Starting phenix.real_space_refine on Wed Mar 4 13:55:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcx_28998/03_2026/8fcx_28998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcx_28998/03_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_28998/03_2026/8fcx_28998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcx_28998/03_2026/8fcx_28998.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcx_28998/03_2026/8fcx_28998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcx_28998/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.09, per 1000 atoms: 0.22 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: 1.27 Conformation dependent library (CDL) restraints added in 431.0 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: 0.29 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: 2.27 Time building geometry restraints manager: 1.63 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: 7282 17.65 - 35.30: 1026 35.30 - 52.95: 297 52.95 - 70.60: 59 70.60 - 88.25: 11 Dihedral angle restraints: 8675 sinusoidal: 3660 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 8672 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 17.789 88.249 5435 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 covalent geometry : bond 0.00266 (14225) covalent geometry : angle 0.59899 (19285) hydrogen bonds : bond 0.18484 ( 753) hydrogen bonds : angle 5.88902 ( 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 : 0.522 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: 0.1175 time to fit residues: 44.3620 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 : 0.542 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3645 r_free = 0.3645 target = 0.064440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047471 restraints weight = 63694.814| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 5.48 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2885 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= 0.206 Angle : 0.632 8.113 19285 Z= 0.330 Chirality : 0.043 0.180 2160 Planarity : 0.005 0.043 2455 Dihedral : 9.999 82.284 2081 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.16 % Favored : 95.48 % Rotamer: Outliers : 2.91 % Allowed : 25.00 % Favored : 72.09 % 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: 0.53 (0.21), residues: 1705 helix: 1.15 (0.17), residues: 1065 sheet: -0.54 (0.47), residues: 140 loop : -1.00 (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 0.018 0.002 PHE U 126 TRP 0.021 0.002 TRP V 267 HIS 0.004 0.001 HIS S 254 Details of bonding type rmsd covalent geometry : bond 0.00447 (14225) covalent geometry : angle 0.63202 (19285) hydrogen bonds : bond 0.04267 ( 753) hydrogen bonds : angle 4.38112 ( 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 179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8785 (mp) REVERT: R 277 CYS cc_start: 0.7897 (m) cc_final: 0.7662 (m) REVERT: S 172 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8595 (mm-30) REVERT: S 318 MET cc_start: 0.9006 (mtm) cc_final: 0.8764 (mtt) REVERT: S 333 GLU cc_start: 0.8708 (tp30) cc_final: 0.8495 (tm-30) REVERT: T 164 HIS cc_start: 0.9102 (t-90) cc_final: 0.8847 (t-90) REVERT: T 277 CYS cc_start: 0.8988 (m) cc_final: 0.8645 (m) REVERT: U 164 HIS cc_start: 0.9067 (t-90) cc_final: 0.8795 (t-90) REVERT: U 172 GLU cc_start: 0.9252 (pt0) cc_final: 0.8766 (pm20) REVERT: U 318 MET cc_start: 0.9494 (mtp) cc_final: 0.9251 (mtm) REVERT: U 328 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9008 (mt0) REVERT: U 338 ASN cc_start: 0.9331 (m110) cc_final: 0.9071 (m110) REVERT: V 30 HIS cc_start: 0.8084 (p90) cc_final: 0.7691 (p90) REVERT: V 172 GLU cc_start: 0.9313 (tp30) cc_final: 0.8912 (tp30) REVERT: V 190 ASP cc_start: 0.9254 (m-30) cc_final: 0.8848 (m-30) REVERT: V 220 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8142 (tp40) REVERT: V 278 ILE cc_start: 0.8356 (mm) cc_final: 0.7932 (tt) REVERT: V 281 LEU cc_start: 0.8825 (tp) cc_final: 0.8621 (tt) REVERT: V 315 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7638 (m) outliers start: 43 outliers final: 16 residues processed: 173 average time/residue: 0.1048 time to fit residues: 27.4259 Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 301 THR Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 36 VAL 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 332 THR 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: 7.9990 chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 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 = 0.3642 r_free = 0.3642 target = 0.064034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.047264 restraints weight = 64359.424| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 5.47 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14225 Z= 0.146 Angle : 0.559 8.287 19285 Z= 0.289 Chirality : 0.041 0.187 2160 Planarity : 0.004 0.043 2455 Dihedral : 9.176 84.468 2076 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.58 % Favored : 96.07 % Rotamer: Outliers : 3.24 % Allowed : 24.59 % Favored : 72.16 % 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: 0.74 (0.21), residues: 1705 helix: 1.33 (0.17), residues: 1065 sheet: -0.57 (0.48), residues: 140 loop : -0.93 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 327 TYR 0.022 0.001 TYR V 109 PHE 0.015 0.001 PHE U 126 TRP 0.018 0.001 TRP V 267 HIS 0.004 0.001 HIS R 30 Details of bonding type rmsd covalent geometry : bond 0.00319 (14225) covalent geometry : angle 0.55862 (19285) hydrogen bonds : bond 0.03840 ( 753) hydrogen bonds : angle 4.07955 ( 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 166 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8856 (mp) REVERT: R 277 CYS cc_start: 0.7817 (m) cc_final: 0.7569 (m) REVERT: R 307 LYS cc_start: 0.9508 (mttt) cc_final: 0.9070 (tmtt) REVERT: S 172 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8644 (mm-30) REVERT: S 283 ASP cc_start: 0.9098 (m-30) cc_final: 0.8858 (m-30) REVERT: T 164 HIS cc_start: 0.9094 (t-90) cc_final: 0.8614 (t-90) REVERT: T 277 CYS cc_start: 0.8994 (m) cc_final: 0.8688 (m) REVERT: U 164 HIS cc_start: 0.9060 (t-90) cc_final: 0.8559 (t-90) REVERT: U 172 GLU cc_start: 0.9168 (pt0) cc_final: 0.8927 (pm20) REVERT: V 30 HIS cc_start: 0.8073 (p90) cc_final: 0.7670 (p90) REVERT: V 81 LYS cc_start: 0.9330 (mmtm) cc_final: 0.9009 (tptp) REVERT: V 172 GLU cc_start: 0.9258 (tp30) cc_final: 0.8913 (tp30) REVERT: V 190 ASP cc_start: 0.9216 (m-30) cc_final: 0.8801 (m-30) REVERT: V 278 ILE cc_start: 0.8437 (mm) cc_final: 0.8084 (tt) outliers start: 48 outliers final: 22 residues processed: 157 average time/residue: 0.0927 time to fit residues: 22.5730 Evaluate side-chains 125 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 MET 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 214 PHE Chi-restraints excluded: chain R residue 301 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 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 266 HIS 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 U residue 311 SER Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 284 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 220 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.047467 restraints weight = 65124.016| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 5.49 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3818 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= 0.127 Angle : 0.547 8.683 19285 Z= 0.278 Chirality : 0.041 0.197 2160 Planarity : 0.004 0.043 2455 Dihedral : 8.877 81.756 2076 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % Rotamer: Outliers : 2.64 % Allowed : 24.86 % Favored : 72.50 % 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: 0.96 (0.22), residues: 1705 helix: 1.50 (0.17), residues: 1060 sheet: -0.57 (0.48), residues: 140 loop : -0.78 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 224 TYR 0.018 0.001 TYR V 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 covalent geometry : bond 0.00278 (14225) covalent geometry : angle 0.54743 (19285) hydrogen bonds : bond 0.03538 ( 753) hydrogen bonds : angle 3.92644 ( 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 156 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8822 (mp) REVERT: R 277 CYS cc_start: 0.7800 (m) cc_final: 0.7544 (m) REVERT: R 307 LYS cc_start: 0.9510 (mttt) cc_final: 0.9074 (tmtt) REVERT: S 172 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8672 (mm-30) REVERT: S 283 ASP cc_start: 0.9068 (m-30) cc_final: 0.8799 (m-30) REVERT: T 164 HIS cc_start: 0.9123 (t-90) cc_final: 0.8613 (t-90) REVERT: T 277 CYS cc_start: 0.8976 (m) cc_final: 0.8681 (m) REVERT: U 19 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8624 (mtt90) REVERT: U 164 HIS cc_start: 0.9096 (t-90) cc_final: 0.8567 (t-90) REVERT: V 30 HIS cc_start: 0.8139 (p90) cc_final: 0.7737 (p90) REVERT: V 81 LYS cc_start: 0.9351 (mmtm) cc_final: 0.9057 (tptp) REVERT: V 172 GLU cc_start: 0.9282 (tp30) cc_final: 0.9015 (tp30) REVERT: V 190 ASP cc_start: 0.9176 (m-30) cc_final: 0.8773 (m-30) REVERT: V 251 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8228 (t80) REVERT: V 278 ILE cc_start: 0.8434 (mm) cc_final: 0.8106 (tt) outliers start: 39 outliers final: 22 residues processed: 146 average time/residue: 0.0973 time to fit residues: 22.2610 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 214 PHE Chi-restraints excluded: chain R residue 272 GLU 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 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 19 ARG Chi-restraints excluded: chain U residue 94 ILE 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 26 TYR Chi-restraints excluded: chain V residue 124 HIS Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL 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: 0.9980 chunk 136 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 188 GLN ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3647 r_free = 0.3647 target = 0.064026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.047513 restraints weight = 64989.161| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 5.48 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4130 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= 0.121 Angle : 0.534 8.411 19285 Z= 0.273 Chirality : 0.040 0.204 2160 Planarity : 0.004 0.043 2455 Dihedral : 8.717 83.257 2075 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.17 % Favored : 96.48 % Rotamer: Outliers : 2.77 % Allowed : 24.80 % Favored : 72.43 % 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: 1.10 (0.22), residues: 1705 helix: 1.54 (0.17), residues: 1065 sheet: -0.53 (0.48), residues: 140 loop : -0.57 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 224 TYR 0.025 0.001 TYR T 183 PHE 0.026 0.001 PHE T 138 TRP 0.009 0.001 TRP V 267 HIS 0.004 0.001 HIS R 30 Details of bonding type rmsd covalent geometry : bond 0.00262 (14225) covalent geometry : angle 0.53353 (19285) hydrogen bonds : bond 0.03444 ( 753) hydrogen bonds : angle 3.85259 ( 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 151 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (mp) REVERT: R 277 CYS cc_start: 0.7740 (m) cc_final: 0.7448 (m) REVERT: S 172 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8647 (mm-30) REVERT: S 283 ASP cc_start: 0.9104 (m-30) cc_final: 0.8818 (m-30) REVERT: T 164 HIS cc_start: 0.9132 (t-90) cc_final: 0.8595 (t-90) REVERT: T 277 CYS cc_start: 0.8971 (m) cc_final: 0.8686 (m) REVERT: U 164 HIS cc_start: 0.9142 (t-90) cc_final: 0.8798 (t70) REVERT: U 172 GLU cc_start: 0.8827 (pm20) cc_final: 0.8521 (pm20) REVERT: V 30 HIS cc_start: 0.8210 (p90) cc_final: 0.7816 (p90) REVERT: V 172 GLU cc_start: 0.9260 (tp30) cc_final: 0.8914 (tp30) REVERT: V 190 ASP cc_start: 0.9171 (m-30) cc_final: 0.8787 (m-30) REVERT: V 251 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8284 (t80) REVERT: V 278 ILE cc_start: 0.8299 (mm) cc_final: 0.7836 (tt) REVERT: V 281 LEU cc_start: 0.8977 (tp) cc_final: 0.8385 (tt) outliers start: 41 outliers final: 24 residues processed: 144 average time/residue: 0.0870 time to fit residues: 20.0984 Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 94 ILE 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 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 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 T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain V residue 26 TYR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 252 GLN Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN 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 = 0.3616 r_free = 0.3616 target = 0.063140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046741 restraints weight = 64402.360| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 5.36 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14225 Z= 0.140 Angle : 0.546 8.269 19285 Z= 0.280 Chirality : 0.041 0.208 2160 Planarity : 0.004 0.043 2455 Dihedral : 8.826 87.232 2075 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.46 % Favored : 96.19 % Rotamer: Outliers : 2.50 % Allowed : 25.00 % Favored : 72.50 % 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: 1.16 (0.22), residues: 1705 helix: 1.59 (0.17), residues: 1060 sheet: -0.48 (0.49), residues: 140 loop : -0.55 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 287 TYR 0.019 0.001 TYR V 109 PHE 0.023 0.001 PHE T 138 TRP 0.010 0.001 TRP V 106 HIS 0.003 0.001 HIS S 30 Details of bonding type rmsd covalent geometry : bond 0.00306 (14225) covalent geometry : angle 0.54646 (19285) hydrogen bonds : bond 0.03466 ( 753) hydrogen bonds : angle 3.81162 ( 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 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8958 (mp) REVERT: R 277 CYS cc_start: 0.7929 (m) cc_final: 0.7708 (m) REVERT: S 172 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8579 (mm-30) REVERT: S 283 ASP cc_start: 0.9114 (m-30) cc_final: 0.8816 (m-30) REVERT: T 164 HIS cc_start: 0.9155 (t-90) cc_final: 0.8590 (t-90) REVERT: T 277 CYS cc_start: 0.9065 (m) cc_final: 0.8779 (m) REVERT: U 19 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8628 (mtt90) REVERT: U 164 HIS cc_start: 0.9181 (t-90) cc_final: 0.8805 (t70) REVERT: U 172 GLU cc_start: 0.8820 (pm20) cc_final: 0.8523 (pm20) REVERT: V 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7028 (mm) REVERT: V 41 MET cc_start: 0.9413 (mmm) cc_final: 0.9022 (tpp) REVERT: V 172 GLU cc_start: 0.9267 (tp30) cc_final: 0.8888 (tp30) REVERT: V 190 ASP cc_start: 0.9190 (m-30) cc_final: 0.8761 (m-30) REVERT: V 251 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (t80) REVERT: V 281 LEU cc_start: 0.9015 (tp) cc_final: 0.8372 (tt) outliers start: 37 outliers final: 23 residues processed: 132 average time/residue: 0.0899 time to fit residues: 19.3393 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 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 272 GLU 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 19 ARG Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 143 VAL Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 284 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 107 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 15 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 66 optimal weight: 0.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.063012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046586 restraints weight = 64604.974| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 5.37 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4557 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= 0.137 Angle : 0.542 8.357 19285 Z= 0.278 Chirality : 0.040 0.211 2160 Planarity : 0.004 0.048 2455 Dihedral : 8.802 84.625 2075 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.46 % Favored : 96.19 % Rotamer: Outliers : 2.70 % Allowed : 25.00 % Favored : 72.30 % 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: 1.56 (0.17), residues: 1060 sheet: -0.51 (0.48), residues: 140 loop : -0.52 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 224 TYR 0.016 0.001 TYR V 109 PHE 0.019 0.001 PHE T 138 TRP 0.005 0.001 TRP V 267 HIS 0.003 0.001 HIS S 30 Details of bonding type rmsd covalent geometry : bond 0.00300 (14225) covalent geometry : angle 0.54213 (19285) hydrogen bonds : bond 0.03478 ( 753) hydrogen bonds : angle 3.82389 ( 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 148 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8966 (mp) REVERT: R 277 CYS cc_start: 0.7946 (m) cc_final: 0.7723 (m) REVERT: S 172 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8589 (mm-30) REVERT: S 283 ASP cc_start: 0.9083 (m-30) cc_final: 0.8773 (m-30) REVERT: T 164 HIS cc_start: 0.9163 (t-90) cc_final: 0.8709 (t-90) REVERT: T 277 CYS cc_start: 0.9089 (m) cc_final: 0.8797 (m) REVERT: U 19 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8616 (mtt90) REVERT: U 164 HIS cc_start: 0.9128 (t-90) cc_final: 0.8643 (t70) REVERT: U 172 GLU cc_start: 0.8832 (pm20) cc_final: 0.8510 (pm20) REVERT: V 12 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6939 (mm) REVERT: V 172 GLU cc_start: 0.9270 (tp30) cc_final: 0.8895 (tp30) REVERT: V 190 ASP cc_start: 0.9159 (m-30) cc_final: 0.8720 (m-30) REVERT: V 251 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8219 (t80) outliers start: 40 outliers final: 25 residues processed: 140 average time/residue: 0.0933 time to fit residues: 20.7745 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 : 0.516 ------------------------------------------------------------------------------- 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 94 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 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 272 GLU 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 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 143 VAL Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 164 HIS Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 316 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 = 0.063258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.046814 restraints weight = 64873.272| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 5.39 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4705 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= 0.122 Angle : 0.548 9.023 19285 Z= 0.281 Chirality : 0.041 0.259 2160 Planarity : 0.004 0.043 2455 Dihedral : 8.687 82.361 2075 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.58 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 25.61 % 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: 1.17 (0.22), residues: 1705 helix: 1.59 (0.17), residues: 1060 sheet: -0.55 (0.48), residues: 140 loop : -0.48 (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 S 109 PHE 0.015 0.001 PHE T 138 TRP 0.007 0.001 TRP V 284 HIS 0.003 0.001 HIS S 30 Details of bonding type rmsd covalent geometry : bond 0.00267 (14225) covalent geometry : angle 0.54827 (19285) hydrogen bonds : bond 0.03385 ( 753) hydrogen bonds : angle 3.80795 ( 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 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8944 (mp) REVERT: R 277 CYS cc_start: 0.7893 (m) cc_final: 0.7646 (m) REVERT: S 172 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8575 (mm-30) REVERT: S 283 ASP cc_start: 0.9073 (m-30) cc_final: 0.8732 (m-30) REVERT: T 41 MET cc_start: 0.9133 (mmt) cc_final: 0.8877 (mmm) REVERT: T 164 HIS cc_start: 0.9159 (t-90) cc_final: 0.8596 (t-90) REVERT: T 198 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (mtm) REVERT: T 277 CYS cc_start: 0.9012 (m) cc_final: 0.8736 (m) REVERT: U 19 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8799 (mtt180) REVERT: U 164 HIS cc_start: 0.9143 (t-90) cc_final: 0.8649 (t70) REVERT: U 172 GLU cc_start: 0.8818 (pm20) cc_final: 0.8514 (pm20) REVERT: V 12 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6837 (mm) REVERT: V 190 ASP cc_start: 0.9192 (m-30) cc_final: 0.8758 (m-30) REVERT: V 251 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8270 (t80) outliers start: 35 outliers final: 26 residues processed: 132 average time/residue: 0.0897 time to fit residues: 19.2289 Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 94 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 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 272 GLU 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 198 MET Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR 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 12 LEU 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 281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 154 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS V 197 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 316 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 = 0.3619 r_free = 0.3619 target = 0.062943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046499 restraints weight = 64912.351| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 5.37 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4821 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= 0.129 Angle : 0.554 9.222 19285 Z= 0.286 Chirality : 0.041 0.280 2160 Planarity : 0.004 0.043 2455 Dihedral : 8.695 81.480 2075 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % Rotamer: Outliers : 2.30 % Allowed : 25.88 % Favored : 71.82 % Cbeta Deviations : 0.06 % 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: 1.16 (0.22), residues: 1705 helix: 1.57 (0.17), residues: 1060 sheet: -0.51 (0.48), residues: 140 loop : -0.47 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 327 TYR 0.028 0.001 TYR S 109 PHE 0.015 0.001 PHE S 214 TRP 0.006 0.001 TRP V 267 HIS 0.004 0.001 HIS V 162 Details of bonding type rmsd covalent geometry : bond 0.00283 (14225) covalent geometry : angle 0.55401 (19285) hydrogen bonds : bond 0.03385 ( 753) hydrogen bonds : angle 3.78627 ( 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 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8940 (mp) REVERT: R 277 CYS cc_start: 0.7940 (m) cc_final: 0.7730 (m) REVERT: S 172 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8617 (mm-30) REVERT: S 283 ASP cc_start: 0.9075 (m-30) cc_final: 0.8729 (m-30) REVERT: T 41 MET cc_start: 0.9142 (mmt) cc_final: 0.8887 (mmm) REVERT: T 164 HIS cc_start: 0.9168 (t-90) cc_final: 0.8716 (t-90) REVERT: T 198 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: T 277 CYS cc_start: 0.9028 (m) cc_final: 0.8732 (m) REVERT: U 19 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8708 (mtt90) REVERT: U 164 HIS cc_start: 0.9152 (t-90) cc_final: 0.8644 (t70) REVERT: U 172 GLU cc_start: 0.8828 (pm20) cc_final: 0.8570 (pm20) REVERT: V 12 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6861 (mm) REVERT: V 172 GLU cc_start: 0.9198 (tp30) cc_final: 0.8889 (tp30) REVERT: V 190 ASP cc_start: 0.9199 (m-30) cc_final: 0.8768 (m-30) REVERT: V 251 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8290 (t80) outliers start: 34 outliers final: 23 residues processed: 125 average time/residue: 0.0806 time to fit residues: 16.7140 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 94 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 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 272 GLU Chi-restraints excluded: chain S residue 128 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 198 MET Chi-restraints excluded: chain T residue 305 LEU Chi-restraints excluded: chain T residue 332 THR 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 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 281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.0270 chunk 131 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** T 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 316 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 = 0.3636 r_free = 0.3636 target = 0.063740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047385 restraints weight = 64088.510| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 5.35 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14225 Z= 0.114 Angle : 0.566 10.634 19285 Z= 0.288 Chirality : 0.041 0.284 2160 Planarity : 0.003 0.043 2455 Dihedral : 8.514 83.794 2075 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.34 % Favored : 96.30 % Rotamer: Outliers : 1.96 % Allowed : 26.55 % Favored : 71.49 % 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: 1.49 (0.22), residues: 1705 helix: 1.83 (0.17), residues: 1015 sheet: -0.44 (0.49), residues: 140 loop : -0.13 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 42 TYR 0.029 0.001 TYR S 109 PHE 0.012 0.001 PHE S 214 TRP 0.021 0.001 TRP V 267 HIS 0.004 0.001 HIS S 30 Details of bonding type rmsd covalent geometry : bond 0.00247 (14225) covalent geometry : angle 0.56597 (19285) hydrogen bonds : bond 0.03298 ( 753) hydrogen bonds : angle 3.79570 ( 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 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8942 (mp) REVERT: R 277 CYS cc_start: 0.7905 (m) cc_final: 0.7678 (m) REVERT: R 283 ASP cc_start: 0.8964 (m-30) cc_final: 0.8748 (t0) REVERT: S 172 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8617 (mm-30) REVERT: S 283 ASP cc_start: 0.9062 (m-30) cc_final: 0.8694 (m-30) REVERT: T 41 MET cc_start: 0.9117 (mmt) cc_final: 0.8851 (mmm) REVERT: T 164 HIS cc_start: 0.9163 (t-90) cc_final: 0.8617 (t-90) REVERT: T 198 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: T 277 CYS cc_start: 0.8885 (m) cc_final: 0.8653 (m) REVERT: U 19 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8710 (mtt90) REVERT: U 164 HIS cc_start: 0.9137 (t-90) cc_final: 0.8646 (t70) REVERT: U 172 GLU cc_start: 0.8818 (pm20) cc_final: 0.8467 (pm20) REVERT: V 12 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6808 (mm) REVERT: V 105 ASN cc_start: 0.8679 (p0) cc_final: 0.8191 (p0) REVERT: V 190 ASP cc_start: 0.9156 (m-30) cc_final: 0.8714 (m-30) REVERT: V 251 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8192 (t80) outliers start: 29 outliers final: 21 residues processed: 125 average time/residue: 0.0887 time to fit residues: 17.9233 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 94 ILE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 156 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 272 GLU 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 198 MET Chi-restraints excluded: chain T residue 305 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 164 HIS ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 316 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 = 0.3616 r_free = 0.3616 target = 0.062922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046668 restraints weight = 64666.141| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 5.36 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5092 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= 0.133 Angle : 0.579 12.089 19285 Z= 0.294 Chirality : 0.041 0.270 2160 Planarity : 0.004 0.042 2455 Dihedral : 8.641 82.780 2075 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.52 % Favored : 96.13 % Rotamer: Outliers : 2.03 % Allowed : 26.42 % 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: 1.44 (0.22), residues: 1705 helix: 1.73 (0.17), residues: 1030 sheet: -0.51 (0.49), residues: 140 loop : -0.06 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 163 TYR 0.029 0.001 TYR S 109 PHE 0.014 0.001 PHE U 126 TRP 0.013 0.001 TRP V 267 HIS 0.005 0.001 HIS V 164 Details of bonding type rmsd covalent geometry : bond 0.00292 (14225) covalent geometry : angle 0.57860 (19285) hydrogen bonds : bond 0.03338 ( 753) hydrogen bonds : angle 3.80834 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.98 seconds wall clock time: 50 minutes 17.63 seconds (3017.63 seconds total)