Starting phenix.real_space_refine on Wed Mar 4 17:54:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcw_28997/03_2026/8fcw_28997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcw_28997/03_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_28997/03_2026/8fcw_28997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcw_28997/03_2026/8fcw_28997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/03_2026/8fcw_28997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcw_28997/03_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-5986/lib/python3.9/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: 3.34, per 1000 atoms: 0.22 Number of scatterers: 15170 At special positions: 0 Unit cell: (112.778, 124.372, 153.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 75 15.00 Mg 5 11.99 O 2965 8.00 N 2665 7.00 C 9420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 448.5 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: 1.87 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: 2.56 Time building geometry restraints manager: 1.71 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: 20628 2.04 - 4.08: 681 4.08 - 6.12: 78 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: 7450 17.72 - 35.44: 1187 35.44 - 53.16: 551 53.16 - 70.88: 127 70.88 - 88.60: 14 Dihedral angle restraints: 9329 sinusoidal: 4314 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 9326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1773 0.063 - 0.125: 559 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: 1.050 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: 0.030 Set scattering table: 0.030 Process input model: 15.030 Find NCS groups from input model: 0.380 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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= 0.659 Angle : 0.903 10.196 21407 Z= 0.553 Chirality : 0.058 0.313 2400 Planarity : 0.005 0.048 2515 Dihedral : 20.726 88.596 6089 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 covalent geometry : bond 0.00994 (15603) covalent geometry : angle 0.90265 (21407) hydrogen bonds : bond 0.17998 ( 833) hydrogen bonds : angle 5.87032 ( 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 : 0.406 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: 0.5841 time to fit residues: 177.8066 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 : 0.445 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 252 GLN T 25 ASN T 142 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 V 142 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.086139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055530 restraints weight = 52207.482| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.96 r_work: 0.2895 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15603 Z= 0.142 Angle : 0.640 11.555 21407 Z= 0.329 Chirality : 0.041 0.146 2400 Planarity : 0.004 0.046 2515 Dihedral : 19.112 79.655 2740 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.76 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 26.35 % Favored : 70.54 % 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: 0.31 (0.21), residues: 1705 helix: 1.05 (0.16), residues: 1060 sheet: -0.52 (0.46), residues: 140 loop : -1.33 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 102 TYR 0.018 0.002 TYR U 103 PHE 0.022 0.001 PHE U 138 TRP 0.020 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00312 (15603) covalent geometry : angle 0.64040 (21407) hydrogen bonds : bond 0.04200 ( 833) hydrogen bonds : angle 4.19551 ( 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 192 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.353 Fit side-chains REVERT: R 18 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: R 186 GLN cc_start: 0.8841 (mp10) cc_final: 0.8631 (mp10) REVERT: R 192 LEU cc_start: 0.9047 (tp) cc_final: 0.8617 (pp) REVERT: R 248 LEU cc_start: 0.9814 (mt) cc_final: 0.9518 (pp) REVERT: R 318 MET cc_start: 0.8486 (mmt) cc_final: 0.7776 (mmt) REVERT: R 321 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8764 (pp20) REVERT: S 71 GLU cc_start: 0.9566 (tt0) cc_final: 0.9267 (tm-30) REVERT: S 103 TYR cc_start: 0.9098 (p90) cc_final: 0.8794 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9285 (t0) cc_final: 0.9007 (t0) REVERT: S 138 PHE cc_start: 0.9228 (m-80) cc_final: 0.8906 (m-80) REVERT: S 146 LYS cc_start: 0.8721 (pttp) cc_final: 0.8346 (pptt) REVERT: S 186 GLN cc_start: 0.8562 (mp10) cc_final: 0.8225 (mp10) REVERT: S 190 ASP cc_start: 0.9418 (m-30) cc_final: 0.9206 (m-30) REVERT: S 318 MET cc_start: 0.9392 (mtm) cc_final: 0.9086 (mtp) REVERT: S 328 GLN cc_start: 0.9359 (mt0) cc_final: 0.9146 (mt0) REVERT: S 337 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8620 (tm-30) REVERT: T 103 TYR cc_start: 0.8747 (p90) cc_final: 0.8123 (p90) REVERT: T 108 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9207 (mm-30) REVERT: T 164 HIS cc_start: 0.9398 (t-170) cc_final: 0.8909 (t-90) REVERT: T 210 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8961 (pm20) REVERT: U 19 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8763 (mtp85) REVERT: U 108 GLU cc_start: 0.9468 (tp30) cc_final: 0.9084 (tp30) REVERT: U 190 ASP cc_start: 0.9273 (m-30) cc_final: 0.9033 (m-30) REVERT: U 321 GLU cc_start: 0.9540 (tp30) cc_final: 0.9166 (mt-10) REVERT: V 121 LEU cc_start: 0.9272 (tt) cc_final: 0.9053 (tm) REVERT: V 158 ASN cc_start: 0.9676 (m-40) cc_final: 0.9424 (m110) REVERT: V 321 GLU cc_start: 0.9444 (mp0) cc_final: 0.9175 (mm-30) REVERT: V 339 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8819 (tp) outliers start: 46 outliers final: 13 residues processed: 185 average time/residue: 0.5214 time to fit residues: 107.3236 Evaluate side-chains 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU 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 128 TYR Chi-restraints excluded: chain T residue 145 SER 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 123 ASP Chi-restraints excluded: chain U residue 145 SER Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 339 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 110 optimal weight: 0.0270 chunk 161 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.084387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053748 restraints weight = 53353.818| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.00 r_work: 0.2840 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15603 Z= 0.150 Angle : 0.611 12.847 21407 Z= 0.314 Chirality : 0.041 0.166 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.680 80.554 2735 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.83 % Rotamer: Outliers : 3.72 % Allowed : 25.14 % Favored : 71.15 % 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: 0.67 (0.21), residues: 1705 helix: 1.34 (0.17), residues: 1060 sheet: -0.50 (0.45), residues: 140 loop : -1.14 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 153 TYR 0.012 0.001 TYR S 26 PHE 0.024 0.001 PHE V 126 TRP 0.021 0.001 TRP R 267 HIS 0.004 0.001 HIS R 30 Details of bonding type rmsd covalent geometry : bond 0.00335 (15603) covalent geometry : angle 0.61065 (21407) hydrogen bonds : bond 0.03809 ( 833) hydrogen bonds : angle 3.89839 ( 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 191 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.554 Fit side-chains REVERT: R 186 GLN cc_start: 0.8879 (mp10) cc_final: 0.8618 (mp10) REVERT: R 192 LEU cc_start: 0.9010 (tp) cc_final: 0.8729 (tp) REVERT: R 248 LEU cc_start: 0.9816 (mt) cc_final: 0.9525 (pp) REVERT: S 71 GLU cc_start: 0.9560 (tt0) cc_final: 0.9241 (tm-30) REVERT: S 103 TYR cc_start: 0.9106 (p90) cc_final: 0.8716 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9309 (t0) cc_final: 0.8972 (t0) REVERT: S 138 PHE cc_start: 0.9260 (m-80) cc_final: 0.8922 (m-80) REVERT: S 144 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: S 146 LYS cc_start: 0.9035 (pttp) cc_final: 0.8622 (pptt) REVERT: S 185 LEU cc_start: 0.9270 (tp) cc_final: 0.9060 (pt) REVERT: S 318 MET cc_start: 0.9364 (mtm) cc_final: 0.9119 (mtp) REVERT: S 337 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8621 (tm-30) REVERT: T 108 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9151 (mm-30) REVERT: T 164 HIS cc_start: 0.9455 (t-170) cc_final: 0.8901 (t-90) REVERT: T 210 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8950 (mp0) REVERT: T 293 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9217 (mm) REVERT: T 321 GLU cc_start: 0.9539 (mt-10) cc_final: 0.9269 (mt-10) REVERT: U 19 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.8768 (mtp85) REVERT: U 108 GLU cc_start: 0.9487 (tp30) cc_final: 0.9086 (tp30) REVERT: U 164 HIS cc_start: 0.8765 (t-90) cc_final: 0.8516 (t-90) REVERT: U 190 ASP cc_start: 0.9352 (m-30) cc_final: 0.9045 (m-30) REVERT: U 321 GLU cc_start: 0.9536 (tp30) cc_final: 0.9196 (mt-10) REVERT: V 121 LEU cc_start: 0.9270 (tt) cc_final: 0.9034 (tm) REVERT: V 158 ASN cc_start: 0.9676 (m-40) cc_final: 0.9427 (m110) REVERT: V 210 GLU cc_start: 0.9298 (mp0) cc_final: 0.9090 (mp0) REVERT: V 321 GLU cc_start: 0.9509 (mp0) cc_final: 0.9152 (mm-30) REVERT: V 345 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8779 (mp) outliers start: 55 outliers final: 20 residues processed: 184 average time/residue: 0.5009 time to fit residues: 103.1726 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 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 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 128 TYR Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS 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: 4.9990 chunk 11 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 197 ASN ** 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 ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.082538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052093 restraints weight = 53344.126| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.89 r_work: 0.2801 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15603 Z= 0.192 Angle : 0.616 12.215 21407 Z= 0.319 Chirality : 0.041 0.149 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.646 84.608 2730 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.92 % Allowed : 25.14 % 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: 0.80 (0.21), residues: 1705 helix: 1.44 (0.17), residues: 1055 sheet: -0.54 (0.45), residues: 140 loop : -1.00 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 102 TYR 0.024 0.001 TYR T 103 PHE 0.017 0.002 PHE V 138 TRP 0.023 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00427 (15603) covalent geometry : angle 0.61619 (21407) hydrogen bonds : bond 0.03951 ( 833) hydrogen bonds : angle 3.90761 ( 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 182 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: R 186 GLN cc_start: 0.8792 (mp10) cc_final: 0.8511 (mp10) REVERT: R 192 LEU cc_start: 0.9025 (tp) cc_final: 0.8693 (tp) REVERT: R 193 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8730 (tttt) REVERT: R 248 LEU cc_start: 0.9821 (mt) cc_final: 0.9527 (pp) REVERT: S 71 GLU cc_start: 0.9574 (tt0) cc_final: 0.9268 (tm-30) REVERT: S 103 TYR cc_start: 0.9109 (p90) cc_final: 0.8699 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9352 (t0) cc_final: 0.8986 (t0) REVERT: S 138 PHE cc_start: 0.9294 (m-80) cc_final: 0.9008 (m-80) REVERT: S 144 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: S 146 LYS cc_start: 0.9340 (pttp) cc_final: 0.8865 (pptt) REVERT: S 185 LEU cc_start: 0.9255 (tp) cc_final: 0.8985 (pt) REVERT: S 318 MET cc_start: 0.9367 (mtm) cc_final: 0.9125 (mtp) REVERT: S 324 GLU cc_start: 0.9186 (pp20) cc_final: 0.8898 (tm-30) REVERT: S 337 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8566 (tm-30) REVERT: T 103 TYR cc_start: 0.9036 (p90) cc_final: 0.8317 (p90) REVERT: T 108 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9145 (mm-30) REVERT: T 118 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8238 (tm-30) REVERT: T 164 HIS cc_start: 0.9492 (t-170) cc_final: 0.8876 (t-90) REVERT: T 210 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8968 (mp0) REVERT: T 321 GLU cc_start: 0.9547 (OUTLIER) cc_final: 0.9276 (mt-10) REVERT: U 19 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.8812 (mtp85) REVERT: U 128 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: U 164 HIS cc_start: 0.8913 (t-90) cc_final: 0.8521 (t-90) REVERT: U 190 ASP cc_start: 0.9397 (OUTLIER) cc_final: 0.9065 (m-30) REVERT: V 103 TYR cc_start: 0.8625 (p90) cc_final: 0.8341 (p90) REVERT: V 121 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9134 (tm) REVERT: V 158 ASN cc_start: 0.9671 (m-40) cc_final: 0.9421 (m110) REVERT: V 210 GLU cc_start: 0.9345 (mp0) cc_final: 0.9132 (mp0) REVERT: V 321 GLU cc_start: 0.9539 (mp0) cc_final: 0.9198 (mm-30) REVERT: V 339 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8867 (tp) REVERT: V 345 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9014 (mp) outliers start: 58 outliers final: 23 residues processed: 173 average time/residue: 0.4822 time to fit residues: 93.8055 Evaluate side-chains 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 145 SER Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 114 LEU 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 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 138 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.083762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053254 restraints weight = 52751.772| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.94 r_work: 0.2829 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15603 Z= 0.125 Angle : 0.593 12.111 21407 Z= 0.301 Chirality : 0.040 0.170 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.444 85.952 2729 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.52 % Favored : 97.07 % Rotamer: Outliers : 3.31 % Allowed : 26.08 % Favored : 70.61 % 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: 1.70 (0.17), residues: 1030 sheet: -0.56 (0.45), residues: 140 loop : -0.52 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 112 TYR 0.027 0.001 TYR S 183 PHE 0.027 0.001 PHE U 138 TRP 0.025 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00275 (15603) covalent geometry : angle 0.59286 (21407) hydrogen bonds : bond 0.03524 ( 833) hydrogen bonds : angle 3.77880 ( 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 176 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: R 52 PHE cc_start: 0.8413 (m-10) cc_final: 0.7945 (m-10) REVERT: R 146 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8351 (mttt) REVERT: R 186 GLN cc_start: 0.8809 (mp10) cc_final: 0.8585 (mp10) REVERT: R 192 LEU cc_start: 0.8959 (tp) cc_final: 0.8752 (tp) REVERT: R 193 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8623 (tttt) REVERT: R 248 LEU cc_start: 0.9820 (mt) cc_final: 0.9504 (pp) REVERT: S 71 GLU cc_start: 0.9575 (tt0) cc_final: 0.9238 (tm-30) REVERT: S 103 TYR cc_start: 0.9124 (p90) cc_final: 0.8683 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9328 (t0) cc_final: 0.8972 (t0) REVERT: S 138 PHE cc_start: 0.9296 (m-80) cc_final: 0.9036 (m-80) REVERT: S 146 LYS cc_start: 0.9349 (pttp) cc_final: 0.8948 (pptt) REVERT: S 185 LEU cc_start: 0.9206 (tp) cc_final: 0.8988 (pt) REVERT: S 324 GLU cc_start: 0.9171 (pp20) cc_final: 0.8920 (tm-30) REVERT: S 337 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8586 (tm-30) REVERT: T 108 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9154 (mm-30) REVERT: T 164 HIS cc_start: 0.9480 (t-170) cc_final: 0.8898 (t-90) REVERT: T 210 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.9015 (mp0) REVERT: T 321 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9280 (mt-10) REVERT: U 19 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.9097 (mpp80) REVERT: U 20 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9209 (tm) REVERT: U 128 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: U 158 ASN cc_start: 0.9698 (m110) cc_final: 0.9205 (m110) REVERT: U 164 HIS cc_start: 0.8885 (t-90) cc_final: 0.8360 (t-90) REVERT: U 190 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8916 (m-30) REVERT: U 252 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.9237 (tt0) REVERT: V 19 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7950 (mpp80) REVERT: V 103 TYR cc_start: 0.8687 (p90) cc_final: 0.8410 (p90) REVERT: V 121 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9072 (tm) REVERT: V 158 ASN cc_start: 0.9691 (m-40) cc_final: 0.9437 (m110) REVERT: V 210 GLU cc_start: 0.9337 (mp0) cc_final: 0.9129 (mp0) REVERT: V 321 GLU cc_start: 0.9541 (mp0) cc_final: 0.9194 (mm-30) REVERT: V 345 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8972 (mp) outliers start: 49 outliers final: 21 residues processed: 166 average time/residue: 0.5113 time to fit residues: 95.2736 Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 20 LEU 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 190 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 61 VAL 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 315 CYS 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: 0.6980 chunk 127 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.082934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052445 restraints weight = 52742.591| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.94 r_work: 0.2806 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15603 Z= 0.143 Angle : 0.590 11.477 21407 Z= 0.304 Chirality : 0.040 0.183 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.236 87.767 2729 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.58 % Favored : 97.01 % Rotamer: Outliers : 3.58 % Allowed : 26.96 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1705 helix: 1.83 (0.17), residues: 1020 sheet: -0.63 (0.46), residues: 140 loop : -0.72 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 215 TYR 0.022 0.001 TYR U 103 PHE 0.021 0.001 PHE V 138 TRP 0.029 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00317 (15603) covalent geometry : angle 0.58999 (21407) hydrogen bonds : bond 0.03564 ( 833) hydrogen bonds : angle 3.75915 ( 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 173 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: R 52 PHE cc_start: 0.8444 (m-10) cc_final: 0.7983 (m-10) REVERT: R 146 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8371 (tttt) REVERT: R 186 GLN cc_start: 0.8783 (mp10) cc_final: 0.8522 (mp10) REVERT: R 193 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8642 (tttt) REVERT: R 248 LEU cc_start: 0.9805 (mt) cc_final: 0.9507 (pp) REVERT: R 318 MET cc_start: 0.8132 (mtt) cc_final: 0.7838 (mtt) REVERT: S 71 GLU cc_start: 0.9583 (tt0) cc_final: 0.9263 (tm-30) REVERT: S 103 TYR cc_start: 0.9088 (p90) cc_final: 0.8640 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9369 (t0) cc_final: 0.9013 (t0) REVERT: S 138 PHE cc_start: 0.9343 (m-80) cc_final: 0.9108 (m-80) REVERT: S 144 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: S 146 LYS cc_start: 0.9472 (pttp) cc_final: 0.8963 (pptt) REVERT: S 324 GLU cc_start: 0.9231 (pp20) cc_final: 0.8927 (tm-30) REVERT: S 337 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8562 (tm-30) REVERT: T 25 ASN cc_start: 0.9357 (p0) cc_final: 0.9129 (p0) REVERT: T 108 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.9159 (mm-30) REVERT: T 164 HIS cc_start: 0.9459 (t-170) cc_final: 0.8843 (t-90) REVERT: T 210 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.9015 (mp0) REVERT: T 321 GLU cc_start: 0.9555 (OUTLIER) cc_final: 0.9277 (mt-10) REVERT: U 19 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9161 (mpp80) REVERT: U 41 MET cc_start: 0.9382 (tpp) cc_final: 0.9127 (mmm) REVERT: U 128 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: U 158 ASN cc_start: 0.9685 (m110) cc_final: 0.9191 (m110) REVERT: U 164 HIS cc_start: 0.8956 (t-90) cc_final: 0.8349 (t-90) REVERT: U 190 ASP cc_start: 0.9334 (OUTLIER) cc_final: 0.8992 (m-30) REVERT: U 252 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.9187 (tt0) REVERT: V 19 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7920 (mpp80) REVERT: V 103 TYR cc_start: 0.8729 (p90) cc_final: 0.8417 (p90) REVERT: V 121 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (tm) REVERT: V 158 ASN cc_start: 0.9675 (m-40) cc_final: 0.9385 (m110) REVERT: V 210 GLU cc_start: 0.9358 (mp0) cc_final: 0.9112 (mp0) REVERT: V 321 GLU cc_start: 0.9557 (mp0) cc_final: 0.9231 (mm-30) REVERT: V 345 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 53 outliers final: 19 residues processed: 166 average time/residue: 0.5126 time to fit residues: 95.0500 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 142 ASN Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU 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 S residue 208 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 215 ARG Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 121 LEU 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 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS 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: 6.9990 chunk 175 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 164 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.083323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.052977 restraints weight = 52124.426| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.89 r_work: 0.2826 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15603 Z= 0.126 Angle : 0.602 12.088 21407 Z= 0.304 Chirality : 0.040 0.206 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.125 88.256 2729 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 2.91 % Allowed : 27.43 % Favored : 69.66 % 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: 1.31 (0.22), residues: 1705 helix: 1.83 (0.17), residues: 1030 sheet: -0.62 (0.45), residues: 140 loop : -0.55 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 215 TYR 0.028 0.001 TYR T 103 PHE 0.025 0.001 PHE U 138 TRP 0.030 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00280 (15603) covalent geometry : angle 0.60246 (21407) hydrogen bonds : bond 0.03359 ( 833) hydrogen bonds : angle 3.70422 ( 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 161 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: R 186 GLN cc_start: 0.8781 (mp10) cc_final: 0.8526 (mp10) REVERT: R 248 LEU cc_start: 0.9808 (mt) cc_final: 0.9503 (pp) REVERT: R 318 MET cc_start: 0.8075 (mtt) cc_final: 0.7805 (mtt) REVERT: S 71 GLU cc_start: 0.9583 (tt0) cc_final: 0.9252 (tm-30) REVERT: S 95 GLU cc_start: 0.9088 (pm20) cc_final: 0.8688 (pm20) REVERT: S 103 TYR cc_start: 0.9121 (p90) cc_final: 0.8664 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9390 (t0) cc_final: 0.9036 (t0) REVERT: S 138 PHE cc_start: 0.9358 (m-80) cc_final: 0.9126 (m-80) REVERT: S 318 MET cc_start: 0.9484 (mtp) cc_final: 0.9283 (mtp) REVERT: S 324 GLU cc_start: 0.9211 (pp20) cc_final: 0.8916 (tm-30) REVERT: S 337 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8557 (tm-30) REVERT: T 103 TYR cc_start: 0.9192 (p90) cc_final: 0.8324 (p90) REVERT: T 108 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9143 (mm-30) REVERT: T 164 HIS cc_start: 0.9448 (t-170) cc_final: 0.8854 (t-90) REVERT: T 210 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.9003 (mp0) REVERT: T 321 GLU cc_start: 0.9543 (OUTLIER) cc_final: 0.9271 (mt-10) REVERT: U 38 GLU cc_start: 0.8645 (pp20) cc_final: 0.8444 (pp20) REVERT: U 41 MET cc_start: 0.9371 (tpp) cc_final: 0.9126 (mmm) REVERT: U 128 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: U 158 ASN cc_start: 0.9690 (m110) cc_final: 0.9199 (m110) REVERT: U 164 HIS cc_start: 0.8989 (t-90) cc_final: 0.8343 (t-90) REVERT: U 190 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: U 252 GLN cc_start: 0.9525 (OUTLIER) cc_final: 0.9209 (tt0) REVERT: U 305 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9271 (mm) REVERT: V 103 TYR cc_start: 0.8779 (p90) cc_final: 0.8442 (p90) REVERT: V 121 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9072 (tm) REVERT: V 158 ASN cc_start: 0.9685 (m-40) cc_final: 0.9403 (m110) REVERT: V 210 GLU cc_start: 0.9389 (mp0) cc_final: 0.9149 (mp0) REVERT: V 321 GLU cc_start: 0.9557 (OUTLIER) cc_final: 0.9226 (mm-30) REVERT: V 345 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9015 (mp) outliers start: 43 outliers final: 22 residues processed: 153 average time/residue: 0.5232 time to fit residues: 89.6868 Evaluate side-chains 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 142 ASN 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 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 215 ARG Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain V residue 121 LEU 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 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU 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: 0.9990 chunk 42 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.082809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052672 restraints weight = 52796.825| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.91 r_work: 0.2810 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15603 Z= 0.139 Angle : 0.609 13.047 21407 Z= 0.307 Chirality : 0.040 0.249 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.101 88.690 2729 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 27.97 % Favored : 68.92 % 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: 1.30 (0.22), residues: 1705 helix: 1.91 (0.17), residues: 1020 sheet: -0.67 (0.45), residues: 140 loop : -0.69 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 215 TYR 0.024 0.001 TYR T 103 PHE 0.021 0.001 PHE V 138 TRP 0.033 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00310 (15603) covalent geometry : angle 0.60911 (21407) hydrogen bonds : bond 0.03449 ( 833) hydrogen bonds : angle 3.70209 ( 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 160 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: R 186 GLN cc_start: 0.8785 (mp10) cc_final: 0.8534 (mp10) REVERT: R 248 LEU cc_start: 0.9809 (mt) cc_final: 0.9511 (pp) REVERT: R 318 MET cc_start: 0.8067 (mtt) cc_final: 0.7861 (mtt) REVERT: S 71 GLU cc_start: 0.9576 (tt0) cc_final: 0.9253 (tm-30) REVERT: S 103 TYR cc_start: 0.9129 (p90) cc_final: 0.8672 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9392 (t0) cc_final: 0.9023 (t0) REVERT: S 138 PHE cc_start: 0.9407 (m-80) cc_final: 0.9196 (m-80) REVERT: S 324 GLU cc_start: 0.9244 (pp20) cc_final: 0.8917 (tm-30) REVERT: S 337 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8562 (tm-30) REVERT: T 108 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9161 (mm-30) REVERT: T 164 HIS cc_start: 0.9468 (t-170) cc_final: 0.8851 (t-90) REVERT: T 210 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9018 (mp0) REVERT: T 321 GLU cc_start: 0.9569 (OUTLIER) cc_final: 0.9299 (mt-10) REVERT: U 19 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.9132 (mpp80) REVERT: U 41 MET cc_start: 0.9373 (tpp) cc_final: 0.9132 (mmm) REVERT: U 128 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: U 158 ASN cc_start: 0.9683 (m110) cc_final: 0.9192 (m110) REVERT: U 164 HIS cc_start: 0.9029 (t-90) cc_final: 0.8370 (t-90) REVERT: U 190 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8951 (m-30) REVERT: U 252 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9189 (tt0) REVERT: U 305 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9262 (mm) REVERT: V 19 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7900 (mpp80) REVERT: V 103 TYR cc_start: 0.8807 (p90) cc_final: 0.8491 (p90) REVERT: V 121 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9071 (tm) REVERT: V 158 ASN cc_start: 0.9672 (m-40) cc_final: 0.9399 (m110) REVERT: V 210 GLU cc_start: 0.9383 (mp0) cc_final: 0.9125 (mp0) REVERT: V 321 GLU cc_start: 0.9567 (OUTLIER) cc_final: 0.9243 (mm-30) REVERT: V 339 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8998 (tm) REVERT: V 345 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9006 (mp) outliers start: 46 outliers final: 21 residues processed: 151 average time/residue: 0.5386 time to fit residues: 90.7459 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 : 0.536 ------------------------------------------------------------------------------- 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 142 ASN Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 215 ARG Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 121 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 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 LEU 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: 9.9990 chunk 147 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 GLN ** 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.082180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051813 restraints weight = 52823.695| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.93 r_work: 0.2794 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4295 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= 0.162 Angle : 0.635 12.745 21407 Z= 0.323 Chirality : 0.041 0.336 2400 Planarity : 0.004 0.044 2515 Dihedral : 18.102 89.122 2729 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.76 % Favored : 96.77 % Rotamer: Outliers : 3.04 % Allowed : 28.65 % Favored : 68.31 % 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: 1.31 (0.22), residues: 1705 helix: 1.93 (0.17), residues: 1020 sheet: -0.68 (0.45), residues: 140 loop : -0.72 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 131 TYR 0.013 0.001 TYR S 128 PHE 0.025 0.001 PHE U 138 TRP 0.036 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00362 (15603) covalent geometry : angle 0.63542 (21407) hydrogen bonds : bond 0.03590 ( 833) hydrogen bonds : angle 3.72608 ( 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 158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8725 (mp0) REVERT: R 41 MET cc_start: 0.8563 (mmm) cc_final: 0.8334 (tpt) REVERT: R 146 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8142 (tttt) REVERT: R 186 GLN cc_start: 0.8764 (mp10) cc_final: 0.8494 (mp10) REVERT: R 248 LEU cc_start: 0.9807 (mt) cc_final: 0.9506 (pp) REVERT: S 71 GLU cc_start: 0.9588 (tt0) cc_final: 0.9266 (tm-30) REVERT: S 95 GLU cc_start: 0.9069 (pm20) cc_final: 0.8725 (pm20) REVERT: S 103 TYR cc_start: 0.9162 (p90) cc_final: 0.8681 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9410 (t0) cc_final: 0.9035 (t0) REVERT: S 138 PHE cc_start: 0.9427 (m-80) cc_final: 0.9205 (m-80) REVERT: S 144 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: S 146 LYS cc_start: 0.9549 (pttp) cc_final: 0.9029 (pptt) REVERT: S 210 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: S 324 GLU cc_start: 0.9269 (pp20) cc_final: 0.8933 (tm-30) REVERT: S 337 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8567 (tm-30) REVERT: T 25 ASN cc_start: 0.9519 (p0) cc_final: 0.9305 (p0) REVERT: T 108 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9172 (mm-30) REVERT: T 164 HIS cc_start: 0.9478 (t-170) cc_final: 0.8849 (t-90) REVERT: T 210 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.9020 (mp0) REVERT: T 321 GLU cc_start: 0.9568 (OUTLIER) cc_final: 0.9297 (mt-10) REVERT: U 19 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9106 (mpp80) REVERT: U 41 MET cc_start: 0.9382 (tpp) cc_final: 0.9136 (mmm) REVERT: U 158 ASN cc_start: 0.9690 (m110) cc_final: 0.9202 (m110) REVERT: U 164 HIS cc_start: 0.9063 (t-90) cc_final: 0.8386 (t-90) REVERT: U 190 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9006 (m-30) REVERT: U 252 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9226 (tt0) REVERT: U 305 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9258 (mm) REVERT: V 19 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7886 (mpp80) REVERT: V 103 TYR cc_start: 0.8850 (p90) cc_final: 0.8552 (p90) REVERT: V 121 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9082 (tm) REVERT: V 128 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8360 (m-10) REVERT: V 158 ASN cc_start: 0.9672 (m-40) cc_final: 0.9403 (m110) REVERT: V 210 GLU cc_start: 0.9392 (mp0) cc_final: 0.9126 (mp0) REVERT: V 321 GLU cc_start: 0.9573 (OUTLIER) cc_final: 0.9257 (mm-30) REVERT: V 339 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9055 (tm) REVERT: V 345 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9011 (mp) outliers start: 45 outliers final: 22 residues processed: 151 average time/residue: 0.5386 time to fit residues: 90.7334 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 142 ASN Chi-restraints excluded: chain R residue 146 LYS 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 36 VAL Chi-restraints excluded: chain S residue 114 LEU 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 S residue 210 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 215 ARG Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 128 TYR 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 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 339 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 113 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052910 restraints weight = 52919.484| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.95 r_work: 0.2828 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15603 Z= 0.129 Angle : 0.645 12.734 21407 Z= 0.325 Chirality : 0.041 0.379 2400 Planarity : 0.004 0.044 2515 Dihedral : 17.965 89.233 2729 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.99 % Favored : 96.60 % Rotamer: Outliers : 2.77 % Allowed : 29.32 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1705 helix: 1.88 (0.17), residues: 1030 sheet: -0.63 (0.45), residues: 140 loop : -0.59 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 131 TYR 0.028 0.001 TYR T 103 PHE 0.025 0.001 PHE U 138 TRP 0.038 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00286 (15603) covalent geometry : angle 0.64459 (21407) hydrogen bonds : bond 0.03430 ( 833) hydrogen bonds : angle 3.73562 ( 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 149 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8743 (mp0) REVERT: R 146 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8093 (mttt) REVERT: R 186 GLN cc_start: 0.8766 (mp10) cc_final: 0.8499 (mp10) REVERT: R 248 LEU cc_start: 0.9811 (mt) cc_final: 0.9505 (pp) REVERT: S 71 GLU cc_start: 0.9596 (tt0) cc_final: 0.9269 (tm-30) REVERT: S 95 GLU cc_start: 0.9059 (pm20) cc_final: 0.8758 (pm20) REVERT: S 103 TYR cc_start: 0.9141 (p90) cc_final: 0.8666 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9385 (t0) cc_final: 0.9024 (t0) REVERT: S 131 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8312 (mmp80) REVERT: S 138 PHE cc_start: 0.9437 (m-80) cc_final: 0.9220 (m-80) REVERT: S 324 GLU cc_start: 0.9270 (pp20) cc_final: 0.8896 (tm-30) REVERT: S 337 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8562 (tm-30) REVERT: T 108 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9144 (mm-30) REVERT: T 164 HIS cc_start: 0.9451 (t-170) cc_final: 0.8858 (t-90) REVERT: T 210 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: T 321 GLU cc_start: 0.9577 (OUTLIER) cc_final: 0.9309 (mt-10) REVERT: U 41 MET cc_start: 0.9363 (tpp) cc_final: 0.9124 (mmm) REVERT: U 158 ASN cc_start: 0.9686 (m110) cc_final: 0.9201 (m110) REVERT: U 164 HIS cc_start: 0.9060 (t-90) cc_final: 0.8367 (t-90) REVERT: U 190 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8852 (m-30) REVERT: U 252 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9195 (tt0) REVERT: U 305 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9274 (mm) REVERT: V 19 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7951 (mpp80) REVERT: V 103 TYR cc_start: 0.8840 (p90) cc_final: 0.8505 (p90) REVERT: V 121 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9075 (tm) REVERT: V 158 ASN cc_start: 0.9669 (m-40) cc_final: 0.9402 (m110) REVERT: V 210 GLU cc_start: 0.9390 (mp0) cc_final: 0.9171 (mp0) REVERT: V 318 MET cc_start: 0.9377 (mmm) cc_final: 0.8915 (mpm) REVERT: V 321 GLU cc_start: 0.9568 (OUTLIER) cc_final: 0.9243 (mm-30) REVERT: V 345 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8992 (mp) outliers start: 41 outliers final: 23 residues processed: 142 average time/residue: 0.5328 time to fit residues: 84.3676 Evaluate side-chains 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 109 TYR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 146 LYS 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 145 SER Chi-restraints excluded: chain S residue 167 VAL 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 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 215 ARG Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 121 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 315 CYS Chi-restraints excluded: chain V residue 321 GLU 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: 0.3980 chunk 136 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 HIS ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.082368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052282 restraints weight = 52757.066| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.91 r_work: 0.2802 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4522 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= 0.153 Angle : 0.648 12.595 21407 Z= 0.328 Chirality : 0.041 0.390 2400 Planarity : 0.004 0.045 2515 Dihedral : 17.958 89.444 2729 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.83 % Rotamer: Outliers : 2.50 % Allowed : 29.32 % Favored : 68.18 % 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: 1.35 (0.22), residues: 1705 helix: 1.89 (0.17), residues: 1030 sheet: -0.67 (0.45), residues: 140 loop : -0.59 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 131 TYR 0.032 0.001 TYR S 183 PHE 0.025 0.001 PHE U 138 TRP 0.038 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00341 (15603) covalent geometry : angle 0.64807 (21407) hydrogen bonds : bond 0.03557 ( 833) hydrogen bonds : angle 3.78042 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5741.20 seconds wall clock time: 98 minutes 28.83 seconds (5908.83 seconds total)