 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7771 (mm-30) REVERT: E 298 ASP cc_start: 0.7340 (m-30) cc_final: 0.6902 (m-30) REVERT: E 299 LEU cc_start: 0.8679 (mt) cc_final: 0.8329 (mt) REVERT: E 300 LYS cc_start: 0.8703 (tttt) cc_final: 0.8409 (tttt) REVERT: E 302 MET cc_start: 0.8183 (tmm) cc_final: 0.7899 (tmm) REVERT: E 304 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.8229 (mmm-85) REVERT: E 313 GLU cc_start: 0.8513 (pt0) cc_final: 0.8236 (pt0) REVERT: E 335 ASP cc_start: 0.8391 (m-30) cc_final: 0.8121 (m-30) REVERT: E 336 LEU cc_start: 0.8882 (mp) cc_final: 0.8644 (mp) REVERT: E 341 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7700 (mm-30) REVERT: F 68 LYS cc_start: 0.7542 (mppt) cc_final: 0.7069 (mppt) REVERT: F 74 MET cc_start: 0.7671 (mtm) cc_final: 0.7248 (mtm) REVERT: F 82 ASP cc_start: 0.8422 (t0) cc_final: 0.8211 (t0) REVERT: F 91 SER cc_start: 0.8787 (m) cc_final: 0.8358 (p) REVERT: F 102 ASP cc_start: 0.8053 (m-30) cc_final: 0.7720 (m-30) REVERT: F 104 LYS cc_start: 0.8417 (tttt) cc_final: 0.8084 (ttmt) REVERT: F 112 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7608 (mtmt) REVERT: F 124 GLN cc_start: 0.7579 (pp30) cc_final: 0.7223 (pp30) REVERT: F 131 LEU cc_start: 0.8465 (mp) cc_final: 0.8160 (mt) REVERT: F 183 LYS cc_start: 0.8524 (mptt) cc_final: 0.8151 (mptt) REVERT: F 211 MET cc_start: 0.7461 (mmp) cc_final: 0.7035 (mmp) REVERT: F 212 MET cc_start: 0.8045 (mmp) cc_final: 0.7673 (mmp) REVERT: F 215 GLN cc_start: 0.6976 (tp-100) cc_final: 0.6747 (tp-100) REVERT: F 219 LEU cc_start: 0.7961 (mt) cc_final: 0.7361 (mt) REVERT: F 248 MET cc_start: 0.7256 (mtp) cc_final: 0.6740 (mtp) REVERT: F 250 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7448 (ttt-90) REVERT: F 263 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7665 (mmmm) REVERT: F 265 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7193 (ptp-170) REVERT: F 270 LYS cc_start: 0.8418 (pttp) cc_final: 0.7986 (ptmm) REVERT: F 300 LYS cc_start: 0.8407 (tptm) cc_final: 0.7912 (tptm) REVERT: F 302 MET cc_start: 0.7808 (tmm) cc_final: 0.7446 (tmm) REVERT: F 304 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6639 (tpp-160) REVERT: F 308 LEU cc_start: 0.8293 (pp) cc_final: 0.7955 (pp) REVERT: F 332 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7681 (mm-40) REVERT: F 337 HIS cc_start: 0.7854 (m170) cc_final: 0.7500 (m170) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.2779 time to fit residues: 238.7010 Evaluate side-chains 593 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 118 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 132 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 58 optimal weight: 30.0000 chunk 67 optimal weight: 0.4980 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.154033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126702 restraints weight = 30053.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131422 restraints weight = 17990.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134709 restraints weight = 12155.355| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14142 Z= 0.122 Angle : 0.600 13.147 19146 Z= 0.310 Chirality : 0.043 0.211 2190 Planarity : 0.004 0.051 2448 Dihedral : 11.223 108.290 1962 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1728 helix: 1.08 (0.16), residues: 990 sheet: 0.48 (0.40), residues: 192 loop : 0.64 (0.31), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 220 HIS 0.012 0.001 HIS A 337 PHE 0.029 0.002 PHE C 216 TYR 0.016 0.002 TYR A 72 ARG 0.009 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 738) hydrogen bonds : angle 4.32845 ( 2052) covalent geometry : bond 0.00260 (14142) covalent geometry : angle 0.59973 (19146) *********************** 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 611 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 611 time to evaluate : 1.536 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: 0.8097 (mtm) cc_final: 0.7586 (mtm) REVERT: A 118 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 124 GLN cc_start: 0.8191 (pp30) cc_final: 0.7928 (pp30) REVERT: A 125 PRO cc_start: 0.8545 (Cg_endo) cc_final: 0.8110 (Cg_exo) REVERT: A 148 LYS cc_start: 0.7974 (tttt) cc_final: 0.7755 (ttmt) REVERT: A 157 LEU cc_start: 0.7934 (tp) cc_final: 0.7575 (tp) REVERT: A 167 TYR cc_start: 0.6700 (m-10) cc_final: 0.6108 (m-10) REVERT: A 169 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 179 SER cc_start: 0.8774 (t) cc_final: 0.8487 (p) REVERT: A 199 ARG cc_start: 0.7404 (tpp80) cc_final: 0.6329 (tpp80) REVERT: A 206 HIS cc_start: 0.8076 (p90) cc_final: 0.7397 (p90) REVERT: A 211 MET cc_start: 0.7961 (mmp) cc_final: 0.7345 (mmp) REVERT: A 212 MET cc_start: 0.7895 (mmp) cc_final: 0.7612 (mmp) REVERT: A 213 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7753 (mtmt) REVERT: A 215 GLN cc_start: 0.7723 (tp-100) cc_final: 0.6584 (tp-100) REVERT: A 217 MET cc_start: 0.8028 (mpp) cc_final: 0.7611 (mpp) REVERT: A 218 SER cc_start: 0.8613 (p) cc_final: 0.8174 (p) REVERT: A 219 LEU cc_start: 0.8790 (mt) cc_final: 0.7697 (mt) REVERT: A 243 LEU cc_start: 0.8371 (mt) cc_final: 0.8115 (mt) REVERT: A 250 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7601 (ttm170) REVERT: A 251 MET cc_start: 0.7900 (mmm) cc_final: 0.7640 (mmm) REVERT: A 259 GLN cc_start: 0.7688 (mt0) cc_final: 0.7337 (mt0) REVERT: A 266 GLU cc_start: 0.7822 (tp30) cc_final: 0.7432 (tp30) REVERT: A 270 LYS cc_start: 0.8303 (mmpt) cc_final: 0.7976 (mmtt) REVERT: A 301 GLU cc_start: 0.8107 (tt0) cc_final: 0.7088 (tt0) REVERT: A 305 ASP cc_start: 0.8299 (t0) cc_final: 0.7874 (m-30) REVERT: A 338 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7866 (mtp85) REVERT: A 341 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 342 LYS cc_start: 0.8723 (mptt) cc_final: 0.8113 (mptt) REVERT: A 343 MET cc_start: 0.8091 (mmm) cc_final: 0.7682 (mmm) REVERT: A 345 LYS cc_start: 0.8723 (pptt) cc_final: 0.8504 (pptt) REVERT: B 74 MET cc_start: 0.8071 (mtm) cc_final: 0.7356 (mtm) REVERT: B 90 TRP cc_start: 0.7958 (m100) cc_final: 0.6949 (m100) REVERT: B 96 LEU cc_start: 0.7620 (mt) cc_final: 0.7318 (mm) REVERT: B 104 LYS cc_start: 0.8603 (tttt) cc_final: 0.8223 (tttt) REVERT: B 144 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8267 (mtpt) REVERT: B 146 THR cc_start: 0.8315 (p) cc_final: 0.7648 (p) REVERT: B 148 LYS cc_start: 0.8254 (tttt) cc_final: 0.7807 (ttmt) REVERT: B 154 PHE cc_start: 0.7715 (t80) cc_final: 0.7088 (t80) REVERT: B 157 LEU cc_start: 0.8078 (tp) cc_final: 0.7699 (tp) REVERT: B 158 GLN cc_start: 0.7193 (pm20) cc_final: 0.6635 (pm20) REVERT: B 211 MET cc_start: 0.8044 (mmp) cc_final: 0.7663 (mmp) REVERT: B 213 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7664 (mtmt) REVERT: B 215 GLN cc_start: 0.7504 (tp-100) cc_final: 0.6223 (tp-100) REVERT: B 217 MET cc_start: 0.8139 (mpp) cc_final: 0.7364 (mpp) REVERT: B 219 LEU cc_start: 0.8767 (mt) cc_final: 0.7595 (mt) REVERT: B 259 GLN cc_start: 0.7905 (mt0) cc_final: 0.7461 (mt0) REVERT: B 266 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7047 (tm-30) REVERT: B 270 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7821 (mptt) REVERT: B 273 LEU cc_start: 0.8024 (mm) cc_final: 0.7768 (mm) REVERT: B 283 ASP cc_start: 0.5748 (p0) cc_final: 0.5527 (p0) REVERT: B 305 ASP cc_start: 0.8308 (m-30) cc_final: 0.7610 (m-30) REVERT: B 338 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8124 (mtp85) REVERT: B 341 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 342 LYS cc_start: 0.8540 (mptt) cc_final: 0.7879 (mptt) REVERT: B 343 MET cc_start: 0.8248 (tpt) cc_final: 0.6812 (tpt) REVERT: B 345 LYS cc_start: 0.8721 (pptt) cc_final: 0.8492 (pptt) REVERT: B 347 LYS cc_start: 0.8906 (mptt) cc_final: 0.8401 (mptt) REVERT: C 167 TYR cc_start: 0.7498 (m-10) cc_final: 0.7028 (m-10) REVERT: C 170 SER cc_start: 0.8142 (p) cc_final: 0.7603 (p) REVERT: C 171 GLN cc_start: 0.8523 (mm110) cc_final: 0.8085 (mp10) REVERT: C 212 MET cc_start: 0.7773 (mmp) cc_final: 0.7477 (mmp) REVERT: C 215 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7575 (tm-30) REVERT: C 219 LEU cc_start: 0.7192 (mt) cc_final: 0.6878 (mt) REVERT: C 245 SER cc_start: 0.8288 (t) cc_final: 0.8042 (t) REVERT: C 248 MET cc_start: 0.7793 (mtp) cc_final: 0.7152 (mtp) REVERT: C 262 LEU cc_start: 0.8695 (mm) cc_final: 0.8169 (mm) REVERT: C 264 GLN cc_start: 0.8365 (mp10) cc_final: 0.7920 (mp10) REVERT: C 265 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7523 (mtt180) REVERT: C 270 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7728 (mmmt) REVERT: C 289 GLN cc_start: 0.7990 (mt0) cc_final: 0.7630 (mt0) REVERT: C 299 LEU cc_start: 0.8650 (mt) cc_final: 0.8277 (mt) REVERT: C 300 LYS cc_start: 0.8859 (tttt) cc_final: 0.8505 (tttt) REVERT: C 302 MET cc_start: 0.8167 (tmm) cc_final: 0.7849 (tmm) REVERT: C 304 ARG cc_start: 0.8445 (mtp85) cc_final: 0.7893 (mtp85) REVERT: C 309 LEU cc_start: 0.8647 (tp) cc_final: 0.8404 (tp) REVERT: C 313 GLU cc_start: 0.8198 (pt0) cc_final: 0.7816 (pt0) REVERT: C 343 MET cc_start: 0.8156 (tpt) cc_final: 0.7539 (tpt) REVERT: C 344 LYS cc_start: 0.8936 (mttm) cc_final: 0.8590 (mttm) REVERT: C 347 LYS cc_start: 0.7961 (mppt) cc_final: 0.7723 (mmtt) REVERT: D 82 ASP cc_start: 0.8207 (t0) cc_final: 0.7924 (t70) REVERT: D 90 TRP cc_start: 0.8379 (m100) cc_final: 0.7758 (m100) REVERT: D 104 LYS cc_start: 0.8390 (tttt) cc_final: 0.8032 (ttmt) REVERT: D 139 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7443 (mtmm) REVERT: D 179 SER cc_start: 0.8068 (p) cc_final: 0.7826 (p) REVERT: D 180 LEU cc_start: 0.8033 (tt) cc_final: 0.7818 (tt) REVERT: D 183 LYS cc_start: 0.8467 (mptt) cc_final: 0.8080 (mptt) REVERT: D 212 MET cc_start: 0.8085 (mmp) cc_final: 0.7547 (mmp) REVERT: D 213 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7554 (mtmm) REVERT: D 217 MET cc_start: 0.7294 (mmm) cc_final: 0.6737 (mmm) REVERT: D 250 ARG cc_start: 0.7726 (ttt-90) cc_final: 0.7498 (ttt180) REVERT: D 251 MET cc_start: 0.7984 (mmt) cc_final: 0.7646 (mmt) REVERT: D 300 LYS cc_start: 0.8571 (tptm) cc_final: 0.8230 (tptm) REVERT: D 305 ASP cc_start: 0.7502 (t0) cc_final: 0.7191 (t0) REVERT: D 309 LEU cc_start: 0.8307 (tp) cc_final: 0.7954 (tp) REVERT: D 337 HIS cc_start: 0.7714 (m170) cc_final: 0.7422 (m90) REVERT: E 139 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7902 (ptpt) REVERT: E 158 GLN cc_start: 0.7920 (pm20) cc_final: 0.7517 (pm20) REVERT: E 171 GLN cc_start: 0.8549 (mm110) cc_final: 0.8152 (mp10) REVERT: E 193 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7263 (mt-10) REVERT: E 212 MET cc_start: 0.7855 (mmp) cc_final: 0.7259 (mmp) REVERT: E 213 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7902 (mtmm) REVERT: E 215 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7154 (tm-30) REVERT: E 217 MET cc_start: 0.8494 (ptp) cc_final: 0.8260 (mmm) REVERT: E 239 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7290 (ttp-110) REVERT: E 248 MET cc_start: 0.7720 (mtp) cc_final: 0.7159 (mtp) REVERT: E 250 ARG cc_start: 0.5817 (mmm160) cc_final: 0.5507 (tpt90) REVERT: E 251 MET cc_start: 0.6741 (mpp) cc_final: 0.6045 (tpp) REVERT: E 256 HIS cc_start: 0.7677 (t70) cc_final: 0.7435 (t70) REVERT: E 264 GLN cc_start: 0.8512 (mp10) cc_final: 0.8193 (mp10) REVERT: E 266 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7569 (tm-30) REVERT: E 270 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7442 (mmmt) REVERT: E 290 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7759 (mm-30) REVERT: E 298 ASP cc_start: 0.7287 (m-30) cc_final: 0.6972 (m-30) REVERT: E 299 LEU cc_start: 0.8638 (mt) cc_final: 0.8323 (mt) REVERT: E 300 LYS cc_start: 0.8651 (tttt) cc_final: 0.8347 (tttt) REVERT: E 301 GLU cc_start: 0.8405 (tt0) cc_final: 0.8056 (tt0) REVERT: E 302 MET cc_start: 0.8112 (tmm) cc_final: 0.7843 (tmm) REVERT: E 304 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8248 (mmm-85) REVERT: E 313 GLU cc_start: 0.8519 (pt0) cc_final: 0.8236 (pt0) REVERT: E 335 ASP cc_start: 0.8327 (m-30) cc_final: 0.8075 (m-30) REVERT: E 341 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7660 (mm-30) REVERT: E 343 MET cc_start: 0.8024 (mmp) cc_final: 0.7586 (mmp) REVERT: F 68 LYS cc_start: 0.7540 (mppt) cc_final: 0.7126 (mppt) REVERT: F 74 MET cc_start: 0.7658 (mtm) cc_final: 0.7224 (mtm) REVERT: F 82 ASP cc_start: 0.8361 (t0) cc_final: 0.8158 (t0) REVERT: F 102 ASP cc_start: 0.8026 (m-30) cc_final: 0.7642 (m-30) REVERT: F 104 LYS cc_start: 0.8395 (tttt) cc_final: 0.8047 (ttmt) REVERT: F 112 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7527 (mtmt) REVERT: F 124 GLN cc_start: 0.7543 (pp30) cc_final: 0.7173 (pp30) REVERT: F 125 PRO cc_start: 0.7929 (Cg_endo) cc_final: 0.7534 (Cg_exo) REVERT: F 131 LEU cc_start: 0.8425 (mp) cc_final: 0.8220 (mt) REVERT: F 180 LEU cc_start: 0.8292 (tt) cc_final: 0.8070 (tt) REVERT: F 183 LYS cc_start: 0.8526 (mptt) cc_final: 0.8195 (mptt) REVERT: F 211 MET cc_start: 0.7488 (mmp) cc_final: 0.7052 (mmp) REVERT: F 212 MET cc_start: 0.8013 (mmp) cc_final: 0.7701 (mmp) REVERT: F 219 LEU cc_start: 0.7907 (mt) cc_final: 0.7247 (mt) REVERT: F 251 MET cc_start: 0.7810 (mpp) cc_final: 0.6846 (mpp) REVERT: F 263 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7702 (mmmm) REVERT: F 265 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7033 (ptp-110) REVERT: F 270 LYS cc_start: 0.8374 (pttp) cc_final: 0.7909 (ptmm) REVERT: F 298 ASP cc_start: 0.8144 (m-30) cc_final: 0.7937 (m-30) REVERT: F 300 LYS cc_start: 0.8399 (tptm) cc_final: 0.7929 (tptm) REVERT: F 302 MET cc_start: 0.7756 (tmm) cc_final: 0.7470 (tmm) REVERT: F 337 HIS cc_start: 0.7735 (m170) cc_final: 0.7375 (m170) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.2798 time to fit residues: 239.6530 Evaluate side-chains 593 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.154161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127072 restraints weight = 29536.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131681 restraints weight = 17662.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134979 restraints weight = 11991.676| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14142 Z= 0.118 Angle : 0.601 13.522 19146 Z= 0.310 Chirality : 0.043 0.195 2190 Planarity : 0.004 0.050 2448 Dihedral : 11.143 108.782 1962 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1728 helix: 1.01 (0.16), residues: 1026 sheet: 0.51 (0.40), residues: 192 loop : 0.59 (0.32), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 220 HIS 0.012 0.001 HIS B 337 PHE 0.033 0.002 PHE B 216 TYR 0.013 0.002 TYR A 72 ARG 0.011 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 738) hydrogen bonds : angle 4.21744 ( 2052) covalent geometry : bond 0.00251 (14142) covalent geometry : angle 0.60144 (19146) *********************** 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 593 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.404 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: 0.8169 (mtm) cc_final: 0.7671 (mtm) REVERT: A 109 LEU cc_start: 0.8458 (mt) cc_final: 0.8228 (mm) REVERT: A 123 LEU cc_start: 0.8440 (tp) cc_final: 0.8218 (tp) REVERT: A 124 GLN cc_start: 0.8210 (pp30) cc_final: 0.7989 (pp30) REVERT: A 125 PRO cc_start: 0.8513 (Cg_endo) cc_final: 0.8053 (Cg_exo) REVERT: A 157 LEU cc_start: 0.7918 (tp) cc_final: 0.7515 (tp) REVERT: A 158 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 167 TYR cc_start: 0.6774 (m-10) cc_final: 0.6230 (m-10) REVERT: A 169 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 178 PHE cc_start: 0.8913 (m-10) cc_final: 0.8499 (m-10) REVERT: A 179 SER cc_start: 0.8787 (t) cc_final: 0.8462 (p) REVERT: A 199 ARG cc_start: 0.7364 (tpp80) cc_final: 0.6332 (tpp80) REVERT: A 206 HIS cc_start: 0.8053 (p90) cc_final: 0.7381 (p90) REVERT: A 211 MET cc_start: 0.8014 (mmp) cc_final: 0.7409 (mmp) REVERT: A 212 MET cc_start: 0.7813 (mmp) cc_final: 0.7568 (mmp) REVERT: A 213 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7726 (mtmt) REVERT: A 215 GLN cc_start: 0.7716 (tp-100) cc_final: 0.6829 (tp-100) REVERT: A 217 MET cc_start: 0.7945 (mpp) cc_final: 0.7503 (mpp) REVERT: A 250 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7536 (ttm170) REVERT: A 251 MET cc_start: 0.7846 (mmm) cc_final: 0.7629 (mmm) REVERT: A 259 GLN cc_start: 0.7689 (mt0) cc_final: 0.7381 (mt0) REVERT: A 262 LEU cc_start: 0.8181 (tp) cc_final: 0.7909 (mm) REVERT: A 266 GLU cc_start: 0.7834 (tp30) cc_final: 0.7456 (tp30) REVERT: A 270 LYS cc_start: 0.8339 (mmpt) cc_final: 0.7998 (mmtt) REVERT: A 283 ASP cc_start: 0.6720 (p0) cc_final: 0.6502 (p0) REVERT: A 300 LYS cc_start: 0.8515 (tptm) cc_final: 0.8195 (tttm) REVERT: A 301 GLU cc_start: 0.8085 (tt0) cc_final: 0.7471 (tt0) REVERT: A 304 ARG cc_start: 0.7740 (mmp-170) cc_final: 0.7274 (mmm160) REVERT: A 338 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7885 (mtp85) REVERT: A 341 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 342 LYS cc_start: 0.8769 (mptt) cc_final: 0.8085 (mptt) REVERT: A 343 MET cc_start: 0.8098 (mmm) cc_final: 0.7611 (mmm) REVERT: A 345 LYS cc_start: 0.8730 (pptt) cc_final: 0.8502 (pptt) REVERT: B 74 MET cc_start: 0.8076 (mtm) cc_final: 0.7354 (mtm) REVERT: B 90 TRP cc_start: 0.7995 (m100) cc_final: 0.7035 (m100) REVERT: B 92 ASP cc_start: 0.7495 (m-30) cc_final: 0.7287 (m-30) REVERT: B 104 LYS cc_start: 0.8617 (tttt) cc_final: 0.8260 (tttt) REVERT: B 144 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8211 (mtpt) REVERT: B 146 THR cc_start: 0.8304 (p) cc_final: 0.7678 (p) REVERT: B 148 LYS cc_start: 0.8305 (tttt) cc_final: 0.8016 (ttmt) REVERT: B 152 CYS cc_start: 0.7412 (p) cc_final: 0.6988 (m) REVERT: B 154 PHE cc_start: 0.7759 (t80) cc_final: 0.7140 (t80) REVERT: B 157 LEU cc_start: 0.8062 (tp) cc_final: 0.7660 (tp) REVERT: B 158 GLN cc_start: 0.7295 (pm20) cc_final: 0.6473 (pm20) REVERT: B 211 MET cc_start: 0.8038 (mmp) cc_final: 0.7649 (mmp) REVERT: B 213 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7684 (mtmt) REVERT: B 215 GLN cc_start: 0.7399 (tp-100) cc_final: 0.6014 (tp-100) REVERT: B 217 MET cc_start: 0.8104 (mpp) cc_final: 0.7554 (mpp) REVERT: B 219 LEU cc_start: 0.8768 (mt) cc_final: 0.7491 (mt) REVERT: B 245 SER cc_start: 0.8583 (p) cc_final: 0.8302 (t) REVERT: B 250 ARG cc_start: 0.7508 (mtt180) cc_final: 0.7198 (mtm180) REVERT: B 259 GLN cc_start: 0.7753 (mt0) cc_final: 0.7311 (mt0) REVERT: B 266 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 270 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7840 (mptt) REVERT: B 273 LEU cc_start: 0.8046 (mm) cc_final: 0.7836 (mm) REVERT: B 283 ASP cc_start: 0.5871 (p0) cc_final: 0.5631 (p0) REVERT: B 305 ASP cc_start: 0.8319 (m-30) cc_final: 0.7653 (m-30) REVERT: B 338 ARG cc_start: 0.8408 (mtp85) cc_final: 0.7975 (mmm-85) REVERT: B 341 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7032 (mm-30) REVERT: B 342 LYS cc_start: 0.8561 (mptt) cc_final: 0.7682 (mptt) REVERT: B 343 MET cc_start: 0.8221 (tpt) cc_final: 0.6815 (tpt) REVERT: B 344 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7274 (pttt) REVERT: B 345 LYS cc_start: 0.8729 (pptt) cc_final: 0.8345 (pptt) REVERT: B 347 LYS cc_start: 0.8893 (mptt) cc_final: 0.8395 (mptt) REVERT: C 167 TYR cc_start: 0.7430 (m-10) cc_final: 0.7131 (m-10) REVERT: C 171 GLN cc_start: 0.8524 (mm110) cc_final: 0.7999 (mp10) REVERT: C 212 MET cc_start: 0.7758 (mmp) cc_final: 0.7443 (mmp) REVERT: C 215 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7592 (tm-30) REVERT: C 219 LEU cc_start: 0.7227 (mt) cc_final: 0.6886 (mt) REVERT: C 239 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7049 (ttm110) REVERT: C 248 MET cc_start: 0.7699 (mtp) cc_final: 0.7076 (mtp) REVERT: C 250 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6664 (mmm160) REVERT: C 264 GLN cc_start: 0.8390 (mp10) cc_final: 0.7929 (mp10) REVERT: C 270 LYS cc_start: 0.8614 (mmmt) cc_final: 0.7719 (mmmt) REVERT: C 289 GLN cc_start: 0.8019 (mt0) cc_final: 0.7685 (mt0) REVERT: C 299 LEU cc_start: 0.8620 (mt) cc_final: 0.8099 (mt) REVERT: C 300 LYS cc_start: 0.8846 (tttt) cc_final: 0.8493 (tttt) REVERT: C 302 MET cc_start: 0.8188 (tmm) cc_final: 0.7928 (tmm) REVERT: C 303 CYS cc_start: 0.8682 (m) cc_final: 0.8117 (m) REVERT: C 304 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7919 (mtp85) REVERT: C 313 GLU cc_start: 0.8196 (pt0) cc_final: 0.7840 (pt0) REVERT: C 335 ASP cc_start: 0.8413 (m-30) cc_final: 0.8133 (m-30) REVERT: C 343 MET cc_start: 0.8150 (tpt) cc_final: 0.7537 (tpt) REVERT: C 344 LYS cc_start: 0.8936 (mttm) cc_final: 0.8585 (mttm) REVERT: D 82 ASP cc_start: 0.8308 (t0) cc_final: 0.7952 (t70) REVERT: D 90 TRP cc_start: 0.8369 (m100) cc_final: 0.7710 (m100) REVERT: D 104 LYS cc_start: 0.8380 (tttt) cc_final: 0.8055 (ttmt) REVERT: D 139 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7508 (mtmm) REVERT: D 183 LYS cc_start: 0.8484 (mptt) cc_final: 0.8084 (mptt) REVERT: D 212 MET cc_start: 0.8040 (mmp) cc_final: 0.7560 (mmp) REVERT: D 213 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7544 (mtmm) REVERT: D 217 MET cc_start: 0.7295 (mmm) cc_final: 0.6743 (mmm) REVERT: D 250 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7174 (ttt180) REVERT: D 251 MET cc_start: 0.8013 (mmt) cc_final: 0.7647 (mmt) REVERT: D 300 LYS cc_start: 0.8496 (tptm) cc_final: 0.8126 (tptm) REVERT: D 305 ASP cc_start: 0.7552 (t0) cc_final: 0.7218 (t0) REVERT: D 309 LEU cc_start: 0.8304 (tp) cc_final: 0.7991 (tp) REVERT: D 312 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7936 (ptp-170) REVERT: D 317 SER cc_start: 0.8912 (m) cc_final: 0.8552 (p) REVERT: D 336 LEU cc_start: 0.7507 (pp) cc_final: 0.7293 (pp) REVERT: D 337 HIS cc_start: 0.7667 (m170) cc_final: 0.7239 (m90) REVERT: E 139 LYS cc_start: 0.8436 (ptpp) cc_final: 0.7984 (ptpt) REVERT: E 158 GLN cc_start: 0.7951 (pm20) cc_final: 0.7518 (pm20) REVERT: E 171 GLN cc_start: 0.8530 (mm110) cc_final: 0.8164 (mp10) REVERT: E 193 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7218 (mt-10) REVERT: E 212 MET cc_start: 0.7871 (mmp) cc_final: 0.7234 (mmp) REVERT: E 213 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7429 (mtmm) REVERT: E 215 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7071 (tm-30) REVERT: E 217 MET cc_start: 0.8419 (ptp) cc_final: 0.8163 (tpp) REVERT: E 239 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7260 (ttp-110) REVERT: E 248 MET cc_start: 0.7624 (mtp) cc_final: 0.7245 (mtp) REVERT: E 250 ARG cc_start: 0.5494 (mmm160) cc_final: 0.5003 (tpt90) REVERT: E 251 MET cc_start: 0.6608 (mpp) cc_final: 0.6151 (mpp) REVERT: E 256 HIS cc_start: 0.7655 (t70) cc_final: 0.7419 (t70) REVERT: E 264 GLN cc_start: 0.8463 (mp10) cc_final: 0.8170 (mp10) REVERT: E 266 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7562 (tm-30) REVERT: E 270 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7473 (mmmt) REVERT: E 290 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7702 (mm-30) REVERT: E 295 SER cc_start: 0.7726 (p) cc_final: 0.7364 (p) REVERT: E 299 LEU cc_start: 0.8645 (mt) cc_final: 0.8252 (mt) REVERT: E 300 LYS cc_start: 0.8635 (tttt) cc_final: 0.8337 (tttt) REVERT: E 301 GLU cc_start: 0.8427 (tt0) cc_final: 0.8079 (tt0) REVERT: E 303 CYS cc_start: 0.8630 (m) cc_final: 0.8044 (m) REVERT: E 304 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8278 (mmm-85) REVERT: E 313 GLU cc_start: 0.8518 (pt0) cc_final: 0.8233 (pt0) REVERT: E 335 ASP cc_start: 0.8312 (m-30) cc_final: 0.8006 (m-30) REVERT: E 341 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7638 (mm-30) REVERT: E 343 MET cc_start: 0.8044 (mmp) cc_final: 0.7566 (mmp) REVERT: F 68 LYS cc_start: 0.7531 (mppt) cc_final: 0.7107 (mppt) REVERT: F 74 MET cc_start: 0.7683 (mtm) cc_final: 0.7228 (mtm) REVERT: F 82 ASP cc_start: 0.8366 (t0) cc_final: 0.8157 (t70) REVERT: F 102 ASP cc_start: 0.8006 (m-30) cc_final: 0.7641 (m-30) REVERT: F 104 LYS cc_start: 0.8330 (tttt) cc_final: 0.7992 (ttmt) REVERT: F 112 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7457 (mtmt) REVERT: F 124 GLN cc_start: 0.7550 (pp30) cc_final: 0.7169 (pp30) REVERT: F 125 PRO cc_start: 0.7765 (Cg_endo) cc_final: 0.7373 (Cg_exo) REVERT: F 131 LEU cc_start: 0.8414 (mp) cc_final: 0.8119 (mt) REVERT: F 180 LEU cc_start: 0.8328 (tt) cc_final: 0.8072 (tt) REVERT: F 183 LYS cc_start: 0.8534 (mptt) cc_final: 0.8170 (mptt) REVERT: F 211 MET cc_start: 0.7562 (mmp) cc_final: 0.7081 (mmp) REVERT: F 212 MET cc_start: 0.8058 (mmp) cc_final: 0.7695 (mmp) REVERT: F 219 LEU cc_start: 0.7963 (mt) cc_final: 0.7322 (mt) REVERT: F 244 ASP cc_start: 0.7733 (p0) cc_final: 0.7525 (p0) REVERT: F 248 MET cc_start: 0.7167 (mtp) cc_final: 0.6748 (mtp) REVERT: F 250 ARG cc_start: 0.7798 (ttt-90) cc_final: 0.7524 (ttt180) REVERT: F 251 MET cc_start: 0.7752 (mpp) cc_final: 0.7507 (mpp) REVERT: F 263 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7678 (mmmm) REVERT: F 270 LYS cc_start: 0.8375 (pttp) cc_final: 0.7939 (ptmm) REVERT: F 298 ASP cc_start: 0.8123 (m-30) cc_final: 0.7920 (m-30) REVERT: F 300 LYS cc_start: 0.8448 (tptm) cc_final: 0.7985 (tptm) REVERT: F 302 MET cc_start: 0.7765 (tmm) cc_final: 0.7501 (tmm) REVERT: F 337 HIS cc_start: 0.7716 (m170) cc_final: 0.7326 (m170) outliers start: 0 outliers final: 0 residues processed: 593 average time/residue: 0.3033 time to fit residues: 254.3853 Evaluate side-chains 580 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 164 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 0.0040 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 161 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 GLN ** 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 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126595 restraints weight = 29662.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131219 restraints weight = 17761.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134464 restraints weight = 11976.340| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14142 Z= 0.122 Angle : 0.603 13.911 19146 Z= 0.311 Chirality : 0.043 0.200 2190 Planarity : 0.004 0.050 2448 Dihedral : 11.115 108.574 1962 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1728 helix: 1.09 (0.16), residues: 1026 sheet: 0.47 (0.40), residues: 192 loop : 0.60 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 220 HIS 0.012 0.001 HIS E 337 PHE 0.041 0.002 PHE D 216 TYR 0.024 0.002 TYR F 72 ARG 0.008 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 738) hydrogen bonds : angle 4.17521 ( 2052) covalent geometry : bond 0.00261 (14142) covalent geometry : angle 0.60256 (19146) *********************** 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 593 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.526 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: A 74 MET cc_start: 0.8194 (mtm) cc_final: 0.7659 (mtm) REVERT: A 109 LEU cc_start: 0.8456 (mt) cc_final: 0.8226 (mm) REVERT: A 123 LEU cc_start: 0.8457 (tp) cc_final: 0.8243 (tp) REVERT: A 124 GLN cc_start: 0.8189 (pp30) cc_final: 0.7964 (pp30) REVERT: A 125 PRO cc_start: 0.8506 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: A 157 LEU cc_start: 0.8013 (tp) cc_final: 0.7519 (tt) REVERT: A 158 GLN cc_start: 0.7382 (tm-30) cc_final: 0.7097 (tm-30) REVERT: A 167 TYR cc_start: 0.6747 (m-10) cc_final: 0.6309 (m-10) REVERT: A 178 PHE cc_start: 0.8927 (m-10) cc_final: 0.8559 (m-10) REVERT: A 179 SER cc_start: 0.8783 (t) cc_final: 0.8451 (p) REVERT: A 199 ARG cc_start: 0.7390 (tpp80) cc_final: 0.6345 (tpp80) REVERT: A 206 HIS cc_start: 0.8054 (p90) cc_final: 0.7423 (p90) REVERT: A 211 MET cc_start: 0.8027 (mmp) cc_final: 0.7464 (mmp) REVERT: A 212 MET cc_start: 0.7829 (mmp) cc_final: 0.7589 (mmp) REVERT: A 213 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7746 (mtmt) REVERT: A 215 GLN cc_start: 0.7723 (tp-100) cc_final: 0.6820 (tp-100) REVERT: A 217 MET cc_start: 0.7950 (mpp) cc_final: 0.7526 (mpp) REVERT: A 250 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7554 (ttm170) REVERT: A 251 MET cc_start: 0.7908 (mmm) cc_final: 0.7611 (mmm) REVERT: A 258 ASN cc_start: 0.8323 (p0) cc_final: 0.8006 (p0) REVERT: A 259 GLN cc_start: 0.7683 (mt0) cc_final: 0.7109 (mt0) REVERT: A 262 LEU cc_start: 0.8188 (tp) cc_final: 0.7896 (mm) REVERT: A 266 GLU cc_start: 0.7850 (tp30) cc_final: 0.7473 (tp30) REVERT: A 270 LYS cc_start: 0.8359 (mmpt) cc_final: 0.8023 (mmtt) REVERT: A 283 ASP cc_start: 0.6708 (p0) cc_final: 0.6505 (p0) REVERT: A 301 GLU cc_start: 0.8113 (tt0) cc_final: 0.7520 (tt0) REVERT: A 304 ARG cc_start: 0.7740 (mmp-170) cc_final: 0.7305 (mmm160) REVERT: A 338 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7890 (mtp85) REVERT: A 341 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 342 LYS cc_start: 0.8768 (mptt) cc_final: 0.8113 (mptt) REVERT: A 343 MET cc_start: 0.8119 (mmm) cc_final: 0.7647 (mmm) REVERT: A 345 LYS cc_start: 0.8722 (pptt) cc_final: 0.8506 (pptt) REVERT: B 74 MET cc_start: 0.8082 (mtm) cc_final: 0.7379 (mtm) REVERT: B 90 TRP cc_start: 0.8013 (m100) cc_final: 0.7125 (m100) REVERT: B 104 LYS cc_start: 0.8610 (tttt) cc_final: 0.8262 (tttt) REVERT: B 118 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6926 (mt-10) REVERT: B 123 LEU cc_start: 0.8346 (tp) cc_final: 0.8111 (tp) REVERT: B 144 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8235 (mtpt) REVERT: B 146 THR cc_start: 0.8352 (p) cc_final: 0.7694 (p) REVERT: B 148 LYS cc_start: 0.8327 (tttt) cc_final: 0.8001 (ttmt) REVERT: B 154 PHE cc_start: 0.7686 (t80) cc_final: 0.7239 (t80) REVERT: B 157 LEU cc_start: 0.8059 (tp) cc_final: 0.7641 (tp) REVERT: B 158 GLN cc_start: 0.7300 (pm20) cc_final: 0.6408 (pm20) REVERT: B 211 MET cc_start: 0.8066 (mmp) cc_final: 0.7690 (mmp) REVERT: B 213 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7716 (mtmt) REVERT: B 215 GLN cc_start: 0.7458 (tp-100) cc_final: 0.6059 (tp-100) REVERT: B 217 MET cc_start: 0.8022 (mpp) cc_final: 0.7618 (mpp) REVERT: B 219 LEU cc_start: 0.8783 (mt) cc_final: 0.7614 (mt) REVERT: B 259 GLN cc_start: 0.7754 (mt0) cc_final: 0.7321 (mt0) REVERT: B 266 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7024 (tm-30) REVERT: B 270 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7818 (mptt) REVERT: B 273 LEU cc_start: 0.8051 (mm) cc_final: 0.7841 (mm) REVERT: B 305 ASP cc_start: 0.8329 (m-30) cc_final: 0.7995 (m-30) REVERT: B 334 GLN cc_start: 0.7809 (mp10) cc_final: 0.7573 (mp10) REVERT: B 338 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7987 (mmm-85) REVERT: B 341 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 342 LYS cc_start: 0.8587 (mptt) cc_final: 0.7710 (mptt) REVERT: B 343 MET cc_start: 0.8225 (tpt) cc_final: 0.6863 (tpt) REVERT: B 344 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7255 (pttt) REVERT: B 345 LYS cc_start: 0.8700 (pptt) cc_final: 0.8360 (pptt) REVERT: B 347 LYS cc_start: 0.8896 (mptt) cc_final: 0.8406 (mptt) REVERT: C 167 TYR cc_start: 0.7398 (m-10) cc_final: 0.7054 (m-10) REVERT: C 171 GLN cc_start: 0.8525 (mm110) cc_final: 0.8015 (mp10) REVERT: C 212 MET cc_start: 0.7770 (mmp) cc_final: 0.7477 (mmp) REVERT: C 215 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7593 (tm-30) REVERT: C 219 LEU cc_start: 0.7269 (mt) cc_final: 0.6939 (mt) REVERT: C 239 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7031 (ttm110) REVERT: C 248 MET cc_start: 0.7703 (mtp) cc_final: 0.7065 (mtp) REVERT: C 262 LEU cc_start: 0.8668 (mm) cc_final: 0.8166 (mm) REVERT: C 264 GLN cc_start: 0.8443 (mp10) cc_final: 0.7969 (mp10) REVERT: C 265 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7461 (mtt180) REVERT: C 270 LYS cc_start: 0.8613 (mmmt) cc_final: 0.7733 (mmmt) REVERT: C 289 GLN cc_start: 0.8122 (mt0) cc_final: 0.7856 (mt0) REVERT: C 299 LEU cc_start: 0.8635 (mt) cc_final: 0.8089 (mt) REVERT: C 300 LYS cc_start: 0.8801 (tttt) cc_final: 0.8426 (tttt) REVERT: C 302 MET cc_start: 0.8190 (tmm) cc_final: 0.7949 (tmm) REVERT: C 303 CYS cc_start: 0.8691 (m) cc_final: 0.8142 (m) REVERT: C 304 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7911 (mtp85) REVERT: C 313 GLU cc_start: 0.8292 (pt0) cc_final: 0.7920 (pt0) REVERT: C 335 ASP cc_start: 0.8424 (m-30) cc_final: 0.8159 (m-30) REVERT: C 343 MET cc_start: 0.8207 (tpt) cc_final: 0.7594 (tpt) REVERT: C 344 LYS cc_start: 0.8952 (mttm) cc_final: 0.8583 (mttm) REVERT: C 347 LYS cc_start: 0.7987 (mppt) cc_final: 0.7763 (mmtt) REVERT: D 82 ASP cc_start: 0.8268 (t0) cc_final: 0.7971 (t70) REVERT: D 90 TRP cc_start: 0.8388 (m100) cc_final: 0.7705 (m100) REVERT: D 104 LYS cc_start: 0.8380 (tttt) cc_final: 0.8079 (ttmt) REVERT: D 112 LYS cc_start: 0.8037 (mttt) cc_final: 0.7830 (mttt) REVERT: D 131 LEU cc_start: 0.8541 (mp) cc_final: 0.8099 (mt) REVERT: D 139 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7454 (mtmm) REVERT: D 179 SER cc_start: 0.8196 (p) cc_final: 0.7943 (p) REVERT: D 183 LYS cc_start: 0.8404 (mptt) cc_final: 0.8023 (mptt) REVERT: D 211 MET cc_start: 0.7629 (mmp) cc_final: 0.7206 (mmp) REVERT: D 212 MET cc_start: 0.8115 (mmp) cc_final: 0.7602 (mmp) REVERT: D 213 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7544 (mtmm) REVERT: D 217 MET cc_start: 0.7360 (mmm) cc_final: 0.6808 (mmm) REVERT: D 250 ARG cc_start: 0.7974 (ttt-90) cc_final: 0.7345 (ttt180) REVERT: D 251 MET cc_start: 0.8054 (mmt) cc_final: 0.7605 (mmt) REVERT: D 300 LYS cc_start: 0.8527 (tptm) cc_final: 0.8146 (tptm) REVERT: D 305 ASP cc_start: 0.7564 (t0) cc_final: 0.7137 (t0) REVERT: D 308 LEU cc_start: 0.8111 (pp) cc_final: 0.7805 (pp) REVERT: D 317 SER cc_start: 0.8928 (m) cc_final: 0.8566 (p) REVERT: D 337 HIS cc_start: 0.7716 (m170) cc_final: 0.7353 (m90) REVERT: E 139 LYS cc_start: 0.8448 (ptpp) cc_final: 0.7990 (ptpt) REVERT: E 158 GLN cc_start: 0.7909 (pm20) cc_final: 0.7462 (pm20) REVERT: E 171 GLN cc_start: 0.8533 (mm110) cc_final: 0.8186 (mp10) REVERT: E 193 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7263 (mt-10) REVERT: E 212 MET cc_start: 0.7900 (mmp) cc_final: 0.7265 (mmp) REVERT: E 213 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7485 (mtmm) REVERT: E 215 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7110 (tm-30) REVERT: E 217 MET cc_start: 0.8429 (ptp) cc_final: 0.8122 (tpp) REVERT: E 239 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7174 (ttp-110) REVERT: E 248 MET cc_start: 0.7650 (mtp) cc_final: 0.7266 (mtp) REVERT: E 250 ARG cc_start: 0.5509 (mmm160) cc_final: 0.5017 (tpt90) REVERT: E 251 MET cc_start: 0.6592 (mpp) cc_final: 0.6093 (mpp) REVERT: E 264 GLN cc_start: 0.8561 (mp10) cc_final: 0.8289 (mp10) REVERT: E 266 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7570 (tm-30) REVERT: E 270 LYS cc_start: 0.8558 (mmmt) cc_final: 0.7486 (mmmt) REVERT: E 290 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7824 (mm-30) REVERT: E 299 LEU cc_start: 0.8632 (mt) cc_final: 0.8183 (mt) REVERT: E 300 LYS cc_start: 0.8660 (tttt) cc_final: 0.8371 (tttt) REVERT: E 301 GLU cc_start: 0.8377 (tt0) cc_final: 0.7984 (tt0) REVERT: E 303 CYS cc_start: 0.8605 (m) cc_final: 0.8086 (m) REVERT: E 312 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7832 (mtp-110) REVERT: E 313 GLU cc_start: 0.8520 (pt0) cc_final: 0.8241 (pt0) REVERT: E 335 ASP cc_start: 0.8168 (m-30) cc_final: 0.7849 (m-30) REVERT: E 336 LEU cc_start: 0.8914 (mp) cc_final: 0.8669 (mp) REVERT: E 341 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 343 MET cc_start: 0.8091 (mmp) cc_final: 0.7621 (mmp) REVERT: F 68 LYS cc_start: 0.7549 (mppt) cc_final: 0.7112 (mppt) REVERT: F 74 MET cc_start: 0.7717 (mtm) cc_final: 0.7238 (mtm) REVERT: F 82 ASP cc_start: 0.8304 (t0) cc_final: 0.8098 (t70) REVERT: F 102 ASP cc_start: 0.8036 (m-30) cc_final: 0.7675 (m-30) REVERT: F 104 LYS cc_start: 0.8328 (tttt) cc_final: 0.7988 (ttmt) REVERT: F 112 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7502 (mtmt) REVERT: F 124 GLN cc_start: 0.7524 (pp30) cc_final: 0.7165 (pp30) REVERT: F 125 PRO cc_start: 0.7789 (Cg_endo) cc_final: 0.7424 (Cg_exo) REVERT: F 131 LEU cc_start: 0.8450 (mp) cc_final: 0.8247 (mt) REVERT: F 183 LYS cc_start: 0.8520 (mptt) cc_final: 0.8186 (mptt) REVERT: F 211 MET cc_start: 0.7636 (mmp) cc_final: 0.7134 (mmp) REVERT: F 212 MET cc_start: 0.8057 (mmp) cc_final: 0.7688 (mmp) REVERT: F 219 LEU cc_start: 0.7970 (mt) cc_final: 0.7310 (mt) REVERT: F 244 ASP cc_start: 0.7761 (p0) cc_final: 0.7553 (p0) REVERT: F 248 MET cc_start: 0.7204 (mtp) cc_final: 0.6787 (mtp) REVERT: F 250 ARG cc_start: 0.7844 (ttt-90) cc_final: 0.7618 (ttt180) REVERT: F 251 MET cc_start: 0.7733 (mpp) cc_final: 0.7526 (mpp) REVERT: F 263 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7701 (mmmm) REVERT: F 270 LYS cc_start: 0.8369 (pttp) cc_final: 0.7939 (ptmm) REVERT: F 300 LYS cc_start: 0.8464 (tptm) cc_final: 0.7988 (tptm) REVERT: F 302 MET cc_start: 0.7811 (tmm) cc_final: 0.7554 (tmm) REVERT: F 337 HIS cc_start: 0.7764 (m170) cc_final: 0.7405 (m170) outliers start: 0 outliers final: 0 residues processed: 593 average time/residue: 0.3528 time to fit residues: 291.0134 Evaluate side-chains 576 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN F 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.153807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126681 restraints weight = 29596.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131320 restraints weight = 17753.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.134575 restraints weight = 12022.481| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14142 Z= 0.122 Angle : 0.609 14.003 19146 Z= 0.312 Chirality : 0.043 0.238 2190 Planarity : 0.004 0.051 2448 Dihedral : 11.079 107.124 1962 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1728 helix: 1.16 (0.16), residues: 1026 sheet: 0.38 (0.39), residues: 192 loop : 0.62 (0.32), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 220 HIS 0.004 0.001 HIS E 337 PHE 0.037 0.002 PHE D 216 TYR 0.017 0.002 TYR E 132 ARG 0.009 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 738) hydrogen bonds : angle 4.10702 ( 2052) covalent geometry : bond 0.00261 (14142) covalent geometry : angle 0.60869 (19146) ********************** 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 599 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.640 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: 0.8208 (mtm) cc_final: 0.7660 (mtm) REVERT: A 92 ASP cc_start: 0.7574 (m-30) cc_final: 0.7317 (m-30) REVERT: A 109 LEU cc_start: 0.8464 (mt) cc_final: 0.8212 (mm) REVERT: A 123 LEU cc_start: 0.8457 (tp) cc_final: 0.8239 (tp) REVERT: A 124 GLN cc_start: 0.8189 (pp30) cc_final: 0.7971 (pp30) REVERT: A 125 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.8087 (Cg_exo) REVERT: A 157 LEU cc_start: 0.8020 (tp) cc_final: 0.7511 (tt) REVERT: A 158 GLN cc_start: 0.7318 (tm-30) cc_final: 0.7031 (tm-30) REVERT: A 178 PHE cc_start: 0.8928 (m-10) cc_final: 0.8531 (m-10) REVERT: A 179 SER cc_start: 0.8783 (t) cc_final: 0.8447 (p) REVERT: A 199 ARG cc_start: 0.7361 (tpp80) cc_final: 0.6344 (tpp80) REVERT: A 206 HIS cc_start: 0.8045 (p90) cc_final: 0.7428 (p90) REVERT: A 211 MET cc_start: 0.8011 (mmp) cc_final: 0.7462 (mmp) REVERT: A 212 MET cc_start: 0.7828 (mmp) cc_final: 0.7619 (mmp) REVERT: A 213 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7734 (mtmt) REVERT: A 215 GLN cc_start: 0.7687 (tp-100) cc_final: 0.6822 (tp-100) REVERT: A 217 MET cc_start: 0.7960 (mpp) cc_final: 0.7498 (mpp) REVERT: A 250 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7345 (ttp-170) REVERT: A 251 MET cc_start: 0.7831 (mmm) cc_final: 0.7561 (mmm) REVERT: A 259 GLN cc_start: 0.7699 (mt0) cc_final: 0.7360 (mt0) REVERT: A 262 LEU cc_start: 0.8145 (tp) cc_final: 0.7843 (mm) REVERT: A 270 LYS cc_start: 0.8387 (mmpt) cc_final: 0.8028 (mmtt) REVERT: A 301 GLU cc_start: 0.8102 (tt0) cc_final: 0.7530 (tt0) REVERT: A 304 ARG cc_start: 0.7531 (mmp-170) cc_final: 0.7241 (mmm160) REVERT: A 338 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7876 (mtp85) REVERT: A 341 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 342 LYS cc_start: 0.8757 (mptt) cc_final: 0.8105 (mptt) REVERT: A 343 MET cc_start: 0.8152 (mmm) cc_final: 0.7650 (mmm) REVERT: A 345 LYS cc_start: 0.8718 (pptt) cc_final: 0.8479 (pptt) REVERT: B 74 MET cc_start: 0.8079 (mtm) cc_final: 0.7384 (mtm) REVERT: B 90 TRP cc_start: 0.8033 (m100) cc_final: 0.7151 (m100) REVERT: B 92 ASP cc_start: 0.7526 (m-30) cc_final: 0.7301 (m-30) REVERT: B 104 LYS cc_start: 0.8602 (tttt) cc_final: 0.8273 (tttt) REVERT: B 114 LYS cc_start: 0.7653 (ptmm) cc_final: 0.7446 (ptmm) REVERT: B 118 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 123 LEU cc_start: 0.8370 (tp) cc_final: 0.8130 (tp) REVERT: B 132 TYR cc_start: 0.7344 (p90) cc_final: 0.6686 (p90) REVERT: B 144 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8221 (mtpt) REVERT: B 146 THR cc_start: 0.8310 (p) cc_final: 0.7693 (p) REVERT: B 148 LYS cc_start: 0.8287 (tttt) cc_final: 0.7996 (ttmt) REVERT: B 154 PHE cc_start: 0.7602 (t80) cc_final: 0.7190 (t80) REVERT: B 157 LEU cc_start: 0.8069 (tp) cc_final: 0.7650 (tp) REVERT: B 158 GLN cc_start: 0.7300 (pm20) cc_final: 0.6417 (pm20) REVERT: B 211 MET cc_start: 0.8066 (mmp) cc_final: 0.7738 (mmp) REVERT: B 213 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7687 (mtmt) REVERT: B 215 GLN cc_start: 0.7449 (tp-100) cc_final: 0.5996 (tp-100) REVERT: B 217 MET cc_start: 0.8108 (mpp) cc_final: 0.7639 (mpp) REVERT: B 219 LEU cc_start: 0.8769 (mt) cc_final: 0.7510 (mt) REVERT: B 250 ARG cc_start: 0.7660 (ttm170) cc_final: 0.6991 (ttp-170) REVERT: B 259 GLN cc_start: 0.7763 (mt0) cc_final: 0.7525 (mt0) REVERT: B 266 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7315 (tm-30) REVERT: B 286 GLU cc_start: 0.6854 (pm20) cc_final: 0.6387 (pm20) REVERT: B 299 LEU cc_start: 0.8791 (mt) cc_final: 0.8442 (mt) REVERT: B 304 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6929 (mmp80) REVERT: B 305 ASP cc_start: 0.8292 (m-30) cc_final: 0.7922 (m-30) REVERT: B 334 GLN cc_start: 0.7758 (mp10) cc_final: 0.7557 (mp10) REVERT: B 338 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7973 (mtp85) REVERT: B 341 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 342 LYS cc_start: 0.8598 (mptt) cc_final: 0.7718 (mptt) REVERT: B 343 MET cc_start: 0.8220 (tpt) cc_final: 0.6835 (tpt) REVERT: B 344 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7157 (pttt) REVERT: B 345 LYS cc_start: 0.8693 (pptt) cc_final: 0.8352 (pptt) REVERT: B 347 LYS cc_start: 0.8905 (mptt) cc_final: 0.8396 (mptt) REVERT: C 74 MET cc_start: 0.5651 (mtm) cc_final: 0.5421 (mtm) REVERT: C 167 TYR cc_start: 0.7334 (m-10) cc_final: 0.6907 (m-10) REVERT: C 171 GLN cc_start: 0.8527 (mm110) cc_final: 0.8003 (mp10) REVERT: C 212 MET cc_start: 0.7751 (mmp) cc_final: 0.7469 (mmp) REVERT: C 215 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7593 (tm-30) REVERT: C 219 LEU cc_start: 0.7272 (mt) cc_final: 0.6938 (mt) REVERT: C 229 CYS cc_start: 0.7496 (t) cc_final: 0.6494 (p) REVERT: C 239 ARG cc_start: 0.7934 (mtt90) cc_final: 0.6967 (ttm110) REVERT: C 248 MET cc_start: 0.7624 (mtp) cc_final: 0.7014 (mtp) REVERT: C 262 LEU cc_start: 0.8664 (mm) cc_final: 0.8132 (mm) REVERT: C 264 GLN cc_start: 0.8427 (mp10) cc_final: 0.7966 (mp10) REVERT: C 265 ARG cc_start: 0.7846 (mtt180) cc_final: 0.7452 (mtt180) REVERT: C 270 LYS cc_start: 0.8624 (mmmt) cc_final: 0.7736 (mmmt) REVERT: C 289 GLN cc_start: 0.8048 (mt0) cc_final: 0.7766 (mt0) REVERT: C 299 LEU cc_start: 0.8628 (mt) cc_final: 0.8095 (mt) REVERT: C 300 LYS cc_start: 0.8795 (tttt) cc_final: 0.8430 (tttt) REVERT: C 303 CYS cc_start: 0.8731 (m) cc_final: 0.8183 (m) REVERT: C 304 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7891 (mtp85) REVERT: C 313 GLU cc_start: 0.8298 (pt0) cc_final: 0.7922 (pt0) REVERT: C 335 ASP cc_start: 0.8393 (m-30) cc_final: 0.8023 (m-30) REVERT: C 344 LYS cc_start: 0.8962 (mttm) cc_final: 0.8505 (mttm) REVERT: D 82 ASP cc_start: 0.8171 (t0) cc_final: 0.7926 (t70) REVERT: D 90 TRP cc_start: 0.8414 (m100) cc_final: 0.7718 (m100) REVERT: D 104 LYS cc_start: 0.8371 (tttt) cc_final: 0.8047 (ttmt) REVERT: D 112 LYS cc_start: 0.8059 (mttt) cc_final: 0.7842 (mttt) REVERT: D 131 LEU cc_start: 0.8549 (mp) cc_final: 0.8064 (mt) REVERT: D 139 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7471 (mtmm) REVERT: D 179 SER cc_start: 0.8253 (p) cc_final: 0.8019 (p) REVERT: D 183 LYS cc_start: 0.8396 (mptt) cc_final: 0.8038 (mptt) REVERT: D 212 MET cc_start: 0.8065 (mmp) cc_final: 0.7539 (mmp) REVERT: D 213 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7692 (mtmm) REVERT: D 241 GLN cc_start: 0.8215 (mp-120) cc_final: 0.7388 (mp-120) REVERT: D 250 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7376 (ttt180) REVERT: D 251 MET cc_start: 0.8054 (mmt) cc_final: 0.7613 (mmt) REVERT: D 300 LYS cc_start: 0.8533 (tptm) cc_final: 0.8135 (tptm) REVERT: D 305 ASP cc_start: 0.7593 (t0) cc_final: 0.7163 (t0) REVERT: D 317 SER cc_start: 0.8925 (m) cc_final: 0.8590 (p) REVERT: D 336 LEU cc_start: 0.7543 (pp) cc_final: 0.7325 (pp) REVERT: D 337 HIS cc_start: 0.7710 (m170) cc_final: 0.7322 (m90) REVERT: E 139 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7998 (ptpt) REVERT: E 158 GLN cc_start: 0.7841 (pm20) cc_final: 0.7404 (pm20) REVERT: E 171 GLN cc_start: 0.8496 (mm110) cc_final: 0.8108 (mp10) REVERT: E 193 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7270 (mt-10) REVERT: E 212 MET cc_start: 0.7978 (mmp) cc_final: 0.7298 (mmp) REVERT: E 213 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7495 (mtmm) REVERT: E 215 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7135 (tm-30) REVERT: E 217 MET cc_start: 0.8330 (ptp) cc_final: 0.8066 (tpp) REVERT: E 239 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7199 (ttp-110) REVERT: E 248 MET cc_start: 0.7657 (mtp) cc_final: 0.7244 (mtp) REVERT: E 250 ARG cc_start: 0.5591 (mmm160) cc_final: 0.5220 (tpt90) REVERT: E 251 MET cc_start: 0.6551 (mpp) cc_final: 0.6120 (mpp) REVERT: E 264 GLN cc_start: 0.8590 (mp10) cc_final: 0.8288 (mp10) REVERT: E 266 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 270 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7521 (mmmt) REVERT: E 286 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7693 (mm-30) REVERT: E 290 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 299 LEU cc_start: 0.8634 (mt) cc_final: 0.8185 (mt) REVERT: E 300 LYS cc_start: 0.8634 (tttt) cc_final: 0.8383 (tttt) REVERT: E 301 GLU cc_start: 0.8368 (tt0) cc_final: 0.7993 (tt0) REVERT: E 303 CYS cc_start: 0.8668 (m) cc_final: 0.8152 (m) REVERT: E 312 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7826 (mtp-110) REVERT: E 313 GLU cc_start: 0.8545 (pt0) cc_final: 0.8245 (pt0) REVERT: E 338 ARG cc_start: 0.8665 (mtp85) cc_final: 0.8328 (mtp85) REVERT: E 341 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 343 MET cc_start: 0.8097 (mmp) cc_final: 0.7631 (mmp) REVERT: F 74 MET cc_start: 0.7727 (mtm) cc_final: 0.7207 (mtm) REVERT: F 102 ASP cc_start: 0.8020 (m-30) cc_final: 0.7664 (m-30) REVERT: F 104 LYS cc_start: 0.8364 (tttt) cc_final: 0.8076 (ttmt) REVERT: F 123 LEU cc_start: 0.8856 (mt) cc_final: 0.8459 (mt) REVERT: F 124 GLN cc_start: 0.7585 (pp30) cc_final: 0.7252 (pp30) REVERT: F 125 PRO cc_start: 0.7822 (Cg_endo) cc_final: 0.7403 (Cg_exo) REVERT: F 131 LEU cc_start: 0.8440 (mp) cc_final: 0.8160 (mt) REVERT: F 132 TYR cc_start: 0.7606 (p90) cc_final: 0.7366 (p90) REVERT: F 140 THR cc_start: 0.8146 (p) cc_final: 0.7916 (p) REVERT: F 141 LEU cc_start: 0.8126 (tt) cc_final: 0.7926 (tt) REVERT: F 144 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7668 (mtpt) REVERT: F 183 LYS cc_start: 0.8541 (mptt) cc_final: 0.8199 (mptt) REVERT: F 211 MET cc_start: 0.7637 (mmp) cc_final: 0.7132 (mmp) REVERT: F 212 MET cc_start: 0.8057 (mmp) cc_final: 0.7663 (mmp) REVERT: F 215 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6699 (tp-100) REVERT: F 219 LEU cc_start: 0.8000 (mt) cc_final: 0.7287 (mt) REVERT: F 248 MET cc_start: 0.7154 (mtp) cc_final: 0.6641 (mtp) REVERT: F 263 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7845 (mmmm) REVERT: F 270 LYS cc_start: 0.8354 (pttp) cc_final: 0.7904 (ptmm) REVERT: F 298 ASP cc_start: 0.8136 (m-30) cc_final: 0.7933 (m-30) REVERT: F 300 LYS cc_start: 0.8466 (tptm) cc_final: 0.7974 (tptm) REVERT: F 302 MET cc_start: 0.7813 (tmm) cc_final: 0.7583 (tmm) REVERT: F 337 HIS cc_start: 0.7729 (m170) cc_final: 0.7421 (m170) outliers start: 0 outliers final: 0 residues processed: 599 average time/residue: 0.2991 time to fit residues: 249.5111 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 : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 0.0980 chunk 110 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 89 optimal weight: 0.0770 chunk 166 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN F 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.153257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126030 restraints weight = 29789.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130648 restraints weight = 17854.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133838 restraints weight = 12083.674| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14142 Z= 0.127 Angle : 0.613 14.081 19146 Z= 0.315 Chirality : 0.043 0.205 2190 Planarity : 0.005 0.058 2448 Dihedral : 11.083 106.362 1962 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1728 helix: 1.32 (0.17), residues: 996 sheet: 0.60 (0.39), residues: 186 loop : 0.77 (0.32), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 220 HIS 0.004 0.001 HIS D 337 PHE 0.031 0.002 PHE D 216 TYR 0.016 0.002 TYR B 132 ARG 0.008 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 738) hydrogen bonds : angle 4.14619 ( 2052) covalent geometry : bond 0.00267 (14142) covalent geometry : angle 0.61312 (19146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5652.17 seconds wall clock time: 100 minutes 4.47 seconds (6004.47 seconds total)