Starting phenix.real_space_refine on Mon Dec 30 20:59:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxt_43639/12_2024/8vxt_43639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxt_43639/12_2024/8vxt_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_43639/12_2024/8vxt_43639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxt_43639/12_2024/8vxt_43639.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxt_43639/12_2024/8vxt_43639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxt_43639/12_2024/8vxt_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-5532/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: 5.39, per 1000 atoms: 0.39 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: 4.47 Conformation dependent library (CDL) restraints added in 1.9 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: 1.39 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: 3.99 Time building geometry restraints manager: 4.34 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 29.430 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- 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 : 1.747 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: 0.2983 time to fit residues: 244.1123 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 : 1.514 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 1.605 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: 0.8147 (mtm) cc_final: 0.7790 (mtm) REVERT: A 101 THR cc_start: 0.8388 (p) cc_final: 0.8035 (t) REVERT: A 114 LYS cc_start: 0.7839 (tptm) cc_final: 0.7535 (tptm) REVERT: A 117 PHE cc_start: 0.7755 (m-10) cc_final: 0.7419 (m-10) REVERT: A 118 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6289 (mt-10) REVERT: A 122 LEU cc_start: 0.7430 (pt) cc_final: 0.6953 (tt) REVERT: A 124 GLN cc_start: 0.8001 (pp30) cc_final: 0.7752 (pp30) REVERT: A 125 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7860 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7717 (mtmm) REVERT: A 141 LEU cc_start: 0.8446 (tp) cc_final: 0.8213 (tp) REVERT: A 148 LYS cc_start: 0.8219 (tttt) cc_final: 0.7886 (ttmt) REVERT: A 149 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 154 PHE cc_start: 0.7662 (t80) cc_final: 0.7063 (t80) REVERT: A 157 LEU cc_start: 0.7972 (tp) cc_final: 0.7611 (tp) REVERT: A 193 GLU cc_start: 0.7601 (tt0) cc_final: 0.7356 (tt0) REVERT: A 206 HIS cc_start: 0.7987 (p90) cc_final: 0.7323 (p90) REVERT: A 211 MET cc_start: 0.8074 (mmp) cc_final: 0.7375 (mmt) REVERT: A 212 MET cc_start: 0.8023 (mmp) cc_final: 0.7665 (mmp) REVERT: A 213 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7644 (mtmt) REVERT: A 215 GLN cc_start: 0.7563 (tp-100) cc_final: 0.6380 (tp-100) REVERT: A 217 MET cc_start: 0.8022 (mpp) cc_final: 0.7548 (mpp) REVERT: A 219 LEU cc_start: 0.8652 (mt) cc_final: 0.7548 (mt) REVERT: A 232 ILE cc_start: 0.8195 (mt) cc_final: 0.7939 (mt) REVERT: A 237 THR cc_start: 0.7676 (t) cc_final: 0.6889 (m) REVERT: A 259 GLN cc_start: 0.7304 (mt0) cc_final: 0.6954 (mt0) REVERT: A 270 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8341 (mmtt) REVERT: A 273 LEU cc_start: 0.8134 (mm) cc_final: 0.7907 (mm) REVERT: A 305 ASP cc_start: 0.8138 (t0) cc_final: 0.7852 (m-30) REVERT: A 341 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 342 LYS cc_start: 0.8592 (mptt) cc_final: 0.8053 (mptt) REVERT: A 343 MET cc_start: 0.8271 (tpt) cc_final: 0.7955 (tpt) REVERT: B 74 MET cc_start: 0.8015 (mtm) cc_final: 0.7356 (mtm) REVERT: B 113 LYS cc_start: 0.7913 (tppp) cc_final: 0.7687 (tttp) REVERT: B 117 PHE cc_start: 0.7664 (m-10) cc_final: 0.7355 (m-10) REVERT: B 148 LYS cc_start: 0.8330 (tttt) cc_final: 0.7785 (ttmt) REVERT: B 149 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 157 LEU cc_start: 0.8034 (tp) cc_final: 0.7628 (tp) REVERT: B 158 GLN cc_start: 0.6844 (pm20) cc_final: 0.6077 (pm20) REVERT: B 193 GLU cc_start: 0.7518 (tt0) cc_final: 0.7170 (tt0) REVERT: B 199 ARG cc_start: 0.7442 (tpp80) cc_final: 0.6634 (tpp80) REVERT: B 211 MET cc_start: 0.8055 (mmp) cc_final: 0.7636 (mmp) REVERT: B 212 MET cc_start: 0.8059 (mmp) cc_final: 0.7739 (mmp) REVERT: B 213 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7612 (mtmt) REVERT: B 215 GLN cc_start: 0.7510 (tp-100) cc_final: 0.6633 (tp-100) REVERT: B 217 MET cc_start: 0.8076 (mpp) cc_final: 0.7266 (mpp) REVERT: B 221 ASP cc_start: 0.7078 (m-30) cc_final: 0.6840 (m-30) REVERT: B 231 VAL cc_start: 0.7839 (t) cc_final: 0.7591 (p) REVERT: B 232 ILE cc_start: 0.8207 (mt) cc_final: 0.7962 (mt) REVERT: B 243 LEU cc_start: 0.8401 (mt) cc_final: 0.8147 (mt) REVERT: B 259 GLN cc_start: 0.7554 (mt0) cc_final: 0.7207 (mt0) REVERT: B 266 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 273 LEU cc_start: 0.8127 (mm) cc_final: 0.7924 (mm) REVERT: B 286 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 295 SER cc_start: 0.6704 (p) cc_final: 0.6394 (p) REVERT: B 299 LEU cc_start: 0.8680 (mt) cc_final: 0.8309 (mt) REVERT: B 311 VAL cc_start: 0.8164 (t) cc_final: 0.7955 (t) REVERT: B 338 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8111 (mtp85) REVERT: B 341 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7344 (mm-30) REVERT: B 342 LYS cc_start: 0.8527 (mptt) cc_final: 0.7687 (mptt) REVERT: B 345 LYS cc_start: 0.8773 (pptt) cc_final: 0.8475 (pptt) REVERT: C 74 MET cc_start: 0.5776 (mtm) cc_final: 0.5125 (mtm) REVERT: C 184 LEU cc_start: 0.5979 (mm) cc_final: 0.5575 (mt) REVERT: C 190 PHE cc_start: 0.6400 (t80) cc_final: 0.6092 (t80) REVERT: C 199 ARG cc_start: 0.5678 (tpp80) cc_final: 0.5446 (tpp80) REVERT: C 211 MET cc_start: 0.6804 (mmp) cc_final: 0.6582 (mmp) REVERT: C 212 MET cc_start: 0.7101 (mmp) cc_final: 0.6326 (mmp) REVERT: C 239 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7155 (mtt90) REVERT: C 248 MET cc_start: 0.7529 (mtp) cc_final: 0.6957 (mtp) REVERT: C 251 MET cc_start: 0.6480 (mmt) cc_final: 0.5976 (mmt) REVERT: C 289 GLN cc_start: 0.8315 (mt0) cc_final: 0.8087 (mt0) REVERT: C 308 LEU cc_start: 0.8579 (tp) cc_final: 0.8366 (tp) REVERT: C 335 ASP cc_start: 0.7853 (m-30) cc_final: 0.7595 (m-30) REVERT: C 336 LEU cc_start: 0.8642 (mp) cc_final: 0.8385 (mp) REVERT: C 343 MET cc_start: 0.8353 (tpt) cc_final: 0.7489 (tpt) REVERT: C 344 LYS cc_start: 0.8958 (mttm) cc_final: 0.8610 (mttm) REVERT: C 347 LYS cc_start: 0.8098 (mptt) cc_final: 0.7823 (mptt) REVERT: D 82 ASP cc_start: 0.7482 (t0) cc_final: 0.6810 (t70) REVERT: D 89 THR cc_start: 0.7696 (p) cc_final: 0.7414 (p) REVERT: D 104 LYS cc_start: 0.8236 (tttt) cc_final: 0.7934 (tttm) REVERT: D 132 TYR cc_start: 0.7208 (p90) cc_final: 0.6931 (p90) REVERT: D 139 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7102 (mtmm) REVERT: D 173 LEU cc_start: 0.8216 (tp) cc_final: 0.7994 (tp) REVERT: D 196 SER cc_start: 0.7031 (t) cc_final: 0.6744 (p) REVERT: D 212 MET cc_start: 0.7784 (mmp) cc_final: 0.6986 (mmp) REVERT: D 217 MET cc_start: 0.6713 (mmp) cc_final: 0.6317 (mmt) REVERT: D 237 THR cc_start: 0.6923 (t) cc_final: 0.6310 (m) REVERT: D 241 GLN cc_start: 0.8096 (mp-120) cc_final: 0.7276 (mm110) REVERT: D 248 MET cc_start: 0.7040 (mtp) cc_final: 0.6546 (mtp) REVERT: D 300 LYS cc_start: 0.8283 (tptm) cc_final: 0.7954 (tptm) REVERT: D 305 ASP cc_start: 0.7546 (t0) cc_final: 0.7180 (t0) REVERT: D 337 HIS cc_start: 0.7455 (m170) cc_final: 0.7233 (m90) REVERT: E 155 ILE cc_start: 0.7192 (pt) cc_final: 0.6358 (tp) REVERT: E 171 GLN cc_start: 0.8384 (mm110) cc_final: 0.8079 (mm-40) REVERT: E 205 ASP cc_start: 0.4506 (m-30) cc_final: 0.4197 (m-30) REVERT: E 212 MET cc_start: 0.7269 (mmp) cc_final: 0.6367 (mmp) REVERT: E 248 MET cc_start: 0.7573 (mtp) cc_final: 0.7056 (mtp) REVERT: E 251 MET cc_start: 0.5937 (mmt) cc_final: 0.5611 (mmt) REVERT: E 286 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 290 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 298 ASP cc_start: 0.7707 (m-30) cc_final: 0.7332 (m-30) REVERT: E 304 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8185 (mtp-110) REVERT: E 336 LEU cc_start: 0.8600 (mp) cc_final: 0.8393 (mp) REVERT: E 341 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7766 (mm-30) REVERT: E 343 MET cc_start: 0.8357 (tpt) cc_final: 0.7454 (tpt) REVERT: E 347 LYS cc_start: 0.8179 (mptt) cc_final: 0.7962 (mmtt) REVERT: F 74 MET cc_start: 0.7511 (mtm) cc_final: 0.7204 (mtm) REVERT: F 82 ASP cc_start: 0.7082 (t70) cc_final: 0.6805 (t0) REVERT: F 87 HIS cc_start: 0.7656 (m-70) cc_final: 0.6977 (m-70) REVERT: F 102 ASP cc_start: 0.7957 (m-30) cc_final: 0.7659 (m-30) REVERT: F 104 LYS cc_start: 0.8287 (tttt) cc_final: 0.7968 (tttm) REVERT: F 115 HIS cc_start: 0.5696 (OUTLIER) cc_final: 0.5426 (p90) REVERT: F 139 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7294 (mtmm) REVERT: F 149 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6919 (mm-30) REVERT: F 183 LYS cc_start: 0.8710 (mptt) cc_final: 0.8399 (mptt) REVERT: F 199 ARG cc_start: 0.6127 (tpp80) cc_final: 0.4971 (tpp80) REVERT: F 211 MET cc_start: 0.7227 (mmp) cc_final: 0.6883 (mmp) REVERT: F 212 MET cc_start: 0.8008 (mmp) cc_final: 0.7575 (mmp) REVERT: F 215 GLN cc_start: 0.7010 (tp-100) cc_final: 0.6784 (tp-100) REVERT: F 219 LEU cc_start: 0.7524 (mt) cc_final: 0.6759 (mt) REVERT: F 237 THR cc_start: 0.6906 (t) cc_final: 0.6232 (m) REVERT: F 241 GLN cc_start: 0.7854 (mm110) cc_final: 0.7434 (mm-40) REVERT: F 248 MET cc_start: 0.7100 (mtp) cc_final: 0.6645 (mtp) REVERT: F 270 LYS cc_start: 0.8270 (pttp) cc_final: 0.7848 (ptmm) REVERT: F 300 LYS cc_start: 0.8049 (tptm) cc_final: 0.7741 (tptm) REVERT: F 302 MET cc_start: 0.7556 (tmm) cc_final: 0.7223 (tmm) REVERT: F 337 HIS cc_start: 0.7516 (m170) cc_final: 0.7247 (m170) outliers start: 1 outliers final: 0 residues processed: 560 average time/residue: 0.3103 time to fit residues: 238.6428 Evaluate side-chains 548 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 547 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14142 Z= 0.257 Angle : 0.657 10.233 19146 Z= 0.352 Chirality : 0.046 0.273 2190 Planarity : 0.005 0.053 2448 Dihedral : 11.007 104.774 1962 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.13 % Allowed : 3.20 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.21), residues: 1728 helix: 0.87 (0.16), residues: 972 sheet: 0.79 (0.40), residues: 198 loop : 0.37 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 90 HIS 0.006 0.001 HIS B 281 PHE 0.050 0.003 PHE D 216 TYR 0.016 0.002 TYR D 132 ARG 0.008 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 599 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 597 time to evaluate : 1.744 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: 0.8201 (mtm) cc_final: 0.7811 (mtm) REVERT: A 96 LEU cc_start: 0.7476 (mt) cc_final: 0.7231 (mt) REVERT: A 101 THR cc_start: 0.8268 (p) cc_final: 0.7896 (t) REVERT: A 104 LYS cc_start: 0.8642 (tttt) cc_final: 0.8209 (tttt) REVERT: A 117 PHE cc_start: 0.7890 (m-10) cc_final: 0.7619 (m-10) REVERT: A 118 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 124 GLN cc_start: 0.8172 (pp30) cc_final: 0.7835 (pp30) REVERT: A 125 PRO cc_start: 0.8441 (Cg_endo) cc_final: 0.7922 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8090 (mp) cc_final: 0.7842 (mt) REVERT: A 148 LYS cc_start: 0.8332 (tttt) cc_final: 0.7910 (ttmt) REVERT: A 149 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 154 PHE cc_start: 0.7710 (t80) cc_final: 0.7103 (t80) REVERT: A 157 LEU cc_start: 0.7945 (tp) cc_final: 0.7623 (tp) REVERT: A 169 GLU cc_start: 0.7780 (tt0) cc_final: 0.7507 (tt0) REVERT: A 177 VAL cc_start: 0.8632 (t) cc_final: 0.8401 (t) REVERT: A 179 SER cc_start: 0.8738 (t) cc_final: 0.8468 (p) REVERT: A 193 GLU cc_start: 0.7707 (tt0) cc_final: 0.7485 (tt0) REVERT: A 199 ARG cc_start: 0.7452 (tpp80) cc_final: 0.6598 (tpp80) REVERT: A 206 HIS cc_start: 0.8022 (p90) cc_final: 0.7280 (p90) REVERT: A 211 MET cc_start: 0.8077 (mmp) cc_final: 0.7556 (mmp) REVERT: A 212 MET cc_start: 0.7998 (mmp) cc_final: 0.7665 (mmp) REVERT: A 213 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7777 (mtmt) REVERT: A 217 MET cc_start: 0.8091 (mpp) cc_final: 0.7644 (mpp) REVERT: A 218 SER cc_start: 0.8600 (p) cc_final: 0.8340 (p) REVERT: A 219 LEU cc_start: 0.8711 (mt) cc_final: 0.8401 (mt) REVERT: A 237 THR cc_start: 0.8119 (t) cc_final: 0.7490 (m) REVERT: A 251 MET cc_start: 0.7831 (mmm) cc_final: 0.7044 (mmm) REVERT: A 259 GLN cc_start: 0.7429 (mt0) cc_final: 0.7079 (mt0) REVERT: A 266 GLU cc_start: 0.7939 (tp30) cc_final: 0.7663 (tp30) REVERT: A 305 ASP cc_start: 0.8252 (t0) cc_final: 0.7905 (m-30) REVERT: A 338 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7863 (mtp85) REVERT: A 341 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7483 (mm-30) REVERT: A 342 LYS cc_start: 0.8719 (mptt) cc_final: 0.8288 (mptt) REVERT: A 343 MET cc_start: 0.8386 (tpt) cc_final: 0.8160 (tpt) REVERT: B 74 MET cc_start: 0.8051 (mtm) cc_final: 0.7364 (mtm) REVERT: B 85 ASN cc_start: 0.8160 (p0) cc_final: 0.7925 (p0) REVERT: B 86 MET cc_start: 0.7950 (mtm) cc_final: 0.7578 (mtm) REVERT: B 90 TRP cc_start: 0.8150 (m100) cc_final: 0.7325 (m100) REVERT: B 104 LYS cc_start: 0.8490 (tttt) cc_final: 0.8102 (tttt) REVERT: B 114 LYS cc_start: 0.7819 (tptm) cc_final: 0.7558 (tptm) REVERT: B 131 LEU cc_start: 0.8196 (mp) cc_final: 0.7837 (tp) REVERT: B 148 LYS cc_start: 0.8353 (tttt) cc_final: 0.8028 (ttmt) REVERT: B 154 PHE cc_start: 0.7689 (t80) cc_final: 0.7102 (t80) REVERT: B 157 LEU cc_start: 0.8084 (tp) cc_final: 0.7826 (tp) REVERT: B 211 MET cc_start: 0.8011 (mmp) cc_final: 0.7608 (mmp) REVERT: B 212 MET cc_start: 0.7994 (mmp) cc_final: 0.7743 (mmp) REVERT: B 213 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7614 (mtmt) REVERT: B 215 GLN cc_start: 0.7462 (tp-100) cc_final: 0.6595 (tp-100) REVERT: B 217 MET cc_start: 0.8133 (mpp) cc_final: 0.7703 (mpp) REVERT: B 237 THR cc_start: 0.7696 (t) cc_final: 0.6885 (m) REVERT: B 243 LEU cc_start: 0.8437 (mt) cc_final: 0.8219 (mt) REVERT: B 259 GLN cc_start: 0.7671 (mt0) cc_final: 0.7289 (mt0) REVERT: B 266 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 295 SER cc_start: 0.6961 (p) cc_final: 0.6598 (p) REVERT: B 299 LEU cc_start: 0.8855 (mt) cc_final: 0.8514 (mp) REVERT: B 305 ASP cc_start: 0.8185 (t0) cc_final: 0.7807 (m-30) REVERT: B 341 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 342 LYS cc_start: 0.8573 (mptt) cc_final: 0.7768 (mptt) REVERT: B 343 MET cc_start: 0.8231 (tpt) cc_final: 0.6629 (tpt) REVERT: B 345 LYS cc_start: 0.8771 (pptt) cc_final: 0.8450 (pptt) REVERT: B 346 SER cc_start: 0.8581 (p) cc_final: 0.8347 (p) REVERT: B 347 LYS cc_start: 0.8880 (mptt) cc_final: 0.8379 (mptt) REVERT: C 74 MET cc_start: 0.5633 (mtm) cc_final: 0.5392 (mtm) REVERT: C 158 GLN cc_start: 0.8335 (pm20) cc_final: 0.7932 (pm20) REVERT: C 170 SER cc_start: 0.7832 (p) cc_final: 0.7551 (p) REVERT: C 171 GLN cc_start: 0.8259 (mm110) cc_final: 0.7900 (mm-40) REVERT: C 211 MET cc_start: 0.6917 (mmp) cc_final: 0.6696 (mmp) REVERT: C 212 MET cc_start: 0.7159 (mmp) cc_final: 0.6679 (mmp) REVERT: C 239 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7023 (mtt90) REVERT: C 248 MET cc_start: 0.7740 (mtp) cc_final: 0.7167 (mtp) REVERT: C 251 MET cc_start: 0.6543 (mmt) cc_final: 0.6048 (mmt) REVERT: C 289 GLN cc_start: 0.8257 (mt0) cc_final: 0.7959 (mt0) REVERT: C 299 LEU cc_start: 0.8615 (mt) cc_final: 0.8343 (mt) REVERT: C 300 LYS cc_start: 0.8891 (tttt) cc_final: 0.8616 (tttt) REVERT: C 302 MET cc_start: 0.8005 (tmm) cc_final: 0.7724 (tmm) REVERT: C 304 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8074 (mtp-110) REVERT: C 308 LEU cc_start: 0.8657 (tp) cc_final: 0.8398 (tp) REVERT: C 335 ASP cc_start: 0.7823 (m-30) cc_final: 0.7499 (m-30) REVERT: C 343 MET cc_start: 0.8401 (tpt) cc_final: 0.7572 (tpt) REVERT: C 344 LYS cc_start: 0.9040 (mttm) cc_final: 0.8663 (mttm) REVERT: C 347 LYS cc_start: 0.8270 (mptt) cc_final: 0.8008 (mptt) REVERT: D 82 ASP cc_start: 0.7876 (t0) cc_final: 0.7461 (t70) REVERT: D 104 LYS cc_start: 0.8332 (tttt) cc_final: 0.7992 (tttm) REVERT: D 132 TYR cc_start: 0.7331 (p90) cc_final: 0.6949 (p90) REVERT: D 139 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7262 (mtmm) REVERT: D 183 LYS cc_start: 0.8680 (mptt) cc_final: 0.8283 (mptt) REVERT: D 212 MET cc_start: 0.7712 (mmp) cc_final: 0.7267 (mmp) REVERT: D 241 GLN cc_start: 0.8112 (mp-120) cc_final: 0.7165 (mm-40) REVERT: D 248 MET cc_start: 0.7040 (mtp) cc_final: 0.6596 (mtp) REVERT: D 250 ARG cc_start: 0.7198 (ttt180) cc_final: 0.6963 (ttt180) REVERT: D 251 MET cc_start: 0.7666 (mmt) cc_final: 0.7429 (mmt) REVERT: D 300 LYS cc_start: 0.8406 (tptm) cc_final: 0.8033 (tptm) REVERT: D 302 MET cc_start: 0.7708 (tmm) cc_final: 0.7473 (tmm) REVERT: D 305 ASP cc_start: 0.7674 (t0) cc_final: 0.7327 (t0) REVERT: D 337 HIS cc_start: 0.7564 (m170) cc_final: 0.7356 (m90) REVERT: E 171 GLN cc_start: 0.8285 (mm110) cc_final: 0.7919 (mm-40) REVERT: E 193 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7125 (mt-10) REVERT: E 212 MET cc_start: 0.7369 (mmp) cc_final: 0.6400 (mmp) REVERT: E 248 MET cc_start: 0.7827 (mtp) cc_final: 0.7324 (mtp) REVERT: E 266 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 286 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7567 (mm-30) REVERT: E 290 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7631 (mm-30) REVERT: E 298 ASP cc_start: 0.7580 (m-30) cc_final: 0.7167 (m-30) REVERT: E 299 LEU cc_start: 0.8720 (mt) cc_final: 0.8318 (mt) REVERT: E 300 LYS cc_start: 0.8654 (tttt) cc_final: 0.8384 (tttt) REVERT: E 302 MET cc_start: 0.8003 (tmm) cc_final: 0.7711 (tmm) REVERT: E 304 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8222 (mtp85) REVERT: E 309 LEU cc_start: 0.8760 (tp) cc_final: 0.8557 (tp) REVERT: E 341 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 343 MET cc_start: 0.8374 (tpt) cc_final: 0.7602 (tpt) REVERT: F 73 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8000 (mt-10) REVERT: F 74 MET cc_start: 0.7627 (mtm) cc_final: 0.7361 (mtm) REVERT: F 82 ASP cc_start: 0.7730 (t70) cc_final: 0.7348 (t0) REVERT: F 102 ASP cc_start: 0.7991 (m-30) cc_final: 0.7669 (m-30) REVERT: F 104 LYS cc_start: 0.8416 (tttt) cc_final: 0.8075 (tttm) REVERT: F 131 LEU cc_start: 0.8312 (mp) cc_final: 0.7882 (mt) REVERT: F 139 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7501 (mtmm) REVERT: F 149 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6939 (mm-30) REVERT: F 183 LYS cc_start: 0.8698 (mptt) cc_final: 0.8429 (mptt) REVERT: F 199 ARG cc_start: 0.6394 (tpp80) cc_final: 0.5181 (tpp80) REVERT: F 211 MET cc_start: 0.7318 (mmp) cc_final: 0.7063 (mmp) REVERT: F 212 MET cc_start: 0.7986 (mmp) cc_final: 0.7637 (mmp) REVERT: F 217 MET cc_start: 0.7331 (mmt) cc_final: 0.6763 (mmt) REVERT: F 241 GLN cc_start: 0.7905 (mm110) cc_final: 0.7412 (mm-40) REVERT: F 248 MET cc_start: 0.7057 (mtp) cc_final: 0.6453 (mtp) REVERT: F 259 GLN cc_start: 0.7992 (mp10) cc_final: 0.7750 (mp10) REVERT: F 270 LYS cc_start: 0.8324 (pttp) cc_final: 0.7894 (ptmm) REVERT: F 300 LYS cc_start: 0.8130 (tptm) cc_final: 0.7781 (tptm) REVERT: F 302 MET cc_start: 0.7726 (tmm) cc_final: 0.7356 (tmm) REVERT: F 337 HIS cc_start: 0.7626 (m170) cc_final: 0.7367 (m170) outliers start: 2 outliers final: 0 residues processed: 598 average time/residue: 0.2951 time to fit residues: 244.5935 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 : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 0.0870 chunk 168 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- 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** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 206 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3498 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= 0.183 Angle : 0.601 11.534 19146 Z= 0.317 Chirality : 0.043 0.211 2190 Planarity : 0.004 0.055 2448 Dihedral : 10.810 102.350 1962 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.21), residues: 1728 helix: 1.18 (0.16), residues: 942 sheet: 1.08 (0.41), residues: 186 loop : 0.14 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 220 HIS 0.013 0.001 HIS A 337 PHE 0.029 0.002 PHE C 216 TYR 0.012 0.002 TYR E 314 ARG 0.008 0.001 ARG F 250 *********************** 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 575 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8154 (mtm) cc_final: 0.7775 (mtm) REVERT: A 90 TRP cc_start: 0.8019 (m100) cc_final: 0.7197 (m100) REVERT: A 101 THR cc_start: 0.8393 (p) cc_final: 0.7995 (t) REVERT: A 104 LYS cc_start: 0.8631 (tttt) cc_final: 0.8191 (tttt) REVERT: A 125 PRO cc_start: 0.8349 (Cg_endo) cc_final: 0.8106 (Cg_exo) REVERT: A 146 THR cc_start: 0.8282 (p) cc_final: 0.7889 (p) REVERT: A 148 LYS cc_start: 0.8219 (tttt) cc_final: 0.7802 (ttmt) REVERT: A 157 LEU cc_start: 0.7893 (tp) cc_final: 0.7598 (tp) REVERT: A 169 GLU cc_start: 0.7686 (tt0) cc_final: 0.7113 (tt0) REVERT: A 177 VAL cc_start: 0.8677 (t) cc_final: 0.8460 (t) REVERT: A 179 SER cc_start: 0.8751 (t) cc_final: 0.8457 (p) REVERT: A 199 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6475 (tpp80) REVERT: A 206 HIS cc_start: 0.7999 (p90) cc_final: 0.7265 (p90) REVERT: A 211 MET cc_start: 0.7982 (mmp) cc_final: 0.7434 (mmp) REVERT: A 212 MET cc_start: 0.8021 (mmp) cc_final: 0.7651 (mmp) REVERT: A 213 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7816 (mtmt) REVERT: A 217 MET cc_start: 0.8061 (mpp) cc_final: 0.7594 (mpp) REVERT: A 219 LEU cc_start: 0.8743 (mt) cc_final: 0.8384 (mt) REVERT: A 251 MET cc_start: 0.7698 (mmm) cc_final: 0.7096 (mmp) REVERT: A 259 GLN cc_start: 0.7384 (mt0) cc_final: 0.7043 (mt0) REVERT: A 266 GLU cc_start: 0.7879 (tp30) cc_final: 0.7545 (tp30) REVERT: A 273 LEU cc_start: 0.8308 (mm) cc_final: 0.8107 (mm) REVERT: A 286 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 301 GLU cc_start: 0.8105 (tt0) cc_final: 0.6754 (tt0) REVERT: A 304 ARG cc_start: 0.7697 (mmp-170) cc_final: 0.7494 (mmm160) REVERT: A 305 ASP cc_start: 0.8197 (t0) cc_final: 0.7914 (m-30) REVERT: A 338 ARG cc_start: 0.8353 (mtp85) cc_final: 0.7819 (mtp85) REVERT: A 341 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 342 LYS cc_start: 0.8679 (mptt) cc_final: 0.8234 (mptt) REVERT: A 343 MET cc_start: 0.8333 (tpt) cc_final: 0.7910 (tpt) REVERT: B 74 MET cc_start: 0.8007 (mtm) cc_final: 0.7314 (mtm) REVERT: B 85 ASN cc_start: 0.8165 (p0) cc_final: 0.7941 (p0) REVERT: B 86 MET cc_start: 0.7954 (mtm) cc_final: 0.7564 (mtm) REVERT: B 104 LYS cc_start: 0.8482 (tttt) cc_final: 0.8118 (tttt) REVERT: B 130 LEU cc_start: 0.7665 (tp) cc_final: 0.6959 (mp) REVERT: B 131 LEU cc_start: 0.8170 (mp) cc_final: 0.7686 (tp) REVERT: B 148 LYS cc_start: 0.8299 (tttt) cc_final: 0.8027 (ttmt) REVERT: B 149 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7139 (mm-30) REVERT: B 157 LEU cc_start: 0.8015 (tp) cc_final: 0.7601 (tp) REVERT: B 158 GLN cc_start: 0.7017 (pm20) cc_final: 0.6178 (pm20) REVERT: B 211 MET cc_start: 0.7994 (mmp) cc_final: 0.7580 (mmp) REVERT: B 212 MET cc_start: 0.7918 (mmp) cc_final: 0.7701 (mmp) REVERT: B 213 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7607 (mtmt) REVERT: B 215 GLN cc_start: 0.7421 (tp-100) cc_final: 0.6540 (tp-100) REVERT: B 217 MET cc_start: 0.8188 (mpp) cc_final: 0.7717 (mpp) REVERT: B 231 VAL cc_start: 0.7804 (t) cc_final: 0.7525 (p) REVERT: B 243 LEU cc_start: 0.8397 (mt) cc_final: 0.8164 (mt) REVERT: B 250 ARG cc_start: 0.7659 (mmt90) cc_final: 0.7373 (tpp80) REVERT: B 259 GLN cc_start: 0.7691 (mt0) cc_final: 0.7293 (mt0) REVERT: B 266 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7019 (tm-30) REVERT: B 270 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7793 (mptt) REVERT: B 273 LEU cc_start: 0.8119 (mm) cc_final: 0.7907 (mm) REVERT: B 286 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6732 (mm-30) REVERT: B 295 SER cc_start: 0.6947 (p) cc_final: 0.6544 (p) REVERT: B 299 LEU cc_start: 0.8811 (mt) cc_final: 0.8400 (mp) REVERT: B 305 ASP cc_start: 0.8135 (t0) cc_final: 0.7774 (m-30) REVERT: B 341 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 342 LYS cc_start: 0.8558 (mptt) cc_final: 0.7717 (mptt) REVERT: B 343 MET cc_start: 0.8228 (tpt) cc_final: 0.6632 (tpt) REVERT: B 345 LYS cc_start: 0.8747 (pptt) cc_final: 0.8435 (pptt) REVERT: B 346 SER cc_start: 0.8613 (p) cc_final: 0.8385 (p) REVERT: B 347 LYS cc_start: 0.8919 (mptt) cc_final: 0.8408 (mptt) REVERT: C 74 MET cc_start: 0.5638 (mtm) cc_final: 0.5392 (mtm) REVERT: C 158 GLN cc_start: 0.8261 (pm20) cc_final: 0.7841 (pm20) REVERT: C 171 GLN cc_start: 0.8195 (mm110) cc_final: 0.7738 (mm-40) REVERT: C 212 MET cc_start: 0.7129 (mmp) cc_final: 0.6624 (mmp) REVERT: C 239 ARG cc_start: 0.7720 (mtt90) cc_final: 0.6951 (mtt90) REVERT: C 245 SER cc_start: 0.7717 (t) cc_final: 0.7511 (t) REVERT: C 248 MET cc_start: 0.7836 (mtp) cc_final: 0.7210 (mtp) REVERT: C 251 MET cc_start: 0.6648 (mmt) cc_final: 0.6026 (mmt) REVERT: C 270 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7508 (mmmt) REVERT: C 289 GLN cc_start: 0.8200 (mt0) cc_final: 0.7835 (mt0) REVERT: C 299 LEU cc_start: 0.8566 (mt) cc_final: 0.8248 (mt) REVERT: C 300 LYS cc_start: 0.8825 (tttt) cc_final: 0.8572 (tttt) REVERT: C 302 MET cc_start: 0.7926 (tmm) cc_final: 0.7632 (tmm) REVERT: C 308 LEU cc_start: 0.8593 (tp) cc_final: 0.8319 (tp) REVERT: C 335 ASP cc_start: 0.7879 (m-30) cc_final: 0.7597 (m-30) REVERT: C 343 MET cc_start: 0.8388 (tpt) cc_final: 0.7558 (tpt) REVERT: C 344 LYS cc_start: 0.9015 (mttm) cc_final: 0.8628 (mttm) REVERT: C 347 LYS cc_start: 0.8254 (mptt) cc_final: 0.8048 (mptt) REVERT: D 82 ASP cc_start: 0.7888 (t0) cc_final: 0.7529 (t70) REVERT: D 104 LYS cc_start: 0.8284 (tttt) cc_final: 0.7953 (tttm) REVERT: D 132 TYR cc_start: 0.7412 (p90) cc_final: 0.7112 (p90) REVERT: D 139 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7142 (mtmm) REVERT: D 180 LEU cc_start: 0.7876 (tt) cc_final: 0.7639 (tt) REVERT: D 183 LYS cc_start: 0.8656 (mptt) cc_final: 0.8226 (mptt) REVERT: D 196 SER cc_start: 0.7167 (t) cc_final: 0.6701 (p) REVERT: D 212 MET cc_start: 0.7700 (mmp) cc_final: 0.7395 (mmp) REVERT: D 241 GLN cc_start: 0.8071 (mp-120) cc_final: 0.7126 (mm-40) REVERT: D 248 MET cc_start: 0.7012 (mtp) cc_final: 0.6511 (mtp) REVERT: D 259 GLN cc_start: 0.8373 (mp10) cc_final: 0.8033 (mp10) REVERT: D 300 LYS cc_start: 0.8440 (tptm) cc_final: 0.8011 (tptm) REVERT: D 302 MET cc_start: 0.7620 (tmm) cc_final: 0.7381 (tmm) REVERT: D 305 ASP cc_start: 0.7669 (t0) cc_final: 0.7283 (t0) REVERT: D 332 GLN cc_start: 0.7820 (tp40) cc_final: 0.7438 (tp-100) REVERT: D 337 HIS cc_start: 0.7469 (m170) cc_final: 0.7247 (m90) REVERT: E 171 GLN cc_start: 0.8284 (mm110) cc_final: 0.7945 (mp10) REVERT: E 193 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6956 (mt-10) REVERT: E 205 ASP cc_start: 0.4910 (m-30) cc_final: 0.4554 (m-30) REVERT: E 211 MET cc_start: 0.7063 (mmp) cc_final: 0.6807 (mmp) REVERT: E 212 MET cc_start: 0.7338 (mmp) cc_final: 0.6576 (mmp) REVERT: E 239 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7352 (ttm110) REVERT: E 248 MET cc_start: 0.7758 (mtp) cc_final: 0.7178 (mtp) REVERT: E 266 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 270 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7289 (mmmt) REVERT: E 290 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7511 (mm-30) REVERT: E 298 ASP cc_start: 0.7548 (m-30) cc_final: 0.7057 (m-30) REVERT: E 299 LEU cc_start: 0.8700 (mt) cc_final: 0.8334 (mt) REVERT: E 300 LYS cc_start: 0.8650 (tttt) cc_final: 0.8408 (tttt) REVERT: E 302 MET cc_start: 0.7978 (tmm) cc_final: 0.7594 (tmm) REVERT: E 312 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.7985 (mtp-110) REVERT: E 335 ASP cc_start: 0.7985 (m-30) cc_final: 0.7738 (m-30) REVERT: E 341 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7680 (mm-30) REVERT: F 74 MET cc_start: 0.7619 (mtm) cc_final: 0.7275 (mtm) REVERT: F 82 ASP cc_start: 0.7954 (t70) cc_final: 0.7537 (t0) REVERT: F 90 TRP cc_start: 0.7960 (m100) cc_final: 0.7304 (m100) REVERT: F 102 ASP cc_start: 0.7940 (m-30) cc_final: 0.7640 (m-30) REVERT: F 104 LYS cc_start: 0.8349 (tttt) cc_final: 0.7967 (ttmt) REVERT: F 131 LEU cc_start: 0.8355 (mp) cc_final: 0.7986 (mt) REVERT: F 139 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7170 (mtmm) REVERT: F 149 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6991 (mm-30) REVERT: F 180 LEU cc_start: 0.8031 (tt) cc_final: 0.7825 (tt) REVERT: F 183 LYS cc_start: 0.8659 (mptt) cc_final: 0.8247 (mptt) REVERT: F 211 MET cc_start: 0.7320 (mmp) cc_final: 0.7095 (mmp) REVERT: F 212 MET cc_start: 0.7936 (mmp) cc_final: 0.7679 (mmp) REVERT: F 215 GLN cc_start: 0.7042 (tp-100) cc_final: 0.6702 (tp-100) REVERT: F 217 MET cc_start: 0.7194 (mmt) cc_final: 0.6576 (mmt) REVERT: F 219 LEU cc_start: 0.7634 (mt) cc_final: 0.7124 (mt) REVERT: F 241 GLN cc_start: 0.7829 (mm110) cc_final: 0.7363 (mm-40) REVERT: F 248 MET cc_start: 0.7004 (mtp) cc_final: 0.6426 (mtp) REVERT: F 270 LYS cc_start: 0.8374 (pttp) cc_final: 0.7914 (ptmm) REVERT: F 300 LYS cc_start: 0.8164 (tptm) cc_final: 0.7790 (tptm) REVERT: F 302 MET cc_start: 0.7762 (tmm) cc_final: 0.7421 (tmm) REVERT: F 337 HIS cc_start: 0.7529 (m170) cc_final: 0.7283 (m170) outliers start: 0 outliers final: 0 residues processed: 575 average time/residue: 0.3070 time to fit residues: 244.1758 Evaluate side-chains 558 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 0.0570 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS F 115 HIS F 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14142 Z= 0.190 Angle : 0.591 11.561 19146 Z= 0.311 Chirality : 0.043 0.171 2190 Planarity : 0.004 0.049 2448 Dihedral : 10.801 104.084 1962 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.20 % Allowed : 1.70 % Favored : 98.10 % 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: 1.40 (0.21), residues: 1728 helix: 1.24 (0.16), residues: 978 sheet: 1.07 (0.41), residues: 186 loop : 0.54 (0.30), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 220 HIS 0.010 0.001 HIS B 337 PHE 0.035 0.002 PHE F 216 TYR 0.013 0.002 TYR C 132 ARG 0.008 0.001 ARG E 199 *********************** 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 586 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 583 time to evaluate : 1.516 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: 0.8190 (mtm) cc_final: 0.7783 (mtm) REVERT: A 102 ASP cc_start: 0.7883 (m-30) cc_final: 0.7660 (m-30) REVERT: A 114 LYS cc_start: 0.7660 (tttt) cc_final: 0.7454 (tttt) REVERT: A 118 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 124 GLN cc_start: 0.8203 (pp30) cc_final: 0.7870 (pp30) REVERT: A 125 PRO cc_start: 0.8384 (Cg_endo) cc_final: 0.7960 (Cg_exo) REVERT: A 146 THR cc_start: 0.8322 (p) cc_final: 0.7998 (p) REVERT: A 148 LYS cc_start: 0.8331 (tttt) cc_final: 0.7900 (ttmt) REVERT: A 157 LEU cc_start: 0.7896 (tp) cc_final: 0.7613 (tp) REVERT: A 177 VAL cc_start: 0.8710 (t) cc_final: 0.8495 (t) REVERT: A 179 SER cc_start: 0.8801 (t) cc_final: 0.8499 (p) REVERT: A 193 GLU cc_start: 0.7759 (tt0) cc_final: 0.7517 (tt0) REVERT: A 206 HIS cc_start: 0.7996 (p90) cc_final: 0.7278 (p90) REVERT: A 211 MET cc_start: 0.7998 (mmp) cc_final: 0.7458 (mmp) REVERT: A 212 MET cc_start: 0.7995 (mmp) cc_final: 0.7654 (mmp) REVERT: A 213 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7829 (mtmt) REVERT: A 217 MET cc_start: 0.8088 (mpp) cc_final: 0.7602 (mpp) REVERT: A 219 LEU cc_start: 0.8736 (mt) cc_final: 0.8370 (mt) REVERT: A 251 MET cc_start: 0.7703 (mmm) cc_final: 0.7129 (mmp) REVERT: A 259 GLN cc_start: 0.7458 (mt0) cc_final: 0.7150 (mt0) REVERT: A 266 GLU cc_start: 0.7885 (tp30) cc_final: 0.7679 (tp30) REVERT: A 270 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8258 (mmtm) REVERT: A 273 LEU cc_start: 0.8314 (mm) cc_final: 0.8100 (mm) REVERT: A 301 GLU cc_start: 0.8140 (tt0) cc_final: 0.6822 (tt0) REVERT: A 305 ASP cc_start: 0.8253 (t0) cc_final: 0.7928 (m-30) REVERT: A 338 ARG cc_start: 0.8337 (mtp85) cc_final: 0.7792 (mtp85) REVERT: A 341 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 342 LYS cc_start: 0.8685 (mptt) cc_final: 0.8279 (mptt) REVERT: A 343 MET cc_start: 0.8343 (tpt) cc_final: 0.7937 (tpt) REVERT: B 74 MET cc_start: 0.8065 (mtm) cc_final: 0.7351 (mtm) REVERT: B 86 MET cc_start: 0.7957 (mtm) cc_final: 0.7591 (mtm) REVERT: B 101 THR cc_start: 0.8455 (p) cc_final: 0.8001 (t) REVERT: B 104 LYS cc_start: 0.8492 (tttt) cc_final: 0.8114 (tttt) REVERT: B 129 VAL cc_start: 0.6707 (t) cc_final: 0.6480 (t) REVERT: B 131 LEU cc_start: 0.8070 (mp) cc_final: 0.7772 (tp) REVERT: B 148 LYS cc_start: 0.8332 (tttt) cc_final: 0.7993 (ttmt) REVERT: B 149 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 152 CYS cc_start: 0.7196 (p) cc_final: 0.6929 (m) REVERT: B 157 LEU cc_start: 0.7992 (tp) cc_final: 0.7639 (tp) REVERT: B 158 GLN cc_start: 0.7133 (pm20) cc_final: 0.6182 (pm20) REVERT: B 211 MET cc_start: 0.8024 (mmp) cc_final: 0.7627 (mmp) REVERT: B 213 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7621 (mtmt) REVERT: B 215 GLN cc_start: 0.7467 (tp-100) cc_final: 0.6576 (tp-100) REVERT: B 217 MET cc_start: 0.8129 (mpp) cc_final: 0.7691 (mpp) REVERT: B 243 LEU cc_start: 0.8471 (mt) cc_final: 0.8228 (mt) REVERT: B 259 GLN cc_start: 0.7757 (mt0) cc_final: 0.7339 (mt0) REVERT: B 266 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 270 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7828 (mptt) REVERT: B 286 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 295 SER cc_start: 0.7006 (p) cc_final: 0.6603 (p) REVERT: B 299 LEU cc_start: 0.8847 (mt) cc_final: 0.8438 (mp) REVERT: B 305 ASP cc_start: 0.8113 (t0) cc_final: 0.7870 (m-30) REVERT: B 338 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8193 (mtp85) REVERT: B 341 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 342 LYS cc_start: 0.8578 (mptt) cc_final: 0.7716 (mptt) REVERT: B 343 MET cc_start: 0.8242 (tpt) cc_final: 0.6736 (tpt) REVERT: B 345 LYS cc_start: 0.8740 (pptt) cc_final: 0.8434 (pptt) REVERT: B 346 SER cc_start: 0.8670 (p) cc_final: 0.8443 (p) REVERT: B 347 LYS cc_start: 0.8918 (mptt) cc_final: 0.8388 (mptt) REVERT: C 74 MET cc_start: 0.5804 (mtm) cc_final: 0.5574 (mtm) REVERT: C 158 GLN cc_start: 0.8290 (pm20) cc_final: 0.7872 (pm20) REVERT: C 170 SER cc_start: 0.7839 (p) cc_final: 0.7288 (p) REVERT: C 171 GLN cc_start: 0.8223 (mm110) cc_final: 0.7790 (mp10) REVERT: C 212 MET cc_start: 0.7149 (mmp) cc_final: 0.6742 (mmp) REVERT: C 215 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7105 (tm-30) REVERT: C 239 ARG cc_start: 0.7727 (mtt90) cc_final: 0.6976 (mtt90) REVERT: C 248 MET cc_start: 0.7795 (mtp) cc_final: 0.7203 (mtp) REVERT: C 251 MET cc_start: 0.6595 (mmt) cc_final: 0.5999 (mmt) REVERT: C 264 GLN cc_start: 0.8402 (mp10) cc_final: 0.8031 (mp10) REVERT: C 270 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7506 (mmmt) REVERT: C 289 GLN cc_start: 0.8206 (mt0) cc_final: 0.7803 (mt0) REVERT: C 299 LEU cc_start: 0.8616 (mt) cc_final: 0.8342 (mt) REVERT: C 300 LYS cc_start: 0.8835 (tttt) cc_final: 0.8560 (tttt) REVERT: C 302 MET cc_start: 0.7947 (tmm) cc_final: 0.7638 (tmm) REVERT: C 308 LEU cc_start: 0.8599 (tp) cc_final: 0.8344 (tp) REVERT: C 309 LEU cc_start: 0.8783 (tp) cc_final: 0.8397 (tp) REVERT: C 312 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7993 (mtp-110) REVERT: C 313 GLU cc_start: 0.8054 (pt0) cc_final: 0.7817 (pt0) REVERT: C 335 ASP cc_start: 0.7910 (m-30) cc_final: 0.7677 (m-30) REVERT: C 343 MET cc_start: 0.8396 (tpt) cc_final: 0.7568 (tpt) REVERT: C 344 LYS cc_start: 0.9039 (mttm) cc_final: 0.8650 (mttm) REVERT: D 82 ASP cc_start: 0.8049 (t0) cc_final: 0.7512 (t70) REVERT: D 104 LYS cc_start: 0.8248 (tttt) cc_final: 0.7918 (tttm) REVERT: D 132 TYR cc_start: 0.7422 (p90) cc_final: 0.7142 (p90) REVERT: D 139 LYS cc_start: 0.7830 (mtmm) cc_final: 0.7221 (mtmm) REVERT: D 183 LYS cc_start: 0.8590 (mptt) cc_final: 0.8224 (mptt) REVERT: D 212 MET cc_start: 0.7690 (mmp) cc_final: 0.7463 (mmp) REVERT: D 241 GLN cc_start: 0.8066 (mp-120) cc_final: 0.7098 (mm-40) REVERT: D 251 MET cc_start: 0.7610 (mmt) cc_final: 0.7173 (mmt) REVERT: D 300 LYS cc_start: 0.8475 (tptm) cc_final: 0.7998 (tptm) REVERT: D 302 MET cc_start: 0.7633 (tmm) cc_final: 0.7417 (tmm) REVERT: D 305 ASP cc_start: 0.7624 (t0) cc_final: 0.7247 (t0) REVERT: D 308 LEU cc_start: 0.8153 (pp) cc_final: 0.6758 (pp) REVERT: D 309 LEU cc_start: 0.8346 (tp) cc_final: 0.8103 (tp) REVERT: D 312 ARG cc_start: 0.8074 (ptp-170) cc_final: 0.7836 (ptp-170) REVERT: D 332 GLN cc_start: 0.7761 (tp40) cc_final: 0.7413 (tp-100) REVERT: D 337 HIS cc_start: 0.7510 (m170) cc_final: 0.7255 (m170) REVERT: E 158 GLN cc_start: 0.8279 (pm20) cc_final: 0.8078 (pm20) REVERT: E 171 GLN cc_start: 0.8303 (mm110) cc_final: 0.8028 (mp10) REVERT: E 193 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6985 (mt-10) REVERT: E 205 ASP cc_start: 0.4872 (m-30) cc_final: 0.4508 (m-30) REVERT: E 212 MET cc_start: 0.7316 (mmp) cc_final: 0.6737 (mmp) REVERT: E 239 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7744 (mtt90) REVERT: E 248 MET cc_start: 0.7628 (mtp) cc_final: 0.7149 (mtp) REVERT: E 266 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7284 (tm-30) REVERT: E 270 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7296 (mmmt) REVERT: E 290 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7527 (mm-30) REVERT: E 298 ASP cc_start: 0.7574 (m-30) cc_final: 0.7098 (m-30) REVERT: E 299 LEU cc_start: 0.8695 (mt) cc_final: 0.8341 (mt) REVERT: E 300 LYS cc_start: 0.8668 (tttt) cc_final: 0.8404 (tttt) REVERT: E 302 MET cc_start: 0.8011 (tmm) cc_final: 0.7594 (tmm) REVERT: E 335 ASP cc_start: 0.7979 (m-30) cc_final: 0.7723 (m-30) REVERT: E 336 LEU cc_start: 0.8870 (mp) cc_final: 0.8610 (mp) REVERT: E 341 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7623 (mm-30) REVERT: F 74 MET cc_start: 0.7626 (mtm) cc_final: 0.7296 (mtm) REVERT: F 82 ASP cc_start: 0.7991 (t70) cc_final: 0.7577 (t0) REVERT: F 90 TRP cc_start: 0.7999 (m100) cc_final: 0.7241 (m100) REVERT: F 102 ASP cc_start: 0.7941 (m-30) cc_final: 0.7622 (m-30) REVERT: F 104 LYS cc_start: 0.8286 (tttt) cc_final: 0.7988 (ttmt) REVERT: F 131 LEU cc_start: 0.8367 (mp) cc_final: 0.8098 (mt) REVERT: F 149 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7010 (mm-30) REVERT: F 183 LYS cc_start: 0.8683 (mptt) cc_final: 0.8318 (mptt) REVERT: F 211 MET cc_start: 0.7330 (mmp) cc_final: 0.6984 (mmp) REVERT: F 212 MET cc_start: 0.7967 (mmp) cc_final: 0.7640 (mmp) REVERT: F 215 GLN cc_start: 0.6961 (tp-100) cc_final: 0.6631 (tp-100) REVERT: F 217 MET cc_start: 0.7389 (mmt) cc_final: 0.6735 (mmt) REVERT: F 219 LEU cc_start: 0.7709 (mt) cc_final: 0.7215 (mt) REVERT: F 241 GLN cc_start: 0.7823 (mm110) cc_final: 0.7345 (mm-40) REVERT: F 248 MET cc_start: 0.7042 (mtp) cc_final: 0.6448 (mtp) REVERT: F 270 LYS cc_start: 0.8344 (pttp) cc_final: 0.7903 (ptmm) REVERT: F 300 LYS cc_start: 0.8191 (tptm) cc_final: 0.7812 (tptm) REVERT: F 302 MET cc_start: 0.7742 (tmm) cc_final: 0.7423 (tmm) REVERT: F 337 HIS cc_start: 0.7529 (m170) cc_final: 0.7202 (m170) outliers start: 3 outliers final: 2 residues processed: 585 average time/residue: 0.3015 time to fit residues: 245.1474 Evaluate side-chains 568 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 566 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.4201 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= 0.189 Angle : 0.600 12.364 19146 Z= 0.313 Chirality : 0.043 0.320 2190 Planarity : 0.004 0.056 2448 Dihedral : 10.862 105.516 1962 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.21), residues: 1728 helix: 1.47 (0.16), residues: 948 sheet: 1.04 (0.42), residues: 186 loop : 0.67 (0.29), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 220 HIS 0.011 0.001 HIS A 337 PHE 0.025 0.002 PHE F 216 TYR 0.017 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 596 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 595 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8133 (mtm) cc_final: 0.7673 (mtm) REVERT: A 102 ASP cc_start: 0.7796 (m-30) cc_final: 0.7549 (m-30) REVERT: A 104 LYS cc_start: 0.8645 (tttt) cc_final: 0.8223 (tttt) REVERT: A 118 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 123 LEU cc_start: 0.8308 (tp) cc_final: 0.8082 (tp) REVERT: A 124 GLN cc_start: 0.8215 (pp30) cc_final: 0.7921 (pp30) REVERT: A 125 PRO cc_start: 0.8422 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8200 (mp) cc_final: 0.7874 (tp) REVERT: A 148 LYS cc_start: 0.8291 (tttt) cc_final: 0.7776 (ttmt) REVERT: A 157 LEU cc_start: 0.7871 (tp) cc_final: 0.7597 (tp) REVERT: A 177 VAL cc_start: 0.8707 (t) cc_final: 0.8483 (t) REVERT: A 179 SER cc_start: 0.8819 (t) cc_final: 0.8531 (p) REVERT: A 206 HIS cc_start: 0.8040 (p90) cc_final: 0.7345 (p90) REVERT: A 211 MET cc_start: 0.8001 (mmp) cc_final: 0.7373 (mmp) REVERT: A 212 MET cc_start: 0.7908 (mmp) cc_final: 0.7568 (mmp) REVERT: A 213 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7834 (mtmt) REVERT: A 216 PHE cc_start: 0.7928 (t80) cc_final: 0.7722 (t80) REVERT: A 217 MET cc_start: 0.8082 (mpp) cc_final: 0.7588 (mpp) REVERT: A 219 LEU cc_start: 0.8715 (mt) cc_final: 0.8356 (mt) REVERT: A 250 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7456 (tpp80) REVERT: A 251 MET cc_start: 0.7684 (mmm) cc_final: 0.7131 (mmp) REVERT: A 259 GLN cc_start: 0.7516 (mt0) cc_final: 0.7135 (mt0) REVERT: A 266 GLU cc_start: 0.7914 (tp30) cc_final: 0.7292 (tp30) REVERT: A 273 LEU cc_start: 0.8308 (mm) cc_final: 0.8070 (mm) REVERT: A 286 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 301 GLU cc_start: 0.8146 (tt0) cc_final: 0.6848 (tt0) REVERT: A 305 ASP cc_start: 0.8248 (t0) cc_final: 0.7982 (m-30) REVERT: A 338 ARG cc_start: 0.8358 (mtp85) cc_final: 0.7789 (mtp85) REVERT: A 341 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 342 LYS cc_start: 0.8674 (mptt) cc_final: 0.8315 (mptt) REVERT: A 343 MET cc_start: 0.8345 (tpt) cc_final: 0.7916 (tpt) REVERT: B 74 MET cc_start: 0.8069 (mtm) cc_final: 0.7301 (mtm) REVERT: B 86 MET cc_start: 0.7961 (mtm) cc_final: 0.7598 (mtm) REVERT: B 104 LYS cc_start: 0.8501 (tttt) cc_final: 0.8140 (tttt) REVERT: B 123 LEU cc_start: 0.8099 (tp) cc_final: 0.7797 (tp) REVERT: B 130 LEU cc_start: 0.7645 (tp) cc_final: 0.6916 (mp) REVERT: B 131 LEU cc_start: 0.8077 (mp) cc_final: 0.7595 (tp) REVERT: B 148 LYS cc_start: 0.8312 (tttt) cc_final: 0.7933 (ttmt) REVERT: B 149 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7115 (mm-30) REVERT: B 157 LEU cc_start: 0.7938 (tp) cc_final: 0.7582 (tp) REVERT: B 158 GLN cc_start: 0.7183 (pm20) cc_final: 0.6320 (pm20) REVERT: B 211 MET cc_start: 0.8010 (mmp) cc_final: 0.7611 (mmp) REVERT: B 213 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7646 (mtmt) REVERT: B 215 GLN cc_start: 0.7494 (tp-100) cc_final: 0.6616 (tp-100) REVERT: B 217 MET cc_start: 0.8141 (mpp) cc_final: 0.7682 (mpp) REVERT: B 243 LEU cc_start: 0.8447 (mt) cc_final: 0.8218 (mt) REVERT: B 250 ARG cc_start: 0.7683 (mmt90) cc_final: 0.7379 (tpp80) REVERT: B 259 GLN cc_start: 0.7758 (mt0) cc_final: 0.7379 (mt0) REVERT: B 266 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 270 LYS cc_start: 0.8398 (mmmt) cc_final: 0.7837 (mptt) REVERT: B 295 SER cc_start: 0.6953 (p) cc_final: 0.6563 (p) REVERT: B 299 LEU cc_start: 0.8849 (mt) cc_final: 0.8450 (mp) REVERT: B 305 ASP cc_start: 0.8134 (t0) cc_final: 0.7899 (m-30) REVERT: B 338 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8176 (mtp85) REVERT: B 341 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 342 LYS cc_start: 0.8543 (mptt) cc_final: 0.7898 (mptt) REVERT: B 343 MET cc_start: 0.8259 (tpt) cc_final: 0.6825 (tpt) REVERT: B 346 SER cc_start: 0.8679 (p) cc_final: 0.8468 (p) REVERT: B 347 LYS cc_start: 0.8946 (mptt) cc_final: 0.8427 (mptt) REVERT: C 74 MET cc_start: 0.5798 (mtm) cc_final: 0.5572 (mtm) REVERT: C 158 GLN cc_start: 0.8274 (pm20) cc_final: 0.7849 (pm20) REVERT: C 170 SER cc_start: 0.7797 (p) cc_final: 0.7195 (p) REVERT: C 171 GLN cc_start: 0.8243 (mm110) cc_final: 0.7805 (mp10) REVERT: C 212 MET cc_start: 0.7157 (mmp) cc_final: 0.6815 (mmp) REVERT: C 215 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7337 (tm-30) REVERT: C 239 ARG cc_start: 0.7743 (mtt90) cc_final: 0.6946 (mtt90) REVERT: C 245 SER cc_start: 0.7761 (t) cc_final: 0.7530 (t) REVERT: C 248 MET cc_start: 0.7782 (mtp) cc_final: 0.7125 (mtp) REVERT: C 264 GLN cc_start: 0.8415 (mp10) cc_final: 0.8090 (mp10) REVERT: C 270 LYS cc_start: 0.8492 (mmmt) cc_final: 0.7529 (mmmt) REVERT: C 289 GLN cc_start: 0.8393 (mt0) cc_final: 0.8011 (mt0) REVERT: C 299 LEU cc_start: 0.8649 (mt) cc_final: 0.8335 (mt) REVERT: C 300 LYS cc_start: 0.8873 (tttt) cc_final: 0.8563 (tttt) REVERT: C 302 MET cc_start: 0.7978 (tmm) cc_final: 0.7681 (tmm) REVERT: C 309 LEU cc_start: 0.8760 (tp) cc_final: 0.8377 (tp) REVERT: C 313 GLU cc_start: 0.8050 (pt0) cc_final: 0.7799 (pt0) REVERT: C 335 ASP cc_start: 0.8017 (m-30) cc_final: 0.7804 (m-30) REVERT: C 343 MET cc_start: 0.8280 (tpt) cc_final: 0.7476 (tpt) REVERT: C 344 LYS cc_start: 0.9014 (mttm) cc_final: 0.8660 (mttm) REVERT: D 82 ASP cc_start: 0.8151 (t0) cc_final: 0.7696 (t70) REVERT: D 104 LYS cc_start: 0.8274 (tttt) cc_final: 0.8000 (ttmt) REVERT: D 132 TYR cc_start: 0.7496 (p90) cc_final: 0.7208 (p90) REVERT: D 139 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7306 (mtmm) REVERT: D 179 SER cc_start: 0.8192 (p) cc_final: 0.7921 (p) REVERT: D 183 LYS cc_start: 0.8488 (mptt) cc_final: 0.8178 (mptt) REVERT: D 211 MET cc_start: 0.7491 (mmp) cc_final: 0.7153 (mmp) REVERT: D 241 GLN cc_start: 0.8054 (mp-120) cc_final: 0.7086 (mm-40) REVERT: D 250 ARG cc_start: 0.7085 (ttt-90) cc_final: 0.6826 (ttt180) REVERT: D 300 LYS cc_start: 0.8503 (tptm) cc_final: 0.8024 (tptm) REVERT: D 302 MET cc_start: 0.7623 (tmm) cc_final: 0.7410 (tmm) REVERT: D 305 ASP cc_start: 0.7675 (t0) cc_final: 0.7358 (t0) REVERT: D 309 LEU cc_start: 0.8364 (tp) cc_final: 0.8060 (tp) REVERT: D 312 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7859 (ptp-170) REVERT: D 337 HIS cc_start: 0.7517 (m170) cc_final: 0.7196 (m170) REVERT: E 158 GLN cc_start: 0.8263 (pm20) cc_final: 0.8008 (pm20) REVERT: E 171 GLN cc_start: 0.8333 (mm110) cc_final: 0.8022 (mp10) REVERT: E 193 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7010 (mt-10) REVERT: E 212 MET cc_start: 0.7337 (mmp) cc_final: 0.6782 (mmp) REVERT: E 215 GLN cc_start: 0.7793 (tp-100) cc_final: 0.6971 (tm-30) REVERT: E 217 MET cc_start: 0.8160 (ptp) cc_final: 0.7882 (tpp) REVERT: E 248 MET cc_start: 0.7661 (mtp) cc_final: 0.7153 (mtp) REVERT: E 264 GLN cc_start: 0.8427 (mp10) cc_final: 0.8221 (mp10) REVERT: E 266 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7302 (tm-30) REVERT: E 270 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7304 (mmmt) REVERT: E 290 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 295 SER cc_start: 0.8193 (p) cc_final: 0.7930 (p) REVERT: E 298 ASP cc_start: 0.7501 (m-30) cc_final: 0.7200 (m-30) REVERT: E 299 LEU cc_start: 0.8688 (mt) cc_final: 0.8388 (mt) REVERT: E 300 LYS cc_start: 0.8675 (tttt) cc_final: 0.8407 (tttt) REVERT: E 301 GLU cc_start: 0.8040 (tt0) cc_final: 0.7669 (tt0) REVERT: E 302 MET cc_start: 0.8022 (tmm) cc_final: 0.7646 (tmm) REVERT: E 313 GLU cc_start: 0.8351 (pt0) cc_final: 0.8140 (pt0) REVERT: E 336 LEU cc_start: 0.8843 (mp) cc_final: 0.8553 (mp) REVERT: E 341 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7546 (mm-30) REVERT: F 74 MET cc_start: 0.7663 (mtm) cc_final: 0.7282 (mtm) REVERT: F 82 ASP cc_start: 0.8063 (t70) cc_final: 0.7724 (t0) REVERT: F 90 TRP cc_start: 0.8014 (m100) cc_final: 0.7215 (m100) REVERT: F 102 ASP cc_start: 0.7944 (m-30) cc_final: 0.7617 (m-30) REVERT: F 104 LYS cc_start: 0.8294 (tttt) cc_final: 0.8008 (ttmt) REVERT: F 112 LYS cc_start: 0.7852 (mttt) cc_final: 0.7632 (mttt) REVERT: F 131 LEU cc_start: 0.8398 (mp) cc_final: 0.7929 (mt) REVERT: F 139 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7281 (mtmm) REVERT: F 149 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7015 (mm-30) REVERT: F 183 LYS cc_start: 0.8619 (mptt) cc_final: 0.8213 (mptt) REVERT: F 211 MET cc_start: 0.7378 (mmp) cc_final: 0.6998 (mmp) REVERT: F 212 MET cc_start: 0.7957 (mmp) cc_final: 0.7637 (mmp) REVERT: F 217 MET cc_start: 0.7341 (mmt) cc_final: 0.6738 (mmt) REVERT: F 241 GLN cc_start: 0.7805 (mm110) cc_final: 0.7270 (mm110) REVERT: F 248 MET cc_start: 0.7096 (mtp) cc_final: 0.6499 (mtp) REVERT: F 250 ARG cc_start: 0.7330 (ttt180) cc_final: 0.7076 (ttt-90) REVERT: F 270 LYS cc_start: 0.8373 (pttp) cc_final: 0.7877 (ptmm) REVERT: F 300 LYS cc_start: 0.8226 (tptm) cc_final: 0.7784 (tptm) REVERT: F 302 MET cc_start: 0.7646 (tmm) cc_final: 0.7278 (tmm) REVERT: F 337 HIS cc_start: 0.7578 (m170) cc_final: 0.7261 (m170) outliers start: 1 outliers final: 1 residues processed: 596 average time/residue: 0.3032 time to fit residues: 249.9237 Evaluate side-chains 572 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 141 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14142 Z= 0.194 Angle : 0.606 12.915 19146 Z= 0.318 Chirality : 0.044 0.276 2190 Planarity : 0.004 0.054 2448 Dihedral : 10.950 106.309 1962 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % 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: 1.59 (0.21), residues: 1728 helix: 1.42 (0.16), residues: 948 sheet: 0.69 (0.42), residues: 192 loop : 0.81 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 220 HIS 0.004 0.001 HIS B 115 PHE 0.035 0.002 PHE D 216 TYR 0.013 0.002 TYR A 72 ARG 0.010 0.001 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 598 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 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: A 74 MET cc_start: 0.8118 (mtm) cc_final: 0.7634 (mtm) REVERT: A 102 ASP cc_start: 0.7774 (m-30) cc_final: 0.7509 (m-30) REVERT: A 124 GLN cc_start: 0.8224 (pp30) cc_final: 0.7952 (pp30) REVERT: A 125 PRO cc_start: 0.8459 (Cg_endo) cc_final: 0.8000 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8167 (mp) cc_final: 0.7913 (tp) REVERT: A 148 LYS cc_start: 0.8103 (tttt) cc_final: 0.7847 (ttmt) REVERT: A 157 LEU cc_start: 0.7881 (tp) cc_final: 0.7570 (tp) REVERT: A 179 SER cc_start: 0.8840 (t) cc_final: 0.8520 (p) REVERT: A 193 GLU cc_start: 0.7785 (tt0) cc_final: 0.7560 (tt0) REVERT: A 206 HIS cc_start: 0.8072 (p90) cc_final: 0.7369 (p90) REVERT: A 211 MET cc_start: 0.8017 (mmp) cc_final: 0.7414 (mmp) REVERT: A 212 MET cc_start: 0.7914 (mmp) cc_final: 0.7581 (mmp) REVERT: A 213 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7846 (mtmt) REVERT: A 217 MET cc_start: 0.8097 (mpp) cc_final: 0.7557 (mpp) REVERT: A 219 LEU cc_start: 0.8762 (mt) cc_final: 0.8399 (mt) REVERT: A 250 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.6779 (mtt-85) REVERT: A 251 MET cc_start: 0.7398 (mmm) cc_final: 0.6860 (mmm) REVERT: A 259 GLN cc_start: 0.7545 (mt0) cc_final: 0.7270 (mt0) REVERT: A 266 GLU cc_start: 0.8050 (tp30) cc_final: 0.7760 (tp30) REVERT: A 273 LEU cc_start: 0.8286 (mm) cc_final: 0.8069 (mm) REVERT: A 301 GLU cc_start: 0.8139 (tt0) cc_final: 0.6782 (tt0) REVERT: A 305 ASP cc_start: 0.8256 (t0) cc_final: 0.7906 (m-30) REVERT: A 338 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7740 (mtp85) REVERT: A 341 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 342 LYS cc_start: 0.8723 (mptt) cc_final: 0.8345 (mptt) REVERT: A 343 MET cc_start: 0.8352 (tpt) cc_final: 0.7958 (tpt) REVERT: B 74 MET cc_start: 0.8081 (mtm) cc_final: 0.7333 (mtm) REVERT: B 86 MET cc_start: 0.8013 (mtm) cc_final: 0.7734 (mtm) REVERT: B 92 ASP cc_start: 0.7448 (m-30) cc_final: 0.7236 (m-30) REVERT: B 104 LYS cc_start: 0.8526 (tttt) cc_final: 0.8155 (tttt) REVERT: B 122 LEU cc_start: 0.8472 (pp) cc_final: 0.8263 (tt) REVERT: B 123 LEU cc_start: 0.8142 (tp) cc_final: 0.7891 (tp) REVERT: B 124 GLN cc_start: 0.8148 (pp30) cc_final: 0.7796 (pp30) REVERT: B 129 VAL cc_start: 0.6750 (t) cc_final: 0.6530 (t) REVERT: B 131 LEU cc_start: 0.8127 (mp) cc_final: 0.7784 (tp) REVERT: B 149 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7137 (mm-30) REVERT: B 154 PHE cc_start: 0.7709 (t80) cc_final: 0.7207 (t80) REVERT: B 157 LEU cc_start: 0.7962 (tp) cc_final: 0.7609 (tp) REVERT: B 158 GLN cc_start: 0.7181 (pm20) cc_final: 0.6322 (pm20) REVERT: B 167 TYR cc_start: 0.6869 (m-10) cc_final: 0.6647 (m-10) REVERT: B 211 MET cc_start: 0.8049 (mmp) cc_final: 0.7686 (mmp) REVERT: B 213 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7712 (mtmt) REVERT: B 215 GLN cc_start: 0.7559 (tp-100) cc_final: 0.6372 (tp-100) REVERT: B 217 MET cc_start: 0.8178 (mpp) cc_final: 0.7679 (mpp) REVERT: B 219 LEU cc_start: 0.8739 (mt) cc_final: 0.7781 (mt) REVERT: B 243 LEU cc_start: 0.8543 (mt) cc_final: 0.8280 (mt) REVERT: B 253 THR cc_start: 0.7747 (p) cc_final: 0.7543 (p) REVERT: B 259 GLN cc_start: 0.7779 (mt0) cc_final: 0.7406 (mt0) REVERT: B 266 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7025 (tm-30) REVERT: B 270 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7857 (mptt) REVERT: B 286 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 299 LEU cc_start: 0.8866 (mt) cc_final: 0.8444 (mp) REVERT: B 305 ASP cc_start: 0.8147 (t0) cc_final: 0.7912 (m-30) REVERT: B 334 GLN cc_start: 0.7858 (mp10) cc_final: 0.7598 (mp10) REVERT: B 338 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7788 (mmm-85) REVERT: B 341 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 342 LYS cc_start: 0.8550 (mptt) cc_final: 0.8102 (mptt) REVERT: B 343 MET cc_start: 0.8246 (tpt) cc_final: 0.6862 (tpt) REVERT: B 346 SER cc_start: 0.8697 (p) cc_final: 0.8490 (p) REVERT: B 347 LYS cc_start: 0.8936 (mptt) cc_final: 0.8398 (mptt) REVERT: C 74 MET cc_start: 0.5765 (mtm) cc_final: 0.5519 (mtm) REVERT: C 170 SER cc_start: 0.7903 (p) cc_final: 0.7369 (p) REVERT: C 171 GLN cc_start: 0.8413 (mm110) cc_final: 0.8050 (mp10) REVERT: C 212 MET cc_start: 0.7222 (mmp) cc_final: 0.6911 (mmp) REVERT: C 215 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7485 (tm-30) REVERT: C 239 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7043 (mtt90) REVERT: C 245 SER cc_start: 0.7788 (t) cc_final: 0.7562 (t) REVERT: C 248 MET cc_start: 0.7764 (mtp) cc_final: 0.7102 (mtp) REVERT: C 270 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7614 (mmmt) REVERT: C 289 GLN cc_start: 0.8424 (mt0) cc_final: 0.8014 (mt0) REVERT: C 299 LEU cc_start: 0.8682 (mt) cc_final: 0.8390 (mt) REVERT: C 300 LYS cc_start: 0.8785 (tttt) cc_final: 0.8524 (tttt) REVERT: C 302 MET cc_start: 0.8026 (tmm) cc_final: 0.7725 (tmm) REVERT: C 304 ARG cc_start: 0.8338 (ttt90) cc_final: 0.8096 (mmm160) REVERT: C 309 LEU cc_start: 0.8686 (tp) cc_final: 0.8354 (tp) REVERT: C 313 GLU cc_start: 0.8106 (pt0) cc_final: 0.7785 (pt0) REVERT: C 344 LYS cc_start: 0.8951 (mttm) cc_final: 0.8575 (mttm) REVERT: D 82 ASP cc_start: 0.8198 (t0) cc_final: 0.7822 (t70) REVERT: D 104 LYS cc_start: 0.8303 (tttt) cc_final: 0.8039 (ttmt) REVERT: D 139 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7369 (mtmm) REVERT: D 183 LYS cc_start: 0.8478 (mptt) cc_final: 0.8166 (mptt) REVERT: D 211 MET cc_start: 0.7540 (mmp) cc_final: 0.7132 (mmp) REVERT: D 212 MET cc_start: 0.8031 (mmp) cc_final: 0.7537 (mmp) REVERT: D 213 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7633 (mtmm) REVERT: D 251 MET cc_start: 0.7892 (mpp) cc_final: 0.6782 (mpp) REVERT: D 300 LYS cc_start: 0.8433 (tptm) cc_final: 0.8113 (tptm) REVERT: D 305 ASP cc_start: 0.7699 (t0) cc_final: 0.7289 (t0) REVERT: D 308 LEU cc_start: 0.8178 (pp) cc_final: 0.7060 (pp) REVERT: D 309 LEU cc_start: 0.8382 (tp) cc_final: 0.8143 (tp) REVERT: D 312 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7889 (ptp-170) REVERT: D 337 HIS cc_start: 0.7586 (m170) cc_final: 0.7315 (m90) REVERT: E 158 GLN cc_start: 0.8195 (pm20) cc_final: 0.7874 (pm20) REVERT: E 171 GLN cc_start: 0.8428 (mm110) cc_final: 0.8147 (mp10) REVERT: E 193 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6973 (mt-10) REVERT: E 212 MET cc_start: 0.7396 (mmp) cc_final: 0.6825 (mmp) REVERT: E 215 GLN cc_start: 0.7641 (tp-100) cc_final: 0.6841 (tm-30) REVERT: E 239 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7899 (mtt90) REVERT: E 248 MET cc_start: 0.7448 (mtp) cc_final: 0.6892 (mtp) REVERT: E 256 HIS cc_start: 0.7483 (t70) cc_final: 0.7227 (t70) REVERT: E 264 GLN cc_start: 0.8453 (mp10) cc_final: 0.8196 (mp10) REVERT: E 266 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 270 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7323 (mmmt) REVERT: E 290 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7745 (mm-30) REVERT: E 295 SER cc_start: 0.8122 (p) cc_final: 0.7795 (p) REVERT: E 298 ASP cc_start: 0.7408 (m-30) cc_final: 0.7150 (m-30) REVERT: E 299 LEU cc_start: 0.8692 (mt) cc_final: 0.8413 (mt) REVERT: E 300 LYS cc_start: 0.8620 (tttt) cc_final: 0.8348 (tttt) REVERT: E 302 MET cc_start: 0.8077 (tmm) cc_final: 0.7746 (tmm) REVERT: E 313 GLU cc_start: 0.8462 (pt0) cc_final: 0.8224 (pt0) REVERT: E 335 ASP cc_start: 0.8290 (m-30) cc_final: 0.7986 (m-30) REVERT: E 341 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7614 (mm-30) REVERT: E 343 MET cc_start: 0.8256 (tpp) cc_final: 0.7902 (tpp) REVERT: F 68 LYS cc_start: 0.7484 (mppt) cc_final: 0.7061 (mppt) REVERT: F 74 MET cc_start: 0.7650 (mtm) cc_final: 0.7229 (mtm) REVERT: F 82 ASP cc_start: 0.8154 (t70) cc_final: 0.7873 (t0) REVERT: F 90 TRP cc_start: 0.8033 (m100) cc_final: 0.7193 (m100) REVERT: F 102 ASP cc_start: 0.7931 (m-30) cc_final: 0.7667 (m-30) REVERT: F 104 LYS cc_start: 0.8306 (tttt) cc_final: 0.7991 (ttmt) REVERT: F 131 LEU cc_start: 0.8354 (mp) cc_final: 0.7831 (mt) REVERT: F 139 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7267 (mtmm) REVERT: F 149 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6963 (mm-30) REVERT: F 180 LEU cc_start: 0.8170 (tt) cc_final: 0.7950 (tt) REVERT: F 183 LYS cc_start: 0.8595 (mptt) cc_final: 0.8218 (mptt) REVERT: F 211 MET cc_start: 0.7407 (mmp) cc_final: 0.7008 (mmp) REVERT: F 212 MET cc_start: 0.7958 (mmp) cc_final: 0.7663 (mmp) REVERT: F 215 GLN cc_start: 0.6967 (tp-100) cc_final: 0.6634 (tp-100) REVERT: F 217 MET cc_start: 0.7303 (mmt) cc_final: 0.6600 (mmt) REVERT: F 219 LEU cc_start: 0.7789 (mt) cc_final: 0.7143 (mt) REVERT: F 241 GLN cc_start: 0.7872 (mm110) cc_final: 0.7352 (mm110) REVERT: F 248 MET cc_start: 0.7012 (mtp) cc_final: 0.6528 (mtp) REVERT: F 251 MET cc_start: 0.7673 (mmt) cc_final: 0.7328 (mmt) REVERT: F 270 LYS cc_start: 0.8336 (pttp) cc_final: 0.7839 (ptmm) REVERT: F 298 ASP cc_start: 0.8148 (m-30) cc_final: 0.7875 (m-30) REVERT: F 300 LYS cc_start: 0.8242 (tptm) cc_final: 0.7779 (tptm) REVERT: F 302 MET cc_start: 0.7707 (tmm) cc_final: 0.7389 (tmm) REVERT: F 332 GLN cc_start: 0.7921 (tp40) cc_final: 0.7697 (tp-100) REVERT: F 337 HIS cc_start: 0.7615 (m170) cc_final: 0.7263 (m170) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.2943 time to fit residues: 244.0463 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 : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14142 Z= 0.203 Angle : 0.614 13.197 19146 Z= 0.323 Chirality : 0.044 0.271 2190 Planarity : 0.005 0.066 2448 Dihedral : 11.107 105.959 1962 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % 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: 1.20 (0.21), residues: 1728 helix: 1.20 (0.17), residues: 942 sheet: 0.67 (0.41), residues: 192 loop : 0.38 (0.30), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 220 HIS 0.004 0.001 HIS B 115 PHE 0.039 0.003 PHE D 216 TYR 0.019 0.002 TYR F 72 ARG 0.010 0.001 ARG F 250 *********************** 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 607 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8199 (mtm) cc_final: 0.7726 (mtm) REVERT: A 102 ASP cc_start: 0.7791 (m-30) cc_final: 0.7531 (m-30) REVERT: A 104 LYS cc_start: 0.8634 (tttt) cc_final: 0.8237 (tttt) REVERT: A 114 LYS cc_start: 0.7369 (tttt) cc_final: 0.7128 (ttmt) REVERT: A 124 GLN cc_start: 0.8245 (pp30) cc_final: 0.8035 (pp30) REVERT: A 125 PRO cc_start: 0.8504 (Cg_endo) cc_final: 0.8126 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8196 (mp) cc_final: 0.7912 (tp) REVERT: A 148 LYS cc_start: 0.8135 (tttt) cc_final: 0.7744 (ttmt) REVERT: A 157 LEU cc_start: 0.7875 (tp) cc_final: 0.7552 (tp) REVERT: A 169 GLU cc_start: 0.7241 (tt0) cc_final: 0.6967 (tt0) REVERT: A 179 SER cc_start: 0.8848 (t) cc_final: 0.8569 (p) REVERT: A 193 GLU cc_start: 0.7841 (tt0) cc_final: 0.7602 (tt0) REVERT: A 206 HIS cc_start: 0.8069 (p90) cc_final: 0.7392 (p90) REVERT: A 211 MET cc_start: 0.8026 (mmp) cc_final: 0.7416 (mmp) REVERT: A 212 MET cc_start: 0.7903 (mmp) cc_final: 0.7565 (mmp) REVERT: A 213 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7839 (mtmt) REVERT: A 216 PHE cc_start: 0.8060 (t80) cc_final: 0.7836 (t80) REVERT: A 217 MET cc_start: 0.8118 (mpp) cc_final: 0.7692 (mpp) REVERT: A 219 LEU cc_start: 0.8759 (mt) cc_final: 0.8400 (mt) REVERT: A 251 MET cc_start: 0.7339 (mmm) cc_final: 0.6956 (mmm) REVERT: A 259 GLN cc_start: 0.7657 (mt0) cc_final: 0.7320 (mt0) REVERT: A 273 LEU cc_start: 0.8308 (mm) cc_final: 0.8071 (mm) REVERT: A 286 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6984 (mm-30) REVERT: A 301 GLU cc_start: 0.8169 (tt0) cc_final: 0.6821 (tt0) REVERT: A 305 ASP cc_start: 0.8252 (t0) cc_final: 0.7951 (m-30) REVERT: A 338 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7941 (mtp85) REVERT: A 341 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 342 LYS cc_start: 0.8748 (mptt) cc_final: 0.8178 (mptt) REVERT: A 343 MET cc_start: 0.8380 (tpt) cc_final: 0.7987 (tpt) REVERT: A 345 LYS cc_start: 0.8714 (pptt) cc_final: 0.8486 (pptt) REVERT: B 74 MET cc_start: 0.8139 (mtm) cc_final: 0.7411 (mtm) REVERT: B 86 MET cc_start: 0.7993 (mtm) cc_final: 0.7745 (mtm) REVERT: B 92 ASP cc_start: 0.7480 (m-30) cc_final: 0.7268 (m-30) REVERT: B 104 LYS cc_start: 0.8549 (tttt) cc_final: 0.8213 (tttt) REVERT: B 123 LEU cc_start: 0.8143 (tp) cc_final: 0.7870 (tp) REVERT: B 124 GLN cc_start: 0.8135 (pp30) cc_final: 0.7782 (pp30) REVERT: B 129 VAL cc_start: 0.6711 (t) cc_final: 0.6508 (t) REVERT: B 131 LEU cc_start: 0.8112 (mp) cc_final: 0.7767 (tp) REVERT: B 148 LYS cc_start: 0.8257 (tttt) cc_final: 0.7988 (ttpt) REVERT: B 149 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 152 CYS cc_start: 0.7282 (m) cc_final: 0.7053 (m) REVERT: B 154 PHE cc_start: 0.7656 (t80) cc_final: 0.7139 (t80) REVERT: B 157 LEU cc_start: 0.7970 (tp) cc_final: 0.7627 (tp) REVERT: B 158 GLN cc_start: 0.7190 (pm20) cc_final: 0.6353 (pm20) REVERT: B 211 MET cc_start: 0.8077 (mmp) cc_final: 0.7738 (mmp) REVERT: B 213 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7692 (mtmt) REVERT: B 215 GLN cc_start: 0.7667 (tp-100) cc_final: 0.6397 (tp-100) REVERT: B 217 MET cc_start: 0.8248 (mpp) cc_final: 0.7731 (mpp) REVERT: B 219 LEU cc_start: 0.8742 (mt) cc_final: 0.7729 (mt) REVERT: B 243 LEU cc_start: 0.8553 (mt) cc_final: 0.8299 (mt) REVERT: B 259 GLN cc_start: 0.7796 (mt0) cc_final: 0.7408 (mt0) REVERT: B 266 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 299 LEU cc_start: 0.8893 (mt) cc_final: 0.8515 (mt) REVERT: B 305 ASP cc_start: 0.8174 (t0) cc_final: 0.7887 (m-30) REVERT: B 338 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8051 (mmm-85) REVERT: B 341 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 342 LYS cc_start: 0.8587 (mptt) cc_final: 0.8135 (mptt) REVERT: B 343 MET cc_start: 0.8297 (tpt) cc_final: 0.6889 (tpt) REVERT: B 347 LYS cc_start: 0.8951 (mptt) cc_final: 0.8413 (mptt) REVERT: C 74 MET cc_start: 0.5752 (mtm) cc_final: 0.5480 (mtm) REVERT: C 158 GLN cc_start: 0.8074 (pm20) cc_final: 0.7631 (pm20) REVERT: C 170 SER cc_start: 0.7890 (p) cc_final: 0.7369 (p) REVERT: C 171 GLN cc_start: 0.8370 (mm110) cc_final: 0.8041 (mp10) REVERT: C 212 MET cc_start: 0.7366 (mmp) cc_final: 0.7062 (mmp) REVERT: C 215 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7498 (tm-30) REVERT: C 219 LEU cc_start: 0.7196 (mt) cc_final: 0.6916 (mm) REVERT: C 239 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7135 (mtt90) REVERT: C 248 MET cc_start: 0.7775 (mtp) cc_final: 0.7216 (mtp) REVERT: C 270 LYS cc_start: 0.8606 (mmmt) cc_final: 0.7548 (mmmt) REVERT: C 289 GLN cc_start: 0.8408 (mt0) cc_final: 0.8066 (mt0) REVERT: C 299 LEU cc_start: 0.8745 (mt) cc_final: 0.8416 (mt) REVERT: C 300 LYS cc_start: 0.8792 (tttt) cc_final: 0.8463 (tttt) REVERT: C 302 MET cc_start: 0.8125 (tmm) cc_final: 0.7841 (tmm) REVERT: C 309 LEU cc_start: 0.8679 (tp) cc_final: 0.8331 (tp) REVERT: C 313 GLU cc_start: 0.8140 (pt0) cc_final: 0.7793 (pt0) REVERT: C 343 MET cc_start: 0.8231 (tpp) cc_final: 0.7878 (tpp) REVERT: C 344 LYS cc_start: 0.8961 (mttm) cc_final: 0.8558 (mttm) REVERT: D 82 ASP cc_start: 0.8167 (t0) cc_final: 0.7816 (t70) REVERT: D 97 ASP cc_start: 0.7701 (p0) cc_final: 0.7492 (p0) REVERT: D 104 LYS cc_start: 0.8314 (tttt) cc_final: 0.8026 (ttmt) REVERT: D 131 LEU cc_start: 0.8433 (mp) cc_final: 0.7862 (mt) REVERT: D 139 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7430 (mtmm) REVERT: D 183 LYS cc_start: 0.8489 (mptt) cc_final: 0.8133 (mptt) REVERT: D 212 MET cc_start: 0.8019 (mmp) cc_final: 0.7542 (mmp) REVERT: D 213 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7752 (mtmm) REVERT: D 300 LYS cc_start: 0.8502 (tptm) cc_final: 0.8192 (tptm) REVERT: D 305 ASP cc_start: 0.7690 (t0) cc_final: 0.7291 (t0) REVERT: D 308 LEU cc_start: 0.8140 (pp) cc_final: 0.6745 (pp) REVERT: D 309 LEU cc_start: 0.8388 (tp) cc_final: 0.8129 (tp) REVERT: D 312 ARG cc_start: 0.8091 (ptp-170) cc_final: 0.7864 (ptp-170) REVERT: D 337 HIS cc_start: 0.7640 (m170) cc_final: 0.7379 (m90) REVERT: E 139 LYS cc_start: 0.8272 (ptpp) cc_final: 0.8036 (pttm) REVERT: E 158 GLN cc_start: 0.8077 (pm20) cc_final: 0.7773 (pm20) REVERT: E 171 GLN cc_start: 0.8425 (mm110) cc_final: 0.8141 (mp10) REVERT: E 193 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7048 (mt-10) REVERT: E 211 MET cc_start: 0.7134 (mmp) cc_final: 0.6881 (mmp) REVERT: E 212 MET cc_start: 0.7451 (mmp) cc_final: 0.6935 (mmp) REVERT: E 215 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7094 (tm-30) REVERT: E 248 MET cc_start: 0.7373 (mtp) cc_final: 0.6910 (mtp) REVERT: E 256 HIS cc_start: 0.7492 (t70) cc_final: 0.7154 (t70) REVERT: E 266 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7380 (tm-30) REVERT: E 270 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7285 (mmmt) REVERT: E 286 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7529 (mm-30) REVERT: E 290 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7650 (mm-30) REVERT: E 295 SER cc_start: 0.7864 (p) cc_final: 0.7585 (p) REVERT: E 298 ASP cc_start: 0.7322 (m-30) cc_final: 0.7107 (m-30) REVERT: E 299 LEU cc_start: 0.8680 (mt) cc_final: 0.8357 (mt) REVERT: E 300 LYS cc_start: 0.8582 (tttt) cc_final: 0.8310 (tttt) REVERT: E 301 GLU cc_start: 0.8227 (tt0) cc_final: 0.7959 (tt0) REVERT: E 302 MET cc_start: 0.8061 (tmm) cc_final: 0.7784 (tmm) REVERT: E 313 GLU cc_start: 0.8486 (pt0) cc_final: 0.8247 (pt0) REVERT: E 335 ASP cc_start: 0.8340 (m-30) cc_final: 0.8059 (m-30) REVERT: E 341 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 343 MET cc_start: 0.8294 (tpp) cc_final: 0.7890 (tpp) REVERT: F 68 LYS cc_start: 0.7502 (mppt) cc_final: 0.7091 (mppt) REVERT: F 74 MET cc_start: 0.7728 (mtm) cc_final: 0.7273 (mtm) REVERT: F 82 ASP cc_start: 0.8228 (t70) cc_final: 0.7987 (t0) REVERT: F 90 TRP cc_start: 0.8107 (m100) cc_final: 0.7179 (m100) REVERT: F 102 ASP cc_start: 0.7939 (m-30) cc_final: 0.7660 (m-30) REVERT: F 104 LYS cc_start: 0.8351 (tttt) cc_final: 0.8045 (ttmt) REVERT: F 131 LEU cc_start: 0.8342 (mp) cc_final: 0.7725 (mt) REVERT: F 139 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7283 (mtmm) REVERT: F 149 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7014 (mm-30) REVERT: F 180 LEU cc_start: 0.8293 (tt) cc_final: 0.8033 (tt) REVERT: F 183 LYS cc_start: 0.8559 (mptt) cc_final: 0.8157 (mptt) REVERT: F 211 MET cc_start: 0.7418 (mmp) cc_final: 0.7029 (mmp) REVERT: F 212 MET cc_start: 0.7927 (mmp) cc_final: 0.7713 (mmp) REVERT: F 215 GLN cc_start: 0.7003 (tp-100) cc_final: 0.6681 (tp-100) REVERT: F 217 MET cc_start: 0.7388 (mmt) cc_final: 0.6776 (mmt) REVERT: F 219 LEU cc_start: 0.7802 (mt) cc_final: 0.7153 (mt) REVERT: F 241 GLN cc_start: 0.7879 (mm110) cc_final: 0.7364 (mm110) REVERT: F 244 ASP cc_start: 0.7734 (p0) cc_final: 0.7494 (p0) REVERT: F 248 MET cc_start: 0.7076 (mtp) cc_final: 0.6539 (mtp) REVERT: F 250 ARG cc_start: 0.7305 (ttt180) cc_final: 0.6875 (ttt180) REVERT: F 270 LYS cc_start: 0.8315 (pttp) cc_final: 0.7812 (ptmm) REVERT: F 298 ASP cc_start: 0.8071 (m-30) cc_final: 0.7837 (m-30) REVERT: F 300 LYS cc_start: 0.8261 (tptm) cc_final: 0.7785 (tptm) REVERT: F 302 MET cc_start: 0.7697 (tmm) cc_final: 0.7410 (tmm) REVERT: F 332 GLN cc_start: 0.8081 (tp40) cc_final: 0.7814 (tp-100) REVERT: F 337 HIS cc_start: 0.7584 (m170) cc_final: 0.7272 (m170) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 0.3035 time to fit residues: 256.5158 Evaluate side-chains 573 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 141 optimal weight: 0.0010 chunk 147 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.4644 ------------------------------------------------------------------------------- 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 206 HIS ** 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** ** D 215 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14142 Z= 0.163 Angle : 0.603 13.771 19146 Z= 0.309 Chirality : 0.043 0.244 2190 Planarity : 0.004 0.062 2448 Dihedral : 10.982 105.920 1962 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.42 (0.21), residues: 1728 helix: 1.25 (0.16), residues: 984 sheet: 0.68 (0.41), residues: 192 loop : 0.73 (0.31), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 220 HIS 0.012 0.001 HIS B 337 PHE 0.037 0.002 PHE D 216 TYR 0.011 0.002 TYR F 72 ARG 0.012 0.001 ARG E 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 598 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 1.514 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: 0.8109 (mtm) cc_final: 0.7583 (mtm) REVERT: A 92 ASP cc_start: 0.7496 (m-30) cc_final: 0.7274 (m-30) REVERT: A 102 ASP cc_start: 0.7747 (m-30) cc_final: 0.7487 (m-30) REVERT: A 104 LYS cc_start: 0.8644 (tttt) cc_final: 0.8227 (tttt) REVERT: A 114 LYS cc_start: 0.7315 (tttt) cc_final: 0.7070 (ttmt) REVERT: A 124 GLN cc_start: 0.8244 (pp30) cc_final: 0.8039 (pp30) REVERT: A 125 PRO cc_start: 0.8488 (Cg_endo) cc_final: 0.8112 (Cg_exo) REVERT: A 148 LYS cc_start: 0.7999 (tttt) cc_final: 0.7617 (ttmt) REVERT: A 157 LEU cc_start: 0.7867 (tp) cc_final: 0.7431 (tp) REVERT: A 169 GLU cc_start: 0.7122 (tt0) cc_final: 0.6884 (tt0) REVERT: A 179 SER cc_start: 0.8812 (t) cc_final: 0.8477 (p) REVERT: A 199 ARG cc_start: 0.7420 (tpp80) cc_final: 0.6366 (tpp80) REVERT: A 206 HIS cc_start: 0.8044 (p90) cc_final: 0.7374 (p90) REVERT: A 211 MET cc_start: 0.8021 (mmp) cc_final: 0.7379 (mmp) REVERT: A 212 MET cc_start: 0.7897 (mmp) cc_final: 0.7532 (mmp) REVERT: A 213 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7778 (mtmt) REVERT: A 216 PHE cc_start: 0.8012 (t80) cc_final: 0.7805 (t80) REVERT: A 217 MET cc_start: 0.8069 (mpp) cc_final: 0.7592 (mpp) REVERT: A 219 LEU cc_start: 0.8695 (mt) cc_final: 0.8251 (mt) REVERT: A 251 MET cc_start: 0.7543 (mmm) cc_final: 0.6963 (mmm) REVERT: A 258 ASN cc_start: 0.8337 (p0) cc_final: 0.8054 (p0) REVERT: A 259 GLN cc_start: 0.7630 (mt0) cc_final: 0.7006 (mt0) REVERT: A 286 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 301 GLU cc_start: 0.8143 (tt0) cc_final: 0.6787 (tt0) REVERT: A 305 ASP cc_start: 0.8224 (t0) cc_final: 0.7936 (m-30) REVERT: A 338 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7722 (mtp85) REVERT: A 341 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7373 (mm-30) REVERT: A 342 LYS cc_start: 0.8741 (mptt) cc_final: 0.8158 (mptt) REVERT: A 343 MET cc_start: 0.8339 (tpt) cc_final: 0.7939 (tpt) REVERT: A 345 LYS cc_start: 0.8708 (pptt) cc_final: 0.8475 (pptt) REVERT: B 74 MET cc_start: 0.8113 (mtm) cc_final: 0.7414 (mtm) REVERT: B 86 MET cc_start: 0.7938 (mtm) cc_final: 0.7694 (mtm) REVERT: B 96 LEU cc_start: 0.7584 (mt) cc_final: 0.7249 (mm) REVERT: B 104 LYS cc_start: 0.8593 (tttt) cc_final: 0.8191 (tttt) REVERT: B 123 LEU cc_start: 0.8064 (tp) cc_final: 0.7855 (tp) REVERT: B 124 GLN cc_start: 0.8153 (pp30) cc_final: 0.7796 (pp30) REVERT: B 148 LYS cc_start: 0.8188 (tttt) cc_final: 0.7896 (ttmt) REVERT: B 149 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7228 (mm-30) REVERT: B 152 CYS cc_start: 0.7288 (m) cc_final: 0.6990 (m) REVERT: B 157 LEU cc_start: 0.7987 (tp) cc_final: 0.7544 (tp) REVERT: B 158 GLN cc_start: 0.7134 (pm20) cc_final: 0.6332 (pm20) REVERT: B 211 MET cc_start: 0.8061 (mmp) cc_final: 0.7725 (mmp) REVERT: B 213 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7678 (mtmt) REVERT: B 215 GLN cc_start: 0.7623 (tp-100) cc_final: 0.6355 (tp-100) REVERT: B 217 MET cc_start: 0.8134 (mpp) cc_final: 0.7659 (mpp) REVERT: B 219 LEU cc_start: 0.8791 (mt) cc_final: 0.7826 (mt) REVERT: B 259 GLN cc_start: 0.7797 (mt0) cc_final: 0.7383 (mt0) REVERT: B 266 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7037 (tm-30) REVERT: B 270 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7839 (mptt) REVERT: B 286 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 299 LEU cc_start: 0.8873 (mt) cc_final: 0.8464 (mt) REVERT: B 304 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7020 (tpm170) REVERT: B 305 ASP cc_start: 0.8152 (t0) cc_final: 0.7851 (m-30) REVERT: B 338 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8072 (mmm-85) REVERT: B 341 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 342 LYS cc_start: 0.8575 (mptt) cc_final: 0.8136 (mptt) REVERT: B 343 MET cc_start: 0.8231 (tpt) cc_final: 0.6992 (tpt) REVERT: B 347 LYS cc_start: 0.8919 (mptt) cc_final: 0.8403 (mptt) REVERT: C 74 MET cc_start: 0.5708 (mtm) cc_final: 0.5390 (mtm) REVERT: C 170 SER cc_start: 0.7865 (p) cc_final: 0.7382 (p) REVERT: C 171 GLN cc_start: 0.8360 (mm110) cc_final: 0.8051 (mp10) REVERT: C 212 MET cc_start: 0.7354 (mmp) cc_final: 0.7043 (mmp) REVERT: C 215 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7494 (tm-30) REVERT: C 219 LEU cc_start: 0.7138 (mt) cc_final: 0.6896 (mm) REVERT: C 239 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7085 (ttm110) REVERT: C 248 MET cc_start: 0.7697 (mtp) cc_final: 0.7110 (mtp) REVERT: C 270 LYS cc_start: 0.8562 (mmmt) cc_final: 0.7594 (mmmt) REVERT: C 284 LEU cc_start: 0.8470 (mp) cc_final: 0.8102 (mp) REVERT: C 289 GLN cc_start: 0.8286 (mt0) cc_final: 0.7853 (mt0) REVERT: C 299 LEU cc_start: 0.8654 (mt) cc_final: 0.8332 (mt) REVERT: C 300 LYS cc_start: 0.8773 (tttt) cc_final: 0.8444 (tttt) REVERT: C 302 MET cc_start: 0.8030 (tmm) cc_final: 0.7771 (tmm) REVERT: C 309 LEU cc_start: 0.8620 (tp) cc_final: 0.8294 (tp) REVERT: C 313 GLU cc_start: 0.8198 (pt0) cc_final: 0.7833 (pt0) REVERT: C 335 ASP cc_start: 0.8300 (m-30) cc_final: 0.8076 (m-30) REVERT: C 343 MET cc_start: 0.8207 (tpp) cc_final: 0.7877 (tpp) REVERT: C 344 LYS cc_start: 0.8940 (mttm) cc_final: 0.8555 (mttm) REVERT: D 82 ASP cc_start: 0.8255 (t0) cc_final: 0.7904 (t70) REVERT: D 97 ASP cc_start: 0.7732 (p0) cc_final: 0.7521 (p0) REVERT: D 104 LYS cc_start: 0.8287 (tttt) cc_final: 0.7996 (ttmt) REVERT: D 131 LEU cc_start: 0.8464 (mp) cc_final: 0.7897 (mt) REVERT: D 139 LYS cc_start: 0.7904 (mtmm) cc_final: 0.7307 (mtmm) REVERT: D 180 LEU cc_start: 0.8112 (tt) cc_final: 0.7905 (tt) REVERT: D 183 LYS cc_start: 0.8446 (mptt) cc_final: 0.8108 (mptt) REVERT: D 211 MET cc_start: 0.7493 (mmp) cc_final: 0.7097 (mmp) REVERT: D 212 MET cc_start: 0.7931 (mmp) cc_final: 0.7536 (mmp) REVERT: D 213 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7545 (mtmm) REVERT: D 217 MET cc_start: 0.6928 (mmm) cc_final: 0.6466 (mmm) REVERT: D 251 MET cc_start: 0.7971 (mpp) cc_final: 0.6408 (mpp) REVERT: D 265 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7064 (ptp-170) REVERT: D 300 LYS cc_start: 0.8499 (tptm) cc_final: 0.8194 (tptm) REVERT: D 305 ASP cc_start: 0.7665 (t0) cc_final: 0.7353 (t0) REVERT: D 309 LEU cc_start: 0.8352 (tp) cc_final: 0.8031 (tp) REVERT: D 312 ARG cc_start: 0.8114 (ptp-170) cc_final: 0.7771 (ptp-170) REVERT: D 337 HIS cc_start: 0.7667 (m170) cc_final: 0.7407 (m90) REVERT: E 158 GLN cc_start: 0.8055 (pm20) cc_final: 0.7757 (pm20) REVERT: E 171 GLN cc_start: 0.8371 (mm110) cc_final: 0.8127 (mp10) REVERT: E 193 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6994 (mt-10) REVERT: E 212 MET cc_start: 0.7448 (mmp) cc_final: 0.6813 (mmp) REVERT: E 215 GLN cc_start: 0.7712 (tp-100) cc_final: 0.6996 (tm-30) REVERT: E 239 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7355 (ttm110) REVERT: E 248 MET cc_start: 0.7313 (mtp) cc_final: 0.6785 (mtp) REVERT: E 256 HIS cc_start: 0.7404 (t70) cc_final: 0.7068 (t70) REVERT: E 266 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7379 (tm-30) REVERT: E 270 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7328 (mmmt) REVERT: E 286 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7411 (mm-30) REVERT: E 290 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 295 SER cc_start: 0.7839 (p) cc_final: 0.7572 (p) REVERT: E 298 ASP cc_start: 0.7319 (m-30) cc_final: 0.7097 (m-30) REVERT: E 299 LEU cc_start: 0.8657 (mt) cc_final: 0.8205 (mt) REVERT: E 300 LYS cc_start: 0.8596 (tttt) cc_final: 0.8290 (tttt) REVERT: E 301 GLU cc_start: 0.8285 (tt0) cc_final: 0.8038 (tt0) REVERT: E 303 CYS cc_start: 0.8604 (m) cc_final: 0.7985 (m) REVERT: E 312 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7913 (mtp-110) REVERT: E 313 GLU cc_start: 0.8471 (pt0) cc_final: 0.8218 (pt0) REVERT: E 335 ASP cc_start: 0.8257 (m-30) cc_final: 0.8007 (m-30) REVERT: E 341 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7615 (mm-30) REVERT: E 343 MET cc_start: 0.8261 (tpp) cc_final: 0.7873 (tpp) REVERT: F 74 MET cc_start: 0.7682 (mtm) cc_final: 0.7185 (mtm) REVERT: F 90 TRP cc_start: 0.8047 (m100) cc_final: 0.7065 (m100) REVERT: F 102 ASP cc_start: 0.7904 (m-30) cc_final: 0.7636 (m-30) REVERT: F 104 LYS cc_start: 0.8380 (tttt) cc_final: 0.8066 (ttmt) REVERT: F 131 LEU cc_start: 0.8394 (mp) cc_final: 0.7832 (mt) REVERT: F 139 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7246 (mtmm) REVERT: F 149 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7090 (mm-30) REVERT: F 180 LEU cc_start: 0.8295 (tt) cc_final: 0.8063 (tt) REVERT: F 183 LYS cc_start: 0.8523 (mptt) cc_final: 0.8216 (mptt) REVERT: F 211 MET cc_start: 0.7430 (mmp) cc_final: 0.6982 (mmp) REVERT: F 212 MET cc_start: 0.7957 (mmp) cc_final: 0.7649 (mmp) REVERT: F 213 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7356 (mtmt) REVERT: F 217 MET cc_start: 0.7334 (mmt) cc_final: 0.6688 (mmt) REVERT: F 248 MET cc_start: 0.6974 (mtp) cc_final: 0.6524 (mtp) REVERT: F 250 ARG cc_start: 0.7353 (ttt180) cc_final: 0.7125 (ttt180) REVERT: F 270 LYS cc_start: 0.8315 (pttp) cc_final: 0.7809 (ptmm) REVERT: F 300 LYS cc_start: 0.8264 (tptm) cc_final: 0.7779 (tptm) REVERT: F 302 MET cc_start: 0.7676 (tmm) cc_final: 0.7318 (tmm) REVERT: F 332 GLN cc_start: 0.8148 (tp40) cc_final: 0.7868 (tp-100) REVERT: F 337 HIS cc_start: 0.7556 (m170) cc_final: 0.7319 (m170) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.3049 time to fit residues: 254.7783 Evaluate side-chains 576 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 14142 Z= 0.191 Angle : 0.626 13.757 19146 Z= 0.321 Chirality : 0.043 0.233 2190 Planarity : 0.004 0.056 2448 Dihedral : 10.985 106.173 1962 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.21), residues: 1728 helix: 1.16 (0.16), residues: 978 sheet: 0.66 (0.40), residues: 192 loop : 0.30 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 220 HIS 0.004 0.001 HIS D 337 PHE 0.033 0.002 PHE D 216 TYR 0.011 0.002 TYR D 132 ARG 0.014 0.001 ARG B 265 ********************** 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 596 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.648 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: 0.8138 (mtm) cc_final: 0.7583 (mtm) REVERT: A 92 ASP cc_start: 0.7499 (m-30) cc_final: 0.7279 (m-30) REVERT: A 102 ASP cc_start: 0.7766 (m-30) cc_final: 0.7474 (m-30) REVERT: A 104 LYS cc_start: 0.8643 (tttt) cc_final: 0.8291 (tttt) REVERT: A 114 LYS cc_start: 0.7383 (tttt) cc_final: 0.7056 (ttmt) REVERT: A 125 PRO cc_start: 0.8491 (Cg_endo) cc_final: 0.8065 (Cg_exo) REVERT: A 131 LEU cc_start: 0.8219 (mp) cc_final: 0.7880 (tp) REVERT: A 148 LYS cc_start: 0.8078 (tttt) cc_final: 0.7701 (ttmt) REVERT: A 157 LEU cc_start: 0.7875 (tp) cc_final: 0.7497 (tp) REVERT: A 158 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 169 GLU cc_start: 0.7112 (tt0) cc_final: 0.6852 (tt0) REVERT: A 178 PHE cc_start: 0.8734 (m-80) cc_final: 0.8496 (m-10) REVERT: A 179 SER cc_start: 0.8838 (t) cc_final: 0.8555 (p) REVERT: A 193 GLU cc_start: 0.7731 (tt0) cc_final: 0.7504 (tt0) REVERT: A 199 ARG cc_start: 0.7432 (tpp80) cc_final: 0.6360 (tpp80) REVERT: A 206 HIS cc_start: 0.8039 (p90) cc_final: 0.7369 (p90) REVERT: A 211 MET cc_start: 0.8034 (mmp) cc_final: 0.7395 (mmp) REVERT: A 212 MET cc_start: 0.7876 (mmp) cc_final: 0.7518 (mmp) REVERT: A 213 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7785 (mtmt) REVERT: A 216 PHE cc_start: 0.8070 (t80) cc_final: 0.7829 (t80) REVERT: A 217 MET cc_start: 0.8028 (mpp) cc_final: 0.7573 (mpp) REVERT: A 251 MET cc_start: 0.7514 (mmm) cc_final: 0.6956 (mmm) REVERT: A 258 ASN cc_start: 0.8300 (p0) cc_final: 0.8006 (p0) REVERT: A 259 GLN cc_start: 0.7645 (mt0) cc_final: 0.7055 (mt0) REVERT: A 266 GLU cc_start: 0.7998 (tp30) cc_final: 0.7269 (tp30) REVERT: A 286 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 301 GLU cc_start: 0.8162 (tt0) cc_final: 0.6817 (tt0) REVERT: A 305 ASP cc_start: 0.8275 (t0) cc_final: 0.7971 (m-30) REVERT: A 338 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7911 (mtp85) REVERT: A 341 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 342 LYS cc_start: 0.8759 (mptt) cc_final: 0.8184 (mptt) REVERT: A 343 MET cc_start: 0.8355 (tpt) cc_final: 0.7952 (tpt) REVERT: A 345 LYS cc_start: 0.8705 (pptt) cc_final: 0.8470 (pptt) REVERT: B 74 MET cc_start: 0.8106 (mtm) cc_final: 0.7429 (mtm) REVERT: B 90 TRP cc_start: 0.8202 (m100) cc_final: 0.6968 (m100) REVERT: B 96 LEU cc_start: 0.7605 (mt) cc_final: 0.7305 (mm) REVERT: B 104 LYS cc_start: 0.8588 (tttt) cc_final: 0.8181 (tttt) REVERT: B 123 LEU cc_start: 0.8111 (tp) cc_final: 0.7853 (tp) REVERT: B 124 GLN cc_start: 0.8207 (pp30) cc_final: 0.7912 (pp30) REVERT: B 146 THR cc_start: 0.8383 (p) cc_final: 0.7790 (p) REVERT: B 148 LYS cc_start: 0.8247 (tttt) cc_final: 0.7924 (ttmt) REVERT: B 152 CYS cc_start: 0.7254 (m) cc_final: 0.7012 (m) REVERT: B 157 LEU cc_start: 0.7999 (tp) cc_final: 0.7543 (tp) REVERT: B 158 GLN cc_start: 0.7132 (pm20) cc_final: 0.6335 (pm20) REVERT: B 211 MET cc_start: 0.8075 (mmp) cc_final: 0.7735 (mmp) REVERT: B 213 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7658 (mtmt) REVERT: B 215 GLN cc_start: 0.7623 (tp-100) cc_final: 0.6355 (tp-100) REVERT: B 217 MET cc_start: 0.8216 (mpp) cc_final: 0.7679 (mpp) REVERT: B 219 LEU cc_start: 0.8785 (mt) cc_final: 0.7809 (mt) REVERT: B 220 TRP cc_start: 0.7646 (m-10) cc_final: 0.6605 (m-10) REVERT: B 250 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7277 (tpp80) REVERT: B 258 ASN cc_start: 0.8252 (p0) cc_final: 0.7986 (p0) REVERT: B 266 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 299 LEU cc_start: 0.8846 (mt) cc_final: 0.8453 (mt) REVERT: B 304 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6941 (mmp80) REVERT: B 334 GLN cc_start: 0.7699 (mp10) cc_final: 0.7495 (mp10) REVERT: B 338 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8083 (mtp85) REVERT: B 341 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7518 (mm-30) REVERT: B 342 LYS cc_start: 0.8601 (mptt) cc_final: 0.7768 (mptt) REVERT: B 343 MET cc_start: 0.8232 (tpt) cc_final: 0.6835 (tpt) REVERT: B 345 LYS cc_start: 0.8670 (pptt) cc_final: 0.8336 (pptt) REVERT: B 347 LYS cc_start: 0.8915 (mptt) cc_final: 0.8396 (mptt) REVERT: C 74 MET cc_start: 0.5693 (mtm) cc_final: 0.5357 (mtm) REVERT: C 158 GLN cc_start: 0.7954 (pm20) cc_final: 0.7564 (pm20) REVERT: C 170 SER cc_start: 0.7876 (p) cc_final: 0.7376 (p) REVERT: C 171 GLN cc_start: 0.8367 (mm110) cc_final: 0.8061 (mp10) REVERT: C 212 MET cc_start: 0.7374 (mmp) cc_final: 0.7077 (mmp) REVERT: C 215 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7514 (tm-30) REVERT: C 219 LEU cc_start: 0.7127 (mt) cc_final: 0.6868 (mm) REVERT: C 239 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7009 (ttm110) REVERT: C 245 SER cc_start: 0.7763 (t) cc_final: 0.7556 (t) REVERT: C 248 MET cc_start: 0.7694 (mtp) cc_final: 0.7101 (mtp) REVERT: C 270 LYS cc_start: 0.8594 (mmmt) cc_final: 0.7618 (mmmt) REVERT: C 284 LEU cc_start: 0.8530 (mp) cc_final: 0.8137 (mp) REVERT: C 289 GLN cc_start: 0.8274 (mt0) cc_final: 0.7857 (mt0) REVERT: C 299 LEU cc_start: 0.8630 (mt) cc_final: 0.8320 (mt) REVERT: C 300 LYS cc_start: 0.8744 (tttt) cc_final: 0.8426 (tttt) REVERT: C 302 MET cc_start: 0.8099 (tmm) cc_final: 0.7830 (tmm) REVERT: C 309 LEU cc_start: 0.8636 (tp) cc_final: 0.8309 (tp) REVERT: C 313 GLU cc_start: 0.8229 (pt0) cc_final: 0.7863 (pt0) REVERT: C 335 ASP cc_start: 0.8348 (m-30) cc_final: 0.7999 (m-30) REVERT: C 343 MET cc_start: 0.8216 (tpp) cc_final: 0.7994 (tpp) REVERT: C 344 LYS cc_start: 0.8858 (mttm) cc_final: 0.8560 (mttm) REVERT: D 82 ASP cc_start: 0.8165 (t0) cc_final: 0.7872 (t70) REVERT: D 97 ASP cc_start: 0.7716 (p0) cc_final: 0.7513 (p0) REVERT: D 104 LYS cc_start: 0.8234 (tttt) cc_final: 0.7968 (ttmt) REVERT: D 131 LEU cc_start: 0.8452 (mp) cc_final: 0.7829 (mt) REVERT: D 139 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7364 (mtmm) REVERT: D 179 SER cc_start: 0.8288 (p) cc_final: 0.8062 (p) REVERT: D 180 LEU cc_start: 0.8178 (tt) cc_final: 0.7954 (tt) REVERT: D 183 LYS cc_start: 0.8468 (mptt) cc_final: 0.8112 (mptt) REVERT: D 211 MET cc_start: 0.7498 (mmp) cc_final: 0.7089 (mmp) REVERT: D 212 MET cc_start: 0.7954 (mmp) cc_final: 0.7515 (mmp) REVERT: D 213 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7579 (mtmm) REVERT: D 217 MET cc_start: 0.6967 (mmm) cc_final: 0.6421 (mmm) REVERT: D 250 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.6852 (ptm160) REVERT: D 251 MET cc_start: 0.7966 (mpp) cc_final: 0.7022 (mpp) REVERT: D 265 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7112 (ptp-170) REVERT: D 300 LYS cc_start: 0.8552 (tptm) cc_final: 0.8205 (tptm) REVERT: D 305 ASP cc_start: 0.7706 (t0) cc_final: 0.7307 (t0) REVERT: D 308 LEU cc_start: 0.8101 (pp) cc_final: 0.7017 (pp) REVERT: D 309 LEU cc_start: 0.8355 (tp) cc_final: 0.8091 (tp) REVERT: D 337 HIS cc_start: 0.7597 (m170) cc_final: 0.7377 (m90) REVERT: E 158 GLN cc_start: 0.7979 (pm20) cc_final: 0.7677 (pm20) REVERT: E 193 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7045 (mt-10) REVERT: E 212 MET cc_start: 0.7554 (mmp) cc_final: 0.6947 (mmp) REVERT: E 239 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7361 (ttm110) REVERT: E 248 MET cc_start: 0.7330 (mtp) cc_final: 0.6786 (mtp) REVERT: E 256 HIS cc_start: 0.7387 (t70) cc_final: 0.7035 (t70) REVERT: E 266 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7469 (tm-30) REVERT: E 270 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7361 (mmmt) REVERT: E 279 ASP cc_start: 0.7340 (p0) cc_final: 0.6911 (t0) REVERT: E 290 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7730 (mm-30) REVERT: E 295 SER cc_start: 0.7847 (p) cc_final: 0.7562 (p) REVERT: E 298 ASP cc_start: 0.7282 (m-30) cc_final: 0.7060 (m-30) REVERT: E 299 LEU cc_start: 0.8641 (mt) cc_final: 0.8224 (mt) REVERT: E 300 LYS cc_start: 0.8580 (tttt) cc_final: 0.8278 (tttt) REVERT: E 301 GLU cc_start: 0.8284 (tt0) cc_final: 0.8039 (tt0) REVERT: E 303 CYS cc_start: 0.8569 (m) cc_final: 0.7969 (m) REVERT: E 313 GLU cc_start: 0.8480 (pt0) cc_final: 0.8221 (pt0) REVERT: E 335 ASP cc_start: 0.8295 (m-30) cc_final: 0.7920 (m-30) REVERT: E 341 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7721 (mm-30) REVERT: E 343 MET cc_start: 0.8298 (tpp) cc_final: 0.7922 (tpp) REVERT: F 74 MET cc_start: 0.7682 (mtm) cc_final: 0.7209 (mtm) REVERT: F 82 ASP cc_start: 0.8287 (t0) cc_final: 0.8063 (t70) REVERT: F 90 TRP cc_start: 0.8056 (m100) cc_final: 0.7052 (m100) REVERT: F 102 ASP cc_start: 0.7909 (m-30) cc_final: 0.7638 (m-30) REVERT: F 104 LYS cc_start: 0.8391 (tttt) cc_final: 0.8060 (ttmt) REVERT: F 131 LEU cc_start: 0.8399 (mp) cc_final: 0.8054 (mt) REVERT: F 132 TYR cc_start: 0.7603 (p90) cc_final: 0.7357 (p90) REVERT: F 149 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7083 (mm-30) REVERT: F 183 LYS cc_start: 0.8523 (mptt) cc_final: 0.8185 (mptt) REVERT: F 211 MET cc_start: 0.7445 (mmp) cc_final: 0.7006 (mmp) REVERT: F 212 MET cc_start: 0.7914 (mmp) cc_final: 0.7638 (mmp) REVERT: F 213 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7363 (mtmt) REVERT: F 217 MET cc_start: 0.7377 (mmt) cc_final: 0.6732 (mmt) REVERT: F 244 ASP cc_start: 0.7788 (p0) cc_final: 0.7581 (p0) REVERT: F 248 MET cc_start: 0.7060 (mtp) cc_final: 0.6532 (mtp) REVERT: F 250 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7125 (ttt180) REVERT: F 263 LYS cc_start: 0.7804 (mmmm) cc_final: 0.7597 (mmmm) REVERT: F 270 LYS cc_start: 0.8305 (pttp) cc_final: 0.7875 (ptmm) REVERT: F 300 LYS cc_start: 0.8266 (tptm) cc_final: 0.7773 (tptm) REVERT: F 302 MET cc_start: 0.7694 (tmm) cc_final: 0.7358 (tmm) REVERT: F 332 GLN cc_start: 0.8088 (tp40) cc_final: 0.7795 (tp-100) REVERT: F 337 HIS cc_start: 0.7635 (m170) cc_final: 0.7328 (m170) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.3022 time to fit residues: 252.1141 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 : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 0.0770 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 206 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128022 restraints weight = 29306.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132531 restraints weight = 17638.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135749 restraints weight = 12069.237| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14142 Z= 0.172 Angle : 0.634 13.895 19146 Z= 0.321 Chirality : 0.043 0.233 2190 Planarity : 0.004 0.051 2448 Dihedral : 10.978 105.889 1962 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: 1.58 (0.22), residues: 1728 helix: 1.34 (0.17), residues: 984 sheet: 0.86 (0.40), residues: 186 loop : 0.84 (0.32), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 220 HIS 0.007 0.001 HIS B 256 PHE 0.034 0.002 PHE D 216 TYR 0.012 0.002 TYR D 132 ARG 0.006 0.001 ARG F 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4176.14 seconds wall clock time: 77 minutes 12.31 seconds (4632.31 seconds total)