Starting phenix.real_space_refine on Thu Aug 6 12:47:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fcw_28997/08_2026/8fcw_28997.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 75 5.49 5 Mg 5 5.21 5 S 40 5.16 5 C 9420 2.51 5 N 2665 2.21 5 O 2965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15170 Number of models: 1 Model: "" Number of chains: 12 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: "N" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "O" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.81, per 1000 atoms: 0.19 Number of scatterers: 15170 At special positions: 0 Unit cell: (112.778, 124.372, 153.884, 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 75 15.00 Mg 5 11.99 O 2965 8.00 N 2665 7.00 C 9420 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: 1.58 Conformation dependent library (CDL) restraints added in 689.4 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 63.4% alpha, 7.1% beta 30 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.583A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.541A 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: 3.625A 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: 3.542A pdb=" N LYS R 178 " --> pdb=" O HIS R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 3.758A 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: 3.509A 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: 3.515A pdb=" N LEU R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 3.822A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 343 removed outlier: 3.690A pdb=" N ASN R 338 " --> pdb=" O ALA R 334 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 14 removed outlier: 3.710A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 removed outlier: 3.501A pdb=" N ARG S 19 " --> pdb=" O PRO S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.540A 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: 3.652A pdb=" N LYS S 178 " --> pdb=" O HIS S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 200 removed outlier: 3.831A pdb=" N ASP S 187 " --> pdb=" O TYR S 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S 198 " --> pdb=" O SER S 194 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.657A 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 273 Processing helix chain 'S' and resid 277 through 295 removed outlier: 3.563A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 309 removed outlier: 3.590A 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 344 removed outlier: 3.652A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 removed outlier: 3.547A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 26 removed outlier: 3.643A 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: 4.104A pdb=" N SER T 84 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 118 Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 172 through 178 removed outlier: 3.602A pdb=" N LYS T 178 " --> pdb=" O HIS T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 200 removed outlier: 3.558A pdb=" N LEU T 185 " --> pdb=" O SER T 181 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN T 186 " --> pdb=" O GLY T 182 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU T 189 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 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: 3.559A 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 344 removed outlier: 3.621A pdb=" N VAL T 336 " --> pdb=" O THR T 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 removed outlier: 3.548A pdb=" N LEU U 11 " --> pdb=" O PRO U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 26 removed outlier: 3.579A pdb=" N ARG U 19 " --> pdb=" O PRO U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 46 Processing helix chain 'U' and resid 62 through 83 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 removed outlier: 3.555A pdb=" N LYS U 178 " --> pdb=" O HIS U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 200 removed outlier: 3.718A pdb=" N ASP U 187 " --> pdb=" O TYR U 183 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.665A 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 266 through 275 removed outlier: 3.557A 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: 3.722A 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: 3.733A pdb=" N VAL U 336 " --> pdb=" O THR U 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 removed outlier: 3.519A 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: 3.987A 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: 3.836A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 200 removed outlier: 4.041A 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: 4.029A 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 263 through 265 No H-bonds generated for 'chain 'V' and resid 263 through 265' Processing helix chain 'V' and resid 266 through 275 Processing helix chain 'V' and resid 277 through 295 Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.658A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.821A pdb=" N LYS V 317 " --> pdb=" O ALA V 313 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.582A pdb=" N VAL R 92 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.897A 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: 3.707A 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: 6.699A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE S 53 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY S 207 " --> pdb=" O ILE S 53 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL S 55 " --> pdb=" O GLY S 207 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.955A 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: 3.528A 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: 6.738A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 7.113A 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: 6.902A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.076A 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: 7.122A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLY V 207 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL V 55 " --> pdb=" O GLY V 207 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.650A 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: 3.829A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2365 1.31 - 1.43: 4382 1.43 - 1.56: 8655 1.56 - 1.69: 146 1.69 - 1.81: 55 Bond restraints: 15603 Sorted by residual: bond pdb=" O2B ATP U 600 " pdb=" PB ATP U 600 " ideal model delta sigma weight residual 1.529 1.284 0.245 2.20e-02 2.07e+03 1.24e+02 bond pdb=" O2B ATP S 600 " pdb=" PB ATP S 600 " ideal model delta sigma weight residual 1.529 1.337 0.192 2.20e-02 2.07e+03 7.61e+01 bond pdb=" O2B ATP T 600 " pdb=" PB ATP T 600 " ideal model delta sigma weight residual 1.529 1.378 0.151 2.20e-02 2.07e+03 4.71e+01 bond pdb=" C4 ATP R 600 " pdb=" C5 ATP R 600 " ideal model delta sigma weight residual 1.388 1.447 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C4 ATP S 600 " pdb=" N9 ATP S 600 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.31e+01 ... (remaining 15598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20641 2.04 - 4.08: 669 4.08 - 6.12: 77 6.12 - 8.16: 17 8.16 - 10.20: 3 Bond angle restraints: 21407 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 108.38 116.17 -7.79 1.35e+00 5.49e-01 3.33e+01 angle pdb=" PA ATP V 600 " pdb=" O3A ATP V 600 " pdb=" PB ATP V 600 " ideal model delta sigma weight residual 136.83 131.73 5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" N GLU U 100 " pdb=" CA GLU U 100 " pdb=" C GLU U 100 " ideal model delta sigma weight residual 112.87 107.07 5.80 1.20e+00 6.94e-01 2.33e+01 angle pdb=" PA ATP T 600 " pdb=" O3A ATP T 600 " pdb=" PB ATP T 600 " ideal model delta sigma weight residual 136.83 132.07 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" N THR U 299 " pdb=" CA THR U 299 " pdb=" C THR U 299 " ideal model delta sigma weight residual 108.74 115.19 -6.45 1.38e+00 5.25e-01 2.19e+01 ... (remaining 21402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7410 17.72 - 35.44: 1135 35.44 - 53.16: 500 53.16 - 70.88: 120 70.88 - 88.60: 9 Dihedral angle restraints: 9174 sinusoidal: 4159 harmonic: 5015 Sorted by residual: dihedral pdb=" CA PHE U 214 " pdb=" C PHE U 214 " pdb=" N ARG U 215 " pdb=" CA ARG U 215 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE T 214 " pdb=" C PHE T 214 " pdb=" N ARG T 215 " pdb=" CA ARG T 215 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE S 214 " pdb=" C PHE S 214 " pdb=" N ARG S 215 " pdb=" CA ARG S 215 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 9171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1772 0.063 - 0.125: 560 0.125 - 0.188: 61 0.188 - 0.250: 5 0.250 - 0.313: 2 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB VAL V 167 " pdb=" CA VAL V 167 " pdb=" CG1 VAL V 167 " pdb=" CG2 VAL V 167 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL V 336 " pdb=" CA VAL V 336 " pdb=" CG1 VAL V 336 " pdb=" CG2 VAL V 336 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU V 248 " pdb=" CB LEU V 248 " pdb=" CD1 LEU V 248 " pdb=" CD2 LEU V 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2397 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 319 " -0.023 2.00e-02 2.50e+03 2.01e-02 7.06e+00 pdb=" CG PHE V 319 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE V 319 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE V 319 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE V 319 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE V 319 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE V 319 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 142 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASN R 142 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN R 142 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 143 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 126 " 0.006 2.00e-02 2.50e+03 1.60e-02 4.48e+00 pdb=" CG PHE V 126 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE V 126 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE V 126 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE V 126 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE V 126 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE V 126 " -0.002 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 165 2.57 - 3.15: 12980 3.15 - 3.74: 25563 3.74 - 4.32: 34886 4.32 - 4.90: 54884 Nonbonded interactions: 128478 Sorted by model distance: nonbonded pdb=" O3B ATP T 600 " pdb="MG MG T 601 " model vdw 1.989 2.170 nonbonded pdb=" O1G ATP V 600 " pdb="MG MG V 601 " model vdw 2.005 2.170 nonbonded pdb=" O3B ATP S 600 " pdb="MG MG S 601 " model vdw 2.007 2.170 nonbonded pdb=" O3B ATP U 600 " pdb="MG MG U 601 " model vdw 2.008 2.170 nonbonded pdb=" O3A ATP V 600 " pdb="MG MG V 601 " model vdw 2.042 2.170 ... (remaining 128473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.010 0.245 15603 Z= 0.662 Angle : 0.901 10.196 21407 Z= 0.561 Chirality : 0.058 0.313 2400 Planarity : 0.005 0.048 2515 Dihedral : 20.160 88.596 5934 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.64 % Favored : 95.95 % Rotamer: Outliers : 2.09 % Allowed : 25.61 % 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: -0.40 (0.20), residues: 1705 helix: 0.35 (0.16), residues: 1055 sheet: -0.59 (0.47), residues: 140 loop : -1.27 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 223 TYR 0.025 0.004 TYR S 128 PHE 0.036 0.005 PHE V 319 TRP 0.030 0.005 TRP S 106 HIS 0.013 0.003 HIS T 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00993 / 0.66 (15603) covalent geometry : angle 0.90144 / 0.56 (21407) hydrogen bonds : bond 0.17998 / 12.09 ( 833) hydrogen bonds : angle 5.87032 / 4.07 ( 2259) *********************** 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 288 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 LEU cc_start: 0.9763 (mt) cc_final: 0.9513 (pp) REVERT: R 277 CYS cc_start: 0.8642 (m) cc_final: 0.8369 (m) REVERT: R 318 MET cc_start: 0.8733 (mmt) cc_final: 0.8010 (mmt) REVERT: R 321 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8911 (pp20) REVERT: S 41 MET cc_start: 0.9449 (tpp) cc_final: 0.9244 (mmm) REVERT: S 71 GLU cc_start: 0.9354 (tt0) cc_final: 0.9149 (pp20) REVERT: S 103 TYR cc_start: 0.8392 (p90) cc_final: 0.8132 (OUTLIER) REVERT: S 138 PHE cc_start: 0.9244 (m-80) cc_final: 0.8921 (m-80) REVERT: S 190 ASP cc_start: 0.9364 (m-30) cc_final: 0.9096 (m-30) REVERT: S 216 ASN cc_start: 0.8105 (m-40) cc_final: 0.7875 (m-40) REVERT: S 234 CYS cc_start: 0.9308 (m) cc_final: 0.9009 (m) REVERT: S 318 MET cc_start: 0.9110 (mtm) cc_final: 0.8515 (mtp) REVERT: T 105 ASN cc_start: 0.9168 (t0) cc_final: 0.8898 (p0) REVERT: T 164 HIS cc_start: 0.9197 (t-170) cc_final: 0.8780 (t-90) REVERT: T 321 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8621 (OUTLIER) REVERT: U 108 GLU cc_start: 0.9114 (tp30) cc_final: 0.8843 (tp30) REVERT: U 126 PHE cc_start: 0.8281 (t80) cc_final: 0.7966 (t80) REVERT: U 321 GLU cc_start: 0.9363 (tp30) cc_final: 0.8902 (mt-10) REVERT: V 41 MET cc_start: 0.9340 (mmm) cc_final: 0.9051 (mmm) REVERT: V 121 LEU cc_start: 0.9324 (tt) cc_final: 0.9010 (tm) REVERT: V 158 ASN cc_start: 0.9657 (m-40) cc_final: 0.9419 (m110) outliers start: 31 outliers final: 8 residues processed: 276 average time/residue: 0.5170 time to fit residues: 158.1614 Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain U 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: 176 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** R 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 124 HIS ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN T 197 ASN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 220 GLN U 338 ASN V 314 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.096661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064659 restraints weight = 50329.523| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.88 r_work: 0.2897 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15603 Z= 0.162 Angle : 0.699 10.541 21407 Z= 0.359 Chirality : 0.044 0.197 2400 Planarity : 0.005 0.056 2515 Dihedral : 18.734 77.609 2585 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 26.82 % Favored : 70.20 % 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: 0.07 (0.21), residues: 1705 helix: 0.83 (0.16), residues: 1080 sheet: -0.62 (0.46), residues: 140 loop : -1.38 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 295 TYR 0.021 0.002 TYR U 103 PHE 0.027 0.002 PHE T 138 TRP 0.018 0.002 TRP R 267 HIS 0.010 0.001 HIS S 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15603) covalent geometry : angle 0.69914 / 0.36 (21407) hydrogen bonds : bond 0.05137 / 3.47 ( 833) hydrogen bonds : angle 4.53834 / 3.20 ( 2259) *********************** 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 191 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 PHE cc_start: 0.8507 (m-80) cc_final: 0.8186 (m-10) REVERT: R 105 ASN cc_start: 0.9130 (t0) cc_final: 0.8898 (t0) REVERT: R 192 LEU cc_start: 0.9021 (tp) cc_final: 0.8733 (tp) REVERT: R 248 LEU cc_start: 0.9797 (mt) cc_final: 0.9504 (pp) REVERT: R 277 CYS cc_start: 0.7445 (m) cc_final: 0.7228 (m) REVERT: R 318 MET cc_start: 0.8504 (mmt) cc_final: 0.7752 (mmt) REVERT: R 321 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8747 (pp20) REVERT: S 71 GLU cc_start: 0.9558 (tt0) cc_final: 0.9243 (tm-30) REVERT: S 103 TYR cc_start: 0.9070 (p90) cc_final: 0.8743 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9343 (t0) cc_final: 0.8983 (t0) REVERT: S 137 ASN cc_start: 0.8798 (p0) cc_final: 0.8565 (p0) REVERT: S 138 PHE cc_start: 0.9201 (m-80) cc_final: 0.8849 (m-80) REVERT: S 146 LYS cc_start: 0.8497 (pttp) cc_final: 0.8162 (pptt) REVERT: S 186 GLN cc_start: 0.8474 (mp10) cc_final: 0.8172 (mp10) REVERT: S 234 CYS cc_start: 0.9384 (m) cc_final: 0.9168 (m) REVERT: S 318 MET cc_start: 0.9390 (mtm) cc_final: 0.9080 (mtp) REVERT: T 105 ASN cc_start: 0.9214 (t0) cc_final: 0.8993 (p0) REVERT: T 108 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9168 (mm-30) REVERT: T 146 LYS cc_start: 0.9414 (mtmm) cc_final: 0.9174 (mtmm) REVERT: T 164 HIS cc_start: 0.9355 (t-170) cc_final: 0.8873 (t-90) REVERT: T 210 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8942 (pm20) REVERT: T 333 GLU cc_start: 0.8590 (pp20) cc_final: 0.8387 (tm-30) REVERT: U 41 MET cc_start: 0.9410 (tpp) cc_final: 0.9182 (mmm) REVERT: U 108 GLU cc_start: 0.9403 (tp30) cc_final: 0.9053 (tp30) REVERT: U 197 ASN cc_start: 0.9403 (m-40) cc_final: 0.9013 (m-40) REVERT: U 206 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8374 (mm) REVERT: U 321 GLU cc_start: 0.9556 (tp30) cc_final: 0.9206 (mt-10) REVERT: V 51 SER cc_start: 0.9147 (m) cc_final: 0.8939 (p) REVERT: V 121 LEU cc_start: 0.9270 (tt) cc_final: 0.9038 (tm) REVERT: V 158 ASN cc_start: 0.9678 (m-40) cc_final: 0.9433 (m110) REVERT: V 206 LEU cc_start: 0.9358 (mt) cc_final: 0.9153 (mp) REVERT: V 321 GLU cc_start: 0.9409 (mp0) cc_final: 0.9178 (mm-30) outliers start: 44 outliers final: 13 residues processed: 186 average time/residue: 0.4181 time to fit residues: 87.5816 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 206 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 GLN ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.085709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054841 restraints weight = 53382.939| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.99 r_work: 0.2877 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15603 Z= 0.156 Angle : 0.639 11.645 21407 Z= 0.328 Chirality : 0.042 0.166 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.610 77.431 2581 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 3.51 % Allowed : 25.27 % Favored : 71.22 % 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: 0.37 (0.21), residues: 1705 helix: 1.10 (0.16), residues: 1055 sheet: -0.56 (0.45), residues: 140 loop : -1.24 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 224 TYR 0.019 0.001 TYR S 128 PHE 0.022 0.001 PHE U 126 TRP 0.019 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (15603) covalent geometry : angle 0.63926 / 0.33 (21407) hydrogen bonds : bond 0.04538 / 3.06 ( 833) hydrogen bonds : angle 4.27890 / 3.02 ( 2259) *********************** 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 185 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 PHE cc_start: 0.8599 (m-80) cc_final: 0.8323 (m-10) REVERT: R 105 ASN cc_start: 0.9144 (t0) cc_final: 0.8843 (t0) REVERT: R 157 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: R 192 LEU cc_start: 0.9055 (tp) cc_final: 0.8818 (tp) REVERT: R 248 LEU cc_start: 0.9808 (mt) cc_final: 0.9519 (pp) REVERT: R 277 CYS cc_start: 0.7440 (m) cc_final: 0.7218 (m) REVERT: R 318 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7745 (mmt) REVERT: R 321 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: S 103 TYR cc_start: 0.9099 (p90) cc_final: 0.8793 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9330 (t0) cc_final: 0.8844 (t0) REVERT: S 137 ASN cc_start: 0.8902 (p0) cc_final: 0.8647 (p0) REVERT: S 138 PHE cc_start: 0.9224 (m-80) cc_final: 0.8861 (m-80) REVERT: S 146 LYS cc_start: 0.8647 (pttp) cc_final: 0.8258 (pptt) REVERT: S 318 MET cc_start: 0.9365 (mtm) cc_final: 0.9037 (mtp) REVERT: S 337 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8584 (tm-30) REVERT: S 338 ASN cc_start: 0.9379 (t0) cc_final: 0.9061 (m110) REVERT: T 102 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7528 (mtm-85) REVERT: T 108 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9218 (mm-30) REVERT: T 164 HIS cc_start: 0.9422 (t-170) cc_final: 0.8912 (t-90) REVERT: T 210 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8968 (mp0) REVERT: T 321 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9296 (mp0) REVERT: U 19 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8776 (mtp85) REVERT: U 41 MET cc_start: 0.9390 (tpp) cc_final: 0.9158 (mmm) REVERT: U 105 ASN cc_start: 0.9572 (t0) cc_final: 0.9277 (t0) REVERT: U 108 GLU cc_start: 0.9421 (tp30) cc_final: 0.9034 (tp30) REVERT: U 321 GLU cc_start: 0.9558 (tp30) cc_final: 0.9215 (mt-10) REVERT: V 51 SER cc_start: 0.9249 (m) cc_final: 0.9039 (p) REVERT: V 121 LEU cc_start: 0.9289 (tt) cc_final: 0.9056 (tm) REVERT: V 158 ASN cc_start: 0.9683 (m-40) cc_final: 0.9446 (m110) REVERT: V 321 GLU cc_start: 0.9460 (mp0) cc_final: 0.9180 (mm-30) REVERT: V 339 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8841 (tp) REVERT: V 345 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8698 (mp) outliers start: 52 outliers final: 20 residues processed: 174 average time/residue: 0.4037 time to fit residues: 79.7778 Evaluate side-chains 148 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 157 GLU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain R residue 321 GLU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 192 LEU Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 163 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.085777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054853 restraints weight = 52980.183| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.99 r_work: 0.2869 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15603 Z= 0.129 Angle : 0.627 12.682 21407 Z= 0.319 Chirality : 0.042 0.186 2400 Planarity : 0.004 0.043 2515 Dihedral : 18.468 78.334 2580 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.93 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 24.93 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1705 helix: 1.18 (0.16), residues: 1060 sheet: -0.64 (0.45), residues: 140 loop : -1.07 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 224 TYR 0.022 0.001 TYR U 103 PHE 0.041 0.001 PHE U 126 TRP 0.024 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15603) covalent geometry : angle 0.62710 / 0.32 (21407) hydrogen bonds : bond 0.04123 / 2.77 ( 833) hydrogen bonds : angle 4.12863 / 2.93 ( 2259) *********************** 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 180 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: R 52 PHE cc_start: 0.8568 (m-80) cc_final: 0.8292 (m-10) REVERT: R 105 ASN cc_start: 0.9168 (t0) cc_final: 0.8841 (t0) REVERT: R 192 LEU cc_start: 0.9043 (tp) cc_final: 0.8799 (tp) REVERT: R 248 LEU cc_start: 0.9812 (mt) cc_final: 0.9517 (pp) REVERT: R 293 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8832 (mp) REVERT: S 71 GLU cc_start: 0.9584 (tt0) cc_final: 0.9270 (tm-30) REVERT: S 103 TYR cc_start: 0.9136 (p90) cc_final: 0.8777 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9304 (t0) cc_final: 0.8782 (t0) REVERT: S 137 ASN cc_start: 0.8915 (p0) cc_final: 0.8647 (p0) REVERT: S 138 PHE cc_start: 0.9238 (m-80) cc_final: 0.8872 (m-80) REVERT: S 146 LYS cc_start: 0.8712 (pttp) cc_final: 0.8301 (pptt) REVERT: S 318 MET cc_start: 0.9356 (mtm) cc_final: 0.9058 (mtp) REVERT: S 337 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8617 (tm-30) REVERT: S 338 ASN cc_start: 0.9400 (t0) cc_final: 0.9056 (m110) REVERT: T 164 HIS cc_start: 0.9411 (t-170) cc_final: 0.8890 (t-90) REVERT: T 210 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: T 293 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9189 (mm) REVERT: T 321 GLU cc_start: 0.9521 (mt-10) cc_final: 0.8970 (tt0) REVERT: U 19 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.9128 (mpp80) REVERT: U 103 TYR cc_start: 0.8657 (p90) cc_final: 0.8425 (p90) REVERT: U 108 GLU cc_start: 0.9428 (tp30) cc_final: 0.9048 (tp30) REVERT: U 321 GLU cc_start: 0.9548 (tp30) cc_final: 0.9241 (mt-10) REVERT: V 51 SER cc_start: 0.9236 (m) cc_final: 0.9035 (p) REVERT: V 121 LEU cc_start: 0.9222 (tt) cc_final: 0.8982 (tm) REVERT: V 158 ASN cc_start: 0.9683 (m-40) cc_final: 0.9435 (m110) REVERT: V 263 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9134 (mp) REVERT: V 321 GLU cc_start: 0.9484 (mp0) cc_final: 0.9160 (mm-30) REVERT: V 339 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8863 (tp) REVERT: V 345 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8710 (mp) outliers start: 51 outliers final: 20 residues processed: 168 average time/residue: 0.3895 time to fit residues: 74.2898 Evaluate side-chains 144 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 263 LEU Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 118 optimal weight: 0.0770 chunk 110 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.085937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055191 restraints weight = 52961.088| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.97 r_work: 0.2879 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15603 Z= 0.122 Angle : 0.617 12.519 21407 Z= 0.312 Chirality : 0.041 0.192 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.358 78.649 2577 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.05 % Favored : 96.60 % Rotamer: Outliers : 3.38 % Allowed : 25.88 % Favored : 70.74 % 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: 0.59 (0.21), residues: 1705 helix: 1.17 (0.16), residues: 1070 sheet: -0.64 (0.45), residues: 140 loop : -0.91 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 131 TYR 0.021 0.001 TYR U 103 PHE 0.024 0.001 PHE U 126 TRP 0.023 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15603) covalent geometry : angle 0.61721 / 0.31 (21407) hydrogen bonds : bond 0.03917 / 2.62 ( 833) hydrogen bonds : angle 4.03581 / 2.87 ( 2259) *********************** 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 180 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: R 52 PHE cc_start: 0.8495 (m-80) cc_final: 0.8256 (m-10) REVERT: R 105 ASN cc_start: 0.9204 (t0) cc_final: 0.8892 (t0) REVERT: R 192 LEU cc_start: 0.9031 (tp) cc_final: 0.8793 (tp) REVERT: R 248 LEU cc_start: 0.9809 (mt) cc_final: 0.9522 (pp) REVERT: S 71 GLU cc_start: 0.9584 (tt0) cc_final: 0.9229 (tm-30) REVERT: S 103 TYR cc_start: 0.9151 (p90) cc_final: 0.8767 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9295 (t0) cc_final: 0.8797 (t0) REVERT: S 137 ASN cc_start: 0.8928 (p0) cc_final: 0.8659 (p0) REVERT: S 138 PHE cc_start: 0.9241 (m-80) cc_final: 0.8874 (m-80) REVERT: S 146 LYS cc_start: 0.8751 (pttp) cc_final: 0.8333 (pptt) REVERT: S 337 GLN cc_start: 0.9182 (mm-40) cc_final: 0.8602 (tm-30) REVERT: S 338 ASN cc_start: 0.9437 (t0) cc_final: 0.9109 (m110) REVERT: T 164 HIS cc_start: 0.9420 (t-170) cc_final: 0.8877 (t-90) REVERT: T 210 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: T 321 GLU cc_start: 0.9527 (OUTLIER) cc_final: 0.8972 (tt0) REVERT: U 19 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.9110 (mpp80) REVERT: U 108 GLU cc_start: 0.9441 (tp30) cc_final: 0.8990 (tp30) REVERT: U 321 GLU cc_start: 0.9543 (tp30) cc_final: 0.9249 (mt-10) REVERT: V 121 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8995 (tm) REVERT: V 158 ASN cc_start: 0.9695 (m-40) cc_final: 0.9444 (m110) REVERT: V 321 GLU cc_start: 0.9508 (mp0) cc_final: 0.9161 (mm-30) REVERT: V 345 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8717 (mp) outliers start: 50 outliers final: 16 residues processed: 168 average time/residue: 0.3917 time to fit residues: 74.6983 Evaluate side-chains 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 140 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.082926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051983 restraints weight = 53893.155| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.94 r_work: 0.2781 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15603 Z= 0.277 Angle : 0.682 11.875 21407 Z= 0.351 Chirality : 0.044 0.203 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.355 79.612 2575 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.05 % Favored : 96.54 % Rotamer: Outliers : 3.18 % Allowed : 26.76 % Favored : 70.07 % 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: 0.70 (0.21), residues: 1705 helix: 1.26 (0.17), residues: 1065 sheet: -0.62 (0.46), residues: 140 loop : -0.84 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 42 TYR 0.024 0.002 TYR U 103 PHE 0.019 0.002 PHE U 126 TRP 0.027 0.002 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (15603) covalent geometry : angle 0.68190 / 0.35 (21407) hydrogen bonds : bond 0.04414 / 2.96 ( 833) hydrogen bonds : angle 4.09549 / 2.91 ( 2259) *********************** 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 166 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8644 (mp0) REVERT: R 105 ASN cc_start: 0.9252 (t0) cc_final: 0.8940 (t0) REVERT: R 166 ASP cc_start: 0.8683 (m-30) cc_final: 0.8469 (p0) REVERT: R 192 LEU cc_start: 0.9048 (tp) cc_final: 0.8798 (tp) REVERT: R 248 LEU cc_start: 0.9816 (mt) cc_final: 0.9513 (pp) REVERT: S 71 GLU cc_start: 0.9582 (tt0) cc_final: 0.9277 (tm-30) REVERT: S 103 TYR cc_start: 0.9155 (p90) cc_final: 0.8790 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9350 (t0) cc_final: 0.8885 (t0) REVERT: S 137 ASN cc_start: 0.8866 (p0) cc_final: 0.8590 (p0) REVERT: S 138 PHE cc_start: 0.9272 (m-80) cc_final: 0.8925 (m-80) REVERT: S 144 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: S 146 LYS cc_start: 0.8947 (pttp) cc_final: 0.8468 (pptt) REVERT: S 183 TYR cc_start: 0.8755 (t80) cc_final: 0.8528 (t80) REVERT: S 337 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8641 (tm-30) REVERT: T 118 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8197 (tm-30) REVERT: T 164 HIS cc_start: 0.9469 (t-170) cc_final: 0.8875 (t-90) REVERT: T 210 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8949 (mp0) REVERT: T 321 GLU cc_start: 0.9535 (OUTLIER) cc_final: 0.9155 (mt-10) REVERT: U 19 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8860 (mtp85) REVERT: U 103 TYR cc_start: 0.8754 (p90) cc_final: 0.8545 (p90) REVERT: U 108 GLU cc_start: 0.9466 (tp30) cc_final: 0.9029 (tp30) REVERT: U 321 GLU cc_start: 0.9569 (tp30) cc_final: 0.9260 (mt-10) REVERT: V 121 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9039 (tm) REVERT: V 158 ASN cc_start: 0.9688 (m-40) cc_final: 0.9439 (m110) REVERT: V 321 GLU cc_start: 0.9520 (mp0) cc_final: 0.9165 (mm-30) REVERT: V 345 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8877 (mp) outliers start: 47 outliers final: 24 residues processed: 155 average time/residue: 0.4288 time to fit residues: 75.7241 Evaluate side-chains 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 145 SER Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 101 optimal weight: 0.9980 chunk 175 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.083123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.052251 restraints weight = 52946.306| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.91 r_work: 0.2791 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15603 Z= 0.190 Angle : 0.661 11.949 21407 Z= 0.333 Chirality : 0.043 0.291 2400 Planarity : 0.004 0.048 2515 Dihedral : 18.330 81.012 2575 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Rotamer: Outliers : 2.70 % Allowed : 27.84 % Favored : 69.46 % 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: 0.75 (0.21), residues: 1705 helix: 1.30 (0.17), residues: 1065 sheet: -0.68 (0.45), residues: 140 loop : -0.81 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 215 TYR 0.024 0.001 TYR U 103 PHE 0.032 0.001 PHE U 138 TRP 0.032 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (15603) covalent geometry : angle 0.66077 / 0.33 (21407) hydrogen bonds : bond 0.04002 / 2.68 ( 833) hydrogen bonds : angle 4.02381 / 2.86 ( 2259) *********************** 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 157 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: R 52 PHE cc_start: 0.8503 (m-10) cc_final: 0.8203 (m-10) REVERT: R 105 ASN cc_start: 0.9242 (t0) cc_final: 0.8911 (t0) REVERT: R 192 LEU cc_start: 0.9092 (tp) cc_final: 0.8860 (tp) REVERT: R 248 LEU cc_start: 0.9827 (mt) cc_final: 0.9531 (pp) REVERT: S 71 GLU cc_start: 0.9573 (tt0) cc_final: 0.9255 (tm-30) REVERT: S 103 TYR cc_start: 0.9167 (p90) cc_final: 0.8763 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9355 (t0) cc_final: 0.8896 (t0) REVERT: S 137 ASN cc_start: 0.8840 (p0) cc_final: 0.8548 (p0) REVERT: S 138 PHE cc_start: 0.9292 (m-80) cc_final: 0.8939 (m-80) REVERT: S 144 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: S 146 LYS cc_start: 0.9076 (pttp) cc_final: 0.8614 (pptt) REVERT: S 183 TYR cc_start: 0.8797 (t80) cc_final: 0.8576 (t80) REVERT: S 337 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8604 (tm-30) REVERT: T 118 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8216 (tm-30) REVERT: T 164 HIS cc_start: 0.9458 (t-170) cc_final: 0.8859 (t-90) REVERT: T 210 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8994 (mp0) REVERT: T 321 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.9103 (mt-10) REVERT: U 19 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.8858 (mtp85) REVERT: U 103 TYR cc_start: 0.8743 (p90) cc_final: 0.8518 (p90) REVERT: U 321 GLU cc_start: 0.9547 (tp30) cc_final: 0.9228 (mt-10) REVERT: V 158 ASN cc_start: 0.9686 (m-40) cc_final: 0.9428 (m110) REVERT: V 321 GLU cc_start: 0.9530 (mp0) cc_final: 0.9194 (mm-30) REVERT: V 345 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 40 outliers final: 20 residues processed: 146 average time/residue: 0.4322 time to fit residues: 71.5620 Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 185 LEU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** 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 = 0.3757 r_free = 0.3757 target = 0.083918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053163 restraints weight = 52887.075| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.93 r_work: 0.2833 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15603 Z= 0.126 Angle : 0.649 12.331 21407 Z= 0.323 Chirality : 0.043 0.351 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.249 80.981 2575 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 28.58 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1705 helix: 1.56 (0.17), residues: 1030 sheet: -0.75 (0.46), residues: 140 loop : -0.50 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 215 TYR 0.029 0.001 TYR R 109 PHE 0.027 0.001 PHE U 126 TRP 0.031 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (15603) covalent geometry : angle 0.64897 / 0.32 (21407) hydrogen bonds : bond 0.03791 / 2.53 ( 833) hydrogen bonds : angle 3.95202 / 2.81 ( 2259) *********************** 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 153 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: R 52 PHE cc_start: 0.8512 (m-10) cc_final: 0.8225 (m-10) REVERT: R 105 ASN cc_start: 0.9232 (t0) cc_final: 0.8893 (t0) REVERT: R 192 LEU cc_start: 0.9104 (tp) cc_final: 0.8876 (tp) REVERT: R 248 LEU cc_start: 0.9825 (mt) cc_final: 0.9537 (pp) REVERT: S 71 GLU cc_start: 0.9563 (tt0) cc_final: 0.9239 (tm-30) REVERT: S 103 TYR cc_start: 0.9142 (p90) cc_final: 0.8726 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9328 (t0) cc_final: 0.8875 (t0) REVERT: S 137 ASN cc_start: 0.8847 (p0) cc_final: 0.8577 (p0) REVERT: S 138 PHE cc_start: 0.9290 (m-80) cc_final: 0.8907 (m-80) REVERT: S 144 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8758 (mp0) REVERT: S 146 LYS cc_start: 0.9095 (pttp) cc_final: 0.8639 (pptt) REVERT: S 183 TYR cc_start: 0.8802 (t80) cc_final: 0.8567 (t80) REVERT: S 337 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8614 (tm-30) REVERT: T 164 HIS cc_start: 0.9462 (t-170) cc_final: 0.8886 (t-90) REVERT: T 210 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8978 (mp0) REVERT: T 321 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9064 (mt-10) REVERT: U 19 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9158 (mpp80) REVERT: U 103 TYR cc_start: 0.8718 (p90) cc_final: 0.8439 (p90) REVERT: U 131 ARG cc_start: 0.8409 (mmp-170) cc_final: 0.8182 (mmp80) REVERT: U 158 ASN cc_start: 0.9708 (m110) cc_final: 0.9242 (m110) REVERT: U 252 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.9167 (tt0) REVERT: U 321 GLU cc_start: 0.9532 (tp30) cc_final: 0.9225 (mt-10) REVERT: V 128 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: V 158 ASN cc_start: 0.9690 (m-40) cc_final: 0.9431 (m110) REVERT: V 210 GLU cc_start: 0.8970 (mp0) cc_final: 0.8629 (pm20) REVERT: V 218 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9185 (p) REVERT: V 321 GLU cc_start: 0.9516 (mp0) cc_final: 0.9175 (mm-30) REVERT: V 345 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8879 (mp) outliers start: 34 outliers final: 18 residues processed: 144 average time/residue: 0.4334 time to fit residues: 70.7140 Evaluate side-chains 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 218 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 166 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 153 optimal weight: 0.0570 chunk 136 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.083786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053116 restraints weight = 52702.118| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.92 r_work: 0.2834 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15603 Z= 0.136 Angle : 0.657 12.097 21407 Z= 0.329 Chirality : 0.042 0.308 2400 Planarity : 0.004 0.048 2515 Dihedral : 18.209 80.951 2575 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.83 % Rotamer: Outliers : 2.36 % Allowed : 28.65 % Favored : 68.99 % 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: 1.08 (0.22), residues: 1705 helix: 1.59 (0.17), residues: 1030 sheet: -0.82 (0.45), residues: 140 loop : -0.48 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 215 TYR 0.030 0.001 TYR R 109 PHE 0.016 0.001 PHE T 168 TRP 0.034 0.001 TRP R 267 HIS 0.005 0.001 HIS R 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (15603) covalent geometry : angle 0.65695 / 0.33 (21407) hydrogen bonds : bond 0.03769 / 2.53 ( 833) hydrogen bonds : angle 3.92431 / 2.79 ( 2259) *********************** 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 147 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8604 (mp0) REVERT: R 52 PHE cc_start: 0.8524 (m-10) cc_final: 0.8252 (m-10) REVERT: R 105 ASN cc_start: 0.9233 (t0) cc_final: 0.8900 (t0) REVERT: R 192 LEU cc_start: 0.9127 (tp) cc_final: 0.8908 (tp) REVERT: R 248 LEU cc_start: 0.9819 (mt) cc_final: 0.9530 (pp) REVERT: S 71 GLU cc_start: 0.9566 (tt0) cc_final: 0.9251 (tm-30) REVERT: S 103 TYR cc_start: 0.9150 (p90) cc_final: 0.8729 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9337 (t0) cc_final: 0.8901 (t0) REVERT: S 137 ASN cc_start: 0.8867 (p0) cc_final: 0.8586 (p0) REVERT: S 138 PHE cc_start: 0.9301 (m-80) cc_final: 0.8930 (m-80) REVERT: S 144 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8736 (mp0) REVERT: S 146 LYS cc_start: 0.9150 (pttp) cc_final: 0.8678 (pptt) REVERT: S 337 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8621 (tm-30) REVERT: T 164 HIS cc_start: 0.9461 (t-170) cc_final: 0.8887 (t-90) REVERT: T 210 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8991 (mp0) REVERT: T 321 GLU cc_start: 0.9526 (OUTLIER) cc_final: 0.9081 (mt-10) REVERT: U 19 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9160 (mpp80) REVERT: U 103 TYR cc_start: 0.8740 (p90) cc_final: 0.8471 (p90) REVERT: U 252 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9175 (tt0) REVERT: U 321 GLU cc_start: 0.9563 (tp30) cc_final: 0.9264 (mt-10) REVERT: V 128 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: V 158 ASN cc_start: 0.9693 (m-40) cc_final: 0.9437 (m110) REVERT: V 210 GLU cc_start: 0.9048 (mp0) cc_final: 0.8726 (pm20) REVERT: V 218 SER cc_start: 0.9412 (OUTLIER) cc_final: 0.9205 (p) REVERT: V 321 GLU cc_start: 0.9520 (mp0) cc_final: 0.9184 (mm-30) REVERT: V 345 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8883 (mp) outliers start: 35 outliers final: 21 residues processed: 139 average time/residue: 0.4124 time to fit residues: 64.8431 Evaluate side-chains 139 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 218 SER Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 146 optimal weight: 0.0270 chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 47 optimal weight: 0.0050 overall best weight: 0.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.084308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053682 restraints weight = 52860.446| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.94 r_work: 0.2847 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15603 Z= 0.123 Angle : 0.665 16.355 21407 Z= 0.329 Chirality : 0.042 0.288 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.178 80.973 2575 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.05 % Favored : 96.60 % Rotamer: Outliers : 2.03 % Allowed : 28.72 % Favored : 69.26 % 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: 1.08 (0.22), residues: 1705 helix: 1.61 (0.17), residues: 1020 sheet: -0.89 (0.45), residues: 140 loop : -0.48 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 215 TYR 0.027 0.001 TYR R 109 PHE 0.030 0.001 PHE U 126 TRP 0.036 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15603) covalent geometry : angle 0.66480 / 0.33 (21407) hydrogen bonds : bond 0.03712 / 2.47 ( 833) hydrogen bonds : angle 3.88539 / 2.77 ( 2259) ********************** 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 147 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: R 105 ASN cc_start: 0.9224 (t0) cc_final: 0.8888 (t0) REVERT: R 192 LEU cc_start: 0.9132 (tp) cc_final: 0.8913 (tp) REVERT: R 248 LEU cc_start: 0.9803 (mt) cc_final: 0.9533 (pp) REVERT: S 71 GLU cc_start: 0.9557 (tt0) cc_final: 0.9243 (tm-30) REVERT: S 103 TYR cc_start: 0.9141 (p90) cc_final: 0.8709 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9325 (t0) cc_final: 0.8899 (t0) REVERT: S 137 ASN cc_start: 0.8853 (p0) cc_final: 0.8581 (p0) REVERT: S 138 PHE cc_start: 0.9315 (m-80) cc_final: 0.8945 (m-80) REVERT: S 144 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: S 146 LYS cc_start: 0.9162 (pttp) cc_final: 0.8699 (pptt) REVERT: S 186 GLN cc_start: 0.8462 (mp10) cc_final: 0.8242 (pm20) REVERT: S 337 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8614 (tm-30) REVERT: T 25 ASN cc_start: 0.9488 (p0) cc_final: 0.9255 (p0) REVERT: T 164 HIS cc_start: 0.9446 (t-170) cc_final: 0.8874 (t-90) REVERT: T 210 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8965 (mp0) REVERT: T 321 GLU cc_start: 0.9524 (OUTLIER) cc_final: 0.9072 (mt-10) REVERT: U 19 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.9164 (mpp80) REVERT: U 41 MET cc_start: 0.9407 (tpp) cc_final: 0.9181 (mmm) REVERT: U 103 TYR cc_start: 0.8659 (p90) cc_final: 0.8357 (p90) REVERT: U 108 GLU cc_start: 0.9380 (tp30) cc_final: 0.8916 (tp30) REVERT: U 158 ASN cc_start: 0.9701 (m110) cc_final: 0.9265 (m110) REVERT: U 252 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9178 (tt0) REVERT: U 321 GLU cc_start: 0.9557 (tp30) cc_final: 0.9270 (mt-10) REVERT: V 128 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: V 158 ASN cc_start: 0.9696 (m-40) cc_final: 0.9434 (m110) REVERT: V 210 GLU cc_start: 0.9083 (mp0) cc_final: 0.8793 (pm20) REVERT: V 318 MET cc_start: 0.9412 (mmm) cc_final: 0.8941 (mmt) REVERT: V 321 GLU cc_start: 0.9519 (mp0) cc_final: 0.9192 (mm-30) REVERT: V 345 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8887 (mp) outliers start: 30 outliers final: 18 residues processed: 138 average time/residue: 0.5056 time to fit residues: 78.3942 Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 142 ASN ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.083806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053167 restraints weight = 52661.030| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.94 r_work: 0.2819 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15603 Z= 0.145 Angle : 0.673 12.384 21407 Z= 0.338 Chirality : 0.042 0.274 2400 Planarity : 0.004 0.050 2515 Dihedral : 18.162 80.941 2575 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.93 % Favored : 96.66 % Rotamer: Outliers : 2.23 % Allowed : 28.99 % Favored : 68.78 % 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: 1.11 (0.22), residues: 1705 helix: 1.65 (0.17), residues: 1020 sheet: -0.88 (0.45), residues: 140 loop : -0.49 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 131 TYR 0.031 0.001 TYR R 109 PHE 0.024 0.001 PHE U 138 TRP 0.034 0.001 TRP R 267 HIS 0.004 0.001 HIS V 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15603) covalent geometry : angle 0.67289 / 0.34 (21407) hydrogen bonds : bond 0.03770 / 2.51 ( 833) hydrogen bonds : angle 3.88110 / 2.76 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4922.55 seconds wall clock time: 84 minutes 34.57 seconds (5074.57 seconds total)