Starting phenix.real_space_refine on Fri Jul 3 17:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcw_28997/07_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_28997/07_2026/8fcw_28997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcw_28997/07_2026/8fcw_28997.map" } 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-dev-6108/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: 2.75, per 1000 atoms: 0.18 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: 0.91 Conformation dependent library (CDL) restraints added in 435.6 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: 1.43 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: 2.15 Time building geometry restraints manager: 1.23 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: 1.010 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- 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= 0.661 Angle : 0.901 10.196 21407 Z= 0.560 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 0.90082 / 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 : 0.595 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: 0.4820 time to fit residues: 147.8427 Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 5.9990 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 ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064685 restraints weight = 50388.627| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.87 r_work: 0.2898 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15603 Z= 0.164 Angle : 0.699 10.251 21407 Z= 0.359 Chirality : 0.044 0.204 2400 Planarity : 0.005 0.056 2515 Dihedral : 18.769 76.852 2585 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 26.96 % 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: 0.08 (0.21), residues: 1705 helix: 0.83 (0.16), residues: 1080 sheet: -0.62 (0.46), residues: 140 loop : -1.37 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 102 TYR 0.022 0.002 TYR U 103 PHE 0.027 0.002 PHE T 138 TRP 0.018 0.001 TRP R 267 HIS 0.008 0.001 HIS S 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (15603) covalent geometry : angle 0.69946 / 0.36 (21407) hydrogen bonds : bond 0.05208 / 3.52 ( 833) hydrogen bonds : angle 4.53256 / 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 190 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 PHE cc_start: 0.8493 (m-80) cc_final: 0.8174 (m-10) REVERT: R 105 ASN cc_start: 0.9126 (t0) cc_final: 0.8900 (t0) REVERT: R 192 LEU cc_start: 0.9016 (tp) cc_final: 0.8731 (tp) REVERT: R 248 LEU cc_start: 0.9797 (mt) cc_final: 0.9505 (pp) REVERT: R 277 CYS cc_start: 0.7422 (m) cc_final: 0.7207 (m) REVERT: R 318 MET cc_start: 0.8505 (mmt) cc_final: 0.7793 (mmt) REVERT: R 321 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (pp20) REVERT: S 71 GLU cc_start: 0.9561 (tt0) cc_final: 0.9246 (tm-30) REVERT: S 103 TYR cc_start: 0.9084 (p90) cc_final: 0.8764 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9341 (t0) cc_final: 0.8985 (t0) REVERT: S 137 ASN cc_start: 0.8798 (p0) cc_final: 0.8570 (p0) REVERT: S 138 PHE cc_start: 0.9205 (m-80) cc_final: 0.8853 (m-80) REVERT: S 146 LYS cc_start: 0.8493 (pttp) cc_final: 0.8159 (pptt) REVERT: S 186 GLN cc_start: 0.8470 (mp10) cc_final: 0.8166 (mp10) REVERT: S 234 CYS cc_start: 0.9382 (m) cc_final: 0.9165 (m) REVERT: S 318 MET cc_start: 0.9388 (mtm) cc_final: 0.9080 (mtp) REVERT: T 105 ASN cc_start: 0.9211 (t0) cc_final: 0.8991 (p0) REVERT: T 108 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9178 (mm-30) REVERT: T 146 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9178 (mtmm) REVERT: T 164 HIS cc_start: 0.9362 (t-170) cc_final: 0.8879 (t-90) REVERT: T 210 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: T 333 GLU cc_start: 0.8591 (pp20) cc_final: 0.8389 (tm-30) REVERT: U 41 MET cc_start: 0.9414 (tpp) cc_final: 0.9185 (mmm) REVERT: U 108 GLU cc_start: 0.9403 (tp30) cc_final: 0.9051 (tp30) REVERT: U 197 ASN cc_start: 0.9405 (m-40) cc_final: 0.9014 (m-40) REVERT: U 206 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8383 (mm) REVERT: U 321 GLU cc_start: 0.9553 (tp30) cc_final: 0.9199 (mt-10) REVERT: V 41 MET cc_start: 0.9410 (mmm) cc_final: 0.9178 (mmm) REVERT: V 51 SER cc_start: 0.9168 (m) cc_final: 0.8959 (p) REVERT: V 121 LEU cc_start: 0.9266 (tt) cc_final: 0.9027 (tm) REVERT: V 158 ASN cc_start: 0.9676 (m-40) cc_final: 0.9429 (m110) REVERT: V 206 LEU cc_start: 0.9349 (mt) cc_final: 0.9124 (mp) REVERT: V 321 GLU cc_start: 0.9405 (mp0) cc_final: 0.9174 (mm-30) outliers start: 44 outliers final: 14 residues processed: 185 average time/residue: 0.4369 time to fit residues: 91.1249 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 U residue 283 ASP 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: 1.9990 chunk 121 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.3799 r_free = 0.3799 target = 0.086359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055528 restraints weight = 53146.170| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.00 r_work: 0.2897 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15603 Z= 0.136 Angle : 0.641 11.572 21407 Z= 0.328 Chirality : 0.041 0.191 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.649 77.092 2581 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.93 % Favored : 96.72 % Rotamer: Outliers : 3.45 % Allowed : 25.27 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.21), residues: 1705 helix: 1.08 (0.16), residues: 1055 sheet: -0.60 (0.45), residues: 140 loop : -1.24 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 102 TYR 0.019 0.001 TYR S 128 PHE 0.023 0.001 PHE U 126 TRP 0.020 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15603) covalent geometry : angle 0.64077 / 0.33 (21407) hydrogen bonds : bond 0.04434 / 2.99 ( 833) hydrogen bonds : angle 4.24813 / 3.00 ( 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 193 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8674 (mp0) REVERT: R 52 PHE cc_start: 0.8612 (m-80) cc_final: 0.8361 (m-10) REVERT: R 105 ASN cc_start: 0.9141 (t0) cc_final: 0.8835 (t0) REVERT: R 157 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: R 192 LEU cc_start: 0.9070 (tp) cc_final: 0.8855 (tp) REVERT: R 248 LEU cc_start: 0.9806 (mt) cc_final: 0.9522 (pp) REVERT: R 318 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: R 321 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: S 103 TYR cc_start: 0.9085 (p90) cc_final: 0.8791 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9301 (t0) cc_final: 0.8802 (t0) REVERT: S 137 ASN cc_start: 0.8897 (p0) cc_final: 0.8643 (p0) REVERT: S 138 PHE cc_start: 0.9218 (m-80) cc_final: 0.8852 (m-80) REVERT: S 146 LYS cc_start: 0.8620 (pttp) cc_final: 0.8238 (pptt) REVERT: S 234 CYS cc_start: 0.9401 (m) cc_final: 0.9189 (m) REVERT: S 318 MET cc_start: 0.9399 (mtm) cc_final: 0.9078 (mtp) REVERT: S 324 GLU cc_start: 0.9151 (pp20) cc_final: 0.8926 (pp20) REVERT: S 337 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8582 (tm-30) REVERT: S 338 ASN cc_start: 0.9384 (t0) cc_final: 0.9036 (m110) REVERT: T 103 TYR cc_start: 0.8581 (p90) cc_final: 0.8109 (p90) REVERT: T 108 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9224 (mm-30) REVERT: T 164 HIS cc_start: 0.9422 (t-170) cc_final: 0.8949 (t-90) REVERT: T 210 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: T 321 GLU cc_start: 0.9524 (mt-10) cc_final: 0.9291 (mp0) REVERT: U 19 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8774 (mtp85) REVERT: U 108 GLU cc_start: 0.9403 (tp30) cc_final: 0.9020 (tp30) REVERT: U 252 GLN cc_start: 0.9542 (OUTLIER) cc_final: 0.9331 (tt0) REVERT: U 321 GLU cc_start: 0.9542 (tp30) cc_final: 0.9239 (mt-10) REVERT: V 121 LEU cc_start: 0.9271 (tt) cc_final: 0.9024 (tm) REVERT: V 158 ASN cc_start: 0.9682 (m-40) cc_final: 0.9444 (m110) REVERT: V 263 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9131 (mp) REVERT: V 321 GLU cc_start: 0.9456 (mp0) cc_final: 0.9161 (mm-30) REVERT: V 345 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8682 (mp) outliers start: 51 outliers final: 20 residues processed: 184 average time/residue: 0.4158 time to fit residues: 86.4083 Evaluate side-chains 151 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU 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 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 126 PHE Chi-restraints excluded: chain U residue 252 GLN 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 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 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: 7.9990 chunk 158 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 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 = 0.3780 r_free = 0.3780 target = 0.085329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054498 restraints weight = 53279.468| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.96 r_work: 0.2865 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15603 Z= 0.149 Angle : 0.638 12.775 21407 Z= 0.324 Chirality : 0.042 0.190 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.513 80.629 2580 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.87 % Favored : 96.77 % Rotamer: Outliers : 3.45 % Allowed : 25.07 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1705 helix: 1.17 (0.17), residues: 1060 sheet: -0.56 (0.45), residues: 140 loop : -1.01 (0.29), 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 0.019 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 0.00325 / 0.15 (15603) covalent geometry : angle 0.63817 / 0.32 (21407) hydrogen bonds : bond 0.04153 / 2.79 ( 833) hydrogen bonds : angle 4.09559 / 2.90 ( 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 174 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8643 (mp0) REVERT: R 52 PHE cc_start: 0.8555 (m-80) cc_final: 0.8268 (m-10) REVERT: R 105 ASN cc_start: 0.9191 (t0) cc_final: 0.8854 (t0) REVERT: R 192 LEU cc_start: 0.9070 (tp) cc_final: 0.8823 (tp) REVERT: R 197 ASN cc_start: 0.8007 (t0) cc_final: 0.7762 (m-40) REVERT: R 248 LEU cc_start: 0.9815 (mt) cc_final: 0.9516 (pp) REVERT: R 293 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8828 (mp) REVERT: S 71 GLU cc_start: 0.9571 (tt0) cc_final: 0.9219 (tm-30) REVERT: S 103 TYR cc_start: 0.9110 (p90) cc_final: 0.8760 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9310 (t0) cc_final: 0.8803 (t0) REVERT: S 137 ASN cc_start: 0.8924 (p0) cc_final: 0.8664 (p0) REVERT: S 138 PHE cc_start: 0.9242 (m-80) cc_final: 0.8894 (m-80) REVERT: S 146 LYS cc_start: 0.8741 (pttp) cc_final: 0.8326 (pptt) REVERT: S 318 MET cc_start: 0.9370 (mtm) cc_final: 0.9077 (mtp) REVERT: S 337 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8622 (tm-30) REVERT: S 338 ASN cc_start: 0.9403 (t0) cc_final: 0.9056 (m110) REVERT: T 103 TYR cc_start: 0.8723 (p90) cc_final: 0.8173 (p90) REVERT: T 164 HIS cc_start: 0.9418 (t-170) cc_final: 0.8890 (t-90) REVERT: T 210 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: T 293 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9188 (mm) REVERT: T 321 GLU cc_start: 0.9521 (mt-10) cc_final: 0.8976 (tt0) REVERT: U 19 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8773 (mtp85) REVERT: U 41 MET cc_start: 0.9334 (mmm) cc_final: 0.9110 (mmm) REVERT: U 108 GLU cc_start: 0.9426 (tp30) cc_final: 0.9032 (tp30) REVERT: U 252 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.9337 (tt0) REVERT: U 321 GLU cc_start: 0.9547 (tp30) cc_final: 0.9215 (mt-10) REVERT: V 121 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8979 (tm) REVERT: V 158 ASN cc_start: 0.9684 (m-40) cc_final: 0.9430 (m110) REVERT: V 321 GLU cc_start: 0.9491 (mp0) cc_final: 0.9168 (mm-30) REVERT: V 345 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8771 (mp) outliers start: 51 outliers final: 24 residues processed: 162 average time/residue: 0.4371 time to fit residues: 79.7103 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 102 ARG Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 189 LEU 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 252 GLN Chi-restraints excluded: chain U residue 283 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 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 308 ARG 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: 0.7980 chunk 101 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.085514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054686 restraints weight = 52829.404| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.98 r_work: 0.2862 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15603 Z= 0.126 Angle : 0.610 12.369 21407 Z= 0.309 Chirality : 0.041 0.190 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.425 81.614 2577 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.87 % Favored : 96.77 % Rotamer: Outliers : 3.45 % Allowed : 25.61 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1705 helix: 1.18 (0.16), residues: 1070 sheet: -0.60 (0.46), residues: 140 loop : -0.83 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 102 TYR 0.022 0.001 TYR S 183 PHE 0.010 0.001 PHE S 319 TRP 0.021 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 0.60968 / 0.31 (21407) hydrogen bonds : bond 0.03886 / 2.60 ( 833) hydrogen bonds : angle 3.99288 / 2.84 ( 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 174 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: R 52 PHE cc_start: 0.8459 (m-80) cc_final: 0.8183 (m-10) REVERT: R 105 ASN cc_start: 0.9217 (t0) cc_final: 0.8901 (t0) REVERT: R 192 LEU cc_start: 0.9005 (tp) cc_final: 0.8766 (tp) REVERT: R 248 LEU cc_start: 0.9811 (mt) cc_final: 0.9524 (pp) REVERT: S 71 GLU cc_start: 0.9575 (tt0) cc_final: 0.9227 (tm-30) REVERT: S 103 TYR cc_start: 0.9105 (p90) cc_final: 0.8712 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9305 (t0) cc_final: 0.8816 (t0) REVERT: S 137 ASN cc_start: 0.8912 (p0) cc_final: 0.8636 (p0) REVERT: S 138 PHE cc_start: 0.9243 (m-80) cc_final: 0.8890 (m-80) REVERT: S 144 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8777 (mp0) REVERT: S 146 LYS cc_start: 0.8817 (pttp) cc_final: 0.8357 (pptt) REVERT: S 190 ASP cc_start: 0.9355 (m-30) cc_final: 0.8576 (p0) REVERT: S 318 MET cc_start: 0.9340 (mtm) cc_final: 0.9117 (mtp) REVERT: S 337 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8574 (tm-30) REVERT: T 103 TYR cc_start: 0.8790 (p90) cc_final: 0.8151 (p90) REVERT: T 164 HIS cc_start: 0.9425 (t-170) cc_final: 0.8867 (t-90) REVERT: T 210 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: T 321 GLU cc_start: 0.9531 (OUTLIER) cc_final: 0.8994 (tt0) REVERT: U 19 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.9112 (mpp80) REVERT: U 41 MET cc_start: 0.9331 (mmm) cc_final: 0.9102 (mmm) REVERT: U 108 GLU cc_start: 0.9458 (tp30) cc_final: 0.9008 (tp30) REVERT: U 210 GLU cc_start: 0.8921 (mp0) cc_final: 0.8718 (pm20) REVERT: U 252 GLN cc_start: 0.9561 (OUTLIER) cc_final: 0.9359 (tt0) REVERT: U 321 GLU cc_start: 0.9536 (tp30) cc_final: 0.9210 (mt-10) REVERT: V 121 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9018 (tm) REVERT: V 128 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: V 158 ASN cc_start: 0.9692 (m-40) cc_final: 0.9438 (m110) REVERT: V 308 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8854 (ttp-170) REVERT: V 321 GLU cc_start: 0.9508 (mp0) cc_final: 0.9136 (mm-30) REVERT: V 345 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8738 (mp) outliers start: 51 outliers final: 18 residues processed: 165 average time/residue: 0.4042 time to fit residues: 75.7337 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 T residue 91 VAL Chi-restraints excluded: chain T residue 123 ASP 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 U residue 283 ASP Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR 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 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: 5.9990 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 GLN ** 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** V 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053056 restraints weight = 53115.373| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.89 r_work: 0.2819 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15603 Z= 0.186 Angle : 0.642 12.048 21407 Z= 0.324 Chirality : 0.042 0.194 2400 Planarity : 0.004 0.042 2515 Dihedral : 18.383 82.526 2575 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.17 % Favored : 96.42 % Rotamer: Outliers : 3.31 % Allowed : 26.35 % Favored : 70.34 % 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: 0.83 (0.21), residues: 1705 helix: 1.37 (0.17), residues: 1055 sheet: -0.63 (0.46), residues: 140 loop : -0.72 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 42 TYR 0.025 0.001 TYR R 109 PHE 0.021 0.001 PHE U 138 TRP 0.028 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (15603) covalent geometry : angle 0.64158 / 0.32 (21407) hydrogen bonds : bond 0.04050 / 2.71 ( 833) hydrogen bonds : angle 3.96747 / 2.82 ( 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 168 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8627 (mp0) REVERT: R 41 MET cc_start: 0.8573 (mmm) cc_final: 0.8324 (tpt) REVERT: R 52 PHE cc_start: 0.8481 (m-80) cc_final: 0.8224 (m-10) REVERT: R 105 ASN cc_start: 0.9254 (t0) cc_final: 0.8928 (t0) REVERT: R 192 LEU cc_start: 0.9060 (tp) cc_final: 0.8814 (tp) REVERT: R 248 LEU cc_start: 0.9816 (mt) cc_final: 0.9523 (pp) REVERT: S 71 GLU cc_start: 0.9577 (tt0) cc_final: 0.9263 (tm-30) REVERT: S 103 TYR cc_start: 0.9101 (p90) cc_final: 0.8707 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9337 (t0) cc_final: 0.8859 (t0) REVERT: S 137 ASN cc_start: 0.8858 (p0) cc_final: 0.8573 (p0) REVERT: S 138 PHE cc_start: 0.9266 (m-80) cc_final: 0.8912 (m-80) REVERT: S 144 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8658 (mp0) REVERT: S 146 LYS cc_start: 0.8959 (pttp) cc_final: 0.8539 (pptt) REVERT: S 318 MET cc_start: 0.9300 (mtm) cc_final: 0.9069 (mtp) REVERT: S 337 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8607 (tm-30) REVERT: T 103 TYR cc_start: 0.8892 (p90) cc_final: 0.8208 (p90) REVERT: T 128 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: T 164 HIS cc_start: 0.9455 (t-170) cc_final: 0.8850 (t-90) REVERT: T 210 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8875 (mp0) REVERT: T 321 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9248 (mt-10) REVERT: U 19 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.9155 (mpp80) REVERT: U 108 GLU cc_start: 0.9439 (tp30) cc_final: 0.9005 (tp30) REVERT: U 128 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: U 321 GLU cc_start: 0.9542 (tp30) cc_final: 0.9229 (mt-10) REVERT: V 128 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: V 158 ASN cc_start: 0.9688 (m-40) cc_final: 0.9438 (m110) REVERT: V 321 GLU cc_start: 0.9521 (mp0) cc_final: 0.9184 (mm-30) REVERT: V 345 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8826 (mp) outliers start: 49 outliers final: 22 residues processed: 158 average time/residue: 0.4231 time to fit residues: 75.4854 Evaluate side-chains 140 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 167 VAL 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 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 128 TYR Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 128 TYR 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 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 101 optimal weight: 1.9990 chunk 175 optimal weight: 50.0000 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** V 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.083526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052888 restraints weight = 52665.020| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.87 r_work: 0.2813 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15603 Z= 0.170 Angle : 0.645 11.989 21407 Z= 0.324 Chirality : 0.043 0.268 2400 Planarity : 0.004 0.048 2515 Dihedral : 18.350 84.215 2575 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.87 % Favored : 96.77 % Rotamer: Outliers : 2.84 % Allowed : 27.97 % Favored : 69.19 % 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: 0.88 (0.22), residues: 1705 helix: 1.39 (0.17), residues: 1055 sheet: -0.67 (0.46), residues: 140 loop : -0.66 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 102 TYR 0.028 0.001 TYR S 183 PHE 0.012 0.001 PHE V 251 TRP 0.029 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15603) covalent geometry : angle 0.64522 / 0.32 (21407) hydrogen bonds : bond 0.03948 / 2.65 ( 833) hydrogen bonds : angle 3.96420 / 2.82 ( 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 159 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: R 52 PHE cc_start: 0.8482 (m-80) cc_final: 0.8232 (m-10) REVERT: R 105 ASN cc_start: 0.9247 (t0) cc_final: 0.8921 (t0) REVERT: R 192 LEU cc_start: 0.9075 (tp) cc_final: 0.8831 (tp) REVERT: R 248 LEU cc_start: 0.9815 (mt) cc_final: 0.9529 (pp) REVERT: S 71 GLU cc_start: 0.9571 (tt0) cc_final: 0.9254 (tm-30) REVERT: S 103 TYR cc_start: 0.9095 (p90) cc_final: 0.8690 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9350 (t0) cc_final: 0.8889 (t0) REVERT: S 137 ASN cc_start: 0.8834 (p0) cc_final: 0.8547 (p0) REVERT: S 138 PHE cc_start: 0.9271 (m-80) cc_final: 0.8912 (m-80) REVERT: S 144 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: S 146 LYS cc_start: 0.9054 (pttp) cc_final: 0.8613 (pptt) REVERT: S 337 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8618 (tm-30) REVERT: T 103 TYR cc_start: 0.8936 (p90) cc_final: 0.8240 (p90) REVERT: T 118 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8149 (tm-30) REVERT: T 164 HIS cc_start: 0.9460 (t-170) cc_final: 0.8864 (t-90) REVERT: T 210 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8934 (mp0) REVERT: T 321 GLU cc_start: 0.9527 (OUTLIER) cc_final: 0.9260 (mt-10) REVERT: T 333 GLU cc_start: 0.8818 (pp20) cc_final: 0.8597 (tm-30) REVERT: U 19 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.9151 (mpp80) REVERT: U 41 MET cc_start: 0.9262 (mmm) cc_final: 0.9052 (mmm) REVERT: U 103 TYR cc_start: 0.8572 (p90) cc_final: 0.8339 (p90) REVERT: U 108 GLU cc_start: 0.9448 (tp30) cc_final: 0.8976 (tp30) REVERT: U 128 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: U 252 GLN cc_start: 0.9571 (OUTLIER) cc_final: 0.9297 (tt0) REVERT: U 321 GLU cc_start: 0.9539 (tp30) cc_final: 0.9226 (mt-10) REVERT: V 128 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.8036 (m-10) REVERT: V 138 PHE cc_start: 0.9026 (m-10) cc_final: 0.8794 (m-80) REVERT: V 158 ASN cc_start: 0.9693 (m-40) cc_final: 0.9443 (m110) REVERT: V 321 GLU cc_start: 0.9533 (mp0) cc_final: 0.9192 (mm-30) REVERT: V 345 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8873 (mp) outliers start: 42 outliers final: 21 residues processed: 151 average time/residue: 0.4163 time to fit residues: 71.1761 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 114 LEU 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 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 128 TYR 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 275 LEU 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: 5.9990 chunk 127 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 131 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 145 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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** ** 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 = 0.3764 r_free = 0.3764 target = 0.084302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053726 restraints weight = 52629.527| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.89 r_work: 0.2839 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3368 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= 0.126 Angle : 0.650 12.250 21407 Z= 0.323 Chirality : 0.042 0.319 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.292 85.136 2575 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 28.38 % 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: 1.15 (0.22), residues: 1705 helix: 1.64 (0.17), residues: 1020 sheet: -0.78 (0.46), residues: 140 loop : -0.41 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 215 TYR 0.028 0.001 TYR U 103 PHE 0.026 0.001 PHE U 138 TRP 0.031 0.001 TRP R 267 HIS 0.006 0.001 HIS R 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15603) covalent geometry : angle 0.65026 / 0.32 (21407) hydrogen bonds : bond 0.03775 / 2.53 ( 833) hydrogen bonds : angle 3.91960 / 2.79 ( 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: 35 poor density : 118 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: R 52 PHE cc_start: 0.8449 (m-80) cc_final: 0.8195 (m-10) REVERT: R 105 ASN cc_start: 0.9227 (t0) cc_final: 0.8894 (t0) REVERT: R 192 LEU cc_start: 0.9066 (tp) cc_final: 0.8828 (tp) REVERT: R 248 LEU cc_start: 0.9820 (mt) cc_final: 0.9539 (pp) REVERT: S 71 GLU cc_start: 0.9574 (tt0) cc_final: 0.9239 (tm-30) REVERT: S 103 TYR cc_start: 0.9079 (p90) cc_final: 0.8659 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9343 (t0) cc_final: 0.8895 (t0) REVERT: S 137 ASN cc_start: 0.8821 (p0) cc_final: 0.8529 (p0) REVERT: S 138 PHE cc_start: 0.9277 (m-80) cc_final: 0.8908 (m-80) REVERT: S 144 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: S 146 LYS cc_start: 0.9081 (pttp) cc_final: 0.8637 (pptt) REVERT: S 337 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8616 (tm-30) REVERT: T 103 TYR cc_start: 0.8946 (p90) cc_final: 0.8206 (p90) REVERT: T 164 HIS cc_start: 0.9462 (t-170) cc_final: 0.8884 (t-90) REVERT: T 210 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8928 (mp0) REVERT: T 321 GLU cc_start: 0.9532 (OUTLIER) cc_final: 0.9242 (mt-10) REVERT: U 19 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.9147 (mpp80) REVERT: U 41 MET cc_start: 0.9290 (mmm) cc_final: 0.9031 (mmm) REVERT: U 103 TYR cc_start: 0.8516 (p90) cc_final: 0.8262 (p90) REVERT: U 108 GLU cc_start: 0.9432 (tp30) cc_final: 0.8960 (tp30) REVERT: U 128 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: U 158 ASN cc_start: 0.9705 (m110) cc_final: 0.9278 (m110) REVERT: U 252 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.9224 (tt0) REVERT: U 321 GLU cc_start: 0.9523 (tp30) cc_final: 0.9219 (mt-10) REVERT: V 138 PHE cc_start: 0.9039 (m-10) cc_final: 0.8821 (m-80) REVERT: V 158 ASN cc_start: 0.9695 (m-40) cc_final: 0.9441 (m110) REVERT: V 210 GLU cc_start: 0.9006 (mp0) cc_final: 0.8649 (pm20) REVERT: V 218 SER cc_start: 0.9398 (OUTLIER) cc_final: 0.9187 (p) REVERT: V 321 GLU cc_start: 0.9523 (mp0) cc_final: 0.9189 (mm-30) REVERT: V 345 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8852 (mp) outliers start: 35 outliers final: 17 residues processed: 146 average time/residue: 0.4124 time to fit residues: 68.6125 Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 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 167 VAL Chi-restraints excluded: chain T residue 91 VAL 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 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 218 SER Chi-restraints excluded: chain V residue 226 VAL 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: 2.9990 chunk 147 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 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** V 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.083691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053159 restraints weight = 52577.839| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.89 r_work: 0.2822 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3483 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= 0.146 Angle : 0.649 12.350 21407 Z= 0.326 Chirality : 0.042 0.245 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.258 85.781 2575 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.23 % Favored : 96.42 % Rotamer: Outliers : 2.30 % Allowed : 28.51 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1705 helix: 1.69 (0.17), residues: 1020 sheet: -0.85 (0.45), residues: 140 loop : -0.35 (0.30), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 215 TYR 0.030 0.001 TYR R 109 PHE 0.014 0.001 PHE R 214 TRP 0.034 0.001 TRP R 267 HIS 0.005 0.001 HIS V 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15603) covalent geometry : angle 0.64889 / 0.33 (21407) hydrogen bonds : bond 0.03825 / 2.57 ( 833) hydrogen bonds : angle 3.91226 / 2.78 ( 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 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: R 52 PHE cc_start: 0.8462 (m-80) cc_final: 0.8241 (m-10) REVERT: R 105 ASN cc_start: 0.9246 (t0) cc_final: 0.8907 (t0) REVERT: R 192 LEU cc_start: 0.9106 (tp) cc_final: 0.8887 (tp) REVERT: R 248 LEU cc_start: 0.9809 (mt) cc_final: 0.9527 (pp) REVERT: S 71 GLU cc_start: 0.9565 (tt0) cc_final: 0.9251 (tm-30) REVERT: S 103 TYR cc_start: 0.9088 (p90) cc_final: 0.8667 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9352 (t0) cc_final: 0.8907 (t0) REVERT: S 137 ASN cc_start: 0.8828 (p0) cc_final: 0.8536 (p0) REVERT: S 138 PHE cc_start: 0.9292 (m-80) cc_final: 0.8927 (m-80) REVERT: S 144 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: S 146 LYS cc_start: 0.9152 (pttp) cc_final: 0.8693 (pptt) REVERT: S 337 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8609 (tm-30) REVERT: T 164 HIS cc_start: 0.9468 (t-170) cc_final: 0.8847 (t-90) REVERT: T 210 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: T 321 GLU cc_start: 0.9545 (OUTLIER) cc_final: 0.9274 (mt-10) REVERT: U 19 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.9139 (mpp80) REVERT: U 108 GLU cc_start: 0.9411 (tp30) cc_final: 0.8937 (tp30) REVERT: U 128 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: U 252 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.9204 (tt0) REVERT: U 321 GLU cc_start: 0.9558 (tp30) cc_final: 0.9251 (mt-10) REVERT: V 128 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: V 138 PHE cc_start: 0.9089 (m-10) cc_final: 0.8857 (m-80) REVERT: V 158 ASN cc_start: 0.9694 (m-40) cc_final: 0.9440 (m110) REVERT: V 210 GLU cc_start: 0.9053 (mp0) cc_final: 0.8767 (pm20) REVERT: V 321 GLU cc_start: 0.9530 (mp0) cc_final: 0.9190 (mm-30) REVERT: V 345 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8866 (mp) outliers start: 34 outliers final: 19 residues processed: 138 average time/residue: 0.4055 time to fit residues: 63.9058 Evaluate side-chains 135 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 263 LEU 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 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 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 226 VAL 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: 0.0470 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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 158 ASN ** 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 = 0.3746 r_free = 0.3746 target = 0.083354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052768 restraints weight = 52825.473| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.90 r_work: 0.2812 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15603 Z= 0.161 Angle : 0.667 12.364 21407 Z= 0.336 Chirality : 0.042 0.230 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.246 86.560 2575 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.05 % Favored : 96.54 % Rotamer: Outliers : 2.09 % Allowed : 28.65 % 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: 1.23 (0.22), residues: 1705 helix: 1.73 (0.17), residues: 1020 sheet: -0.90 (0.45), residues: 140 loop : -0.36 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 42 TYR 0.028 0.001 TYR T 103 PHE 0.011 0.001 PHE T 168 TRP 0.037 0.001 TRP R 267 HIS 0.005 0.001 HIS V 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (15603) covalent geometry : angle 0.66695 / 0.34 (21407) hydrogen bonds : bond 0.03839 / 2.57 ( 833) hydrogen bonds : angle 3.91473 / 2.78 ( 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 139 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: R 52 PHE cc_start: 0.8467 (m-80) cc_final: 0.7787 (m-10) REVERT: R 105 ASN cc_start: 0.9238 (t0) cc_final: 0.8903 (t0) REVERT: R 192 LEU cc_start: 0.9129 (tp) cc_final: 0.8744 (pp) REVERT: R 248 LEU cc_start: 0.9810 (mt) cc_final: 0.9535 (pp) REVERT: S 71 GLU cc_start: 0.9567 (tt0) cc_final: 0.9253 (tm-30) REVERT: S 103 TYR cc_start: 0.9099 (p90) cc_final: 0.8676 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9366 (t0) cc_final: 0.8932 (t0) REVERT: S 137 ASN cc_start: 0.8837 (p0) cc_final: 0.8538 (p0) REVERT: S 138 PHE cc_start: 0.9297 (m-80) cc_final: 0.8933 (m-80) REVERT: S 144 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: S 146 LYS cc_start: 0.9226 (pttp) cc_final: 0.8758 (pptt) REVERT: S 337 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8612 (tm-30) REVERT: T 103 TYR cc_start: 0.8973 (p90) cc_final: 0.8305 (p90) REVERT: T 164 HIS cc_start: 0.9426 (t-170) cc_final: 0.8852 (t-90) REVERT: T 210 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8994 (mp0) REVERT: T 321 GLU cc_start: 0.9527 (OUTLIER) cc_final: 0.9101 (mt-10) REVERT: U 19 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.9156 (mpp80) REVERT: U 103 TYR cc_start: 0.8444 (p90) cc_final: 0.8215 (p90) REVERT: U 108 GLU cc_start: 0.9359 (tp30) cc_final: 0.8903 (tp30) REVERT: U 128 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: U 252 GLN cc_start: 0.9518 (OUTLIER) cc_final: 0.9188 (tt0) REVERT: U 273 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8807 (mmm-85) REVERT: V 103 TYR cc_start: 0.8609 (p90) cc_final: 0.8302 (p90) REVERT: V 128 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.8092 (m-10) REVERT: V 138 PHE cc_start: 0.9103 (m-10) cc_final: 0.8874 (m-80) REVERT: V 158 ASN cc_start: 0.9693 (m-40) cc_final: 0.9440 (m110) REVERT: V 210 GLU cc_start: 0.9072 (mp0) cc_final: 0.8837 (pm20) REVERT: V 318 MET cc_start: 0.9362 (mmm) cc_final: 0.8970 (mmt) REVERT: V 321 GLU cc_start: 0.9539 (mp0) cc_final: 0.9219 (mm-30) REVERT: V 345 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8915 (mp) outliers start: 31 outliers final: 17 residues processed: 135 average time/residue: 0.4424 time to fit residues: 67.0309 Evaluate side-chains 126 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 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 128 TYR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 273 ARG Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 275 LEU 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: 0.9990 chunk 136 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 157 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 142 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.084195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053508 restraints weight = 52159.707| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.91 r_work: 0.2831 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15603 Z= 0.125 Angle : 0.665 12.386 21407 Z= 0.332 Chirality : 0.042 0.212 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.215 87.017 2574 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.87 % Favored : 96.72 % Rotamer: Outliers : 1.96 % Allowed : 29.05 % 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: 1.20 (0.22), residues: 1705 helix: 1.69 (0.17), residues: 1020 sheet: -0.91 (0.45), residues: 140 loop : -0.37 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 131 TYR 0.028 0.001 TYR R 109 PHE 0.015 0.001 PHE T 168 TRP 0.033 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15603) covalent geometry : angle 0.66455 / 0.33 (21407) hydrogen bonds : bond 0.03727 / 2.48 ( 833) hydrogen bonds : angle 3.86708 / 2.75 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.83 seconds wall clock time: 84 minutes 46.88 seconds (5086.88 seconds total)