Starting phenix.real_space_refine on Sun Jan 19 16:24:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxt_43639/01_2025/8vxt_43639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxt_43639/01_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_43639/01_2025/8vxt_43639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxt_43639/01_2025/8vxt_43639.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxt_43639/01_2025/8vxt_43639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxt_43639/01_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-5571/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: 5.31, per 1000 atoms: 0.38 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: 3.33 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: 1.19 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: 3.77 Time building geometry restraints manager: 3.91 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: 0.12 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: 0.970 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 28.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- 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= 0.198 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 *********************** 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 : 1.667 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: 0.3014 time to fit residues: 245.7977 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 : 1.561 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134063 restraints weight = 30039.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138738 restraints weight = 18618.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141895 restraints weight = 12771.086| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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= 0.215 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 *********************** 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 : 1.555 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: 0.8144 (mtm) cc_final: 0.7791 (mtm) REVERT: A 101 THR cc_start: 0.8395 (p) cc_final: 0.8040 (t) REVERT: A 114 LYS cc_start: 0.7777 (tptm) cc_final: 0.7462 (tptm) REVERT: A 117 PHE cc_start: 0.7838 (m-10) cc_final: 0.7490 (m-10) REVERT: A 118 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6262 (mt-10) REVERT: A 122 LEU cc_start: 0.7514 (pt) cc_final: 0.6994 (tt) REVERT: A 124 GLN cc_start: 0.7932 (pp30) cc_final: 0.7705 (pp30) REVERT: A 125 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7785 (Cg_exo) REVERT: A 141 LEU cc_start: 0.8462 (tp) cc_final: 0.8226 (tp) REVERT: A 148 LYS cc_start: 0.8230 (tttt) cc_final: 0.7906 (ttmt) REVERT: A 149 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 154 PHE cc_start: 0.7700 (t80) cc_final: 0.7085 (t80) REVERT: A 157 LEU cc_start: 0.8056 (tp) cc_final: 0.7729 (tp) REVERT: A 193 GLU cc_start: 0.7699 (tt0) cc_final: 0.7462 (tt0) REVERT: A 206 HIS cc_start: 0.7963 (p90) cc_final: 0.7305 (p90) REVERT: A 211 MET cc_start: 0.8048 (mmp) cc_final: 0.7326 (mmt) REVERT: A 212 MET cc_start: 0.7850 (mmp) cc_final: 0.7552 (mmp) REVERT: A 213 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7623 (mtmt) REVERT: A 215 GLN cc_start: 0.7546 (tp-100) cc_final: 0.6308 (tp-100) REVERT: A 217 MET cc_start: 0.8027 (mpp) cc_final: 0.7562 (mpp) REVERT: A 219 LEU cc_start: 0.8667 (mt) cc_final: 0.7489 (mt) REVERT: A 232 ILE cc_start: 0.8328 (mt) cc_final: 0.8050 (mt) REVERT: A 237 THR cc_start: 0.7730 (t) cc_final: 0.6950 (m) REVERT: A 259 GLN cc_start: 0.7344 (mt0) cc_final: 0.6993 (mt0) REVERT: A 273 LEU cc_start: 0.8108 (mm) cc_final: 0.7888 (mm) REVERT: A 305 ASP cc_start: 0.8166 (t0) cc_final: 0.7869 (m-30) REVERT: A 341 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 342 LYS cc_start: 0.8569 (mptt) cc_final: 0.8028 (mptt) REVERT: A 343 MET cc_start: 0.8225 (tpt) cc_final: 0.7942 (tpt) REVERT: B 74 MET cc_start: 0.8026 (mtm) cc_final: 0.7367 (mtm) REVERT: B 85 ASN cc_start: 0.8021 (p0) cc_final: 0.7813 (p0) REVERT: B 113 LYS cc_start: 0.7946 (tppp) cc_final: 0.7696 (tttp) REVERT: B 117 PHE cc_start: 0.7733 (m-10) cc_final: 0.7424 (m-10) REVERT: B 148 LYS cc_start: 0.8424 (tttt) cc_final: 0.7874 (ttmt) REVERT: B 149 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7219 (mm-30) REVERT: B 157 LEU cc_start: 0.8121 (tp) cc_final: 0.7744 (tp) REVERT: B 158 GLN cc_start: 0.6978 (pm20) cc_final: 0.6157 (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: 0.6602 (tpp80) REVERT: B 211 MET cc_start: 0.8033 (mmp) cc_final: 0.7615 (mmp) REVERT: B 212 MET cc_start: 0.7917 (mmp) cc_final: 0.7650 (mmp) REVERT: B 213 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7561 (mtmt) REVERT: B 215 GLN cc_start: 0.7503 (tp-100) cc_final: 0.6583 (tp-100) REVERT: B 217 MET cc_start: 0.8073 (mpp) cc_final: 0.7269 (mpp) REVERT: B 221 ASP cc_start: 0.7153 (m-30) cc_final: 0.6913 (m-30) REVERT: B 231 VAL cc_start: 0.7884 (t) cc_final: 0.7597 (p) REVERT: B 232 ILE cc_start: 0.8316 (mt) cc_final: 0.8053 (mt) REVERT: B 243 LEU cc_start: 0.8420 (mt) cc_final: 0.8135 (mt) REVERT: B 259 GLN cc_start: 0.7586 (mt0) cc_final: 0.7241 (mt0) REVERT: B 266 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7220 (tm-30) REVERT: B 286 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 295 SER cc_start: 0.6799 (p) cc_final: 0.6501 (p) REVERT: B 299 LEU cc_start: 0.8624 (mt) cc_final: 0.8249 (mt) REVERT: B 311 VAL cc_start: 0.8203 (t) cc_final: 0.7987 (t) REVERT: B 338 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8116 (mtp85) REVERT: B 341 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 342 LYS cc_start: 0.8517 (mptt) cc_final: 0.7685 (mptt) REVERT: B 345 LYS cc_start: 0.8775 (pptt) cc_final: 0.8478 (pptt) REVERT: C 74 MET cc_start: 0.5641 (mtm) cc_final: 0.5214 (mtm) REVERT: C 184 LEU cc_start: 0.6239 (mm) cc_final: 0.5864 (mt) REVERT: C 190 PHE cc_start: 0.6491 (t80) cc_final: 0.6213 (t80) REVERT: C 199 ARG cc_start: 0.5959 (tpp80) cc_final: 0.5714 (tpp80) REVERT: C 211 MET cc_start: 0.7169 (mmp) cc_final: 0.6937 (mmp) REVERT: C 212 MET cc_start: 0.7522 (mmp) cc_final: 0.6718 (mmp) REVERT: C 239 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7247 (mtt90) REVERT: C 248 MET cc_start: 0.7617 (mtp) cc_final: 0.7051 (mtp) REVERT: C 251 MET cc_start: 0.6346 (mmt) cc_final: 0.5804 (mmt) REVERT: C 289 GLN cc_start: 0.8286 (mt0) cc_final: 0.8066 (mt0) REVERT: C 308 LEU cc_start: 0.8582 (tp) cc_final: 0.8358 (tp) REVERT: C 335 ASP cc_start: 0.7868 (m-30) cc_final: 0.7600 (m-30) REVERT: C 336 LEU cc_start: 0.8638 (mp) cc_final: 0.8368 (mp) REVERT: C 343 MET cc_start: 0.8241 (tpt) cc_final: 0.7403 (tpt) REVERT: C 344 LYS cc_start: 0.8925 (mttm) cc_final: 0.8560 (mttm) REVERT: C 347 LYS cc_start: 0.8147 (mptt) cc_final: 0.7883 (mptt) REVERT: D 82 ASP cc_start: 0.7587 (t0) cc_final: 0.6949 (t70) REVERT: D 89 THR cc_start: 0.7743 (p) cc_final: 0.7475 (p) REVERT: D 104 LYS cc_start: 0.8304 (tttt) cc_final: 0.7989 (tttm) REVERT: D 132 TYR cc_start: 0.7250 (p90) cc_final: 0.6978 (p90) REVERT: D 139 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7208 (mtmm) REVERT: D 173 LEU cc_start: 0.8233 (tp) cc_final: 0.8026 (tp) REVERT: D 196 SER cc_start: 0.7154 (t) cc_final: 0.6836 (p) REVERT: D 212 MET cc_start: 0.7880 (mmp) cc_final: 0.7037 (mmp) REVERT: D 217 MET cc_start: 0.7085 (mmp) cc_final: 0.6639 (mmt) REVERT: D 237 THR cc_start: 0.7052 (t) cc_final: 0.6410 (m) REVERT: D 241 GLN cc_start: 0.8233 (mp-120) cc_final: 0.7371 (mm110) REVERT: D 248 MET cc_start: 0.7037 (mtp) cc_final: 0.6507 (mtp) REVERT: D 259 GLN cc_start: 0.7983 (mp10) cc_final: 0.7776 (mp10) REVERT: D 300 LYS cc_start: 0.8463 (tptm) cc_final: 0.8129 (tptm) REVERT: D 305 ASP cc_start: 0.7461 (t0) cc_final: 0.7082 (t0) REVERT: D 337 HIS cc_start: 0.7573 (m170) cc_final: 0.7271 (m90) REVERT: E 155 ILE cc_start: 0.7188 (pt) cc_final: 0.6375 (tp) REVERT: E 171 GLN cc_start: 0.8554 (mm110) cc_final: 0.8163 (mm-40) REVERT: E 205 ASP cc_start: 0.4653 (m-30) cc_final: 0.4349 (m-30) REVERT: E 212 MET cc_start: 0.7640 (mmp) cc_final: 0.6734 (mmp) REVERT: E 248 MET cc_start: 0.7712 (mtp) cc_final: 0.7201 (mtp) REVERT: E 251 MET cc_start: 0.5684 (mmt) cc_final: 0.5316 (mmt) REVERT: E 286 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7544 (mm-30) REVERT: E 290 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7623 (mm-30) REVERT: E 298 ASP cc_start: 0.7696 (m-30) cc_final: 0.7332 (m-30) REVERT: E 304 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8213 (mtp-110) REVERT: E 336 LEU cc_start: 0.8604 (mp) cc_final: 0.8386 (mp) REVERT: E 341 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7785 (mm-30) REVERT: E 343 MET cc_start: 0.8273 (tpt) cc_final: 0.7415 (tpt) REVERT: E 347 LYS cc_start: 0.8229 (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: 0.7153 (t70) cc_final: 0.6939 (t0) REVERT: F 87 HIS cc_start: 0.7598 (m-70) cc_final: 0.6934 (m-70) REVERT: F 102 ASP cc_start: 0.8000 (m-30) cc_final: 0.7695 (m-30) REVERT: F 104 LYS cc_start: 0.8335 (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: 0.7892 (mtmm) cc_final: 0.7392 (mtmm) REVERT: F 183 LYS cc_start: 0.8596 (mptt) cc_final: 0.8311 (mptt) REVERT: F 199 ARG cc_start: 0.5986 (tpp80) cc_final: 0.4851 (tpp80) REVERT: F 211 MET cc_start: 0.7312 (mmp) cc_final: 0.6955 (mmp) REVERT: F 212 MET cc_start: 0.7954 (mmp) cc_final: 0.7505 (mmp) REVERT: F 215 GLN cc_start: 0.6984 (tp-100) cc_final: 0.6732 (tp-100) REVERT: F 219 LEU cc_start: 0.7590 (mt) cc_final: 0.6793 (mt) REVERT: F 237 THR cc_start: 0.6982 (t) cc_final: 0.6317 (m) REVERT: F 241 GLN cc_start: 0.8002 (mm110) cc_final: 0.7556 (mm-40) REVERT: F 248 MET cc_start: 0.7138 (mtp) cc_final: 0.6640 (mtp) REVERT: F 270 LYS cc_start: 0.8281 (pttp) cc_final: 0.7860 (ptmm) REVERT: F 300 LYS cc_start: 0.8238 (tptm) cc_final: 0.7923 (tptm) REVERT: F 302 MET cc_start: 0.7691 (tmm) cc_final: 0.7356 (tmm) REVERT: F 337 HIS cc_start: 0.7706 (m170) cc_final: 0.7360 (m170) outliers start: 1 outliers final: 0 residues processed: 560 average time/residue: 0.3167 time to fit residues: 244.0350 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 : 1.470 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS A 256 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121995 restraints weight = 30818.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126680 restraints weight = 18494.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129904 restraints weight = 12519.253| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14142 Z= 0.318 Angle : 0.733 10.128 19146 Z= 0.392 Chirality : 0.049 0.285 2190 Planarity : 0.005 0.056 2448 Dihedral : 11.185 107.527 1962 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 0.26 % Allowed : 3.92 % Favored : 95.82 % 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: 0.65 (0.21), residues: 1728 helix: 0.60 (0.16), residues: 978 sheet: 0.58 (0.40), residues: 204 loop : 0.38 (0.30), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 90 HIS 0.009 0.002 HIS C 281 PHE 0.046 0.003 PHE D 216 TYR 0.020 0.003 TYR D 132 ARG 0.009 0.001 ARG E 199 *********************** 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 617 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 613 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8236 (mtm) cc_final: 0.7872 (mtm) REVERT: A 96 LEU cc_start: 0.7563 (mt) cc_final: 0.7331 (mt) REVERT: A 99 VAL cc_start: 0.8274 (t) cc_final: 0.7962 (m) REVERT: A 101 THR cc_start: 0.8318 (p) cc_final: 0.7951 (p) REVERT: A 104 LYS cc_start: 0.8621 (tttt) cc_final: 0.8234 (tttt) REVERT: A 105 ASP cc_start: 0.7225 (p0) cc_final: 0.7016 (p0) REVERT: A 114 LYS cc_start: 0.7582 (tptm) cc_final: 0.7255 (tptm) REVERT: A 117 PHE cc_start: 0.7916 (m-10) cc_final: 0.7688 (m-10) REVERT: A 124 GLN cc_start: 0.8144 (pp30) cc_final: 0.7827 (pp30) REVERT: A 125 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.7918 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8143 (mp) cc_final: 0.7858 (tp) REVERT: A 148 LYS cc_start: 0.8411 (tttt) cc_final: 0.8047 (ttmt) REVERT: A 149 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6981 (mm-30) REVERT: A 154 PHE cc_start: 0.7714 (t80) cc_final: 0.7097 (t80) REVERT: A 157 LEU cc_start: 0.8044 (tp) cc_final: 0.7769 (tp) REVERT: A 169 GLU cc_start: 0.7987 (tt0) cc_final: 0.7655 (tt0) REVERT: A 177 VAL cc_start: 0.8677 (t) cc_final: 0.8453 (t) REVERT: A 179 SER cc_start: 0.8760 (t) cc_final: 0.8501 (p) REVERT: A 193 GLU cc_start: 0.7827 (tt0) cc_final: 0.7597 (tt0) REVERT: A 206 HIS cc_start: 0.8120 (p90) cc_final: 0.7357 (p90) REVERT: A 211 MET cc_start: 0.8030 (mmp) cc_final: 0.7490 (mmp) REVERT: A 212 MET cc_start: 0.7898 (mmp) cc_final: 0.7653 (mmp) REVERT: A 213 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7738 (mtmt) REVERT: A 215 GLN cc_start: 0.7599 (tp-100) cc_final: 0.6500 (tp-100) REVERT: A 217 MET cc_start: 0.8077 (mpp) cc_final: 0.7650 (mpp) REVERT: A 218 SER cc_start: 0.8666 (p) cc_final: 0.8240 (p) REVERT: A 219 LEU cc_start: 0.8743 (mt) cc_final: 0.7749 (mt) REVERT: A 237 THR cc_start: 0.8438 (t) cc_final: 0.7878 (m) REVERT: A 259 GLN cc_start: 0.7536 (mt0) cc_final: 0.7175 (mt0) REVERT: A 270 LYS cc_start: 0.8634 (mmpt) cc_final: 0.8403 (mmtt) REVERT: A 341 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 342 LYS cc_start: 0.8752 (mptt) cc_final: 0.8355 (mptt) REVERT: B 74 MET cc_start: 0.8082 (mtm) cc_final: 0.7353 (mtm) REVERT: B 85 ASN cc_start: 0.8084 (p0) cc_final: 0.7763 (p0) REVERT: B 86 MET cc_start: 0.7773 (mtm) cc_final: 0.7482 (mtm) REVERT: B 104 LYS cc_start: 0.8480 (tttt) cc_final: 0.8112 (tttt) REVERT: B 131 LEU cc_start: 0.8224 (mp) cc_final: 0.7814 (mt) REVERT: B 148 LYS cc_start: 0.8496 (tttt) cc_final: 0.8173 (ttmt) REVERT: B 149 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 154 PHE cc_start: 0.7727 (t80) cc_final: 0.7010 (t80) REVERT: B 157 LEU cc_start: 0.8180 (tp) cc_final: 0.7802 (tp) REVERT: B 158 GLN cc_start: 0.7281 (pm20) cc_final: 0.6439 (pm20) REVERT: B 211 MET cc_start: 0.7988 (mmp) cc_final: 0.7614 (mmp) REVERT: B 213 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7547 (mtmt) REVERT: B 215 GLN cc_start: 0.7477 (tp-100) cc_final: 0.6299 (tp-100) REVERT: B 217 MET cc_start: 0.8141 (mpp) cc_final: 0.7633 (mpp) REVERT: B 218 SER cc_start: 0.8565 (p) cc_final: 0.8033 (p) REVERT: B 219 LEU cc_start: 0.8726 (mt) cc_final: 0.7685 (mt) REVERT: B 243 LEU cc_start: 0.8459 (mt) cc_final: 0.8206 (mt) REVERT: B 259 GLN cc_start: 0.7738 (mt0) cc_final: 0.7369 (mt0) REVERT: B 266 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 270 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7928 (mptt) REVERT: B 295 SER cc_start: 0.7202 (p) cc_final: 0.6900 (p) REVERT: B 299 LEU cc_start: 0.8858 (mt) cc_final: 0.8498 (mt) REVERT: B 341 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 342 LYS cc_start: 0.8568 (mptt) cc_final: 0.7758 (mptt) REVERT: B 343 MET cc_start: 0.8202 (tpt) cc_final: 0.6807 (tpt) REVERT: B 344 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7822 (ptpp) REVERT: B 345 LYS cc_start: 0.8771 (pptt) cc_final: 0.8426 (pptt) REVERT: B 346 SER cc_start: 0.8626 (p) cc_final: 0.8403 (p) REVERT: B 347 LYS cc_start: 0.8882 (mptt) cc_final: 0.8387 (mptt) REVERT: C 86 MET cc_start: 0.5661 (pmm) cc_final: 0.5389 (pmm) REVERT: C 158 GLN cc_start: 0.8300 (pm20) cc_final: 0.7907 (pm20) REVERT: C 170 SER cc_start: 0.8021 (p) cc_final: 0.7635 (p) REVERT: C 171 GLN cc_start: 0.8418 (mm110) cc_final: 0.8000 (mm-40) REVERT: C 212 MET cc_start: 0.7553 (mmp) cc_final: 0.7132 (mmp) REVERT: C 239 ARG cc_start: 0.7951 (mtt90) cc_final: 0.7643 (mtt90) REVERT: C 248 MET cc_start: 0.7962 (mtp) cc_final: 0.7457 (mtp) REVERT: C 251 MET cc_start: 0.6451 (mmt) cc_final: 0.5827 (mmt) REVERT: C 270 LYS cc_start: 0.8563 (mmmt) cc_final: 0.7618 (mmmt) REVERT: C 289 GLN cc_start: 0.8202 (mt0) cc_final: 0.7895 (mt0) REVERT: C 299 LEU cc_start: 0.8664 (mt) cc_final: 0.8354 (mt) REVERT: C 300 LYS cc_start: 0.8980 (tttt) cc_final: 0.8711 (tttt) REVERT: C 302 MET cc_start: 0.8100 (tmm) cc_final: 0.7789 (tmm) REVERT: C 304 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8146 (mmm-85) REVERT: C 308 LEU cc_start: 0.8653 (tp) cc_final: 0.8339 (tp) REVERT: C 313 GLU cc_start: 0.8126 (pt0) cc_final: 0.7891 (pt0) REVERT: C 343 MET cc_start: 0.8309 (tpt) cc_final: 0.7484 (tpt) REVERT: C 344 LYS cc_start: 0.9036 (mttm) cc_final: 0.8637 (mttm) REVERT: C 347 LYS cc_start: 0.8321 (mptt) cc_final: 0.8075 (mptt) REVERT: D 82 ASP cc_start: 0.8201 (t0) cc_final: 0.7774 (t70) REVERT: D 104 LYS cc_start: 0.8448 (tttt) cc_final: 0.8085 (tttm) REVERT: D 178 PHE cc_start: 0.7655 (m-10) cc_final: 0.7200 (m-10) REVERT: D 183 LYS cc_start: 0.8547 (mptt) cc_final: 0.8130 (mptt) REVERT: D 211 MET cc_start: 0.7584 (mmp) cc_final: 0.7108 (mmp) REVERT: D 212 MET cc_start: 0.7734 (mmp) cc_final: 0.7203 (mmp) REVERT: D 223 LEU cc_start: 0.8039 (mt) cc_final: 0.7609 (mt) REVERT: D 241 GLN cc_start: 0.8201 (mp-120) cc_final: 0.7276 (mm110) REVERT: D 248 MET cc_start: 0.7023 (mtp) cc_final: 0.6473 (mtp) REVERT: D 250 ARG cc_start: 0.7456 (ttt180) cc_final: 0.6851 (ttt-90) REVERT: D 300 LYS cc_start: 0.8572 (tptm) cc_final: 0.8129 (tptm) REVERT: D 302 MET cc_start: 0.7779 (tmm) cc_final: 0.7499 (tmm) REVERT: D 305 ASP cc_start: 0.7608 (t0) cc_final: 0.7255 (t0) REVERT: D 337 HIS cc_start: 0.7719 (m170) cc_final: 0.7473 (m-70) REVERT: E 117 PHE cc_start: 0.6226 (m-80) cc_final: 0.5910 (m-80) REVERT: E 158 GLN cc_start: 0.8306 (pm20) cc_final: 0.7959 (pm20) REVERT: E 171 GLN cc_start: 0.8578 (mm110) cc_final: 0.8141 (mp10) REVERT: E 193 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 205 ASP cc_start: 0.5235 (m-30) cc_final: 0.4942 (m-30) REVERT: E 212 MET cc_start: 0.7707 (mmp) cc_final: 0.6976 (mmp) REVERT: E 248 MET cc_start: 0.7906 (mtp) cc_final: 0.7429 (mtp) REVERT: E 266 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7636 (tm-30) REVERT: E 286 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7663 (mm-30) REVERT: E 290 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 298 ASP cc_start: 0.7584 (m-30) cc_final: 0.7195 (m-30) REVERT: E 299 LEU cc_start: 0.8756 (mt) cc_final: 0.8322 (mt) REVERT: E 300 LYS cc_start: 0.8800 (tttt) cc_final: 0.8531 (tttt) REVERT: E 302 MET cc_start: 0.8141 (tmm) cc_final: 0.7804 (tmm) REVERT: E 304 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8210 (mtp-110) REVERT: E 309 LEU cc_start: 0.8751 (tp) cc_final: 0.8546 (tp) REVERT: E 312 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8072 (mtp-110) REVERT: E 335 ASP cc_start: 0.7887 (m-30) cc_final: 0.7640 (m-30) REVERT: E 341 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7735 (mm-30) REVERT: F 74 MET cc_start: 0.7639 (mtm) cc_final: 0.7288 (mtm) REVERT: F 90 TRP cc_start: 0.8148 (m100) cc_final: 0.7706 (m100) REVERT: F 102 ASP cc_start: 0.8080 (m-30) cc_final: 0.7782 (m-30) REVERT: F 104 LYS cc_start: 0.8478 (tttt) cc_final: 0.8104 (ttmt) REVERT: F 112 LYS cc_start: 0.7865 (mttt) cc_final: 0.7653 (mttt) REVERT: F 131 LEU cc_start: 0.8369 (mp) cc_final: 0.7856 (mt) REVERT: F 139 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7616 (mtmm) REVERT: F 178 PHE cc_start: 0.7725 (m-10) cc_final: 0.7355 (m-10) REVERT: F 183 LYS cc_start: 0.8587 (mptt) cc_final: 0.8278 (mptt) REVERT: F 211 MET cc_start: 0.7381 (mmp) cc_final: 0.7143 (mmp) REVERT: F 212 MET cc_start: 0.7983 (mmp) cc_final: 0.7576 (mmp) REVERT: F 217 MET cc_start: 0.7546 (mmt) cc_final: 0.6937 (mmt) REVERT: F 223 LEU cc_start: 0.7775 (mt) cc_final: 0.7375 (mt) REVERT: F 241 GLN cc_start: 0.8019 (mm110) cc_final: 0.7497 (mm-40) REVERT: F 244 ASP cc_start: 0.7479 (p0) cc_final: 0.7278 (p0) REVERT: F 248 MET cc_start: 0.6957 (mtp) cc_final: 0.6327 (mtp) REVERT: F 259 GLN cc_start: 0.7926 (mp10) cc_final: 0.7711 (mp10) REVERT: F 270 LYS cc_start: 0.8424 (pttp) cc_final: 0.7994 (ptmm) REVERT: F 300 LYS cc_start: 0.8359 (tptm) cc_final: 0.7966 (tptm) REVERT: F 302 MET cc_start: 0.7801 (tmm) cc_final: 0.7456 (tmm) REVERT: F 304 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.7214 (tpp-160) REVERT: F 337 HIS cc_start: 0.7734 (m170) cc_final: 0.7457 (m170) outliers start: 4 outliers final: 1 residues processed: 615 average time/residue: 0.2952 time to fit residues: 253.1038 Evaluate side-chains 590 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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: 2.9990 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 275 ASN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN F 332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126214 restraints weight = 30410.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.130691 restraints weight = 18550.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133810 restraints weight = 12649.140| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3786 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= 0.186 Angle : 0.608 11.707 19146 Z= 0.320 Chirality : 0.044 0.194 2190 Planarity : 0.004 0.054 2448 Dihedral : 10.904 104.156 1962 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % 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: 1.17 (0.21), residues: 1728 helix: 1.05 (0.16), residues: 984 sheet: 1.00 (0.41), residues: 186 loop : 0.42 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 90 HIS 0.012 0.001 HIS B 337 PHE 0.026 0.002 PHE C 216 TYR 0.014 0.002 TYR D 132 ARG 0.007 0.001 ARG B 304 *********************** 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 595 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 1.669 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: A 74 MET cc_start: 0.8161 (mtm) cc_final: 0.7764 (mtm) REVERT: A 90 TRP cc_start: 0.8059 (m100) cc_final: 0.7155 (m100) REVERT: A 96 LEU cc_start: 0.7522 (mt) cc_final: 0.7268 (mt) REVERT: A 101 THR cc_start: 0.8269 (p) cc_final: 0.7837 (t) REVERT: A 104 LYS cc_start: 0.8657 (tttt) cc_final: 0.8227 (tttt) REVERT: A 117 PHE cc_start: 0.7872 (m-10) cc_final: 0.7662 (m-10) REVERT: A 118 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 124 GLN cc_start: 0.8196 (pp30) cc_final: 0.7924 (pp30) REVERT: A 125 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.7900 (Cg_exo) REVERT: A 146 THR cc_start: 0.8264 (p) cc_final: 0.7897 (p) REVERT: A 148 LYS cc_start: 0.8298 (tttt) cc_final: 0.7855 (ttmt) REVERT: A 157 LEU cc_start: 0.8020 (tp) cc_final: 0.7745 (tp) REVERT: A 169 GLU cc_start: 0.7688 (tt0) cc_final: 0.7108 (tt0) REVERT: A 177 VAL cc_start: 0.8618 (t) cc_final: 0.8407 (t) REVERT: A 179 SER cc_start: 0.8785 (t) cc_final: 0.8481 (p) REVERT: A 180 LEU cc_start: 0.8268 (tp) cc_final: 0.8062 (tt) REVERT: A 193 GLU cc_start: 0.7716 (tt0) cc_final: 0.7497 (tt0) REVERT: A 206 HIS cc_start: 0.7994 (p90) cc_final: 0.7263 (p90) REVERT: A 211 MET cc_start: 0.7921 (mmp) cc_final: 0.7354 (mmp) REVERT: A 212 MET cc_start: 0.7782 (mmp) cc_final: 0.7554 (mmp) REVERT: A 213 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7789 (mtmt) REVERT: A 215 GLN cc_start: 0.7643 (tp-100) cc_final: 0.6542 (tp-100) REVERT: A 217 MET cc_start: 0.8049 (mpp) cc_final: 0.7606 (mpp) REVERT: A 218 SER cc_start: 0.8624 (p) cc_final: 0.8225 (p) REVERT: A 219 LEU cc_start: 0.8723 (mt) cc_final: 0.7724 (mt) REVERT: A 251 MET cc_start: 0.7668 (mmm) cc_final: 0.7243 (mmm) REVERT: A 259 GLN cc_start: 0.7451 (mt0) cc_final: 0.7164 (mt0) REVERT: A 270 LYS cc_start: 0.8552 (mmpt) cc_final: 0.8275 (mmtt) REVERT: A 305 ASP cc_start: 0.8323 (m-30) cc_final: 0.8084 (m-30) REVERT: A 338 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7693 (mtp85) REVERT: A 341 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 342 LYS cc_start: 0.8711 (mptt) cc_final: 0.8270 (mptt) REVERT: B 74 MET cc_start: 0.8024 (mtm) cc_final: 0.7395 (mtm) REVERT: B 85 ASN cc_start: 0.8054 (p0) cc_final: 0.7854 (p0) REVERT: B 104 LYS cc_start: 0.8462 (tttt) cc_final: 0.8148 (tttt) REVERT: B 149 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7185 (mm-30) REVERT: B 152 CYS cc_start: 0.6938 (m) cc_final: 0.6688 (m) REVERT: B 157 LEU cc_start: 0.8125 (tp) cc_final: 0.7696 (tp) REVERT: B 158 GLN cc_start: 0.7251 (pm20) cc_final: 0.6331 (pm20) REVERT: B 211 MET cc_start: 0.7930 (mmp) cc_final: 0.7590 (mmp) REVERT: B 213 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7578 (mtmt) REVERT: B 215 GLN cc_start: 0.7438 (tp-100) cc_final: 0.6516 (tp-100) REVERT: B 217 MET cc_start: 0.8056 (mpp) cc_final: 0.7566 (mpp) REVERT: B 231 VAL cc_start: 0.7780 (t) cc_final: 0.7491 (p) REVERT: B 237 THR cc_start: 0.7990 (t) cc_final: 0.7246 (m) REVERT: B 241 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8103 (mm-40) REVERT: B 243 LEU cc_start: 0.8399 (mt) cc_final: 0.8152 (mt) REVERT: B 259 GLN cc_start: 0.7777 (mt0) cc_final: 0.7357 (mt0) REVERT: B 266 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6939 (tm-30) REVERT: B 270 LYS cc_start: 0.8413 (mmmt) cc_final: 0.7927 (mptt) REVERT: B 295 SER cc_start: 0.7129 (p) cc_final: 0.6781 (p) REVERT: B 299 LEU cc_start: 0.8783 (mt) cc_final: 0.8440 (mt) REVERT: B 305 ASP cc_start: 0.8319 (m-30) cc_final: 0.7704 (m-30) REVERT: B 338 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8067 (mtp85) REVERT: B 341 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 342 LYS cc_start: 0.8564 (mptt) cc_final: 0.7679 (mptt) REVERT: B 343 MET cc_start: 0.8178 (tpt) cc_final: 0.6736 (tpt) REVERT: B 345 LYS cc_start: 0.8766 (pptt) cc_final: 0.8450 (pptt) REVERT: B 346 SER cc_start: 0.8613 (p) cc_final: 0.8406 (p) REVERT: B 347 LYS cc_start: 0.8923 (mptt) cc_final: 0.8399 (mptt) REVERT: C 86 MET cc_start: 0.5494 (pmm) cc_final: 0.5206 (pmm) REVERT: C 158 GLN cc_start: 0.8193 (pm20) cc_final: 0.7757 (pm20) REVERT: C 167 TYR cc_start: 0.7311 (m-10) cc_final: 0.6960 (m-10) REVERT: C 171 GLN cc_start: 0.8323 (mm110) cc_final: 0.7847 (mm-40) REVERT: C 212 MET cc_start: 0.7476 (mmp) cc_final: 0.6988 (mmp) REVERT: C 215 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7223 (tm-30) REVERT: C 239 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7046 (mtt90) REVERT: C 245 SER cc_start: 0.8181 (t) cc_final: 0.7901 (t) REVERT: C 248 MET cc_start: 0.7754 (mtp) cc_final: 0.7120 (mtp) REVERT: C 264 GLN cc_start: 0.8271 (mp10) cc_final: 0.7879 (mp10) REVERT: C 270 LYS cc_start: 0.8505 (mmmt) cc_final: 0.7473 (mmmt) REVERT: C 289 GLN cc_start: 0.8117 (mt0) cc_final: 0.7768 (mt0) REVERT: C 299 LEU cc_start: 0.8558 (mt) cc_final: 0.8221 (mt) REVERT: C 300 LYS cc_start: 0.8923 (tttt) cc_final: 0.8656 (tttt) REVERT: C 302 MET cc_start: 0.7962 (tmm) cc_final: 0.7651 (tmm) REVERT: C 304 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8241 (mmm160) REVERT: C 308 LEU cc_start: 0.8559 (tp) cc_final: 0.8256 (tp) REVERT: C 313 GLU cc_start: 0.8089 (pt0) cc_final: 0.7834 (pt0) REVERT: C 335 ASP cc_start: 0.7930 (m-30) cc_final: 0.7665 (m-30) REVERT: C 343 MET cc_start: 0.8214 (tpt) cc_final: 0.7394 (tpt) REVERT: C 344 LYS cc_start: 0.9026 (mttm) cc_final: 0.8624 (mttm) REVERT: D 82 ASP cc_start: 0.8115 (t0) cc_final: 0.7759 (t70) REVERT: D 104 LYS cc_start: 0.8336 (tttt) cc_final: 0.7974 (tttm) REVERT: D 132 TYR cc_start: 0.7550 (p90) cc_final: 0.7265 (p90) REVERT: D 139 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7165 (mtmm) REVERT: D 183 LYS cc_start: 0.8483 (mptt) cc_final: 0.8071 (mptt) REVERT: D 212 MET cc_start: 0.7681 (mmp) cc_final: 0.7392 (mmp) REVERT: D 241 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7230 (mm-40) REVERT: D 291 THR cc_start: 0.6481 (p) cc_final: 0.5862 (t) REVERT: D 300 LYS cc_start: 0.8613 (tptm) cc_final: 0.8126 (tptm) REVERT: D 302 MET cc_start: 0.7701 (tmm) cc_final: 0.7440 (tmm) REVERT: D 305 ASP cc_start: 0.7520 (t0) cc_final: 0.7095 (t0) REVERT: D 337 HIS cc_start: 0.7547 (m170) cc_final: 0.7252 (m90) REVERT: E 158 GLN cc_start: 0.8195 (pm20) cc_final: 0.7824 (pm20) REVERT: E 171 GLN cc_start: 0.8539 (mm110) cc_final: 0.8129 (mp10) REVERT: E 193 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7179 (mt-10) REVERT: E 205 ASP cc_start: 0.4916 (m-30) cc_final: 0.4652 (m-30) REVERT: E 212 MET cc_start: 0.7700 (mmp) cc_final: 0.7039 (mmp) REVERT: E 217 MET cc_start: 0.8561 (ptp) cc_final: 0.7874 (tpp) REVERT: E 239 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7294 (ttp-110) REVERT: E 248 MET cc_start: 0.7893 (mtp) cc_final: 0.7347 (mtp) REVERT: E 250 ARG cc_start: 0.6119 (mmm160) cc_final: 0.5813 (mmm160) REVERT: E 266 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7260 (tm-30) REVERT: E 270 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7340 (mmmt) REVERT: E 286 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7591 (mm-30) REVERT: E 290 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7450 (mm-30) REVERT: E 298 ASP cc_start: 0.7471 (m-30) cc_final: 0.7020 (m-30) REVERT: E 299 LEU cc_start: 0.8704 (mt) cc_final: 0.8243 (mt) REVERT: E 300 LYS cc_start: 0.8757 (tttt) cc_final: 0.8487 (tttt) REVERT: E 301 GLU cc_start: 0.8090 (tt0) cc_final: 0.7623 (tt0) REVERT: E 302 MET cc_start: 0.8044 (tmm) cc_final: 0.7669 (tmm) REVERT: E 304 ARG cc_start: 0.8559 (mtp-110) cc_final: 0.8296 (mmm-85) REVERT: E 313 GLU cc_start: 0.8358 (pt0) cc_final: 0.8122 (pt0) REVERT: E 336 LEU cc_start: 0.8846 (mp) cc_final: 0.8612 (mp) REVERT: E 341 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 343 MET cc_start: 0.8261 (tpt) cc_final: 0.7300 (tpt) REVERT: F 74 MET cc_start: 0.7503 (mtm) cc_final: 0.7150 (mtm) REVERT: F 82 ASP cc_start: 0.8317 (t0) cc_final: 0.7925 (t0) REVERT: F 90 TRP cc_start: 0.8167 (m100) cc_final: 0.7561 (m100) REVERT: F 102 ASP cc_start: 0.7950 (m-30) cc_final: 0.7654 (m-30) REVERT: F 104 LYS cc_start: 0.8345 (tttt) cc_final: 0.8056 (ttmt) REVERT: F 112 LYS cc_start: 0.7835 (mttt) cc_final: 0.7630 (mttt) REVERT: F 131 LEU cc_start: 0.8446 (mp) cc_final: 0.8212 (mt) REVERT: F 180 LEU cc_start: 0.7954 (tt) cc_final: 0.7722 (tt) REVERT: F 183 LYS cc_start: 0.8487 (mptt) cc_final: 0.8097 (mptt) REVERT: F 212 MET cc_start: 0.7903 (mmp) cc_final: 0.7694 (mmp) REVERT: F 217 MET cc_start: 0.7459 (mmt) cc_final: 0.6935 (mmt) REVERT: F 241 GLN cc_start: 0.7926 (mm110) cc_final: 0.7441 (mm-40) REVERT: F 248 MET cc_start: 0.6962 (mtp) cc_final: 0.6362 (mtp) REVERT: F 270 LYS cc_start: 0.8417 (pttp) cc_final: 0.7957 (ptmm) REVERT: F 300 LYS cc_start: 0.8282 (tptm) cc_final: 0.7912 (tptm) REVERT: F 302 MET cc_start: 0.7712 (tmm) cc_final: 0.7378 (tmm) REVERT: F 304 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.7140 (tpp-160) REVERT: F 337 HIS cc_start: 0.7679 (m170) cc_final: 0.7357 (m170) outliers start: 1 outliers final: 1 residues processed: 595 average time/residue: 0.3040 time to fit residues: 251.4242 Evaluate side-chains 568 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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: 3.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 241 GLN ** 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 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** 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 = 0.4069 r_free = 0.4069 target = 0.150526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123344 restraints weight = 30589.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.128089 restraints weight = 18275.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131334 restraints weight = 12341.356| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4282 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= 0.213 Angle : 0.619 11.721 19146 Z= 0.327 Chirality : 0.044 0.305 2190 Planarity : 0.005 0.054 2448 Dihedral : 10.882 105.265 1962 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % 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: 1.19 (0.21), residues: 1728 helix: 1.07 (0.16), residues: 978 sheet: 0.68 (0.41), residues: 192 loop : 0.57 (0.31), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 90 HIS 0.010 0.001 HIS B 337 PHE 0.036 0.003 PHE F 216 TYR 0.014 0.002 TYR F 132 ARG 0.009 0.001 ARG E 265 *********************** 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 609 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 1.618 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: A 74 MET cc_start: 0.8223 (mtm) cc_final: 0.7812 (mtm) REVERT: A 104 LYS cc_start: 0.8630 (tttt) cc_final: 0.8198 (tttt) REVERT: A 118 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 124 GLN cc_start: 0.8179 (pp30) cc_final: 0.7951 (pp30) REVERT: A 125 PRO cc_start: 0.8455 (Cg_endo) cc_final: 0.7978 (Cg_exo) REVERT: A 146 THR cc_start: 0.8329 (p) cc_final: 0.7980 (p) REVERT: A 148 LYS cc_start: 0.8332 (tttt) cc_final: 0.7807 (ttmt) REVERT: A 157 LEU cc_start: 0.8004 (tp) cc_final: 0.7662 (tp) REVERT: A 169 GLU cc_start: 0.7589 (tt0) cc_final: 0.7367 (tt0) REVERT: A 179 SER cc_start: 0.8808 (t) cc_final: 0.8508 (p) REVERT: A 180 LEU cc_start: 0.8378 (tp) cc_final: 0.8162 (tt) REVERT: A 206 HIS cc_start: 0.8086 (p90) cc_final: 0.7406 (p90) REVERT: A 211 MET cc_start: 0.7999 (mmp) cc_final: 0.7457 (mmp) REVERT: A 212 MET cc_start: 0.7952 (mmp) cc_final: 0.7674 (mmp) REVERT: A 213 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7754 (mtmt) REVERT: A 215 GLN cc_start: 0.7766 (tp-100) cc_final: 0.6714 (tp-100) REVERT: A 217 MET cc_start: 0.8122 (mpp) cc_final: 0.7605 (mpp) REVERT: A 218 SER cc_start: 0.8627 (p) cc_final: 0.8182 (p) REVERT: A 219 LEU cc_start: 0.8751 (mt) cc_final: 0.7867 (mt) REVERT: A 251 MET cc_start: 0.7665 (mmm) cc_final: 0.7174 (mmm) REVERT: A 259 GLN cc_start: 0.7585 (mt0) cc_final: 0.7238 (mt0) REVERT: A 270 LYS cc_start: 0.8520 (mmpt) cc_final: 0.8210 (mmtt) REVERT: A 304 ARG cc_start: 0.7626 (mmp-170) cc_final: 0.7395 (mmm160) REVERT: A 305 ASP cc_start: 0.8360 (m-30) cc_final: 0.8126 (m-30) REVERT: A 338 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7776 (mtp85) REVERT: A 341 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 342 LYS cc_start: 0.8747 (mptt) cc_final: 0.8333 (mptt) REVERT: B 74 MET cc_start: 0.8060 (mtm) cc_final: 0.7399 (mtm) REVERT: B 86 MET cc_start: 0.7970 (mtm) cc_final: 0.7659 (mtm) REVERT: B 104 LYS cc_start: 0.8508 (tttt) cc_final: 0.8150 (tttt) REVERT: B 123 LEU cc_start: 0.8067 (tp) cc_final: 0.7840 (tp) REVERT: B 124 GLN cc_start: 0.8072 (pp30) cc_final: 0.7696 (pp30) REVERT: B 131 LEU cc_start: 0.8128 (mp) cc_final: 0.7814 (tp) REVERT: B 144 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8423 (mtpt) REVERT: B 149 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 152 CYS cc_start: 0.7274 (m) cc_final: 0.6992 (m) REVERT: B 154 PHE cc_start: 0.7681 (t80) cc_final: 0.7049 (t80) REVERT: B 157 LEU cc_start: 0.8056 (tp) cc_final: 0.7671 (tp) REVERT: B 158 GLN cc_start: 0.7355 (pm20) cc_final: 0.6462 (pm20) REVERT: B 211 MET cc_start: 0.8031 (mmp) cc_final: 0.7681 (mmp) REVERT: B 213 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7589 (mtmt) REVERT: B 215 GLN cc_start: 0.7481 (tp-100) cc_final: 0.6551 (tp-100) REVERT: B 217 MET cc_start: 0.8231 (mpp) cc_final: 0.7722 (mpp) REVERT: B 237 THR cc_start: 0.8172 (t) cc_final: 0.7496 (m) REVERT: B 241 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8585 (mm-40) REVERT: B 243 LEU cc_start: 0.8503 (mt) cc_final: 0.8263 (mt) REVERT: B 259 GLN cc_start: 0.7834 (mt0) cc_final: 0.7420 (mt0) REVERT: B 266 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 270 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7865 (mptt) REVERT: B 273 LEU cc_start: 0.8098 (mm) cc_final: 0.7884 (mm) REVERT: B 295 SER cc_start: 0.6947 (p) cc_final: 0.6625 (p) REVERT: B 299 LEU cc_start: 0.8833 (mt) cc_final: 0.8491 (mt) REVERT: B 305 ASP cc_start: 0.8292 (m-30) cc_final: 0.7677 (m-30) REVERT: B 331 VAL cc_start: 0.7736 (t) cc_final: 0.7517 (t) REVERT: B 338 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8217 (mtp85) REVERT: B 341 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 342 LYS cc_start: 0.8652 (mptt) cc_final: 0.7786 (mptt) REVERT: B 343 MET cc_start: 0.8306 (tpt) cc_final: 0.6938 (tpt) REVERT: B 345 LYS cc_start: 0.8747 (pptt) cc_final: 0.8425 (pptt) REVERT: B 346 SER cc_start: 0.8671 (p) cc_final: 0.8456 (p) REVERT: B 347 LYS cc_start: 0.8894 (mptt) cc_final: 0.8372 (mptt) REVERT: C 86 MET cc_start: 0.5480 (pmm) cc_final: 0.5163 (pmm) REVERT: C 158 GLN cc_start: 0.8123 (pm20) cc_final: 0.7647 (pm20) REVERT: C 167 TYR cc_start: 0.7603 (m-10) cc_final: 0.7207 (m-10) REVERT: C 170 SER cc_start: 0.8128 (p) cc_final: 0.7742 (p) REVERT: C 171 GLN cc_start: 0.8362 (mm110) cc_final: 0.7878 (mp10) REVERT: C 212 MET cc_start: 0.7614 (mmp) cc_final: 0.7143 (mmp) REVERT: C 215 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7416 (tm-30) REVERT: C 239 ARG cc_start: 0.7829 (mtt90) cc_final: 0.6990 (mtt90) REVERT: C 245 SER cc_start: 0.8212 (t) cc_final: 0.7727 (t) REVERT: C 248 MET cc_start: 0.7807 (mtp) cc_final: 0.7223 (mtp) REVERT: C 264 GLN cc_start: 0.8412 (mp10) cc_final: 0.7999 (mp10) REVERT: C 270 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7496 (mmmt) REVERT: C 289 GLN cc_start: 0.8161 (mt0) cc_final: 0.7771 (mt0) REVERT: C 295 SER cc_start: 0.8125 (p) cc_final: 0.7772 (p) REVERT: C 298 ASP cc_start: 0.7524 (m-30) cc_final: 0.7133 (m-30) REVERT: C 299 LEU cc_start: 0.8631 (mt) cc_final: 0.8266 (mt) REVERT: C 300 LYS cc_start: 0.8954 (tttt) cc_final: 0.8613 (tttt) REVERT: C 302 MET cc_start: 0.8104 (tmm) cc_final: 0.7746 (tmm) REVERT: C 304 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8041 (mtp85) REVERT: C 308 LEU cc_start: 0.8592 (tp) cc_final: 0.8345 (tp) REVERT: C 309 LEU cc_start: 0.8795 (tp) cc_final: 0.8433 (tp) REVERT: C 312 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8086 (mtp-110) REVERT: C 313 GLU cc_start: 0.8141 (pt0) cc_final: 0.7885 (pt0) REVERT: C 343 MET cc_start: 0.8262 (tpt) cc_final: 0.7602 (tpt) REVERT: C 344 LYS cc_start: 0.9041 (mttm) cc_final: 0.8701 (mttm) REVERT: D 82 ASP cc_start: 0.8227 (t0) cc_final: 0.7846 (t70) REVERT: D 104 LYS cc_start: 0.8403 (tttt) cc_final: 0.8058 (tttm) REVERT: D 132 TYR cc_start: 0.7584 (p90) cc_final: 0.7259 (p90) REVERT: D 139 LYS cc_start: 0.7801 (mtmm) cc_final: 0.7388 (mtmm) REVERT: D 179 SER cc_start: 0.8202 (p) cc_final: 0.7991 (p) REVERT: D 183 LYS cc_start: 0.8488 (mptt) cc_final: 0.8138 (mptt) REVERT: D 211 MET cc_start: 0.7629 (mmp) cc_final: 0.7221 (mmp) REVERT: D 212 MET cc_start: 0.7771 (mmp) cc_final: 0.7475 (mmp) REVERT: D 241 GLN cc_start: 0.8259 (mp-120) cc_final: 0.7208 (mm-40) REVERT: D 250 ARG cc_start: 0.7474 (ttt-90) cc_final: 0.7043 (ttt180) REVERT: D 259 GLN cc_start: 0.8422 (mp-120) cc_final: 0.8141 (mp10) REVERT: D 291 THR cc_start: 0.6719 (p) cc_final: 0.6216 (p) REVERT: D 300 LYS cc_start: 0.8695 (tptm) cc_final: 0.8372 (tptm) REVERT: D 302 MET cc_start: 0.7857 (tmm) cc_final: 0.7288 (tmm) REVERT: D 305 ASP cc_start: 0.7552 (t0) cc_final: 0.7242 (t0) REVERT: D 309 LEU cc_start: 0.8348 (tp) cc_final: 0.8030 (tp) REVERT: D 312 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7835 (ptp-170) REVERT: D 337 HIS cc_start: 0.7697 (m170) cc_final: 0.7339 (m170) REVERT: E 139 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7854 (pttm) REVERT: E 158 GLN cc_start: 0.8091 (pm20) cc_final: 0.7650 (pm20) REVERT: E 167 TYR cc_start: 0.7293 (m-10) cc_final: 0.6900 (m-10) REVERT: E 171 GLN cc_start: 0.8600 (mm110) cc_final: 0.8163 (mp10) REVERT: E 193 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7348 (mt-10) REVERT: E 205 ASP cc_start: 0.5248 (m-30) cc_final: 0.4990 (m-30) REVERT: E 212 MET cc_start: 0.7798 (mmp) cc_final: 0.7155 (mmp) REVERT: E 215 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7135 (tm-30) REVERT: E 217 MET cc_start: 0.8523 (ptp) cc_final: 0.7867 (tpp) REVERT: E 248 MET cc_start: 0.7840 (mtp) cc_final: 0.7307 (mtp) REVERT: E 251 MET cc_start: 0.6796 (mpp) cc_final: 0.6275 (mpp) REVERT: E 256 HIS cc_start: 0.7809 (t70) cc_final: 0.7521 (t70) REVERT: E 264 GLN cc_start: 0.8533 (mp10) cc_final: 0.8178 (mp10) REVERT: E 266 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7534 (tm-30) REVERT: E 270 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7371 (mmmt) REVERT: E 284 LEU cc_start: 0.8888 (mt) cc_final: 0.8677 (mt) REVERT: E 290 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7608 (mm-30) REVERT: E 298 ASP cc_start: 0.7542 (m-30) cc_final: 0.7058 (m-30) REVERT: E 299 LEU cc_start: 0.8704 (mt) cc_final: 0.8300 (mt) REVERT: E 300 LYS cc_start: 0.8774 (tttt) cc_final: 0.8522 (tttt) REVERT: E 302 MET cc_start: 0.8183 (tmm) cc_final: 0.7776 (tmm) REVERT: E 304 ARG cc_start: 0.8610 (mtp-110) cc_final: 0.8358 (mmm-85) REVERT: E 313 GLU cc_start: 0.8404 (pt0) cc_final: 0.8157 (pt0) REVERT: E 335 ASP cc_start: 0.8449 (m-30) cc_final: 0.7743 (m-30) REVERT: E 336 LEU cc_start: 0.8903 (mp) cc_final: 0.8580 (mp) REVERT: E 341 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7800 (mm-30) REVERT: F 74 MET cc_start: 0.7675 (mtm) cc_final: 0.7282 (mtm) REVERT: F 82 ASP cc_start: 0.8296 (t0) cc_final: 0.7944 (t0) REVERT: F 90 TRP cc_start: 0.8214 (m100) cc_final: 0.7615 (m100) REVERT: F 102 ASP cc_start: 0.8046 (m-30) cc_final: 0.7739 (m-30) REVERT: F 104 LYS cc_start: 0.8372 (tttt) cc_final: 0.8130 (tttt) REVERT: F 131 LEU cc_start: 0.8418 (mp) cc_final: 0.8063 (mt) REVERT: F 132 TYR cc_start: 0.7584 (p90) cc_final: 0.7350 (p90) REVERT: F 180 LEU cc_start: 0.8152 (tt) cc_final: 0.7934 (tt) REVERT: F 183 LYS cc_start: 0.8622 (mptt) cc_final: 0.8206 (mptt) REVERT: F 211 MET cc_start: 0.7445 (mmp) cc_final: 0.7097 (mmp) REVERT: F 212 MET cc_start: 0.8125 (mmp) cc_final: 0.7830 (mmp) REVERT: F 215 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7567 (tm-30) REVERT: F 217 MET cc_start: 0.7659 (mmt) cc_final: 0.6981 (mmt) REVERT: F 241 GLN cc_start: 0.8083 (mm110) cc_final: 0.7474 (mm110) REVERT: F 248 MET cc_start: 0.6999 (mtp) cc_final: 0.6645 (mtp) REVERT: F 251 MET cc_start: 0.7777 (mpp) cc_final: 0.7063 (mpp) REVERT: F 270 LYS cc_start: 0.8404 (pttp) cc_final: 0.7931 (ptmm) REVERT: F 298 ASP cc_start: 0.8102 (m-30) cc_final: 0.7830 (m-30) REVERT: F 300 LYS cc_start: 0.8406 (tptm) cc_final: 0.7986 (tptm) REVERT: F 302 MET cc_start: 0.7828 (tmm) cc_final: 0.7388 (tmm) REVERT: F 304 ARG cc_start: 0.7272 (tpp-160) cc_final: 0.6856 (tpp-160) REVERT: F 308 LEU cc_start: 0.8269 (pp) cc_final: 0.7955 (pp) REVERT: F 337 HIS cc_start: 0.7771 (m170) cc_final: 0.7434 (m170) outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 0.3111 time to fit residues: 267.3757 Evaluate side-chains 587 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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: 0.9990 chunk 145 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 142 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 B 79 HIS B 241 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4087 r_free = 0.4087 target = 0.154392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127208 restraints weight = 30262.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131917 restraints weight = 18300.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.135177 restraints weight = 12445.254| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14142 Z= 0.195 Angle : 0.605 12.424 19146 Z= 0.318 Chirality : 0.044 0.245 2190 Planarity : 0.004 0.052 2448 Dihedral : 10.835 105.251 1962 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.07 % Allowed : 1.18 % Favored : 98.76 % 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: 1.29 (0.21), residues: 1728 helix: 1.16 (0.16), residues: 978 sheet: 0.59 (0.41), residues: 192 loop : 0.64 (0.31), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 220 HIS 0.003 0.001 HIS A 115 PHE 0.040 0.002 PHE C 216 TYR 0.013 0.002 TYR A 72 ARG 0.009 0.001 ARG B 304 *********************** 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: 1 poor density : 613 time to evaluate : 1.464 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: 0.8183 (mtm) cc_final: 0.7727 (mtm) REVERT: A 104 LYS cc_start: 0.8650 (tttt) cc_final: 0.8226 (tttt) REVERT: A 118 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 123 LEU cc_start: 0.8353 (tp) cc_final: 0.8136 (tp) REVERT: A 124 GLN cc_start: 0.8126 (pp30) cc_final: 0.7910 (pp30) REVERT: A 125 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8024 (Cg_exo) REVERT: A 148 LYS cc_start: 0.8285 (tttt) cc_final: 0.7733 (ttmt) REVERT: A 157 LEU cc_start: 0.7965 (tp) cc_final: 0.7603 (tp) REVERT: A 158 GLN cc_start: 0.7203 (pm20) cc_final: 0.6708 (pm20) REVERT: A 169 GLU cc_start: 0.7135 (tt0) cc_final: 0.6871 (tt0) REVERT: A 179 SER cc_start: 0.8831 (t) cc_final: 0.8535 (p) REVERT: A 180 LEU cc_start: 0.8392 (tp) cc_final: 0.8183 (tp) REVERT: A 193 GLU cc_start: 0.7788 (tt0) cc_final: 0.7581 (tt0) REVERT: A 206 HIS cc_start: 0.8048 (p90) cc_final: 0.7392 (p90) REVERT: A 211 MET cc_start: 0.7933 (mmp) cc_final: 0.7321 (mmp) REVERT: A 212 MET cc_start: 0.7881 (mmp) cc_final: 0.7597 (mmp) REVERT: A 213 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7772 (mtmt) REVERT: A 215 GLN cc_start: 0.7661 (tp-100) cc_final: 0.6535 (tp-100) REVERT: A 217 MET cc_start: 0.8009 (mpp) cc_final: 0.7601 (mpp) REVERT: A 218 SER cc_start: 0.8669 (p) cc_final: 0.8270 (p) REVERT: A 219 LEU cc_start: 0.8777 (mt) cc_final: 0.7683 (mt) REVERT: A 248 MET cc_start: 0.7841 (mtp) cc_final: 0.7568 (mtp) REVERT: A 251 MET cc_start: 0.7651 (mmm) cc_final: 0.7183 (mmm) REVERT: A 259 GLN cc_start: 0.7620 (mt0) cc_final: 0.7319 (mt0) REVERT: A 266 GLU cc_start: 0.7902 (tp30) cc_final: 0.7426 (tp30) REVERT: A 270 LYS cc_start: 0.8517 (mmpt) cc_final: 0.8226 (mmtt) REVERT: A 301 GLU cc_start: 0.7853 (tt0) cc_final: 0.7040 (tt0) REVERT: A 304 ARG cc_start: 0.7600 (mmp-170) cc_final: 0.7386 (mmm160) REVERT: A 305 ASP cc_start: 0.8342 (m-30) cc_final: 0.8067 (m-30) REVERT: A 338 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7719 (mtp85) REVERT: A 341 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 342 LYS cc_start: 0.8743 (mptt) cc_final: 0.8313 (mptt) REVERT: A 343 MET cc_start: 0.8059 (mmm) cc_final: 0.7800 (mmm) REVERT: B 74 MET cc_start: 0.8059 (mtm) cc_final: 0.7336 (mtm) REVERT: B 104 LYS cc_start: 0.8536 (tttt) cc_final: 0.8225 (tttt) REVERT: B 122 LEU cc_start: 0.8378 (pt) cc_final: 0.7867 (tp) REVERT: B 123 LEU cc_start: 0.8162 (tp) cc_final: 0.7779 (tp) REVERT: B 124 GLN cc_start: 0.8126 (pp30) cc_final: 0.7812 (pp30) REVERT: B 131 LEU cc_start: 0.8236 (mp) cc_final: 0.7854 (tp) REVERT: B 144 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8398 (mtpt) REVERT: B 149 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 152 CYS cc_start: 0.7171 (m) cc_final: 0.6870 (m) REVERT: B 154 PHE cc_start: 0.7727 (t80) cc_final: 0.7148 (t80) REVERT: B 157 LEU cc_start: 0.8058 (tp) cc_final: 0.7689 (tp) REVERT: B 158 GLN cc_start: 0.7403 (pm20) cc_final: 0.6478 (pm20) REVERT: B 211 MET cc_start: 0.7982 (mmp) cc_final: 0.7619 (mmp) REVERT: B 213 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7649 (mtmt) REVERT: B 215 GLN cc_start: 0.7487 (tp-100) cc_final: 0.6218 (tp-100) REVERT: B 217 MET cc_start: 0.8106 (mpp) cc_final: 0.7653 (mpp) REVERT: B 219 LEU cc_start: 0.8763 (mt) cc_final: 0.7642 (mt) REVERT: B 241 GLN cc_start: 0.8849 (mm110) cc_final: 0.8641 (mm-40) REVERT: B 243 LEU cc_start: 0.8527 (mt) cc_final: 0.8263 (mt) REVERT: B 259 GLN cc_start: 0.7856 (mt0) cc_final: 0.7430 (mt0) REVERT: B 266 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 270 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7863 (mptt) REVERT: B 295 SER cc_start: 0.6945 (p) cc_final: 0.6606 (p) REVERT: B 299 LEU cc_start: 0.8821 (mt) cc_final: 0.8476 (mt) REVERT: B 305 ASP cc_start: 0.8291 (m-30) cc_final: 0.7624 (m-30) REVERT: B 338 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8117 (mtp85) REVERT: B 341 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7353 (mm-30) REVERT: B 342 LYS cc_start: 0.8575 (mptt) cc_final: 0.7853 (mptt) REVERT: B 343 MET cc_start: 0.8280 (tpt) cc_final: 0.6838 (tpt) REVERT: B 347 LYS cc_start: 0.8951 (mptt) cc_final: 0.8426 (mptt) REVERT: C 86 MET cc_start: 0.5505 (pmm) cc_final: 0.5187 (pmm) REVERT: C 158 GLN cc_start: 0.8114 (pm20) cc_final: 0.7615 (pm20) REVERT: C 167 TYR cc_start: 0.7561 (m-10) cc_final: 0.7141 (m-10) REVERT: C 170 SER cc_start: 0.8028 (p) cc_final: 0.7340 (p) REVERT: C 171 GLN cc_start: 0.8397 (mm110) cc_final: 0.7873 (mp10) REVERT: C 212 MET cc_start: 0.7744 (mmp) cc_final: 0.7388 (mmp) REVERT: C 215 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7549 (tm-30) REVERT: C 219 LEU cc_start: 0.7222 (mt) cc_final: 0.6999 (mt) REVERT: C 226 ASP cc_start: 0.5566 (t0) cc_final: 0.5361 (t0) REVERT: C 239 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7059 (mtt90) REVERT: C 245 SER cc_start: 0.8227 (t) cc_final: 0.7885 (t) REVERT: C 248 MET cc_start: 0.7772 (mtp) cc_final: 0.7137 (mtp) REVERT: C 264 GLN cc_start: 0.8406 (mp10) cc_final: 0.8017 (mp10) REVERT: C 270 LYS cc_start: 0.8535 (mmmt) cc_final: 0.7683 (mmmt) REVERT: C 289 GLN cc_start: 0.8224 (mt0) cc_final: 0.7772 (mt0) REVERT: C 295 SER cc_start: 0.8131 (p) cc_final: 0.7779 (p) REVERT: C 298 ASP cc_start: 0.7424 (m-30) cc_final: 0.7079 (m-30) REVERT: C 299 LEU cc_start: 0.8643 (mt) cc_final: 0.8292 (mt) REVERT: C 300 LYS cc_start: 0.8888 (tttt) cc_final: 0.8546 (tttt) REVERT: C 302 MET cc_start: 0.8119 (tmm) cc_final: 0.7785 (tmm) REVERT: C 304 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7996 (mtp85) REVERT: C 309 LEU cc_start: 0.8775 (tp) cc_final: 0.8455 (tp) REVERT: C 313 GLU cc_start: 0.8136 (pt0) cc_final: 0.7850 (pt0) REVERT: C 343 MET cc_start: 0.8164 (tpt) cc_final: 0.7523 (tpp) REVERT: C 344 LYS cc_start: 0.8975 (mttm) cc_final: 0.8645 (mttm) REVERT: C 347 LYS cc_start: 0.8061 (mppt) cc_final: 0.7837 (mmtt) REVERT: D 82 ASP cc_start: 0.8253 (t0) cc_final: 0.7897 (t70) REVERT: D 104 LYS cc_start: 0.8391 (tttt) cc_final: 0.8090 (ttmt) REVERT: D 139 LYS cc_start: 0.7773 (mtmm) cc_final: 0.7363 (mtmm) REVERT: D 183 LYS cc_start: 0.8444 (mptt) cc_final: 0.8153 (mptt) REVERT: D 212 MET cc_start: 0.7740 (mmp) cc_final: 0.7443 (mmp) REVERT: D 213 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7667 (mtmm) REVERT: D 241 GLN cc_start: 0.8254 (mp-120) cc_final: 0.7210 (mm-40) REVERT: D 259 GLN cc_start: 0.8359 (mp-120) cc_final: 0.8138 (mp10) REVERT: D 263 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7571 (mmmm) REVERT: D 291 THR cc_start: 0.6940 (p) cc_final: 0.6675 (t) REVERT: D 300 LYS cc_start: 0.8594 (tptm) cc_final: 0.8289 (tptm) REVERT: D 305 ASP cc_start: 0.7476 (t0) cc_final: 0.7178 (t0) REVERT: D 309 LEU cc_start: 0.8342 (tp) cc_final: 0.8012 (tp) REVERT: D 312 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7765 (ptp-170) REVERT: D 337 HIS cc_start: 0.7711 (m170) cc_final: 0.7442 (m90) REVERT: E 139 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7950 (pttm) REVERT: E 158 GLN cc_start: 0.8104 (pm20) cc_final: 0.7730 (pm20) REVERT: E 167 TYR cc_start: 0.7290 (m-10) cc_final: 0.6868 (m-10) REVERT: E 171 GLN cc_start: 0.8538 (mm110) cc_final: 0.8109 (mp10) REVERT: E 193 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 205 ASP cc_start: 0.5189 (m-30) cc_final: 0.4956 (m-30) REVERT: E 212 MET cc_start: 0.7815 (mmp) cc_final: 0.7179 (mmp) REVERT: E 215 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7198 (tm-30) REVERT: E 217 MET cc_start: 0.8576 (ptp) cc_final: 0.7994 (tpp) REVERT: E 248 MET cc_start: 0.7873 (mtp) cc_final: 0.7394 (mtp) REVERT: E 251 MET cc_start: 0.6695 (mpp) cc_final: 0.6258 (tpp) REVERT: E 256 HIS cc_start: 0.7764 (t70) cc_final: 0.7359 (t70) REVERT: E 264 GLN cc_start: 0.8441 (mp10) cc_final: 0.8153 (mp10) REVERT: E 266 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7482 (tm-30) REVERT: E 270 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7416 (mmmt) REVERT: E 290 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7657 (mm-30) REVERT: E 298 ASP cc_start: 0.7335 (m-30) cc_final: 0.6911 (m-30) REVERT: E 299 LEU cc_start: 0.8677 (mt) cc_final: 0.8303 (mt) REVERT: E 300 LYS cc_start: 0.8739 (tttt) cc_final: 0.8512 (tttt) REVERT: E 301 GLU cc_start: 0.8094 (tt0) cc_final: 0.7710 (tt0) REVERT: E 302 MET cc_start: 0.8186 (tmm) cc_final: 0.7753 (tmm) REVERT: E 313 GLU cc_start: 0.8521 (pt0) cc_final: 0.8235 (pt0) REVERT: E 341 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7644 (mm-30) REVERT: F 74 MET cc_start: 0.7619 (mtm) cc_final: 0.7199 (mtm) REVERT: F 82 ASP cc_start: 0.8328 (t0) cc_final: 0.8013 (t0) REVERT: F 102 ASP cc_start: 0.8004 (m-30) cc_final: 0.7724 (m-30) REVERT: F 104 LYS cc_start: 0.8395 (tttt) cc_final: 0.8065 (ttmt) REVERT: F 112 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7558 (mtmt) REVERT: F 131 LEU cc_start: 0.8410 (mp) cc_final: 0.7988 (mt) REVERT: F 139 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7410 (mtmm) REVERT: F 183 LYS cc_start: 0.8554 (mptt) cc_final: 0.8222 (mptt) REVERT: F 211 MET cc_start: 0.7483 (mmp) cc_final: 0.7116 (mmp) REVERT: F 212 MET cc_start: 0.8075 (mmp) cc_final: 0.7703 (mmp) REVERT: F 217 MET cc_start: 0.7546 (mmt) cc_final: 0.6971 (mmt) REVERT: F 241 GLN cc_start: 0.8024 (mm110) cc_final: 0.7478 (mm110) REVERT: F 248 MET cc_start: 0.7015 (mtp) cc_final: 0.6505 (mtp) REVERT: F 270 LYS cc_start: 0.8404 (pttp) cc_final: 0.7934 (ptmm) REVERT: F 298 ASP cc_start: 0.8087 (m-30) cc_final: 0.7817 (m-30) REVERT: F 300 LYS cc_start: 0.8421 (tptm) cc_final: 0.7956 (tptm) REVERT: F 302 MET cc_start: 0.7792 (tmm) cc_final: 0.7422 (tmm) REVERT: F 304 ARG cc_start: 0.7082 (tpp-160) cc_final: 0.6652 (tpp-160) REVERT: F 308 LEU cc_start: 0.8243 (pp) cc_final: 0.7913 (pp) REVERT: F 337 HIS cc_start: 0.7720 (m170) cc_final: 0.7394 (m170) outliers start: 1 outliers final: 1 residues processed: 614 average time/residue: 0.2941 time to fit residues: 251.3951 Evaluate side-chains 583 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 582 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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: 1.9990 chunk 108 optimal weight: 0.0270 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128337 restraints weight = 29943.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.133061 restraints weight = 18015.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136461 restraints weight = 12250.015| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4820 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= 0.171 Angle : 0.595 13.058 19146 Z= 0.312 Chirality : 0.043 0.218 2190 Planarity : 0.004 0.052 2448 Dihedral : 10.754 105.567 1962 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.21), residues: 1728 helix: 1.19 (0.16), residues: 978 sheet: 0.58 (0.41), residues: 192 loop : 0.72 (0.31), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 90 HIS 0.011 0.001 HIS A 337 PHE 0.031 0.002 PHE A 216 TYR 0.015 0.002 TYR E 72 ARG 0.010 0.000 ARG B 304 *********************** 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 603 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8150 (mtm) cc_final: 0.7639 (mtm) REVERT: A 118 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 123 LEU cc_start: 0.8416 (tp) cc_final: 0.8182 (tp) REVERT: A 148 LYS cc_start: 0.8055 (tttt) cc_final: 0.7820 (ttmt) REVERT: A 157 LEU cc_start: 0.8000 (tp) cc_final: 0.7637 (tp) REVERT: A 158 GLN cc_start: 0.7229 (pm20) cc_final: 0.6507 (pm20) REVERT: A 169 GLU cc_start: 0.7098 (tt0) cc_final: 0.6823 (tt0) REVERT: A 179 SER cc_start: 0.8859 (t) cc_final: 0.8561 (p) REVERT: A 206 HIS cc_start: 0.8069 (p90) cc_final: 0.7393 (p90) REVERT: A 211 MET cc_start: 0.7963 (mmp) cc_final: 0.7323 (mmp) REVERT: A 212 MET cc_start: 0.7900 (mmp) cc_final: 0.7614 (mmp) REVERT: A 213 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7760 (mtmt) REVERT: A 215 GLN cc_start: 0.7513 (tp-100) cc_final: 0.6214 (tp-100) REVERT: A 216 PHE cc_start: 0.7959 (t80) cc_final: 0.7737 (t80) REVERT: A 217 MET cc_start: 0.8095 (mpp) cc_final: 0.7556 (mpp) REVERT: A 219 LEU cc_start: 0.8805 (mt) cc_final: 0.7577 (mt) REVERT: A 248 MET cc_start: 0.7639 (mtp) cc_final: 0.7419 (mtp) REVERT: A 250 ARG cc_start: 0.7573 (mtt-85) cc_final: 0.7095 (mtt-85) REVERT: A 251 MET cc_start: 0.7340 (mmm) cc_final: 0.6873 (mmm) REVERT: A 259 GLN cc_start: 0.7678 (mt0) cc_final: 0.7308 (mt0) REVERT: A 266 GLU cc_start: 0.7841 (tp30) cc_final: 0.7417 (tp30) REVERT: A 270 LYS cc_start: 0.8487 (mmpt) cc_final: 0.8235 (mmtt) REVERT: A 301 GLU cc_start: 0.7813 (tt0) cc_final: 0.6991 (tt0) REVERT: A 304 ARG cc_start: 0.7590 (mmp-170) cc_final: 0.7320 (mmm160) REVERT: A 305 ASP cc_start: 0.8293 (m-30) cc_final: 0.8055 (m-30) REVERT: A 338 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7893 (mtp85) REVERT: A 341 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 342 LYS cc_start: 0.8727 (mptt) cc_final: 0.8318 (mptt) REVERT: A 343 MET cc_start: 0.8070 (mmm) cc_final: 0.7779 (mmm) REVERT: B 74 MET cc_start: 0.8040 (mtm) cc_final: 0.7327 (mtm) REVERT: B 104 LYS cc_start: 0.8585 (tttt) cc_final: 0.8190 (tttt) REVERT: B 123 LEU cc_start: 0.8201 (tp) cc_final: 0.7880 (tp) REVERT: B 124 GLN cc_start: 0.8191 (pp30) cc_final: 0.7893 (pp30) REVERT: B 144 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8317 (mtpt) REVERT: B 149 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 152 CYS cc_start: 0.7088 (m) cc_final: 0.6756 (m) REVERT: B 154 PHE cc_start: 0.7690 (t80) cc_final: 0.7078 (t80) REVERT: B 157 LEU cc_start: 0.8046 (tp) cc_final: 0.7681 (tp) REVERT: B 158 GLN cc_start: 0.7343 (pm20) cc_final: 0.6426 (pm20) REVERT: B 211 MET cc_start: 0.8017 (mmp) cc_final: 0.7642 (mmp) REVERT: B 213 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7715 (mtmt) REVERT: B 215 GLN cc_start: 0.7489 (tp-100) cc_final: 0.6219 (tp-100) REVERT: B 217 MET cc_start: 0.8113 (mpp) cc_final: 0.7551 (mpp) REVERT: B 219 LEU cc_start: 0.8756 (mt) cc_final: 0.7602 (mt) REVERT: B 241 GLN cc_start: 0.8844 (mm110) cc_final: 0.8603 (mm-40) REVERT: B 243 LEU cc_start: 0.8528 (mt) cc_final: 0.8250 (mt) REVERT: B 250 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.7100 (mtt-85) REVERT: B 259 GLN cc_start: 0.7839 (mt0) cc_final: 0.7414 (mt0) REVERT: B 266 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 270 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7833 (mptt) REVERT: B 299 LEU cc_start: 0.8817 (mt) cc_final: 0.8396 (mt) REVERT: B 338 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8191 (mtp85) REVERT: B 341 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 342 LYS cc_start: 0.8535 (mptt) cc_final: 0.8079 (mptt) REVERT: B 343 MET cc_start: 0.8255 (tpt) cc_final: 0.6894 (tpt) REVERT: B 347 LYS cc_start: 0.8926 (mptt) cc_final: 0.8410 (mptt) REVERT: C 86 MET cc_start: 0.5604 (pmm) cc_final: 0.5253 (pmm) REVERT: C 158 GLN cc_start: 0.8072 (pm20) cc_final: 0.7621 (pm20) REVERT: C 167 TYR cc_start: 0.7387 (m-10) cc_final: 0.6993 (m-10) REVERT: C 170 SER cc_start: 0.8140 (p) cc_final: 0.7606 (p) REVERT: C 171 GLN cc_start: 0.8496 (mm110) cc_final: 0.8076 (mp10) REVERT: C 212 MET cc_start: 0.7765 (mmp) cc_final: 0.7380 (mmp) REVERT: C 215 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7545 (tm-30) REVERT: C 219 LEU cc_start: 0.7291 (mt) cc_final: 0.6960 (mt) REVERT: C 239 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7058 (mtt90) REVERT: C 248 MET cc_start: 0.7756 (mtp) cc_final: 0.7103 (mtp) REVERT: C 270 LYS cc_start: 0.8638 (mmmt) cc_final: 0.7751 (mmmt) REVERT: C 289 GLN cc_start: 0.8306 (mt0) cc_final: 0.7871 (mt0) REVERT: C 299 LEU cc_start: 0.8691 (mt) cc_final: 0.8357 (mt) REVERT: C 300 LYS cc_start: 0.8866 (tttt) cc_final: 0.8522 (tttt) REVERT: C 302 MET cc_start: 0.8108 (tmm) cc_final: 0.7788 (tmm) REVERT: C 304 ARG cc_start: 0.8487 (mtp85) cc_final: 0.7954 (mtp85) REVERT: C 309 LEU cc_start: 0.8675 (tp) cc_final: 0.8411 (tp) REVERT: C 313 GLU cc_start: 0.8175 (pt0) cc_final: 0.7855 (pt0) REVERT: C 343 MET cc_start: 0.8155 (tpt) cc_final: 0.7472 (tpt) REVERT: C 344 LYS cc_start: 0.8971 (mttm) cc_final: 0.8613 (mttm) REVERT: D 82 ASP cc_start: 0.8279 (t0) cc_final: 0.7910 (t70) REVERT: D 104 LYS cc_start: 0.8380 (tttt) cc_final: 0.8054 (ttmt) REVERT: D 132 TYR cc_start: 0.7623 (p90) cc_final: 0.7379 (p90) REVERT: D 139 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7420 (mtmm) REVERT: D 183 LYS cc_start: 0.8463 (mptt) cc_final: 0.8142 (mptt) REVERT: D 211 MET cc_start: 0.7623 (mmp) cc_final: 0.7183 (mmp) REVERT: D 212 MET cc_start: 0.7680 (mmp) cc_final: 0.7407 (mmp) REVERT: D 213 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7646 (mtmm) REVERT: D 250 ARG cc_start: 0.7372 (ttt-90) cc_final: 0.7157 (ttt180) REVERT: D 263 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7639 (mmmm) REVERT: D 300 LYS cc_start: 0.8562 (tptm) cc_final: 0.8226 (tptm) REVERT: D 305 ASP cc_start: 0.7468 (t0) cc_final: 0.7184 (t0) REVERT: D 309 LEU cc_start: 0.8326 (tp) cc_final: 0.7954 (tp) REVERT: D 312 ARG cc_start: 0.8099 (ptp-170) cc_final: 0.7796 (ptp-170) REVERT: D 337 HIS cc_start: 0.7716 (m170) cc_final: 0.7454 (m90) REVERT: D 340 ILE cc_start: 0.8768 (mm) cc_final: 0.8532 (mm) REVERT: E 139 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7861 (ptpt) REVERT: E 158 GLN cc_start: 0.8074 (pm20) cc_final: 0.7695 (pm20) REVERT: E 167 TYR cc_start: 0.7164 (m-10) cc_final: 0.6854 (m-10) REVERT: E 171 GLN cc_start: 0.8537 (mm110) cc_final: 0.8155 (mp10) REVERT: E 193 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7184 (mt-10) REVERT: E 212 MET cc_start: 0.7796 (mmp) cc_final: 0.7151 (mmp) REVERT: E 213 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7786 (mtmm) REVERT: E 215 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7192 (tm-30) REVERT: E 217 MET cc_start: 0.8532 (ptp) cc_final: 0.7986 (tpp) REVERT: E 248 MET cc_start: 0.7816 (mtp) cc_final: 0.7314 (mtp) REVERT: E 251 MET cc_start: 0.6835 (mpp) cc_final: 0.6327 (tpp) REVERT: E 256 HIS cc_start: 0.7719 (t70) cc_final: 0.7303 (t70) REVERT: E 264 GLN cc_start: 0.8445 (mp10) cc_final: 0.8111 (mp10) REVERT: E 266 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7568 (tm-30) REVERT: E 270 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7365 (mmmt) REVERT: E 279 ASP cc_start: 0.7174 (p0) cc_final: 0.6816 (t0) REVERT: E 290 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7734 (mm-30) REVERT: E 295 SER cc_start: 0.7706 (p) cc_final: 0.7435 (p) REVERT: E 298 ASP cc_start: 0.7319 (m-30) cc_final: 0.7059 (m-30) REVERT: E 299 LEU cc_start: 0.8674 (mt) cc_final: 0.8354 (mt) REVERT: E 300 LYS cc_start: 0.8688 (tttt) cc_final: 0.8426 (tttt) REVERT: E 301 GLU cc_start: 0.8131 (tt0) cc_final: 0.7672 (tt0) REVERT: E 302 MET cc_start: 0.8214 (tmm) cc_final: 0.7813 (tmm) REVERT: E 304 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8350 (mmm-85) REVERT: E 313 GLU cc_start: 0.8507 (pt0) cc_final: 0.8221 (pt0) REVERT: E 335 ASP cc_start: 0.8335 (m-30) cc_final: 0.7989 (m-30) REVERT: E 341 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7580 (mm-30) REVERT: F 74 MET cc_start: 0.7641 (mtm) cc_final: 0.7186 (mtm) REVERT: F 82 ASP cc_start: 0.8324 (t0) cc_final: 0.8095 (t0) REVERT: F 102 ASP cc_start: 0.7995 (m-30) cc_final: 0.7718 (m-30) REVERT: F 104 LYS cc_start: 0.8385 (tttt) cc_final: 0.8078 (ttmt) REVERT: F 131 LEU cc_start: 0.8448 (mp) cc_final: 0.7986 (mt) REVERT: F 139 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7358 (mtmm) REVERT: F 183 LYS cc_start: 0.8503 (mptt) cc_final: 0.8141 (mptt) REVERT: F 211 MET cc_start: 0.7462 (mmp) cc_final: 0.7063 (mmp) REVERT: F 212 MET cc_start: 0.8128 (mmp) cc_final: 0.7679 (mmp) REVERT: F 217 MET cc_start: 0.7549 (mmt) cc_final: 0.6942 (mmt) REVERT: F 248 MET cc_start: 0.7013 (mtp) cc_final: 0.6503 (mtp) REVERT: F 270 LYS cc_start: 0.8361 (pttp) cc_final: 0.7895 (ptmm) REVERT: F 298 ASP cc_start: 0.8064 (m-30) cc_final: 0.7743 (m-30) REVERT: F 300 LYS cc_start: 0.8415 (tptm) cc_final: 0.7954 (tptm) REVERT: F 302 MET cc_start: 0.7754 (tmm) cc_final: 0.7446 (tmm) REVERT: F 304 ARG cc_start: 0.7089 (tpp-160) cc_final: 0.6620 (tpp-160) REVERT: F 308 LEU cc_start: 0.8184 (pp) cc_final: 0.7826 (pp) REVERT: F 337 HIS cc_start: 0.7728 (m170) cc_final: 0.7402 (m170) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.2932 time to fit residues: 246.3028 Evaluate side-chains 575 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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: 0.2980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 256 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 171 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127666 restraints weight = 29669.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132365 restraints weight = 17869.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135697 restraints weight = 12145.649| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5070 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= 0.191 Angle : 0.611 13.463 19146 Z= 0.322 Chirality : 0.044 0.200 2190 Planarity : 0.004 0.051 2448 Dihedral : 10.798 106.634 1962 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.23 (0.21), residues: 1728 helix: 1.24 (0.17), residues: 942 sheet: 0.63 (0.41), residues: 192 loop : 0.38 (0.30), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 90 HIS 0.011 0.001 HIS E 337 PHE 0.036 0.002 PHE D 216 TYR 0.017 0.002 TYR F 72 ARG 0.011 0.000 ARG B 304 *********************** 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 594 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 1.734 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: 0.8177 (mtm) cc_final: 0.7681 (mtm) REVERT: A 102 ASP cc_start: 0.7796 (m-30) cc_final: 0.7593 (m-30) REVERT: A 104 LYS cc_start: 0.8603 (tttt) cc_final: 0.8181 (tttt) REVERT: A 148 LYS cc_start: 0.8093 (tttt) cc_final: 0.7810 (ttmt) REVERT: A 157 LEU cc_start: 0.8001 (tp) cc_final: 0.7631 (tp) REVERT: A 169 GLU cc_start: 0.7120 (tt0) cc_final: 0.6849 (tt0) REVERT: A 179 SER cc_start: 0.8870 (t) cc_final: 0.8541 (p) REVERT: A 199 ARG cc_start: 0.7396 (tpp80) cc_final: 0.6352 (tpp80) REVERT: A 206 HIS cc_start: 0.8077 (p90) cc_final: 0.7409 (p90) REVERT: A 211 MET cc_start: 0.7966 (mmp) cc_final: 0.7303 (mmp) REVERT: A 212 MET cc_start: 0.7824 (mmp) cc_final: 0.7537 (mmp) REVERT: A 213 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7763 (mtmt) REVERT: A 216 PHE cc_start: 0.8085 (t80) cc_final: 0.7804 (t80) REVERT: A 217 MET cc_start: 0.8091 (mpp) cc_final: 0.7630 (mpp) REVERT: A 219 LEU cc_start: 0.8798 (mt) cc_final: 0.8446 (mt) REVERT: A 251 MET cc_start: 0.7321 (mmm) cc_final: 0.7002 (mmm) REVERT: A 259 GLN cc_start: 0.7686 (mt0) cc_final: 0.7326 (mt0) REVERT: A 266 GLU cc_start: 0.7864 (tp30) cc_final: 0.7374 (tp30) REVERT: A 283 ASP cc_start: 0.7085 (p0) cc_final: 0.6745 (p0) REVERT: A 301 GLU cc_start: 0.7840 (tt0) cc_final: 0.7097 (tt0) REVERT: A 304 ARG cc_start: 0.7419 (mmp-170) cc_final: 0.7068 (tpm170) REVERT: A 305 ASP cc_start: 0.8292 (m-30) cc_final: 0.7995 (m-30) REVERT: A 338 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7666 (mtp85) REVERT: A 341 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 342 LYS cc_start: 0.8782 (mptt) cc_final: 0.8108 (mptt) REVERT: A 343 MET cc_start: 0.8105 (mmm) cc_final: 0.7769 (mmm) REVERT: A 345 LYS cc_start: 0.8726 (pptt) cc_final: 0.8517 (pptt) REVERT: B 74 MET cc_start: 0.8070 (mtm) cc_final: 0.7344 (mtm) REVERT: B 90 TRP cc_start: 0.8206 (m100) cc_final: 0.6933 (m100) REVERT: B 104 LYS cc_start: 0.8542 (tttt) cc_final: 0.8181 (tttt) REVERT: B 123 LEU cc_start: 0.8249 (tp) cc_final: 0.7963 (tp) REVERT: B 124 GLN cc_start: 0.8228 (pp30) cc_final: 0.7965 (pp30) REVERT: B 144 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8266 (mtpt) REVERT: B 146 THR cc_start: 0.8415 (p) cc_final: 0.7792 (p) REVERT: B 152 CYS cc_start: 0.7088 (m) cc_final: 0.6823 (m) REVERT: B 154 PHE cc_start: 0.7655 (t80) cc_final: 0.7113 (t80) REVERT: B 157 LEU cc_start: 0.8062 (tp) cc_final: 0.7704 (tp) REVERT: B 158 GLN cc_start: 0.7350 (pm20) cc_final: 0.6447 (pm20) REVERT: B 211 MET cc_start: 0.8022 (mmp) cc_final: 0.7651 (mmp) REVERT: B 213 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7740 (mtmt) REVERT: B 215 GLN cc_start: 0.7507 (tp-100) cc_final: 0.6217 (tp-100) REVERT: B 217 MET cc_start: 0.8100 (mpp) cc_final: 0.7492 (mpp) REVERT: B 219 LEU cc_start: 0.8783 (mt) cc_final: 0.7625 (mt) REVERT: B 241 GLN cc_start: 0.8828 (mm110) cc_final: 0.8593 (mm-40) REVERT: B 243 LEU cc_start: 0.8535 (mt) cc_final: 0.8233 (mt) REVERT: B 259 GLN cc_start: 0.7845 (mt0) cc_final: 0.7401 (mt0) REVERT: B 266 GLU cc_start: 0.7609 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 270 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7840 (mptt) REVERT: B 286 GLU cc_start: 0.6835 (pm20) cc_final: 0.6449 (pm20) REVERT: B 299 LEU cc_start: 0.8825 (mt) cc_final: 0.8471 (mt) REVERT: B 338 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8038 (mmm-85) REVERT: B 341 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7524 (mm-30) REVERT: B 342 LYS cc_start: 0.8566 (mptt) cc_final: 0.7949 (mptt) REVERT: B 343 MET cc_start: 0.8275 (tpt) cc_final: 0.6897 (tpt) REVERT: B 345 LYS cc_start: 0.8708 (pptt) cc_final: 0.8486 (pptt) REVERT: B 347 LYS cc_start: 0.8943 (mptt) cc_final: 0.8437 (mptt) REVERT: C 86 MET cc_start: 0.5592 (pmm) cc_final: 0.5263 (pmm) REVERT: C 158 GLN cc_start: 0.7925 (pm20) cc_final: 0.7506 (pm20) REVERT: C 167 TYR cc_start: 0.7404 (m-10) cc_final: 0.7006 (m-10) REVERT: C 171 GLN cc_start: 0.8486 (mm110) cc_final: 0.7968 (mp10) REVERT: C 212 MET cc_start: 0.7759 (mmp) cc_final: 0.7421 (mmp) REVERT: C 215 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7546 (tm-30) REVERT: C 219 LEU cc_start: 0.7238 (mt) cc_final: 0.6850 (mm) REVERT: C 248 MET cc_start: 0.7731 (mtp) cc_final: 0.7119 (mtp) REVERT: C 250 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6725 (mmm160) REVERT: C 270 LYS cc_start: 0.8655 (mmmt) cc_final: 0.7585 (mmmt) REVERT: C 289 GLN cc_start: 0.8280 (mt0) cc_final: 0.7892 (mt0) REVERT: C 299 LEU cc_start: 0.8659 (mt) cc_final: 0.8280 (mt) REVERT: C 300 LYS cc_start: 0.8855 (tttt) cc_final: 0.8499 (tttt) REVERT: C 302 MET cc_start: 0.8148 (tmm) cc_final: 0.7851 (tmm) REVERT: C 304 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7898 (mtp85) REVERT: C 309 LEU cc_start: 0.8659 (tp) cc_final: 0.8403 (tp) REVERT: C 313 GLU cc_start: 0.8198 (pt0) cc_final: 0.7851 (pt0) REVERT: C 344 LYS cc_start: 0.8938 (mttm) cc_final: 0.8537 (mttm) REVERT: D 82 ASP cc_start: 0.8201 (t0) cc_final: 0.7916 (t70) REVERT: D 104 LYS cc_start: 0.8355 (tttt) cc_final: 0.8013 (ttmt) REVERT: D 124 GLN cc_start: 0.7575 (pp30) cc_final: 0.7277 (pp30) REVERT: D 131 LEU cc_start: 0.8441 (mp) cc_final: 0.7918 (mt) REVERT: D 139 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7411 (mtmm) REVERT: D 183 LYS cc_start: 0.8471 (mptt) cc_final: 0.8130 (mptt) REVERT: D 211 MET cc_start: 0.7622 (mmp) cc_final: 0.7165 (mmp) REVERT: D 212 MET cc_start: 0.7715 (mmp) cc_final: 0.7439 (mmp) REVERT: D 213 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7562 (mtmm) REVERT: D 217 MET cc_start: 0.7185 (mmm) cc_final: 0.6714 (mmm) REVERT: D 259 GLN cc_start: 0.8366 (mp-120) cc_final: 0.8122 (mp10) REVERT: D 263 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7687 (mmmm) REVERT: D 300 LYS cc_start: 0.8577 (tptm) cc_final: 0.8251 (tptm) REVERT: D 305 ASP cc_start: 0.7541 (t0) cc_final: 0.7216 (t0) REVERT: D 309 LEU cc_start: 0.8336 (tp) cc_final: 0.8002 (tp) REVERT: D 312 ARG cc_start: 0.8144 (ptp-170) cc_final: 0.7794 (ptp-170) REVERT: D 337 HIS cc_start: 0.7708 (m170) cc_final: 0.7440 (m90) REVERT: E 139 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7826 (ptpt) REVERT: E 158 GLN cc_start: 0.7987 (pm20) cc_final: 0.7619 (pm20) REVERT: E 167 TYR cc_start: 0.7207 (m-10) cc_final: 0.6901 (m-10) REVERT: E 171 GLN cc_start: 0.8526 (mm110) cc_final: 0.8141 (mp10) REVERT: E 193 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7209 (mt-10) REVERT: E 212 MET cc_start: 0.7875 (mmp) cc_final: 0.7237 (mmp) REVERT: E 213 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7861 (mtmm) REVERT: E 215 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7248 (tm-30) REVERT: E 217 MET cc_start: 0.8522 (ptp) cc_final: 0.7950 (tpp) REVERT: E 239 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7238 (ttp-110) REVERT: E 248 MET cc_start: 0.7787 (mtp) cc_final: 0.7239 (mtp) REVERT: E 251 MET cc_start: 0.6802 (mpp) cc_final: 0.6360 (tpp) REVERT: E 256 HIS cc_start: 0.7687 (t70) cc_final: 0.7254 (t70) REVERT: E 266 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 270 LYS cc_start: 0.8462 (mmmt) cc_final: 0.7447 (mmmt) REVERT: E 279 ASP cc_start: 0.7205 (p0) cc_final: 0.6836 (t0) REVERT: E 286 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 290 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7694 (mm-30) REVERT: E 298 ASP cc_start: 0.7374 (m-30) cc_final: 0.6941 (m-30) REVERT: E 299 LEU cc_start: 0.8659 (mt) cc_final: 0.8309 (mt) REVERT: E 300 LYS cc_start: 0.8655 (tttt) cc_final: 0.8364 (tttt) REVERT: E 302 MET cc_start: 0.8184 (tmm) cc_final: 0.7844 (tmm) REVERT: E 304 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8341 (mmm-85) REVERT: E 313 GLU cc_start: 0.8487 (pt0) cc_final: 0.8229 (pt0) REVERT: E 335 ASP cc_start: 0.8231 (m-30) cc_final: 0.7964 (m-30) REVERT: E 341 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7763 (mm-30) REVERT: E 343 MET cc_start: 0.8202 (tpp) cc_final: 0.7786 (tpp) REVERT: F 74 MET cc_start: 0.7686 (mtm) cc_final: 0.7216 (mtm) REVERT: F 102 ASP cc_start: 0.7984 (m-30) cc_final: 0.7713 (m-30) REVERT: F 104 LYS cc_start: 0.8399 (tttt) cc_final: 0.8053 (ttmt) REVERT: F 131 LEU cc_start: 0.8413 (mp) cc_final: 0.7942 (mt) REVERT: F 139 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7356 (mtmm) REVERT: F 183 LYS cc_start: 0.8517 (mptt) cc_final: 0.8225 (mptt) REVERT: F 211 MET cc_start: 0.7525 (mmp) cc_final: 0.7124 (mmp) REVERT: F 212 MET cc_start: 0.8093 (mmp) cc_final: 0.7740 (mmp) REVERT: F 217 MET cc_start: 0.7550 (mmt) cc_final: 0.7097 (mmt) REVERT: F 248 MET cc_start: 0.7202 (mtp) cc_final: 0.6694 (mtp) REVERT: F 250 ARG cc_start: 0.7722 (ttt180) cc_final: 0.7477 (ttt180) REVERT: F 263 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7659 (mmmm) REVERT: F 270 LYS cc_start: 0.8358 (pttp) cc_final: 0.7868 (ptmm) REVERT: F 298 ASP cc_start: 0.8036 (m-30) cc_final: 0.7811 (m-30) REVERT: F 300 LYS cc_start: 0.8445 (tptm) cc_final: 0.7989 (tptm) REVERT: F 302 MET cc_start: 0.7785 (tmm) cc_final: 0.7528 (tmm) REVERT: F 337 HIS cc_start: 0.7755 (m170) cc_final: 0.7424 (m170) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.2999 time to fit residues: 247.6692 Evaluate side-chains 577 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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: 0.7980 chunk 114 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 67 optimal weight: 0.0570 chunk 121 optimal weight: 0.0470 chunk 29 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 259 GLN ** 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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** 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 = 0.4108 r_free = 0.4108 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128549 restraints weight = 29452.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133215 restraints weight = 17878.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136455 restraints weight = 12207.711| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14142 Z= 0.170 Angle : 0.600 13.920 19146 Z= 0.312 Chirality : 0.043 0.195 2190 Planarity : 0.004 0.051 2448 Dihedral : 10.760 107.033 1962 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.21), residues: 1728 helix: 1.08 (0.17), residues: 984 sheet: 0.62 (0.41), residues: 192 loop : 0.33 (0.30), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 220 HIS 0.007 0.001 HIS E 337 PHE 0.035 0.002 PHE D 216 TYR 0.012 0.002 TYR F 72 ARG 0.007 0.000 ARG C 265 *********************** 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 588 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.523 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: A 74 MET cc_start: 0.8130 (mtm) cc_final: 0.7620 (mtm) REVERT: A 102 ASP cc_start: 0.7802 (m-30) cc_final: 0.7571 (m-30) REVERT: A 104 LYS cc_start: 0.8594 (tttt) cc_final: 0.8225 (tttt) REVERT: A 114 LYS cc_start: 0.7241 (tttt) cc_final: 0.6903 (ttmt) REVERT: A 148 LYS cc_start: 0.7992 (tttt) cc_final: 0.7613 (ttmt) REVERT: A 157 LEU cc_start: 0.7938 (tp) cc_final: 0.7595 (tp) REVERT: A 158 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 169 GLU cc_start: 0.7040 (tt0) cc_final: 0.6761 (tt0) REVERT: A 178 PHE cc_start: 0.8815 (m-10) cc_final: 0.8488 (m-10) REVERT: A 179 SER cc_start: 0.8863 (t) cc_final: 0.8561 (p) REVERT: A 199 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6353 (tpp80) REVERT: A 206 HIS cc_start: 0.8053 (p90) cc_final: 0.7432 (p90) REVERT: A 211 MET cc_start: 0.7964 (mmp) cc_final: 0.7307 (mmp) REVERT: A 212 MET cc_start: 0.7781 (mmp) cc_final: 0.7499 (mmp) REVERT: A 213 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7759 (mtmt) REVERT: A 217 MET cc_start: 0.8048 (mpp) cc_final: 0.7535 (mpp) REVERT: A 219 LEU cc_start: 0.8736 (mt) cc_final: 0.8416 (mt) REVERT: A 251 MET cc_start: 0.7547 (mmm) cc_final: 0.7002 (mmm) REVERT: A 259 GLN cc_start: 0.7669 (mt0) cc_final: 0.7310 (mt0) REVERT: A 266 GLU cc_start: 0.7823 (tp30) cc_final: 0.7341 (tp30) REVERT: A 286 GLU cc_start: 0.7760 (pm20) cc_final: 0.7317 (pm20) REVERT: A 301 GLU cc_start: 0.7774 (tt0) cc_final: 0.7025 (tt0) REVERT: A 305 ASP cc_start: 0.8243 (m-30) cc_final: 0.7956 (m-30) REVERT: A 338 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7891 (mtp85) REVERT: A 341 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 342 LYS cc_start: 0.8756 (mptt) cc_final: 0.8125 (mptt) REVERT: A 343 MET cc_start: 0.8119 (mmm) cc_final: 0.7795 (mmm) REVERT: A 345 LYS cc_start: 0.8730 (pptt) cc_final: 0.8507 (pptt) REVERT: B 74 MET cc_start: 0.8040 (mtm) cc_final: 0.7336 (mtm) REVERT: B 92 ASP cc_start: 0.7569 (m-30) cc_final: 0.7347 (m-30) REVERT: B 123 LEU cc_start: 0.8292 (tp) cc_final: 0.7978 (tp) REVERT: B 124 GLN cc_start: 0.8199 (pp30) cc_final: 0.7950 (pp30) REVERT: B 144 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8246 (mtpt) REVERT: B 146 THR cc_start: 0.8386 (p) cc_final: 0.7978 (p) REVERT: B 152 CYS cc_start: 0.7162 (m) cc_final: 0.6797 (m) REVERT: B 154 PHE cc_start: 0.7679 (t80) cc_final: 0.7189 (t80) REVERT: B 157 LEU cc_start: 0.8062 (tp) cc_final: 0.7709 (tp) REVERT: B 158 GLN cc_start: 0.7304 (pm20) cc_final: 0.6406 (pm20) REVERT: B 211 MET cc_start: 0.8039 (mmp) cc_final: 0.7706 (mmp) REVERT: B 213 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7695 (mtmt) REVERT: B 215 GLN cc_start: 0.7450 (tp-100) cc_final: 0.6138 (tp-100) REVERT: B 217 MET cc_start: 0.7999 (mpp) cc_final: 0.7687 (mpp) REVERT: B 219 LEU cc_start: 0.8799 (mt) cc_final: 0.7640 (mt) REVERT: B 241 GLN cc_start: 0.8762 (mm110) cc_final: 0.8551 (mm-40) REVERT: B 243 LEU cc_start: 0.8561 (mt) cc_final: 0.8252 (mt) REVERT: B 251 MET cc_start: 0.7031 (mmp) cc_final: 0.6178 (mmm) REVERT: B 266 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6989 (tm-30) REVERT: B 270 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7822 (mptt) REVERT: B 286 GLU cc_start: 0.7096 (pm20) cc_final: 0.6805 (pm20) REVERT: B 299 LEU cc_start: 0.8818 (mt) cc_final: 0.8400 (mt) REVERT: B 301 GLU cc_start: 0.7562 (tt0) cc_final: 0.6790 (tt0) REVERT: B 304 ARG cc_start: 0.7410 (mmp-170) cc_final: 0.6935 (tpm170) REVERT: B 334 GLN cc_start: 0.7756 (mp10) cc_final: 0.7528 (mp10) REVERT: B 338 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8056 (mtp85) REVERT: B 341 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 342 LYS cc_start: 0.8588 (mptt) cc_final: 0.7957 (mptt) REVERT: B 343 MET cc_start: 0.8247 (tpt) cc_final: 0.6748 (tpt) REVERT: B 345 LYS cc_start: 0.8698 (pptt) cc_final: 0.8468 (pptt) REVERT: B 347 LYS cc_start: 0.8903 (mptt) cc_final: 0.8421 (mptt) REVERT: C 167 TYR cc_start: 0.7359 (m-10) cc_final: 0.6982 (m-10) REVERT: C 171 GLN cc_start: 0.8480 (mm110) cc_final: 0.7962 (mp10) REVERT: C 212 MET cc_start: 0.7740 (mmp) cc_final: 0.7391 (mmp) REVERT: C 215 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7552 (tm-30) REVERT: C 219 LEU cc_start: 0.7261 (mt) cc_final: 0.6833 (mm) REVERT: C 239 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7000 (ttm110) REVERT: C 248 MET cc_start: 0.7628 (mtp) cc_final: 0.7012 (mtp) REVERT: C 270 LYS cc_start: 0.8598 (mmmt) cc_final: 0.7632 (mmmt) REVERT: C 284 LEU cc_start: 0.8226 (mp) cc_final: 0.7940 (mp) REVERT: C 289 GLN cc_start: 0.8226 (mt0) cc_final: 0.7804 (mt0) REVERT: C 299 LEU cc_start: 0.8623 (mt) cc_final: 0.8069 (mt) REVERT: C 300 LYS cc_start: 0.8839 (tttt) cc_final: 0.8463 (tttt) REVERT: C 302 MET cc_start: 0.8106 (tmm) cc_final: 0.7870 (tmm) REVERT: C 303 CYS cc_start: 0.8647 (m) cc_final: 0.8083 (m) REVERT: C 304 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7899 (mtp85) REVERT: C 313 GLU cc_start: 0.8259 (pt0) cc_final: 0.7889 (pt0) REVERT: C 335 ASP cc_start: 0.8349 (m-30) cc_final: 0.8134 (m-30) REVERT: C 343 MET cc_start: 0.8090 (tpp) cc_final: 0.7715 (tpp) REVERT: C 344 LYS cc_start: 0.8949 (mttm) cc_final: 0.8522 (mttm) REVERT: D 82 ASP cc_start: 0.8163 (t0) cc_final: 0.7873 (t70) REVERT: D 90 TRP cc_start: 0.8299 (m100) cc_final: 0.7394 (m100) REVERT: D 104 LYS cc_start: 0.8294 (tttt) cc_final: 0.8059 (tttt) REVERT: D 124 GLN cc_start: 0.7580 (pp30) cc_final: 0.7303 (pp30) REVERT: D 131 LEU cc_start: 0.8491 (mp) cc_final: 0.7897 (mt) REVERT: D 139 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7378 (mtmm) REVERT: D 179 SER cc_start: 0.8239 (p) cc_final: 0.8029 (p) REVERT: D 183 LYS cc_start: 0.8446 (mptt) cc_final: 0.8095 (mptt) REVERT: D 211 MET cc_start: 0.7635 (mmp) cc_final: 0.7231 (mmp) REVERT: D 212 MET cc_start: 0.7587 (mmp) cc_final: 0.7339 (mmp) REVERT: D 213 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7604 (mtmm) REVERT: D 217 MET cc_start: 0.7203 (mmm) cc_final: 0.6625 (mmm) REVERT: D 251 MET cc_start: 0.7860 (mpp) cc_final: 0.6507 (mpp) REVERT: D 263 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7674 (mmmm) REVERT: D 300 LYS cc_start: 0.8589 (tptm) cc_final: 0.8232 (tptm) REVERT: D 305 ASP cc_start: 0.7507 (t0) cc_final: 0.7181 (t0) REVERT: D 309 LEU cc_start: 0.8293 (tp) cc_final: 0.7967 (tp) REVERT: D 312 ARG cc_start: 0.8125 (ptp-170) cc_final: 0.7912 (ptp-170) REVERT: D 337 HIS cc_start: 0.7619 (m170) cc_final: 0.7318 (m90) REVERT: E 139 LYS cc_start: 0.8370 (ptpp) cc_final: 0.7946 (ptpt) REVERT: E 158 GLN cc_start: 0.7935 (pm20) cc_final: 0.7598 (pm20) REVERT: E 167 TYR cc_start: 0.7150 (m-10) cc_final: 0.6811 (m-10) REVERT: E 171 GLN cc_start: 0.8503 (mm110) cc_final: 0.8190 (mp10) REVERT: E 193 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7172 (mt-10) REVERT: E 212 MET cc_start: 0.7862 (mmp) cc_final: 0.7217 (mmp) REVERT: E 213 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7820 (mtmm) REVERT: E 215 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7263 (tm-30) REVERT: E 217 MET cc_start: 0.8529 (ptp) cc_final: 0.8007 (tpp) REVERT: E 239 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7200 (ttm110) REVERT: E 248 MET cc_start: 0.7747 (mtp) cc_final: 0.7213 (mtp) REVERT: E 251 MET cc_start: 0.6737 (mpp) cc_final: 0.6134 (tpp) REVERT: E 256 HIS cc_start: 0.7672 (t70) cc_final: 0.7268 (t70) REVERT: E 266 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 270 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7423 (mmmt) REVERT: E 279 ASP cc_start: 0.7240 (p0) cc_final: 0.6727 (t0) REVERT: E 290 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 298 ASP cc_start: 0.7354 (m-30) cc_final: 0.6974 (m-30) REVERT: E 299 LEU cc_start: 0.8647 (mt) cc_final: 0.8368 (mt) REVERT: E 300 LYS cc_start: 0.8619 (tttt) cc_final: 0.8346 (tttt) REVERT: E 301 GLU cc_start: 0.8309 (tt0) cc_final: 0.7933 (tt0) REVERT: E 302 MET cc_start: 0.8108 (tmm) cc_final: 0.7845 (tmm) REVERT: E 304 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.8292 (mmm-85) REVERT: E 313 GLU cc_start: 0.8514 (pt0) cc_final: 0.8260 (pt0) REVERT: E 335 ASP cc_start: 0.8256 (m-30) cc_final: 0.7967 (m-30) REVERT: E 341 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7720 (mm-30) REVERT: E 343 MET cc_start: 0.8170 (tpp) cc_final: 0.7753 (tpp) REVERT: F 74 MET cc_start: 0.7657 (mtm) cc_final: 0.7162 (mtm) REVERT: F 82 ASP cc_start: 0.8344 (t0) cc_final: 0.8141 (t0) REVERT: F 102 ASP cc_start: 0.7983 (m-30) cc_final: 0.7698 (m-30) REVERT: F 104 LYS cc_start: 0.8390 (tttt) cc_final: 0.8051 (ttmt) REVERT: F 123 LEU cc_start: 0.8750 (mt) cc_final: 0.8249 (mt) REVERT: F 131 LEU cc_start: 0.8459 (mp) cc_final: 0.7891 (mt) REVERT: F 139 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7326 (mtmm) REVERT: F 183 LYS cc_start: 0.8515 (mptt) cc_final: 0.8188 (mptt) REVERT: F 211 MET cc_start: 0.7464 (mmp) cc_final: 0.7059 (mmp) REVERT: F 212 MET cc_start: 0.8072 (mmp) cc_final: 0.7717 (mmp) REVERT: F 217 MET cc_start: 0.7516 (mmt) cc_final: 0.7057 (mmt) REVERT: F 248 MET cc_start: 0.7231 (mtp) cc_final: 0.6707 (mtp) REVERT: F 250 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7529 (ttt180) REVERT: F 263 LYS cc_start: 0.7842 (mmmm) cc_final: 0.7598 (mmmm) REVERT: F 265 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7121 (ptp-170) REVERT: F 270 LYS cc_start: 0.8346 (pttp) cc_final: 0.7914 (ptmm) REVERT: F 298 ASP cc_start: 0.8076 (m-30) cc_final: 0.7875 (m-30) REVERT: F 300 LYS cc_start: 0.8443 (tptm) cc_final: 0.8003 (tptm) REVERT: F 302 MET cc_start: 0.7795 (tmm) cc_final: 0.7540 (tmm) REVERT: F 337 HIS cc_start: 0.7710 (m170) cc_final: 0.7390 (m170) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.2977 time to fit residues: 242.9284 Evaluate side-chains 566 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 259 GLN ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS C 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126472 restraints weight = 29634.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131178 restraints weight = 17898.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.134426 restraints weight = 12178.616| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14142 Z= 0.198 Angle : 0.622 13.860 19146 Z= 0.322 Chirality : 0.043 0.197 2190 Planarity : 0.004 0.059 2448 Dihedral : 10.831 109.404 1962 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 1.04 (0.21), residues: 1728 helix: 1.07 (0.16), residues: 978 sheet: 0.60 (0.41), residues: 192 loop : 0.28 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 220 HIS 0.012 0.001 HIS A 337 PHE 0.034 0.002 PHE D 216 TYR 0.021 0.002 TYR B 132 ARG 0.010 0.001 ARG B 250 ********************** 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 586 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.537 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: A 74 MET cc_start: 0.8221 (mtm) cc_final: 0.7722 (mtm) REVERT: A 92 ASP cc_start: 0.7301 (m-30) cc_final: 0.7044 (m-30) REVERT: A 102 ASP cc_start: 0.7772 (m-30) cc_final: 0.7555 (m-30) REVERT: A 104 LYS cc_start: 0.8664 (tttt) cc_final: 0.8253 (tttt) REVERT: A 124 GLN cc_start: 0.8125 (pp30) cc_final: 0.7865 (pp30) REVERT: A 148 LYS cc_start: 0.8165 (tttt) cc_final: 0.7951 (ttmt) REVERT: A 157 LEU cc_start: 0.8036 (tp) cc_final: 0.7552 (tp) REVERT: A 158 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 169 GLU cc_start: 0.7069 (tt0) cc_final: 0.6795 (tt0) REVERT: A 178 PHE cc_start: 0.8888 (m-10) cc_final: 0.8452 (m-10) REVERT: A 179 SER cc_start: 0.8825 (t) cc_final: 0.8506 (p) REVERT: A 199 ARG cc_start: 0.7424 (tpp80) cc_final: 0.6359 (tpp80) REVERT: A 206 HIS cc_start: 0.8067 (p90) cc_final: 0.7445 (p90) REVERT: A 211 MET cc_start: 0.8031 (mmp) cc_final: 0.7395 (mmp) REVERT: A 212 MET cc_start: 0.7874 (mmp) cc_final: 0.7579 (mmp) REVERT: A 213 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7815 (mtmt) REVERT: A 216 PHE cc_start: 0.7964 (t80) cc_final: 0.7754 (t80) REVERT: A 217 MET cc_start: 0.8029 (mpp) cc_final: 0.7548 (mpp) REVERT: A 219 LEU cc_start: 0.8793 (mt) cc_final: 0.8431 (mt) REVERT: A 251 MET cc_start: 0.7520 (mmm) cc_final: 0.7022 (mmm) REVERT: A 259 GLN cc_start: 0.7729 (mt0) cc_final: 0.7380 (mt0) REVERT: A 262 LEU cc_start: 0.8167 (tp) cc_final: 0.7812 (mm) REVERT: A 266 GLU cc_start: 0.7829 (tp30) cc_final: 0.7273 (tp30) REVERT: A 286 GLU cc_start: 0.7767 (pm20) cc_final: 0.7319 (pm20) REVERT: A 301 GLU cc_start: 0.7823 (tt0) cc_final: 0.7081 (tt0) REVERT: A 305 ASP cc_start: 0.8231 (m-30) cc_final: 0.7939 (m-30) REVERT: A 338 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7915 (mtp85) REVERT: A 341 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 342 LYS cc_start: 0.8778 (mptt) cc_final: 0.8197 (mptt) REVERT: A 343 MET cc_start: 0.8164 (mmm) cc_final: 0.7769 (mmm) REVERT: A 345 LYS cc_start: 0.8734 (pptt) cc_final: 0.8520 (pptt) REVERT: B 74 MET cc_start: 0.8044 (mtm) cc_final: 0.7379 (mtm) REVERT: B 86 MET cc_start: 0.7862 (mtm) cc_final: 0.7635 (mtm) REVERT: B 92 ASP cc_start: 0.7602 (m-30) cc_final: 0.7366 (m-30) REVERT: B 104 LYS cc_start: 0.8537 (tttt) cc_final: 0.8237 (tttt) REVERT: B 118 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6835 (mt-10) REVERT: B 123 LEU cc_start: 0.8343 (tp) cc_final: 0.8059 (tp) REVERT: B 124 GLN cc_start: 0.8194 (pp30) cc_final: 0.7952 (pp30) REVERT: B 132 TYR cc_start: 0.7434 (p90) cc_final: 0.6833 (p90) REVERT: B 144 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8204 (mtpt) REVERT: B 146 THR cc_start: 0.8346 (p) cc_final: 0.7724 (p) REVERT: B 152 CYS cc_start: 0.7349 (m) cc_final: 0.6985 (m) REVERT: B 154 PHE cc_start: 0.7682 (t80) cc_final: 0.7287 (t80) REVERT: B 157 LEU cc_start: 0.8088 (tp) cc_final: 0.7620 (tt) REVERT: B 158 GLN cc_start: 0.7319 (pm20) cc_final: 0.6498 (pm20) REVERT: B 211 MET cc_start: 0.8101 (mmp) cc_final: 0.7731 (mmp) REVERT: B 213 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7682 (mtmt) REVERT: B 215 GLN cc_start: 0.7516 (tp-100) cc_final: 0.6182 (tp-100) REVERT: B 217 MET cc_start: 0.8128 (mpp) cc_final: 0.7555 (mpp) REVERT: B 219 LEU cc_start: 0.8742 (mt) cc_final: 0.7489 (mt) REVERT: B 247 ILE cc_start: 0.8160 (mm) cc_final: 0.7851 (mm) REVERT: B 259 GLN cc_start: 0.7860 (mt0) cc_final: 0.7622 (mt0) REVERT: B 262 LEU cc_start: 0.8137 (tp) cc_final: 0.7808 (mm) REVERT: B 266 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 270 LYS cc_start: 0.8399 (mmmt) cc_final: 0.7756 (mmtm) REVERT: B 286 GLU cc_start: 0.7129 (pm20) cc_final: 0.6851 (pm20) REVERT: B 299 LEU cc_start: 0.8842 (mt) cc_final: 0.8415 (mt) REVERT: B 301 GLU cc_start: 0.7580 (tt0) cc_final: 0.6800 (tt0) REVERT: B 338 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8128 (mtp85) REVERT: B 341 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 342 LYS cc_start: 0.8602 (mptt) cc_final: 0.7771 (mptt) REVERT: B 343 MET cc_start: 0.8288 (tpt) cc_final: 0.6876 (tpt) REVERT: B 345 LYS cc_start: 0.8705 (pptt) cc_final: 0.8307 (pptt) REVERT: B 347 LYS cc_start: 0.8902 (mptt) cc_final: 0.8411 (mptt) REVERT: C 74 MET cc_start: 0.5620 (mtm) cc_final: 0.5385 (mtm) REVERT: C 167 TYR cc_start: 0.7396 (m-10) cc_final: 0.6895 (m-10) REVERT: C 171 GLN cc_start: 0.8496 (mm110) cc_final: 0.8006 (mp10) REVERT: C 212 MET cc_start: 0.7796 (mmp) cc_final: 0.7452 (mmp) REVERT: C 215 GLN cc_start: 0.8158 (tp-100) cc_final: 0.7619 (tm-30) REVERT: C 239 ARG cc_start: 0.7888 (mtt90) cc_final: 0.6981 (ttm110) REVERT: C 248 MET cc_start: 0.7690 (mtp) cc_final: 0.7085 (mtp) REVERT: C 270 LYS cc_start: 0.8604 (mmmt) cc_final: 0.7634 (mmmt) REVERT: C 284 LEU cc_start: 0.8342 (mp) cc_final: 0.8038 (mp) REVERT: C 289 GLN cc_start: 0.8232 (mt0) cc_final: 0.7821 (mt0) REVERT: C 299 LEU cc_start: 0.8606 (mt) cc_final: 0.8081 (mt) REVERT: C 300 LYS cc_start: 0.8818 (tttt) cc_final: 0.8432 (tttt) REVERT: C 302 MET cc_start: 0.8156 (tmm) cc_final: 0.7936 (tmm) REVERT: C 303 CYS cc_start: 0.8672 (m) cc_final: 0.8130 (m) REVERT: C 304 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7921 (mtp85) REVERT: C 313 GLU cc_start: 0.8302 (pt0) cc_final: 0.7948 (pt0) REVERT: C 335 ASP cc_start: 0.8364 (m-30) cc_final: 0.8019 (m-30) REVERT: C 343 MET cc_start: 0.8134 (tpp) cc_final: 0.7714 (tpp) REVERT: C 344 LYS cc_start: 0.8882 (mttm) cc_final: 0.8476 (mttm) REVERT: D 82 ASP cc_start: 0.8133 (t0) cc_final: 0.7861 (t70) REVERT: D 104 LYS cc_start: 0.8313 (tttt) cc_final: 0.7993 (ttmt) REVERT: D 124 GLN cc_start: 0.7650 (pp30) cc_final: 0.7381 (pp30) REVERT: D 131 LEU cc_start: 0.8428 (mp) cc_final: 0.8216 (mt) REVERT: D 183 LYS cc_start: 0.8479 (mptt) cc_final: 0.8104 (mptt) REVERT: D 211 MET cc_start: 0.7665 (mmp) cc_final: 0.7219 (mmp) REVERT: D 212 MET cc_start: 0.7673 (mmp) cc_final: 0.7414 (mmp) REVERT: D 213 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7540 (mtmm) REVERT: D 217 MET cc_start: 0.7385 (mmm) cc_final: 0.6839 (mmm) REVERT: D 250 ARG cc_start: 0.7729 (ttt-90) cc_final: 0.6957 (ptm160) REVERT: D 251 MET cc_start: 0.7888 (mpp) cc_final: 0.6966 (mpp) REVERT: D 263 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7763 (mmmm) REVERT: D 265 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.6841 (mtm-85) REVERT: D 300 LYS cc_start: 0.8564 (tptm) cc_final: 0.8197 (tptm) REVERT: D 305 ASP cc_start: 0.7584 (t0) cc_final: 0.7167 (t0) REVERT: D 308 LEU cc_start: 0.8120 (pp) cc_final: 0.7135 (pp) REVERT: D 309 LEU cc_start: 0.8313 (tp) cc_final: 0.8058 (tp) REVERT: D 317 SER cc_start: 0.8932 (m) cc_final: 0.8561 (p) REVERT: D 337 HIS cc_start: 0.7669 (m170) cc_final: 0.7339 (m90) REVERT: E 139 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7886 (ptpt) REVERT: E 158 GLN cc_start: 0.7917 (pm20) cc_final: 0.7507 (pm20) REVERT: E 167 TYR cc_start: 0.7286 (m-10) cc_final: 0.6901 (m-10) REVERT: E 171 GLN cc_start: 0.8506 (mm110) cc_final: 0.8113 (mp10) REVERT: E 193 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7253 (mt-10) REVERT: E 212 MET cc_start: 0.7906 (mmp) cc_final: 0.7275 (mmp) REVERT: E 213 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7842 (mtmm) REVERT: E 215 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7273 (tm-30) REVERT: E 217 MET cc_start: 0.8562 (ptp) cc_final: 0.8049 (tpp) REVERT: E 239 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7246 (ttp-110) REVERT: E 248 MET cc_start: 0.7819 (mtp) cc_final: 0.7328 (mtp) REVERT: E 251 MET cc_start: 0.6783 (mpp) cc_final: 0.6143 (tpp) REVERT: E 256 HIS cc_start: 0.7671 (t70) cc_final: 0.7231 (t70) REVERT: E 266 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7667 (tm-30) REVERT: E 270 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7648 (mmmt) REVERT: E 279 ASP cc_start: 0.7396 (p0) cc_final: 0.6897 (t0) REVERT: E 290 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 298 ASP cc_start: 0.7270 (m-30) cc_final: 0.6894 (m-30) REVERT: E 299 LEU cc_start: 0.8695 (mt) cc_final: 0.8401 (mt) REVERT: E 300 LYS cc_start: 0.8604 (tttt) cc_final: 0.8340 (tttt) REVERT: E 301 GLU cc_start: 0.8283 (tt0) cc_final: 0.7928 (tt0) REVERT: E 302 MET cc_start: 0.8128 (tmm) cc_final: 0.7890 (tmm) REVERT: E 304 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.8299 (mmm-85) REVERT: E 313 GLU cc_start: 0.8515 (pt0) cc_final: 0.8254 (pt0) REVERT: E 335 ASP cc_start: 0.8319 (m-30) cc_final: 0.8027 (m-30) REVERT: E 341 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7781 (mm-30) REVERT: E 343 MET cc_start: 0.8267 (tpp) cc_final: 0.7840 (tpp) REVERT: F 74 MET cc_start: 0.7697 (mtm) cc_final: 0.7191 (mtm) REVERT: F 102 ASP cc_start: 0.8071 (m-30) cc_final: 0.7797 (m-30) REVERT: F 104 LYS cc_start: 0.8435 (tttt) cc_final: 0.8120 (ttmt) REVERT: F 112 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7688 (mtmt) REVERT: F 116 LEU cc_start: 0.7249 (mm) cc_final: 0.6768 (mm) REVERT: F 124 GLN cc_start: 0.7617 (pp30) cc_final: 0.7296 (pp30) REVERT: F 131 LEU cc_start: 0.8375 (mp) cc_final: 0.8107 (mt) REVERT: F 180 LEU cc_start: 0.8353 (tt) cc_final: 0.8128 (tt) REVERT: F 183 LYS cc_start: 0.8518 (mptt) cc_final: 0.8210 (mptt) REVERT: F 211 MET cc_start: 0.7572 (mmp) cc_final: 0.7163 (mmp) REVERT: F 212 MET cc_start: 0.8088 (mmp) cc_final: 0.7741 (mmp) REVERT: F 217 MET cc_start: 0.7597 (mmt) cc_final: 0.7005 (mmt) REVERT: F 248 MET cc_start: 0.7285 (mtp) cc_final: 0.6745 (mtp) REVERT: F 250 ARG cc_start: 0.7895 (ttt180) cc_final: 0.7629 (ttt180) REVERT: F 263 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7698 (mmmm) REVERT: F 265 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7296 (ptp-170) REVERT: F 270 LYS cc_start: 0.8342 (pttp) cc_final: 0.7900 (ptmm) REVERT: F 300 LYS cc_start: 0.8487 (tptm) cc_final: 0.8037 (tptm) REVERT: F 302 MET cc_start: 0.7844 (tmm) cc_final: 0.7584 (tmm) REVERT: F 337 HIS cc_start: 0.7758 (m170) cc_final: 0.7415 (m170) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.3052 time to fit residues: 249.0603 Evaluate side-chains 572 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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: 0.8980 chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 165 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 166 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 259 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 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 256 HIS F 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.154747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127596 restraints weight = 29597.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132209 restraints weight = 17942.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.135373 restraints weight = 12261.983| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14142 Z= 0.179 Angle : 0.618 14.049 19146 Z= 0.320 Chirality : 0.043 0.253 2190 Planarity : 0.004 0.051 2448 Dihedral : 10.720 109.076 1962 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 1.35 (0.22), residues: 1728 helix: 1.34 (0.17), residues: 936 sheet: 0.76 (0.40), residues: 186 loop : 0.42 (0.30), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 220 HIS 0.004 0.001 HIS F 115 PHE 0.036 0.002 PHE D 216 TYR 0.020 0.002 TYR B 132 ARG 0.009 0.001 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5263.10 seconds wall clock time: 96 minutes 44.35 seconds (5804.35 seconds total)