Starting phenix.real_space_refine on Fri Jul 3 12:16:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcx_28998/07_2026/8fcx_28998.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 8835 2.51 5 N 2440 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13940 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.74, per 1000 atoms: 0.20 Number of scatterers: 13940 At special positions: 0 Unit cell: (77.996, 124.372, 151.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 15 15.00 Mg 5 11.99 O 2605 8.00 N 2440 7.00 C 8835 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: 0.74 Conformation dependent library (CDL) restraints added in 397.2 milliseconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 63.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.595A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 3.505A pdb=" N ARG R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.560A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 Proline residue: R 80 - end of helix removed outlier: 3.634A pdb=" N SER R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 118 Processing helix chain 'R' and resid 148 through 164 Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.509A pdb=" N LYS R 178 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 3.527A pdb=" N ASP R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET R 198 " --> pdb=" O SER R 194 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.533A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 275 Processing helix chain 'R' and resid 277 through 296 Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.507A pdb=" N LEU R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 3.849A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 343 removed outlier: 3.727A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 14 removed outlier: 3.661A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 removed outlier: 3.503A pdb=" N ARG S 19 " --> pdb=" O PRO S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.609A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 172 through 178 removed outlier: 3.567A pdb=" N LYS S 178 " --> pdb=" O HIS S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 200 removed outlier: 3.833A pdb=" N ASP S 187 " --> pdb=" O TYR S 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET S 198 " --> pdb=" O SER S 194 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 199 " --> pdb=" O LEU S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 Processing helix chain 'S' and resid 218 through 224 removed outlier: 3.734A pdb=" N ARG S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 254 Processing helix chain 'S' and resid 266 through 275 Processing helix chain 'S' and resid 277 through 295 removed outlier: 3.540A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 309 removed outlier: 3.611A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 343 removed outlier: 3.658A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 removed outlier: 3.512A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 26 removed outlier: 3.736A pdb=" N ARG T 19 " --> pdb=" O PRO T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 85 Proline residue: T 80 - end of helix removed outlier: 4.017A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 118 removed outlier: 4.097A pdb=" N TYR T 109 " --> pdb=" O ASN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 172 through 178 removed outlier: 3.512A pdb=" N LYS T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 200 removed outlier: 3.520A pdb=" N LEU T 185 " --> pdb=" O SER T 181 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 removed outlier: 3.507A pdb=" N THR T 213 " --> pdb=" O GLU T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 Processing helix chain 'T' and resid 301 through 308 removed outlier: 3.550A pdb=" N ARG T 308 " --> pdb=" O ASP T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 329 Processing helix chain 'T' and resid 332 through 343 removed outlier: 3.632A pdb=" N VAL T 336 " --> pdb=" O THR T 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 removed outlier: 3.574A pdb=" N LEU U 11 " --> pdb=" O PRO U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 removed outlier: 3.582A pdb=" N ARG U 19 " --> pdb=" O PRO U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 46 removed outlier: 3.590A pdb=" N GLU U 46 " --> pdb=" O ARG U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 84 Proline residue: U 80 - end of helix Processing helix chain 'U' and resid 105 through 118 Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 183 through 200 removed outlier: 3.726A pdb=" N ASP U 187 " --> pdb=" O TYR U 183 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 215 Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 254 Processing helix chain 'U' and resid 263 through 265 No H-bonds generated for 'chain 'U' and resid 263 through 265' Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.551A pdb=" N PHE U 270 " --> pdb=" O HIS U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 308 removed outlier: 3.716A pdb=" N ARG U 308 " --> pdb=" O ASP U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 329 Processing helix chain 'U' and resid 332 through 344 removed outlier: 3.751A pdb=" N VAL U 336 " --> pdb=" O THR U 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 removed outlier: 3.545A pdb=" N LEU V 11 " --> pdb=" O PRO V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 26 Processing helix chain 'V' and resid 30 through 46 removed outlier: 4.118A pdb=" N GLU V 46 " --> pdb=" O ARG V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 78 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.754A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 200 removed outlier: 4.014A pdb=" N LEU V 189 " --> pdb=" O LEU V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 Processing helix chain 'V' and resid 217 through 224 removed outlier: 4.009A pdb=" N LEU V 221 " --> pdb=" O LEU V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 266 through 275 Processing helix chain 'V' and resid 277 through 295 removed outlier: 3.622A pdb=" N ARG V 295 " --> pdb=" O ASP V 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.605A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.846A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE V 319 " --> pdb=" O CYS V 315 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 344 Processing sheet with id=AA1, first strand: chain 'R' and resid 91 through 95 removed outlier: 3.572A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 133 through 134 removed outlier: 3.791A pdb=" N SER R 134 " --> pdb=" O ASN R 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 91 through 95 removed outlier: 6.660A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE S 53 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY S 207 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL S 55 " --> pdb=" O GLY S 207 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 133 through 134 removed outlier: 3.550A pdb=" N SER S 134 " --> pdb=" O ASN S 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 91 through 95 removed outlier: 6.792A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'U' and resid 91 through 95 removed outlier: 6.951A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE U 53 " --> pdb=" O LEU U 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'V' and resid 92 through 95 removed outlier: 7.137A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY V 207 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL V 55 " --> pdb=" O GLY V 207 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.836A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) 753 hydrogen bonds defined for protein. 2094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4581 1.34 - 1.46: 1901 1.46 - 1.57: 7663 1.57 - 1.69: 25 1.69 - 1.81: 55 Bond restraints: 14225 Sorted by residual: bond pdb=" N SER V 59 " pdb=" CA SER V 59 " ideal model delta sigma weight residual 1.463 1.437 0.027 1.29e-02 6.01e+03 4.23e+00 bond pdb=" CA SER V 59 " pdb=" C SER V 59 " ideal model delta sigma weight residual 1.530 1.514 0.015 1.10e-02 8.26e+03 1.94e+00 bond pdb=" CA ASP V 127 " pdb=" CB ASP V 127 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.93e+00 bond pdb=" CA LEU U 82 " pdb=" C LEU U 82 " ideal model delta sigma weight residual 1.524 1.508 0.017 1.28e-02 6.10e+03 1.75e+00 bond pdb=" CG ASP V 187 " pdb=" OD1 ASP V 187 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.73e+00 ... (remaining 14220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 18844 1.69 - 3.38: 361 3.38 - 5.07: 55 5.07 - 6.76: 15 6.76 - 8.45: 10 Bond angle restraints: 19285 Sorted by residual: angle pdb=" N THR V 299 " pdb=" CA THR V 299 " pdb=" C THR V 299 " ideal model delta sigma weight residual 108.38 115.75 -7.37 1.35e+00 5.49e-01 2.98e+01 angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.57 -6.83 1.38e+00 5.25e-01 2.45e+01 angle pdb=" C VAL S 61 " pdb=" N GLY S 62 " pdb=" CA GLY S 62 " ideal model delta sigma weight residual 122.26 116.29 5.97 1.34e+00 5.57e-01 1.99e+01 angle pdb=" N SER U 59 " pdb=" CA SER U 59 " pdb=" C SER U 59 " ideal model delta sigma weight residual 109.24 102.68 6.56 1.63e+00 3.76e-01 1.62e+01 angle pdb=" N VAL U 61 " pdb=" CA VAL U 61 " pdb=" C VAL U 61 " ideal model delta sigma weight residual 109.34 117.63 -8.29 2.08e+00 2.31e-01 1.59e+01 ... (remaining 19280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7241 17.65 - 35.30: 973 35.30 - 52.95: 248 52.95 - 70.60: 52 70.60 - 88.25: 6 Dihedral angle restraints: 8520 sinusoidal: 3505 harmonic: 5015 Sorted by residual: dihedral pdb=" CA ASP V 187 " pdb=" C ASP V 187 " pdb=" N GLN V 188 " pdb=" CA GLN V 188 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP U 127 " pdb=" C ASP U 127 " pdb=" N TYR U 128 " pdb=" CA TYR U 128 " ideal model delta harmonic sigma weight residual -180.00 -163.33 -16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LEU V 121 " pdb=" C LEU V 121 " pdb=" N ILE V 122 " pdb=" CA ILE V 122 " ideal model delta harmonic sigma weight residual 180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1496 0.033 - 0.067: 454 0.067 - 0.100: 132 0.100 - 0.134: 71 0.134 - 0.167: 7 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ASP V 127 " pdb=" N ASP V 127 " pdb=" C ASP V 127 " pdb=" CB ASP V 127 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ASP T 127 " pdb=" N ASP T 127 " pdb=" C ASP T 127 " pdb=" CB ASP T 127 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE S 94 " pdb=" N ILE S 94 " pdb=" C ILE S 94 " pdb=" CB ILE S 94 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 2157 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " -0.013 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" CG PHE V 126 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 297 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ALA U 297 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA U 297 " -0.015 2.00e-02 2.50e+03 pdb=" N THR U 298 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU S 79 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO S 80 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 80 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 80 " 0.031 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 152 2.57 - 3.15: 11796 3.15 - 3.73: 22939 3.73 - 4.32: 30355 4.32 - 4.90: 50514 Nonbonded interactions: 115756 Sorted by model distance: nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 1.984 2.170 nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.995 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.000 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.005 2.170 nonbonded pdb=" O3A ATP U 600 " pdb="MG MG U 601 " model vdw 2.026 2.170 ... (remaining 115751 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 1.060 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14225 Z= 0.142 Angle : 0.599 8.446 19285 Z= 0.328 Chirality : 0.040 0.167 2160 Planarity : 0.004 0.054 2455 Dihedral : 16.934 88.249 5280 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 3.93 % Favored : 95.37 % Rotamer: Outliers : 0.61 % Allowed : 27.03 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.22), residues: 1705 helix: 0.97 (0.17), residues: 1040 sheet: -0.54 (0.48), residues: 140 loop : -0.94 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 131 TYR 0.014 0.001 TYR T 128 PHE 0.047 0.001 PHE V 126 TRP 0.017 0.001 TRP S 267 HIS 0.006 0.001 HIS S 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (14225) covalent geometry : angle 0.59899 / 0.33 (19285) hydrogen bonds : bond 0.18484 / 12.29 ( 753) hydrogen bonds : angle 5.88902 / 4.29 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 254 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 LEU cc_start: 0.9236 (tp) cc_final: 0.8871 (tp) REVERT: R 190 ASP cc_start: 0.8940 (m-30) cc_final: 0.8691 (m-30) REVERT: S 56 TYR cc_start: 0.8152 (m-80) cc_final: 0.7225 (m-10) REVERT: S 318 MET cc_start: 0.8866 (mtm) cc_final: 0.8345 (mtt) REVERT: S 333 GLU cc_start: 0.8828 (tp30) cc_final: 0.8559 (tm-30) REVERT: T 244 PHE cc_start: 0.9532 (t80) cc_final: 0.9245 (t80) REVERT: T 277 CYS cc_start: 0.8974 (m) cc_final: 0.8420 (m) REVERT: T 333 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8698 (tp30) REVERT: U 172 GLU cc_start: 0.9175 (pt0) cc_final: 0.8756 (pm20) REVERT: U 210 GLU cc_start: 0.9000 (tt0) cc_final: 0.8783 (tt0) REVERT: V 30 HIS cc_start: 0.7327 (p90) cc_final: 0.6807 (p-80) REVERT: V 190 ASP cc_start: 0.9234 (m-30) cc_final: 0.8842 (m-30) REVERT: V 277 CYS cc_start: 0.8892 (m) cc_final: 0.8378 (m) REVERT: V 278 ILE cc_start: 0.8329 (mm) cc_final: 0.8010 (tt) REVERT: V 281 LEU cc_start: 0.8850 (tp) cc_final: 0.8625 (tt) REVERT: V 315 CYS cc_start: 0.7785 (t) cc_final: 0.7281 (p) outliers start: 9 outliers final: 4 residues processed: 261 average time/residue: 0.1268 time to fit residues: 48.1258 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain V residue 59 SER Chi-restraints excluded: chain V residue 301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 GLN S 252 GLN T 25 ASN ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 158 ASN V 158 ASN V 164 HIS V 220 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.064225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047138 restraints weight = 64323.939| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 5.55 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14225 Z= 0.205 Angle : 0.635 8.247 19285 Z= 0.331 Chirality : 0.043 0.184 2160 Planarity : 0.005 0.045 2455 Dihedral : 5.420 64.198 1926 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.22 % Favored : 95.43 % Rotamer: Outliers : 3.18 % Allowed : 24.80 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.21), residues: 1705 helix: 1.12 (0.17), residues: 1065 sheet: -0.57 (0.47), residues: 140 loop : -1.01 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 42 TYR 0.016 0.002 TYR T 103 PHE 0.019 0.002 PHE U 126 TRP 0.021 0.002 TRP V 267 HIS 0.006 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (14225) covalent geometry : angle 0.63456 / 0.33 (19285) hydrogen bonds : bond 0.04220 / 2.84 ( 753) hydrogen bonds : angle 4.36512 / 3.17 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8790 (mp) REVERT: R 277 CYS cc_start: 0.7951 (m) cc_final: 0.7719 (m) REVERT: S 172 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8564 (mm-30) REVERT: S 318 MET cc_start: 0.8986 (mtm) cc_final: 0.8747 (mtt) REVERT: S 333 GLU cc_start: 0.8696 (tp30) cc_final: 0.8494 (tm-30) REVERT: T 164 HIS cc_start: 0.9114 (t-90) cc_final: 0.8842 (t-90) REVERT: T 277 CYS cc_start: 0.8984 (m) cc_final: 0.8652 (m) REVERT: U 164 HIS cc_start: 0.9070 (t-90) cc_final: 0.8780 (t-90) REVERT: U 172 GLU cc_start: 0.9244 (pt0) cc_final: 0.8780 (pm20) REVERT: U 318 MET cc_start: 0.9517 (mtp) cc_final: 0.9286 (mtm) REVERT: U 328 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8996 (mt0) REVERT: U 338 ASN cc_start: 0.9333 (m110) cc_final: 0.9067 (m110) REVERT: V 30 HIS cc_start: 0.8133 (p90) cc_final: 0.7764 (p90) REVERT: V 172 GLU cc_start: 0.9302 (tp30) cc_final: 0.8907 (tp30) REVERT: V 190 ASP cc_start: 0.9240 (m-30) cc_final: 0.8832 (m-30) REVERT: V 220 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: V 278 ILE cc_start: 0.8346 (mm) cc_final: 0.7957 (tt) REVERT: V 281 LEU cc_start: 0.8834 (tp) cc_final: 0.8629 (tt) REVERT: V 315 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7641 (m) outliers start: 47 outliers final: 18 residues processed: 174 average time/residue: 0.1111 time to fit residues: 29.0829 Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain U residue 137 ASN Chi-restraints excluded: chain U residue 328 GLN Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 220 GLN Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 284 TRP Chi-restraints excluded: chain V residue 315 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS V 220 GLN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.061949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.045319 restraints weight = 66062.028| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 5.41 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14225 Z= 0.222 Angle : 0.611 8.010 19285 Z= 0.320 Chirality : 0.042 0.191 2160 Planarity : 0.005 0.045 2455 Dihedral : 4.912 62.461 1921 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.11 % Favored : 95.54 % Rotamer: Outliers : 3.58 % Allowed : 25.14 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.21), residues: 1705 helix: 1.13 (0.16), residues: 1065 sheet: -0.66 (0.47), residues: 140 loop : -1.05 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 131 TYR 0.020 0.002 TYR T 183 PHE 0.022 0.002 PHE U 126 TRP 0.019 0.002 TRP V 267 HIS 0.004 0.001 HIS T 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (14225) covalent geometry : angle 0.61105 / 0.32 (19285) hydrogen bonds : bond 0.04193 / 2.80 ( 753) hydrogen bonds : angle 4.19304 / 3.04 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8878 (mp) REVERT: R 277 CYS cc_start: 0.8213 (m) cc_final: 0.7910 (m) REVERT: S 172 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8626 (mm-30) REVERT: T 164 HIS cc_start: 0.9162 (t-90) cc_final: 0.8649 (t-90) REVERT: T 172 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8999 (mm-30) REVERT: T 277 CYS cc_start: 0.9172 (m) cc_final: 0.8772 (m) REVERT: U 164 HIS cc_start: 0.9095 (t-90) cc_final: 0.8848 (t70) REVERT: U 172 GLU cc_start: 0.9182 (pt0) cc_final: 0.8703 (pm20) REVERT: V 81 LYS cc_start: 0.9325 (mmtm) cc_final: 0.8983 (tptp) REVERT: V 105 ASN cc_start: 0.8749 (p0) cc_final: 0.8545 (p0) REVERT: V 172 GLU cc_start: 0.9316 (tp30) cc_final: 0.8953 (tp30) REVERT: V 190 ASP cc_start: 0.9317 (m-30) cc_final: 0.8862 (m-30) REVERT: V 220 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (tp40) REVERT: V 315 CYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7762 (m) outliers start: 53 outliers final: 23 residues processed: 157 average time/residue: 0.0973 time to fit residues: 24.4559 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 138 PHE Chi-restraints excluded: chain T residue 266 HIS Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 137 ASN Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 220 GLN Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 284 TRP Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 315 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 GLN ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 220 GLN V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.063058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.046398 restraints weight = 65090.841| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 5.47 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14225 Z= 0.126 Angle : 0.547 8.473 19285 Z= 0.278 Chirality : 0.041 0.164 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.616 48.811 1921 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.52 % Favored : 96.13 % Rotamer: Outliers : 2.70 % Allowed : 25.61 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.21), residues: 1705 helix: 1.37 (0.17), residues: 1065 sheet: -0.59 (0.47), residues: 140 loop : -0.97 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 327 TYR 0.020 0.001 TYR R 109 PHE 0.015 0.001 PHE U 126 TRP 0.012 0.001 TRP V 267 HIS 0.004 0.001 HIS R 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14225) covalent geometry : angle 0.54742 / 0.28 (19285) hydrogen bonds : bond 0.03625 / 2.42 ( 753) hydrogen bonds : angle 3.98242 / 2.88 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: R 105 ASN cc_start: 0.9264 (t0) cc_final: 0.9055 (t0) REVERT: R 117 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8967 (mp) REVERT: R 277 CYS cc_start: 0.7977 (m) cc_final: 0.7667 (m) REVERT: S 172 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8642 (mm-30) REVERT: S 224 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8468 (ptp-170) REVERT: S 293 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9411 (mt) REVERT: T 41 MET cc_start: 0.9289 (mmm) cc_final: 0.8996 (mmt) REVERT: T 164 HIS cc_start: 0.9157 (t-90) cc_final: 0.8764 (t-90) REVERT: T 277 CYS cc_start: 0.9044 (m) cc_final: 0.8746 (m) REVERT: U 19 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8645 (mtt180) REVERT: U 164 HIS cc_start: 0.9171 (t-90) cc_final: 0.8859 (t70) REVERT: U 172 GLU cc_start: 0.9055 (pt0) cc_final: 0.8611 (pm20) REVERT: U 318 MET cc_start: 0.9577 (mtp) cc_final: 0.8927 (mtm) REVERT: V 12 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7290 (mm) REVERT: V 30 HIS cc_start: 0.8285 (p90) cc_final: 0.7876 (p90) REVERT: V 172 GLU cc_start: 0.9273 (tp30) cc_final: 0.8979 (tp30) REVERT: V 190 ASP cc_start: 0.9184 (m-30) cc_final: 0.8802 (m-30) REVERT: V 251 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (t80) REVERT: V 278 ILE cc_start: 0.8405 (mm) cc_final: 0.8077 (tt) REVERT: V 315 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7784 (m) outliers start: 40 outliers final: 21 residues processed: 146 average time/residue: 0.1068 time to fit residues: 24.3787 Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 138 PHE Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 137 ASN Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.063330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.046872 restraints weight = 64825.292| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 5.42 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14225 Z= 0.115 Angle : 0.537 8.685 19285 Z= 0.272 Chirality : 0.040 0.163 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.410 45.182 1920 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.48 % Rotamer: Outliers : 2.91 % Allowed : 25.54 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.22), residues: 1705 helix: 1.46 (0.17), residues: 1060 sheet: -0.54 (0.48), residues: 140 loop : -0.75 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 287 TYR 0.026 0.001 TYR T 183 PHE 0.021 0.001 PHE T 138 TRP 0.008 0.001 TRP V 267 HIS 0.005 0.001 HIS V 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (14225) covalent geometry : angle 0.53677 / 0.27 (19285) hydrogen bonds : bond 0.03463 / 2.31 ( 753) hydrogen bonds : angle 3.90661 / 2.83 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 ASN cc_start: 0.9340 (t0) cc_final: 0.9106 (t0) REVERT: R 117 LEU cc_start: 0.9213 (tt) cc_final: 0.8951 (mp) REVERT: R 277 CYS cc_start: 0.8089 (m) cc_final: 0.7795 (m) REVERT: R 283 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (t0) REVERT: S 109 TYR cc_start: 0.9187 (t80) cc_final: 0.8974 (t80) REVERT: S 172 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8616 (mm-30) REVERT: S 224 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8493 (ptp-170) REVERT: S 283 ASP cc_start: 0.9019 (m-30) cc_final: 0.8779 (t0) REVERT: S 293 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9386 (mt) REVERT: T 164 HIS cc_start: 0.9132 (t-90) cc_final: 0.8590 (t-90) REVERT: T 277 CYS cc_start: 0.8987 (m) cc_final: 0.8743 (m) REVERT: T 318 MET cc_start: 0.9062 (mmt) cc_final: 0.8803 (mmt) REVERT: U 19 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8656 (mtt90) REVERT: U 164 HIS cc_start: 0.9195 (t-90) cc_final: 0.8831 (t70) REVERT: V 30 HIS cc_start: 0.8336 (p90) cc_final: 0.7898 (p90) REVERT: V 82 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7641 (mm) REVERT: V 172 GLU cc_start: 0.9183 (tp30) cc_final: 0.8924 (tp30) REVERT: V 190 ASP cc_start: 0.9146 (m-30) cc_final: 0.8732 (m-30) REVERT: V 251 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8145 (t80) REVERT: V 278 ILE cc_start: 0.8440 (mm) cc_final: 0.8126 (tt) outliers start: 43 outliers final: 19 residues processed: 140 average time/residue: 0.0953 time to fit residues: 21.1336 Evaluate side-chains 122 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.062612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046200 restraints weight = 65230.029| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 5.43 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14225 Z= 0.135 Angle : 0.537 8.563 19285 Z= 0.274 Chirality : 0.040 0.159 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.312 45.500 1920 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.40 % Favored : 96.25 % Rotamer: Outliers : 2.57 % Allowed : 25.81 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1705 helix: 1.49 (0.17), residues: 1060 sheet: -0.50 (0.49), residues: 140 loop : -0.64 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 287 TYR 0.010 0.001 TYR V 128 PHE 0.014 0.001 PHE U 126 TRP 0.010 0.001 TRP V 284 HIS 0.003 0.001 HIS S 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14225) covalent geometry : angle 0.53681 / 0.27 (19285) hydrogen bonds : bond 0.03485 / 2.34 ( 753) hydrogen bonds : angle 3.88047 / 2.81 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 ASN cc_start: 0.9374 (t0) cc_final: 0.9129 (t0) REVERT: R 117 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8978 (mp) REVERT: R 277 CYS cc_start: 0.8270 (m) cc_final: 0.7996 (m) REVERT: R 283 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8660 (t0) REVERT: S 109 TYR cc_start: 0.9196 (t80) cc_final: 0.8994 (t80) REVERT: S 172 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8540 (mm-30) REVERT: S 283 ASP cc_start: 0.9008 (m-30) cc_final: 0.8768 (t0) REVERT: T 164 HIS cc_start: 0.9149 (t-90) cc_final: 0.8572 (t-90) REVERT: T 277 CYS cc_start: 0.9068 (m) cc_final: 0.8790 (m) REVERT: U 19 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8609 (mtt90) REVERT: U 164 HIS cc_start: 0.9131 (t-90) cc_final: 0.8641 (t70) REVERT: U 172 GLU cc_start: 0.8869 (pm20) cc_final: 0.8557 (pm20) REVERT: V 12 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6819 (mm) REVERT: V 172 GLU cc_start: 0.9223 (tp30) cc_final: 0.8927 (tp30) REVERT: V 190 ASP cc_start: 0.9152 (m-30) cc_final: 0.8729 (m-30) REVERT: V 251 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8212 (t80) outliers start: 38 outliers final: 19 residues processed: 129 average time/residue: 0.0946 time to fit residues: 19.5623 Evaluate side-chains 123 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 266 HIS Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 107 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 147 optimal weight: 0.2980 chunk 82 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.062037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045716 restraints weight = 65390.793| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 5.38 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14225 Z= 0.150 Angle : 0.558 11.905 19285 Z= 0.283 Chirality : 0.040 0.179 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.328 46.399 1920 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.46 % Favored : 96.19 % Rotamer: Outliers : 2.77 % Allowed : 25.34 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1705 helix: 1.50 (0.17), residues: 1060 sheet: -0.42 (0.49), residues: 140 loop : -0.57 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 153 TYR 0.026 0.001 TYR T 183 PHE 0.017 0.001 PHE U 126 TRP 0.006 0.001 TRP V 106 HIS 0.003 0.001 HIS S 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14225) covalent geometry : angle 0.55763 / 0.28 (19285) hydrogen bonds : bond 0.03530 / 2.36 ( 753) hydrogen bonds : angle 3.88231 / 2.80 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: R 105 ASN cc_start: 0.9367 (t0) cc_final: 0.9111 (t0) REVERT: R 117 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8945 (mp) REVERT: R 277 CYS cc_start: 0.8330 (m) cc_final: 0.8049 (m) REVERT: R 283 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8635 (t0) REVERT: S 172 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8555 (mm-30) REVERT: S 283 ASP cc_start: 0.9028 (m-30) cc_final: 0.8783 (t0) REVERT: T 68 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9274 (mm) REVERT: T 82 LEU cc_start: 0.9008 (tp) cc_final: 0.8719 (mt) REVERT: T 164 HIS cc_start: 0.9176 (t-90) cc_final: 0.8591 (t-90) REVERT: T 198 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8133 (mtm) REVERT: T 277 CYS cc_start: 0.9148 (m) cc_final: 0.8835 (m) REVERT: T 318 MET cc_start: 0.9078 (mmt) cc_final: 0.8862 (mmt) REVERT: U 19 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8626 (mtt90) REVERT: U 164 HIS cc_start: 0.9138 (t-90) cc_final: 0.8608 (t70) REVERT: U 172 GLU cc_start: 0.8766 (pm20) cc_final: 0.8405 (pm20) REVERT: V 172 GLU cc_start: 0.9211 (tp30) cc_final: 0.8932 (tp30) REVERT: V 190 ASP cc_start: 0.9185 (m-30) cc_final: 0.8738 (m-30) REVERT: V 251 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8223 (t80) outliers start: 41 outliers final: 21 residues processed: 135 average time/residue: 0.0956 time to fit residues: 20.3770 Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 68 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 198 MET Chi-restraints excluded: chain T residue 266 HIS Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain V residue 158 ASN Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS V 197 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.062704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.046436 restraints weight = 64890.788| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.40 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14225 Z= 0.116 Angle : 0.545 9.059 19285 Z= 0.275 Chirality : 0.040 0.197 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.308 47.444 1920 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.40 % Favored : 96.25 % Rotamer: Outliers : 2.09 % Allowed : 26.49 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1705 helix: 1.55 (0.17), residues: 1060 sheet: -0.35 (0.50), residues: 140 loop : -0.55 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 163 TYR 0.028 0.001 TYR S 109 PHE 0.013 0.001 PHE S 214 TRP 0.020 0.001 TRP V 267 HIS 0.004 0.001 HIS S 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14225) covalent geometry : angle 0.54543 / 0.28 (19285) hydrogen bonds : bond 0.03357 / 2.26 ( 753) hydrogen bonds : angle 3.85401 / 2.78 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 ASN cc_start: 0.9380 (t0) cc_final: 0.9104 (t0) REVERT: R 117 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8971 (mp) REVERT: R 277 CYS cc_start: 0.8263 (m) cc_final: 0.7998 (m) REVERT: R 283 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8612 (t0) REVERT: S 172 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8510 (mm-30) REVERT: S 283 ASP cc_start: 0.8979 (m-30) cc_final: 0.8720 (t0) REVERT: T 41 MET cc_start: 0.9298 (mmm) cc_final: 0.9071 (mmt) REVERT: T 82 LEU cc_start: 0.8963 (tp) cc_final: 0.8651 (mt) REVERT: T 164 HIS cc_start: 0.9165 (t-90) cc_final: 0.8712 (t-90) REVERT: T 198 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: T 277 CYS cc_start: 0.9007 (m) cc_final: 0.8730 (m) REVERT: T 318 MET cc_start: 0.9055 (mmt) cc_final: 0.8798 (mmt) REVERT: U 19 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8683 (mtt90) REVERT: U 164 HIS cc_start: 0.9152 (t-90) cc_final: 0.8649 (t70) REVERT: U 172 GLU cc_start: 0.8809 (pm20) cc_final: 0.8529 (pm20) REVERT: V 30 HIS cc_start: 0.8380 (p90) cc_final: 0.8118 (p90) REVERT: V 172 GLU cc_start: 0.9111 (tp30) cc_final: 0.8880 (tp30) REVERT: V 190 ASP cc_start: 0.9183 (m-30) cc_final: 0.8763 (m-30) REVERT: V 198 MET cc_start: 0.8565 (mtm) cc_final: 0.8346 (mtm) REVERT: V 251 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8187 (t80) outliers start: 31 outliers final: 20 residues processed: 121 average time/residue: 0.0846 time to fit residues: 16.6818 Evaluate side-chains 122 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 198 MET Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 158 ASN Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 GLN V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.062112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.045835 restraints weight = 65426.391| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 5.41 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14225 Z= 0.137 Angle : 0.561 9.236 19285 Z= 0.285 Chirality : 0.040 0.282 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.281 48.024 1920 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.52 % Favored : 96.13 % Rotamer: Outliers : 1.96 % Allowed : 26.69 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1705 helix: 1.55 (0.17), residues: 1060 sheet: -0.38 (0.49), residues: 140 loop : -0.50 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 327 TYR 0.029 0.001 TYR S 109 PHE 0.015 0.001 PHE S 214 TRP 0.037 0.001 TRP V 267 HIS 0.008 0.001 HIS V 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14225) covalent geometry : angle 0.56109 / 0.28 (19285) hydrogen bonds : bond 0.03380 / 2.29 ( 753) hydrogen bonds : angle 3.84324 / 2.77 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 105 ASN cc_start: 0.9388 (t0) cc_final: 0.9112 (t0) REVERT: R 117 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8960 (mp) REVERT: R 283 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (t0) REVERT: S 172 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8562 (mm-30) REVERT: T 82 LEU cc_start: 0.8974 (tp) cc_final: 0.8668 (mt) REVERT: T 164 HIS cc_start: 0.9178 (t-90) cc_final: 0.8586 (t-90) REVERT: T 198 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8017 (mtm) REVERT: T 277 CYS cc_start: 0.9070 (m) cc_final: 0.8772 (m) REVERT: U 19 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8704 (mtt90) REVERT: U 164 HIS cc_start: 0.9155 (t-90) cc_final: 0.8631 (t70) REVERT: U 172 GLU cc_start: 0.8819 (pm20) cc_final: 0.8491 (pm20) REVERT: V 41 MET cc_start: 0.9496 (tmm) cc_final: 0.9014 (tpp) REVERT: V 190 ASP cc_start: 0.9179 (m-30) cc_final: 0.8719 (m-30) REVERT: V 198 MET cc_start: 0.8564 (mtm) cc_final: 0.8324 (mtm) REVERT: V 251 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8300 (t80) outliers start: 29 outliers final: 17 residues processed: 121 average time/residue: 0.0934 time to fit residues: 18.0888 Evaluate side-chains 116 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 152 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 198 MET Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.046578 restraints weight = 64403.034| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 5.40 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14225 Z= 0.115 Angle : 0.581 11.570 19285 Z= 0.290 Chirality : 0.040 0.258 2160 Planarity : 0.004 0.042 2455 Dihedral : 4.309 48.951 1920 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.52 % Favored : 96.13 % Rotamer: Outliers : 1.76 % Allowed : 27.30 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1705 helix: 1.66 (0.17), residues: 1045 sheet: -0.32 (0.50), residues: 140 loop : -0.52 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 327 TYR 0.030 0.001 TYR S 109 PHE 0.012 0.001 PHE U 126 TRP 0.033 0.001 TRP V 267 HIS 0.007 0.001 HIS V 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14225) covalent geometry : angle 0.58068 / 0.29 (19285) hydrogen bonds : bond 0.03287 / 2.22 ( 753) hydrogen bonds : angle 3.84230 / 2.76 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: R 105 ASN cc_start: 0.9358 (t0) cc_final: 0.9071 (t0) REVERT: R 117 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8992 (mp) REVERT: R 283 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (t0) REVERT: S 172 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8526 (mm-30) REVERT: S 318 MET cc_start: 0.8649 (mmm) cc_final: 0.8320 (mmt) REVERT: T 82 LEU cc_start: 0.8983 (tp) cc_final: 0.8672 (mt) REVERT: T 164 HIS cc_start: 0.9161 (t-90) cc_final: 0.8705 (t-90) REVERT: T 198 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7884 (mtm) REVERT: T 277 CYS cc_start: 0.8909 (m) cc_final: 0.8670 (m) REVERT: T 318 MET cc_start: 0.9078 (mmt) cc_final: 0.8815 (mmt) REVERT: U 19 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8692 (mtt90) REVERT: U 164 HIS cc_start: 0.9168 (t-90) cc_final: 0.8662 (t70) REVERT: U 172 GLU cc_start: 0.8797 (pm20) cc_final: 0.8464 (pm20) REVERT: V 95 GLU cc_start: 0.8557 (pm20) cc_final: 0.8343 (pm20) REVERT: V 190 ASP cc_start: 0.9154 (m-30) cc_final: 0.8701 (m-30) REVERT: V 198 MET cc_start: 0.8529 (mtm) cc_final: 0.8273 (mtm) REVERT: V 251 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8236 (t80) outliers start: 26 outliers final: 17 residues processed: 119 average time/residue: 0.0800 time to fit residues: 15.6032 Evaluate side-chains 121 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 198 MET Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 9 LEU Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 158 ASN Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 254 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.060981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044754 restraints weight = 65713.613| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 5.31 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14225 Z= 0.192 Angle : 0.613 11.904 19285 Z= 0.313 Chirality : 0.041 0.260 2160 Planarity : 0.004 0.041 2455 Dihedral : 4.361 49.373 1920 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.11 % Favored : 95.54 % Rotamer: Outliers : 1.62 % Allowed : 27.57 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1705 helix: 1.68 (0.17), residues: 1015 sheet: -0.42 (0.50), residues: 140 loop : -0.16 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 163 TYR 0.032 0.002 TYR T 183 PHE 0.020 0.002 PHE U 126 TRP 0.032 0.002 TRP V 267 HIS 0.008 0.001 HIS V 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (14225) covalent geometry : angle 0.61274 / 0.31 (19285) hydrogen bonds : bond 0.03594 / 2.44 ( 753) hydrogen bonds : angle 3.92872 / 2.82 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.29 seconds wall clock time: 52 minutes 39.28 seconds (3159.28 seconds total)