Starting phenix.real_space_refine on Sat Oct 24 04:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uek_64084/10_2026/9uek_64084.map" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 8 5.49 5 S 36 5.16 5 C 7608 2.51 5 N 2124 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12108 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "B" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "C" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "D" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'NAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 2.91, per 1000 atoms: 0.24 Number of scatterers: 12108 At special positions: 0 Unit cell: (109.612, 109.612, 119.487, 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 36 16.00 P 8 15.00 O 2332 8.00 N 2124 7.00 C 7608 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: 0.95 Conformation dependent library (CDL) restraints added in 656.2 milliseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 42.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.842A pdb=" N GLU A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 113 through 121 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 273 through 287 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 327 through 346 removed outlier: 4.298A pdb=" N TYR A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 362 through 373 Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.527A pdb=" N GLN B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 273 through 287 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 327 through 347 removed outlier: 4.358A pdb=" N TYR B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 362 through 373 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 59 through 69 removed outlier: 4.410A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 113 through 121 Processing helix chain 'C' and resid 133 through 145 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 273 through 286 Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 327 through 347 removed outlier: 4.375A pdb=" N GLN C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 362 through 374 Processing helix chain 'D' and resid 11 through 21 removed outlier: 3.521A pdb=" N GLN D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 59 through 68 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 273 through 287 Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 327 through 347 removed outlier: 4.304A pdb=" N TYR D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR D 336 " --> pdb=" O THR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 362 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 6.684A pdb=" N VAL A 3 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A 31 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 5 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 4 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER A 96 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 removed outlier: 10.148A pdb=" N ARG A 235 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 150 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU A 237 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 152 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS A 239 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 154 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 241 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 156 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N TYR A 243 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N GLY A 158 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 149 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG A 304 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 309 " --> pdb=" O HIS A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.525A pdb=" N CYS A 270 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.782A pdb=" N VAL B 3 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA B 31 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 5 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER B 96 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 197 removed outlier: 7.750A pdb=" N LEU B 187 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR B 238 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 197 removed outlier: 7.750A pdb=" N LEU B 187 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR B 238 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N ARG B 235 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU B 150 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU B 237 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 152 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LYS B 239 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 154 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 241 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 156 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N TYR B 243 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 11.006A pdb=" N GLY B 158 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL B 149 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 304 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 266 Processing sheet with id=AA9, first strand: chain 'C' and resid 50 through 54 removed outlier: 6.773A pdb=" N VAL C 3 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA C 31 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 5 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER C 96 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.660A pdb=" N LEU C 187 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR C 238 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLY C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE C 208 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.660A pdb=" N LEU C 187 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR C 238 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY C 158 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 149 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG C 304 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 309 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 54 removed outlier: 6.805A pdb=" N VAL D 3 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA D 31 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL D 5 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER D 96 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 204 through 208 removed outlier: 4.851A pdb=" N PHE D 208 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N ARG D 235 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU D 150 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU D 237 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE D 152 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS D 239 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 154 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE D 241 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL D 156 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N TYR D 243 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 11.091A pdb=" N GLY D 158 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 149 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG D 304 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 186 through 190 Processing sheet with id=AB7, first strand: chain 'D' and resid 265 through 267 644 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2368 1.32 - 1.46: 2678 1.46 - 1.59: 7155 1.59 - 1.73: 15 1.73 - 1.86: 64 Bond restraints: 12280 Sorted by residual: bond pdb=" N VAL B 361 " pdb=" CA VAL B 361 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.35e+01 bond pdb=" N VAL C 361 " pdb=" CA VAL C 361 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.34e+01 bond pdb=" N VAL D 361 " pdb=" CA VAL D 361 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.02e+01 bond pdb=" N VAL A 361 " pdb=" CA VAL A 361 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.50e-03 1.78e+04 1.88e+01 bond pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 1.456 1.492 -0.036 8.60e-03 1.35e+04 1.78e+01 ... (remaining 12275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12630 1.96 - 3.91: 3815 3.91 - 5.87: 195 5.87 - 7.82: 17 7.82 - 9.78: 7 Bond angle restraints: 16664 Sorted by residual: angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" O GLY C 353 " ideal model delta sigma weight residual 122.37 117.62 4.75 7.30e-01 1.88e+00 4.24e+01 angle pdb=" CA GLY A 353 " pdb=" C GLY A 353 " pdb=" O GLY A 353 " ideal model delta sigma weight residual 122.33 117.85 4.48 8.10e-01 1.52e+00 3.06e+01 angle pdb=" CA ASP B 293 " pdb=" CB ASP B 293 " pdb=" CG ASP B 293 " ideal model delta sigma weight residual 112.60 117.26 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C THR C 183 " pdb=" CA THR C 183 " pdb=" CB THR C 183 " ideal model delta sigma weight residual 109.34 116.39 -7.05 1.55e+00 4.16e-01 2.07e+01 angle pdb=" C THR B 183 " pdb=" CA THR B 183 " pdb=" CB THR B 183 " ideal model delta sigma weight residual 109.34 116.33 -6.99 1.55e+00 4.16e-01 2.03e+01 ... (remaining 16659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6799 17.79 - 35.58: 585 35.58 - 53.37: 146 53.37 - 71.16: 67 71.16 - 88.95: 7 Dihedral angle restraints: 7604 sinusoidal: 3200 harmonic: 4404 Sorted by residual: dihedral pdb=" CA ALA C 131 " pdb=" C ALA C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta harmonic sigma weight residual 0.00 20.91 -20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C ASP B 255 " pdb=" N ASP B 255 " pdb=" CA ASP B 255 " pdb=" CB ASP B 255 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 dihedral pdb=" CA GLY C 347 " pdb=" C GLY C 347 " pdb=" N VAL C 348 " pdb=" CA VAL C 348 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 855 0.058 - 0.116: 716 0.116 - 0.173: 327 0.173 - 0.231: 58 0.231 - 0.289: 8 Chirality restraints: 1964 Sorted by residual: chirality pdb=" CA ASP B 255 " pdb=" N ASP B 255 " pdb=" C ASP B 255 " pdb=" CB ASP B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA GLN D 342 " pdb=" N GLN D 342 " pdb=" C GLN D 342 " pdb=" CB GLN D 342 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 272 " pdb=" CA VAL B 272 " pdb=" CG1 VAL B 272 " pdb=" CG2 VAL B 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1961 not shown) Planarity restraints: 2128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 355 " -0.025 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR C 355 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR C 355 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 355 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 355 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR C 355 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 355 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 355 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 331 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ARG C 331 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG C 331 " 0.024 2.00e-02 2.50e+03 pdb=" N THR C 332 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 243 " 0.042 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR C 243 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR C 243 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 243 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 243 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 243 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 243 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 243 " 0.011 2.00e-02 2.50e+03 ... (remaining 2125 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1205 2.77 - 3.30: 12407 3.30 - 3.83: 21425 3.83 - 4.37: 28951 4.37 - 4.90: 44668 Nonbonded interactions: 108656 Sorted by model distance: nonbonded pdb=" O2N NAD C 401 " pdb=" O HOH C 501 " model vdw 2.236 3.040 nonbonded pdb=" O2N NAD D 401 " pdb=" O HOH D 501 " model vdw 2.312 3.040 nonbonded pdb=" O LYS C 402 " pdb=" O HOH C 502 " model vdw 2.318 3.040 nonbonded pdb=" O2N NAD A 401 " pdb=" O HOH A 501 " model vdw 2.357 3.040 nonbonded pdb=" O2N NAD B 401 " pdb=" O HOH B 501 " model vdw 2.409 3.040 ... (remaining 108651 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.390 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.013 0.063 12280 Z= 0.977 Angle : 1.627 9.776 16664 Z= 1.196 Chirality : 0.088 0.289 1964 Planarity : 0.012 0.119 2128 Dihedral : 15.313 88.949 4780 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.77 % Allowed : 11.19 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.19), residues: 1528 helix: -1.74 (0.16), residues: 600 sheet: -1.44 (0.24), residues: 396 loop : -0.60 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARG B 298 TYR 0.056 0.010 TYR C 243 PHE 0.027 0.006 PHE D 211 HIS 0.024 0.005 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.01324 / 0.98 (12280) covalent geometry : angle 1.62671 / 1.20 (16664) hydrogen bonds : bond 0.17994 / 12.04 ( 628) hydrogen bonds : angle 7.27044 / 5.24 ( 1827) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 352 time to evaluate : 0.387 Fit side-chains REVERT: A 1 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5748 (mtt) REVERT: A 10 LEU cc_start: 0.7858 (mp) cc_final: 0.7601 (mt) REVERT: A 18 ASP cc_start: 0.7844 (t70) cc_final: 0.7620 (t0) REVERT: A 83 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5799 (mp0) REVERT: A 98 ASP cc_start: 0.8131 (p0) cc_final: 0.7694 (p0) REVERT: A 107 THR cc_start: 0.7160 (t) cc_final: 0.6679 (m) REVERT: A 148 GLU cc_start: 0.6762 (tp30) cc_final: 0.5924 (mt-10) REVERT: A 180 ASP cc_start: 0.8411 (m-30) cc_final: 0.8029 (m-30) REVERT: A 187 LEU cc_start: 0.8248 (tp) cc_final: 0.7834 (mp) REVERT: A 234 LYS cc_start: 0.7811 (tptm) cc_final: 0.7410 (mmpt) REVERT: A 248 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 251 LYS cc_start: 0.7871 (tptt) cc_final: 0.7266 (tppt) REVERT: A 255 ASP cc_start: 0.7034 (t0) cc_final: 0.6823 (m-30) REVERT: A 273 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7548 (ttmt) REVERT: A 293 ASP cc_start: 0.8313 (p0) cc_final: 0.8083 (p0) REVERT: A 309 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6142 (tp30) REVERT: A 323 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6161 (tt0) REVERT: A 367 MET cc_start: 0.7860 (mtp) cc_final: 0.7549 (mtp) REVERT: A 370 MET cc_start: 0.7846 (mmp) cc_final: 0.7600 (mmm) REVERT: A 380 LYS cc_start: 0.6659 (ttpp) cc_final: 0.5764 (mptp) REVERT: B 2 LYS cc_start: 0.6972 (mmtp) cc_final: 0.6667 (mptm) REVERT: B 22 SER cc_start: 0.7623 (m) cc_final: 0.7258 (t) REVERT: B 44 GLN cc_start: 0.6558 (mt0) cc_final: 0.6223 (tm-30) REVERT: B 55 VAL cc_start: 0.7476 (p) cc_final: 0.7165 (t) REVERT: B 68 LYS cc_start: 0.6843 (tttp) cc_final: 0.6532 (tptm) REVERT: B 83 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6225 (mp0) REVERT: B 150 GLU cc_start: 0.8088 (tt0) cc_final: 0.7748 (mt-10) REVERT: B 164 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 193 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6501 (mt0) REVERT: B 251 LYS cc_start: 0.7977 (tttm) cc_final: 0.7387 (ttmm) REVERT: B 260 ARG cc_start: 0.7378 (mtp180) cc_final: 0.6858 (mtm180) REVERT: B 266 GLU cc_start: 0.6749 (tp30) cc_final: 0.6367 (tp30) REVERT: B 285 LEU cc_start: 0.8231 (tp) cc_final: 0.8014 (mt) REVERT: B 293 ASP cc_start: 0.8103 (t70) cc_final: 0.7727 (p0) REVERT: B 329 MET cc_start: 0.8708 (tpp) cc_final: 0.8303 (tpp) REVERT: B 364 ASP cc_start: 0.7104 (p0) cc_final: 0.6695 (p0) REVERT: B 370 MET cc_start: 0.8149 (mmp) cc_final: 0.7891 (mmm) REVERT: B 379 GLU cc_start: 0.8014 (tt0) cc_final: 0.7629 (tt0) REVERT: C 11 MET cc_start: 0.7795 (mmp) cc_final: 0.7304 (mmt) REVERT: C 24 ASP cc_start: 0.4591 (t70) cc_final: 0.4168 (p0) REVERT: C 68 LYS cc_start: 0.7572 (tptt) cc_final: 0.7232 (tmtp) REVERT: C 80 GLN cc_start: 0.7580 (pt0) cc_final: 0.7327 (pp30) REVERT: C 148 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7076 (mp0) REVERT: C 162 ARG cc_start: 0.7747 (mtt-85) cc_final: 0.7145 (mtp180) REVERT: C 193 GLN cc_start: 0.6989 (mp-120) cc_final: 0.6613 (mm-40) REVERT: C 234 LYS cc_start: 0.8041 (tttm) cc_final: 0.7518 (mtmt) REVERT: C 251 LYS cc_start: 0.7741 (tptt) cc_final: 0.7266 (tppt) REVERT: C 323 GLU cc_start: 0.6210 (mp0) cc_final: 0.6000 (tt0) REVERT: C 382 THR cc_start: 0.7246 (m) cc_final: 0.6830 (t) REVERT: D 21 GLN cc_start: 0.6490 (pt0) cc_final: 0.5573 (mm110) REVERT: D 44 GLN cc_start: 0.6137 (mt0) cc_final: 0.5744 (tm-30) REVERT: D 83 GLU cc_start: 0.6955 (tt0) cc_final: 0.6460 (tp30) REVERT: D 107 THR cc_start: 0.5823 (t) cc_final: 0.5597 (m) REVERT: D 176 GLU cc_start: 0.7858 (mp0) cc_final: 0.7580 (mp0) REVERT: D 260 ARG cc_start: 0.7130 (mpt180) cc_final: 0.6715 (mtp180) REVERT: D 266 GLU cc_start: 0.7564 (pt0) cc_final: 0.6861 (tt0) REVERT: D 271 ARG cc_start: 0.6809 (ttm-80) cc_final: 0.6296 (mtp-110) REVERT: D 289 LYS cc_start: 0.6746 (mmtp) cc_final: 0.6522 (tptt) REVERT: D 308 LYS cc_start: 0.6060 (mtpt) cc_final: 0.5823 (mtmt) REVERT: D 368 ASP cc_start: 0.6782 (m-30) cc_final: 0.6414 (t0) outliers start: 10 outliers final: 4 residues processed: 360 average time/residue: 0.7216 time to fit residues: 276.2884 Evaluate side-chains 213 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 62 GLN A 75 ASN A 95 HIS ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 95 HIS B 136 ASN B 170 ASN B 171 HIS B 191 ASN B 261 HIS B 384 HIS C 21 GLN C 75 ASN C 95 HIS C 136 ASN C 170 ASN C 171 HIS ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 246 HIS C 324 ASN C 359 GLN D 75 ASN D 95 HIS D 102 HIS D 136 ASN D 171 HIS D 191 ASN D 268 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127980 restraints weight = 11902.659| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.25 r_work: 0.3220 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12280 Z= 0.142 Angle : 0.559 5.381 16664 Z= 0.299 Chirality : 0.045 0.141 1964 Planarity : 0.004 0.032 2128 Dihedral : 8.665 88.662 1903 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.62 % Allowed : 15.59 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1528 helix: 0.82 (0.21), residues: 616 sheet: -0.48 (0.25), residues: 408 loop : -0.26 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 109 TYR 0.015 0.002 TYR C 79 PHE 0.017 0.001 PHE D 211 HIS 0.007 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12280) covalent geometry : angle 0.55943 / 0.30 (16664) hydrogen bonds : bond 0.04870 / 3.27 ( 628) hydrogen bonds : angle 5.19335 / 3.72 ( 1827) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.464 Fit side-chains REVERT: A 21 GLN cc_start: 0.6976 (mt0) cc_final: 0.6695 (mm110) REVERT: A 83 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6790 (mp0) REVERT: A 148 GLU cc_start: 0.7119 (tp30) cc_final: 0.6402 (mt-10) REVERT: A 150 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 187 LEU cc_start: 0.8689 (tp) cc_final: 0.8390 (mt) REVERT: A 251 LYS cc_start: 0.8846 (tptt) cc_final: 0.8535 (tptm) REVERT: A 271 ARG cc_start: 0.7029 (mmm160) cc_final: 0.6594 (mmt180) REVERT: A 367 MET cc_start: 0.8729 (mtp) cc_final: 0.8465 (mtp) REVERT: A 380 LYS cc_start: 0.7277 (ttpp) cc_final: 0.6716 (mppt) REVERT: A 382 THR cc_start: 0.7844 (m) cc_final: 0.7550 (p) REVERT: B 39 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6353 (mt-10) REVERT: B 55 VAL cc_start: 0.8184 (p) cc_final: 0.7878 (t) REVERT: B 80 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: B 83 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7387 (mp0) REVERT: B 251 LYS cc_start: 0.8764 (tttm) cc_final: 0.8427 (ttmm) REVERT: B 309 GLU cc_start: 0.7205 (tt0) cc_final: 0.6787 (pp20) REVERT: B 367 MET cc_start: 0.8246 (mtt) cc_final: 0.7774 (tpp) REVERT: B 368 ASP cc_start: 0.7212 (t70) cc_final: 0.7011 (m-30) REVERT: C 11 MET cc_start: 0.8372 (mmp) cc_final: 0.7853 (mmt) REVERT: C 24 ASP cc_start: 0.4910 (t70) cc_final: 0.4681 (p0) REVERT: C 54 ARG cc_start: 0.6465 (ttm110) cc_final: 0.6208 (ptm-80) REVERT: C 107 THR cc_start: 0.6789 (t) cc_final: 0.6473 (m) REVERT: C 193 GLN cc_start: 0.7490 (mp-120) cc_final: 0.7241 (mm-40) REVERT: C 251 LYS cc_start: 0.8691 (tptt) cc_final: 0.8420 (tppt) REVERT: C 266 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: D 21 GLN cc_start: 0.7245 (pt0) cc_final: 0.6717 (mm110) REVERT: D 266 GLU cc_start: 0.7628 (pt0) cc_final: 0.7379 (tt0) REVERT: D 304 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7608 (mtt-85) REVERT: D 324 ASN cc_start: 0.8019 (m110) cc_final: 0.7799 (m110) REVERT: D 371 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7648 (mmtm) outliers start: 21 outliers final: 8 residues processed: 247 average time/residue: 0.7100 time to fit residues: 186.9078 Evaluate side-chains 196 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [85, 24, 45, 113, 61, 48, 25, 114, 42, 0, 47] chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 136 ASN A 181 HIS A 218 HIS ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 181 HIS B 261 HIS B 268 ASN C 145 GLN C 181 HIS C 195 GLN C 218 HIS D 102 HIS D 342 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122466 restraints weight = 11930.684| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.26 r_work: 0.3119 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12280 Z= 0.210 Angle : 0.623 5.460 16664 Z= 0.327 Chirality : 0.048 0.174 1964 Planarity : 0.005 0.049 2128 Dihedral : 8.761 73.982 1900 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.85 % Allowed : 16.67 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.22), residues: 1528 helix: 0.98 (0.21), residues: 616 sheet: -0.26 (0.25), residues: 404 loop : -0.09 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 304 TYR 0.019 0.002 TYR C 79 PHE 0.021 0.002 PHE D 211 HIS 0.007 0.002 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (12280) covalent geometry : angle 0.62263 / 0.33 (16664) hydrogen bonds : bond 0.05378 / 3.58 ( 628) hydrogen bonds : angle 5.07910 / 3.59 ( 1827) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.315 Fit side-chains REVERT: A 2 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6878 (mmtm) REVERT: A 21 GLN cc_start: 0.7088 (mt0) cc_final: 0.6760 (mm110) REVERT: A 83 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6902 (mp0) REVERT: A 107 THR cc_start: 0.7632 (t) cc_final: 0.7321 (m) REVERT: A 148 GLU cc_start: 0.7435 (tp30) cc_final: 0.6612 (mt-10) REVERT: A 150 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 251 LYS cc_start: 0.8935 (tptt) cc_final: 0.8692 (tptm) REVERT: A 380 LYS cc_start: 0.7257 (ttpp) cc_final: 0.6646 (mppt) REVERT: B 26 GLU cc_start: 0.7862 (tt0) cc_final: 0.7386 (tt0) REVERT: B 39 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6452 (mt-10) REVERT: B 55 VAL cc_start: 0.8201 (p) cc_final: 0.7841 (t) REVERT: B 80 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: B 83 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7270 (mp0) REVERT: B 148 GLU cc_start: 0.7708 (tt0) cc_final: 0.7305 (pt0) REVERT: B 187 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8511 (tt) REVERT: B 251 LYS cc_start: 0.8810 (tttm) cc_final: 0.8436 (ttmm) REVERT: B 309 GLU cc_start: 0.7176 (tt0) cc_final: 0.6744 (pp20) REVERT: B 364 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7293 (p0) REVERT: B 368 ASP cc_start: 0.7375 (t70) cc_final: 0.7099 (m-30) REVERT: B 379 GLU cc_start: 0.8095 (tt0) cc_final: 0.7892 (tt0) REVERT: C 24 ASP cc_start: 0.5235 (t70) cc_final: 0.4869 (p0) REVERT: C 54 ARG cc_start: 0.6573 (ttm110) cc_final: 0.6100 (ptm-80) REVERT: C 107 THR cc_start: 0.6809 (t) cc_final: 0.6531 (m) REVERT: C 193 GLN cc_start: 0.7645 (mp-120) cc_final: 0.7293 (mm-40) REVERT: C 225 THR cc_start: 0.8764 (p) cc_final: 0.8473 (p) REVERT: C 251 LYS cc_start: 0.8796 (tptt) cc_final: 0.8392 (tppt) REVERT: C 266 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: D 34 ASP cc_start: 0.6509 (t70) cc_final: 0.6051 (t0) REVERT: D 266 GLU cc_start: 0.7774 (pt0) cc_final: 0.7532 (tt0) REVERT: D 324 ASN cc_start: 0.8047 (m110) cc_final: 0.7828 (m110) outliers start: 37 outliers final: 15 residues processed: 212 average time/residue: 0.7188 time to fit residues: 162.6713 Evaluate side-chains 189 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 372 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [75, 86, 44, 144, 25, 92, 110, 134, 105, 39, 69] chunk 75 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 110 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 HIS B 62 GLN B 261 HIS C 70 HIS C 218 HIS D 102 HIS D 218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.156302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126317 restraints weight = 12110.847| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.25 r_work: 0.3176 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12280 Z= 0.121 Angle : 0.502 5.329 16664 Z= 0.266 Chirality : 0.044 0.134 1964 Planarity : 0.003 0.040 2128 Dihedral : 8.268 78.303 1900 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.31 % Allowed : 17.44 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1528 helix: 1.22 (0.21), residues: 616 sheet: -0.19 (0.25), residues: 404 loop : -0.02 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 109 TYR 0.010 0.001 TYR D 366 PHE 0.013 0.001 PHE D 211 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12280) covalent geometry : angle 0.50185 / 0.27 (16664) hydrogen bonds : bond 0.04077 / 2.73 ( 628) hydrogen bonds : angle 4.74395 / 3.36 ( 1827) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.427 Fit side-chains REVERT: A 21 GLN cc_start: 0.7236 (mt0) cc_final: 0.6869 (mm110) REVERT: A 83 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6883 (mp0) REVERT: A 107 THR cc_start: 0.7499 (t) cc_final: 0.7136 (m) REVERT: A 148 GLU cc_start: 0.7253 (tp30) cc_final: 0.6507 (mt-10) REVERT: A 150 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 251 LYS cc_start: 0.8857 (tptt) cc_final: 0.8618 (tptm) REVERT: A 380 LYS cc_start: 0.7315 (ttpp) cc_final: 0.6710 (mppt) REVERT: A 382 THR cc_start: 0.7864 (m) cc_final: 0.7560 (p) REVERT: B 39 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6436 (mt-10) REVERT: B 55 VAL cc_start: 0.8203 (p) cc_final: 0.7855 (t) REVERT: B 80 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: B 83 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7446 (mp0) REVERT: B 148 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: B 251 LYS cc_start: 0.8694 (tttm) cc_final: 0.8358 (ttmm) REVERT: B 260 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7338 (mtt180) REVERT: B 309 GLU cc_start: 0.7115 (tt0) cc_final: 0.6682 (pp20) REVERT: B 364 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7221 (p0) REVERT: B 368 ASP cc_start: 0.7359 (t70) cc_final: 0.7080 (m-30) REVERT: C 24 ASP cc_start: 0.5042 (t70) cc_final: 0.4791 (p0) REVERT: C 54 ARG cc_start: 0.6518 (ttm110) cc_final: 0.6035 (ptm-80) REVERT: C 107 THR cc_start: 0.6777 (t) cc_final: 0.6471 (m) REVERT: C 193 GLN cc_start: 0.7611 (mp-120) cc_final: 0.7272 (mm-40) REVERT: C 251 LYS cc_start: 0.8742 (tptt) cc_final: 0.8315 (tppt) REVERT: C 315 GLU cc_start: 0.8238 (tt0) cc_final: 0.8032 (mt-10) REVERT: C 382 THR cc_start: 0.7366 (p) cc_final: 0.7029 (t) REVERT: D 34 ASP cc_start: 0.6466 (t70) cc_final: 0.6092 (t0) REVERT: D 266 GLU cc_start: 0.7748 (pt0) cc_final: 0.7536 (tt0) REVERT: D 324 ASN cc_start: 0.8096 (m110) cc_final: 0.7865 (m110) outliers start: 30 outliers final: 14 residues processed: 207 average time/residue: 0.7344 time to fit residues: 161.8271 Evaluate side-chains 193 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [116, 82, 81, 32, 142, 14, 50, 22, 19, 73, 62] chunk 116 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 218 HIS C 75 ASN C 218 HIS D 46 HIS D 102 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118746 restraints weight = 12091.201| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.23 r_work: 0.3084 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12280 Z= 0.256 Angle : 0.665 5.475 16664 Z= 0.348 Chirality : 0.050 0.198 1964 Planarity : 0.005 0.055 2128 Dihedral : 8.781 58.227 1900 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.09 % Allowed : 17.59 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.21), residues: 1528 helix: 0.82 (0.21), residues: 616 sheet: -0.30 (0.25), residues: 408 loop : -0.05 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 298 TYR 0.020 0.003 TYR C 79 PHE 0.022 0.003 PHE D 211 HIS 0.009 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.26 (12280) covalent geometry : angle 0.66488 / 0.35 (16664) hydrogen bonds : bond 0.05518 / 3.66 ( 628) hydrogen bonds : angle 5.10883 / 3.61 ( 1827) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.376 Fit side-chains REVERT: A 2 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6949 (mmtm) REVERT: A 21 GLN cc_start: 0.7148 (mt0) cc_final: 0.6774 (mm110) REVERT: A 83 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6969 (mp0) REVERT: A 107 THR cc_start: 0.7637 (t) cc_final: 0.7324 (m) REVERT: A 148 GLU cc_start: 0.7434 (tp30) cc_final: 0.6547 (mt-10) REVERT: A 150 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: A 209 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8228 (t70) REVERT: A 256 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 380 LYS cc_start: 0.7455 (ttpp) cc_final: 0.6791 (mppt) REVERT: A 381 ARG cc_start: 0.7261 (ttt-90) cc_final: 0.6843 (ttt90) REVERT: B 39 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6538 (mt-10) REVERT: B 55 VAL cc_start: 0.8235 (p) cc_final: 0.7820 (t) REVERT: B 80 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8051 (pt0) REVERT: B 83 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7322 (mp0) REVERT: B 148 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: B 251 LYS cc_start: 0.8889 (tttm) cc_final: 0.8491 (ttmm) REVERT: B 264 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 364 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7646 (p0) REVERT: B 368 ASP cc_start: 0.7576 (t70) cc_final: 0.7265 (m-30) REVERT: B 379 GLU cc_start: 0.8206 (tt0) cc_final: 0.7942 (tt0) REVERT: C 24 ASP cc_start: 0.5267 (t70) cc_final: 0.4918 (p0) REVERT: C 54 ARG cc_start: 0.6654 (ttm110) cc_final: 0.6115 (ptm-80) REVERT: C 107 THR cc_start: 0.6765 (t) cc_final: 0.6468 (m) REVERT: C 193 GLN cc_start: 0.7681 (mp-120) cc_final: 0.7341 (mm-40) REVERT: C 225 THR cc_start: 0.8801 (p) cc_final: 0.8532 (p) REVERT: C 251 LYS cc_start: 0.8810 (tptt) cc_final: 0.8287 (tptt) REVERT: C 315 GLU cc_start: 0.8451 (tt0) cc_final: 0.8177 (mt-10) REVERT: D 34 ASP cc_start: 0.6569 (t70) cc_final: 0.6185 (t0) REVERT: D 266 GLU cc_start: 0.7832 (pt0) cc_final: 0.7569 (tt0) REVERT: D 289 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7429 (mptt) REVERT: D 324 ASN cc_start: 0.8100 (m110) cc_final: 0.7885 (m110) outliers start: 40 outliers final: 21 residues processed: 198 average time/residue: 0.7300 time to fit residues: 153.8394 Evaluate side-chains 191 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 289 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [122, 13, 108, 136, 2, 65, 81, 36, 105, 61, 141] chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 HIS B 62 GLN D 102 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122654 restraints weight = 12048.960| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.30 r_work: 0.3110 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12280 Z= 0.139 Angle : 0.530 5.297 16664 Z= 0.280 Chirality : 0.045 0.141 1964 Planarity : 0.004 0.046 2128 Dihedral : 8.096 56.917 1900 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.39 % Allowed : 17.98 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1528 helix: 1.15 (0.21), residues: 616 sheet: -0.24 (0.25), residues: 408 loop : -0.03 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 304 TYR 0.011 0.001 TYR C 79 PHE 0.016 0.001 PHE D 211 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12280) covalent geometry : angle 0.53040 / 0.28 (16664) hydrogen bonds : bond 0.04274 / 2.85 ( 628) hydrogen bonds : angle 4.80775 / 3.40 ( 1827) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.319 Fit side-chains REVERT: A 21 GLN cc_start: 0.7118 (mt0) cc_final: 0.6732 (mm110) REVERT: A 83 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6983 (mp0) REVERT: A 148 GLU cc_start: 0.7313 (tp30) cc_final: 0.6541 (mt-10) REVERT: A 150 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 380 LYS cc_start: 0.7375 (ttpp) cc_final: 0.6689 (mppt) REVERT: B 39 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6512 (mt-10) REVERT: B 55 VAL cc_start: 0.8207 (p) cc_final: 0.7818 (t) REVERT: B 80 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: B 83 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7454 (mp0) REVERT: B 148 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: B 251 LYS cc_start: 0.8805 (tttm) cc_final: 0.8414 (ttmm) REVERT: B 364 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7238 (p0) REVERT: B 368 ASP cc_start: 0.7541 (t70) cc_final: 0.7246 (m-30) REVERT: B 379 GLU cc_start: 0.8077 (tt0) cc_final: 0.7854 (tt0) REVERT: C 24 ASP cc_start: 0.5199 (t70) cc_final: 0.4836 (p0) REVERT: C 54 ARG cc_start: 0.6654 (ttm110) cc_final: 0.6050 (ptm-80) REVERT: C 107 THR cc_start: 0.6792 (t) cc_final: 0.6440 (m) REVERT: C 193 GLN cc_start: 0.7671 (mp-120) cc_final: 0.7332 (mm-40) REVERT: C 251 LYS cc_start: 0.8787 (tptt) cc_final: 0.8309 (tppt) REVERT: C 315 GLU cc_start: 0.8416 (tt0) cc_final: 0.8142 (mt-10) REVERT: C 384 HIS cc_start: 0.6942 (p-80) cc_final: 0.6734 (p-80) REVERT: D 34 ASP cc_start: 0.6437 (t70) cc_final: 0.6110 (t0) REVERT: D 266 GLU cc_start: 0.7834 (pt0) cc_final: 0.7588 (tt0) REVERT: D 324 ASN cc_start: 0.8077 (m110) cc_final: 0.7817 (m110) REVERT: D 371 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7475 (mmtm) outliers start: 31 outliers final: 15 residues processed: 195 average time/residue: 0.7239 time to fit residues: 150.7576 Evaluate side-chains 184 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [136, 130, 19, 131, 103, 92, 141, 32, 122, 91, 78] chunk 136 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 218 HIS B 62 GLN C 75 ASN D 46 HIS D 102 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125427 restraints weight = 12091.199| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.25 r_work: 0.3151 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12280 Z= 0.131 Angle : 0.520 6.724 16664 Z= 0.274 Chirality : 0.044 0.142 1964 Planarity : 0.003 0.043 2128 Dihedral : 7.636 56.376 1900 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.39 % Allowed : 18.44 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1528 helix: 1.27 (0.21), residues: 616 sheet: -0.19 (0.25), residues: 408 loop : -0.01 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.011 0.001 TYR C 79 PHE 0.013 0.001 PHE D 211 HIS 0.012 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12280) covalent geometry : angle 0.52024 / 0.27 (16664) hydrogen bonds : bond 0.04054 / 2.70 ( 628) hydrogen bonds : angle 4.67710 / 3.30 ( 1827) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.445 Fit side-chains REVERT: A 21 GLN cc_start: 0.7261 (mt0) cc_final: 0.6870 (mm110) REVERT: A 83 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6925 (mp0) REVERT: A 87 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7668 (mtpt) REVERT: A 148 GLU cc_start: 0.7274 (tp30) cc_final: 0.6567 (mt-10) REVERT: A 150 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: A 187 LEU cc_start: 0.8761 (tp) cc_final: 0.8388 (mp) REVERT: A 256 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 380 LYS cc_start: 0.7340 (ttpp) cc_final: 0.6743 (mppt) REVERT: A 382 THR cc_start: 0.7955 (m) cc_final: 0.7550 (p) REVERT: B 39 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6524 (mt-10) REVERT: B 55 VAL cc_start: 0.8219 (p) cc_final: 0.7825 (t) REVERT: B 83 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7467 (mp0) REVERT: B 148 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: B 251 LYS cc_start: 0.8731 (tttm) cc_final: 0.8360 (ttmm) REVERT: B 364 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7202 (p0) REVERT: B 368 ASP cc_start: 0.7486 (t70) cc_final: 0.7223 (m-30) REVERT: B 379 GLU cc_start: 0.8020 (tt0) cc_final: 0.7802 (tt0) REVERT: C 24 ASP cc_start: 0.5154 (t70) cc_final: 0.4841 (p0) REVERT: C 54 ARG cc_start: 0.6675 (ttm110) cc_final: 0.6312 (ttp80) REVERT: C 107 THR cc_start: 0.6773 (t) cc_final: 0.6462 (m) REVERT: C 193 GLN cc_start: 0.7583 (mp-120) cc_final: 0.7261 (mm-40) REVERT: C 251 LYS cc_start: 0.8738 (tptt) cc_final: 0.8375 (tppt) REVERT: C 315 GLU cc_start: 0.8228 (tt0) cc_final: 0.8024 (mt-10) REVERT: C 367 MET cc_start: 0.8290 (mtp) cc_final: 0.8055 (mtm) REVERT: D 34 ASP cc_start: 0.6514 (t70) cc_final: 0.6208 (t0) REVERT: D 115 GLU cc_start: 0.7089 (mp0) cc_final: 0.6802 (mm-30) REVERT: D 266 GLU cc_start: 0.7804 (pt0) cc_final: 0.7565 (tt0) REVERT: D 324 ASN cc_start: 0.8104 (m110) cc_final: 0.7852 (m110) REVERT: D 371 LYS cc_start: 0.7786 (mmtm) cc_final: 0.7507 (mmtm) outliers start: 31 outliers final: 19 residues processed: 190 average time/residue: 0.7337 time to fit residues: 148.7346 Evaluate side-chains 189 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [19, 83, 88, 3, 100, 102, 63, 99, 133, 31, 74] chunk 19 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 218 HIS B 62 GLN D 46 HIS D 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124915 restraints weight = 12036.485| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.24 r_work: 0.3150 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12280 Z= 0.135 Angle : 0.525 9.181 16664 Z= 0.276 Chirality : 0.044 0.143 1964 Planarity : 0.004 0.043 2128 Dihedral : 7.570 57.990 1900 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.39 % Allowed : 18.75 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1528 helix: 1.31 (0.21), residues: 616 sheet: -0.17 (0.25), residues: 408 loop : -0.02 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 304 TYR 0.012 0.001 TYR C 79 PHE 0.013 0.001 PHE D 211 HIS 0.011 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (12280) covalent geometry : angle 0.52473 / 0.28 (16664) hydrogen bonds : bond 0.04075 / 2.72 ( 628) hydrogen bonds : angle 4.66313 / 3.30 ( 1827) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.479 Fit side-chains REVERT: A 21 GLN cc_start: 0.7125 (mt0) cc_final: 0.6739 (mm110) REVERT: A 83 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6924 (mp0) REVERT: A 87 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7667 (mtpt) REVERT: A 148 GLU cc_start: 0.7273 (tp30) cc_final: 0.6568 (mt-10) REVERT: A 150 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: A 187 LEU cc_start: 0.8747 (tp) cc_final: 0.8374 (mp) REVERT: A 256 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 380 LYS cc_start: 0.7345 (ttpp) cc_final: 0.6746 (mppt) REVERT: A 382 THR cc_start: 0.7932 (m) cc_final: 0.7526 (p) REVERT: B 39 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6523 (mt-10) REVERT: B 55 VAL cc_start: 0.8225 (p) cc_final: 0.7844 (t) REVERT: B 83 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7429 (mp0) REVERT: B 148 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: B 251 LYS cc_start: 0.8739 (tttm) cc_final: 0.8364 (ttmm) REVERT: B 364 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7177 (p0) REVERT: B 368 ASP cc_start: 0.7421 (t70) cc_final: 0.7169 (m-30) REVERT: B 379 GLU cc_start: 0.7989 (tt0) cc_final: 0.7781 (tt0) REVERT: C 24 ASP cc_start: 0.5128 (t70) cc_final: 0.4820 (p0) REVERT: C 54 ARG cc_start: 0.6645 (ttm110) cc_final: 0.6293 (ttp80) REVERT: C 107 THR cc_start: 0.6730 (t) cc_final: 0.6415 (m) REVERT: C 193 GLN cc_start: 0.7585 (mp-120) cc_final: 0.7264 (mm-40) REVERT: C 251 LYS cc_start: 0.8727 (tptt) cc_final: 0.8362 (tppt) REVERT: C 271 ARG cc_start: 0.7013 (mmm160) cc_final: 0.6743 (tpt-90) REVERT: C 315 GLU cc_start: 0.8311 (tt0) cc_final: 0.8065 (mt-10) REVERT: C 367 MET cc_start: 0.8246 (mtp) cc_final: 0.8024 (mtm) REVERT: D 34 ASP cc_start: 0.6469 (t70) cc_final: 0.6168 (t0) REVERT: D 115 GLU cc_start: 0.7116 (mp0) cc_final: 0.6812 (mm-30) REVERT: D 324 ASN cc_start: 0.8119 (m110) cc_final: 0.7862 (m110) REVERT: D 371 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7541 (mmtm) outliers start: 31 outliers final: 20 residues processed: 192 average time/residue: 0.7247 time to fit residues: 148.5305 Evaluate side-chains 189 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [72, 21, 140, 8, 11, 142, 20, 135, 16, 14, 98] chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 140 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 218 HIS B 62 GLN D 46 HIS D 102 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124578 restraints weight = 11918.000| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.28 r_work: 0.3164 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12280 Z= 0.128 Angle : 0.518 10.034 16664 Z= 0.272 Chirality : 0.044 0.143 1964 Planarity : 0.003 0.042 2128 Dihedral : 7.494 56.685 1900 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.31 % Allowed : 18.67 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1528 helix: 1.35 (0.21), residues: 616 sheet: -0.15 (0.25), residues: 408 loop : 0.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 304 TYR 0.011 0.001 TYR C 79 PHE 0.012 0.001 PHE D 211 HIS 0.007 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12280) covalent geometry : angle 0.51813 / 0.27 (16664) hydrogen bonds : bond 0.03953 / 2.64 ( 628) hydrogen bonds : angle 4.61758 / 3.27 ( 1827) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.470 Fit side-chains REVERT: A 21 GLN cc_start: 0.7072 (mt0) cc_final: 0.6688 (mm110) REVERT: A 83 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6897 (mp0) REVERT: A 148 GLU cc_start: 0.7223 (tp30) cc_final: 0.6528 (mt-10) REVERT: A 150 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 187 LEU cc_start: 0.8764 (tp) cc_final: 0.8356 (mp) REVERT: A 256 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 380 LYS cc_start: 0.7334 (ttpp) cc_final: 0.6749 (mppt) REVERT: A 382 THR cc_start: 0.7923 (m) cc_final: 0.7540 (p) REVERT: B 39 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6469 (mt-10) REVERT: B 55 VAL cc_start: 0.8196 (p) cc_final: 0.7819 (t) REVERT: B 83 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7323 (mp0) REVERT: B 148 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: B 251 LYS cc_start: 0.8712 (tttm) cc_final: 0.8321 (ttmm) REVERT: B 264 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: B 364 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7134 (p0) REVERT: B 368 ASP cc_start: 0.7314 (t70) cc_final: 0.7043 (m-30) REVERT: C 54 ARG cc_start: 0.6585 (ttm110) cc_final: 0.6325 (ttp80) REVERT: C 62 GLN cc_start: 0.7331 (mt0) cc_final: 0.6991 (mt0) REVERT: C 107 THR cc_start: 0.6691 (t) cc_final: 0.6370 (m) REVERT: C 193 GLN cc_start: 0.7501 (mp-120) cc_final: 0.7202 (mm-40) REVERT: C 251 LYS cc_start: 0.8689 (tptt) cc_final: 0.8237 (tppt) REVERT: C 367 MET cc_start: 0.8228 (mtp) cc_final: 0.8000 (mtm) REVERT: C 382 THR cc_start: 0.7418 (p) cc_final: 0.6954 (t) REVERT: D 34 ASP cc_start: 0.6385 (t70) cc_final: 0.6141 (t0) REVERT: D 115 GLU cc_start: 0.7081 (mp0) cc_final: 0.6780 (mm-30) REVERT: D 266 GLU cc_start: 0.7514 (tt0) cc_final: 0.7102 (tt0) REVERT: D 324 ASN cc_start: 0.8107 (m110) cc_final: 0.7845 (m110) REVERT: D 371 LYS cc_start: 0.7804 (mmtm) cc_final: 0.7513 (mmtm) outliers start: 30 outliers final: 20 residues processed: 192 average time/residue: 0.7052 time to fit residues: 144.7709 Evaluate side-chains 194 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [151, 82, 78, 54, 114, 132, 99, 107, 110, 139, 60] chunk 151 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 218 HIS B 62 GLN C 75 ASN D 46 HIS D 102 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125000 restraints weight = 12004.850| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.22 r_work: 0.3172 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12280 Z= 0.118 Angle : 0.506 10.065 16664 Z= 0.266 Chirality : 0.044 0.145 1964 Planarity : 0.003 0.041 2128 Dihedral : 7.388 57.212 1900 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.16 % Allowed : 18.90 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1528 helix: 1.41 (0.21), residues: 616 sheet: -0.13 (0.25), residues: 408 loop : 0.04 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.010 0.001 TYR C 79 PHE 0.011 0.001 PHE D 211 HIS 0.007 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12280) covalent geometry : angle 0.50551 / 0.27 (16664) hydrogen bonds : bond 0.03780 / 2.53 ( 628) hydrogen bonds : angle 4.55448 / 3.22 ( 1827) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.394 Fit side-chains REVERT: A 21 GLN cc_start: 0.7226 (mt0) cc_final: 0.6819 (mm110) REVERT: A 83 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6926 (mp0) REVERT: A 148 GLU cc_start: 0.7335 (tp30) cc_final: 0.6609 (mt-10) REVERT: A 150 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 187 LEU cc_start: 0.8738 (tp) cc_final: 0.8329 (mt) REVERT: A 256 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 380 LYS cc_start: 0.7369 (ttpp) cc_final: 0.6776 (mppt) REVERT: A 382 THR cc_start: 0.7912 (m) cc_final: 0.7565 (p) REVERT: B 39 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6470 (mt-10) REVERT: B 55 VAL cc_start: 0.8222 (p) cc_final: 0.7840 (t) REVERT: B 68 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7124 (tptm) REVERT: B 83 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7441 (mp0) REVERT: B 148 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: B 251 LYS cc_start: 0.8707 (tttm) cc_final: 0.8335 (ttmm) REVERT: B 364 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7190 (p0) REVERT: B 368 ASP cc_start: 0.7384 (t70) cc_final: 0.7107 (m-30) REVERT: C 39 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6201 (mm-30) REVERT: C 54 ARG cc_start: 0.6495 (ttm110) cc_final: 0.6279 (ttp80) REVERT: C 107 THR cc_start: 0.6722 (t) cc_final: 0.6398 (m) REVERT: C 193 GLN cc_start: 0.7494 (mp-120) cc_final: 0.7229 (mm-40) REVERT: C 251 LYS cc_start: 0.8691 (tptt) cc_final: 0.8256 (tppt) REVERT: C 271 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7111 (mmt90) REVERT: C 367 MET cc_start: 0.8247 (mtp) cc_final: 0.8045 (mtm) REVERT: C 382 THR cc_start: 0.7463 (p) cc_final: 0.6992 (t) REVERT: D 34 ASP cc_start: 0.6360 (t70) cc_final: 0.6120 (t0) REVERT: D 266 GLU cc_start: 0.7506 (tt0) cc_final: 0.7097 (tt0) REVERT: D 324 ASN cc_start: 0.8161 (m110) cc_final: 0.7908 (m110) REVERT: D 371 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7551 (mmtm) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.6962 time to fit residues: 138.2777 Evaluate side-chains 187 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [5, 111, 102, 40, 10, 147, 119, 23, 28, 6, 46] chunk 5 optimal weight: 7.9990 chunk 111 optimal weight: 0.0010 chunk 102 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 384 HIS B 62 GLN D 46 HIS D 102 HIS D 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.158324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128045 restraints weight = 11942.933| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.28 r_work: 0.3214 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12280 Z= 0.103 Angle : 0.488 9.911 16664 Z= 0.257 Chirality : 0.043 0.147 1964 Planarity : 0.003 0.039 2128 Dihedral : 7.107 59.465 1900 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.54 % Allowed : 19.60 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1528 helix: 1.52 (0.21), residues: 616 sheet: -0.07 (0.25), residues: 408 loop : 0.07 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 304 TYR 0.012 0.001 TYR B 141 PHE 0.009 0.001 PHE D 211 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (12280) covalent geometry : angle 0.48818 / 0.26 (16664) hydrogen bonds : bond 0.03386 / 2.27 ( 628) hydrogen bonds : angle 4.38763 / 3.10 ( 1827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.47 seconds wall clock time: 86 minutes 17.82 seconds (5177.82 seconds total)