Starting phenix.real_space_refine on Fri Jun 13 18:57:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_28997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_28997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_28997.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_28997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcw_28997/06_2025/8fcw_28997.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.77, per 1000 atoms: 0.64 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: 4.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.87 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: 5.52 Time building geometry restraints manager: 5.00 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: 1.110 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.970 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.005 TRP S 106 HIS 0.013 0.003 HIS T 203 PHE 0.036 0.005 PHE V 319 TYR 0.025 0.004 TYR S 128 ARG 0.016 0.001 ARG U 223 Details of bonding type rmsd hydrogen bonds : bond 0.17998 ( 833) hydrogen bonds : angle 5.87032 ( 2259) covalent geometry : bond 0.00994 (15603) covalent geometry : angle 0.90265 (21407) *********************** 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 : 1.607 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: 1.2158 time to fit residues: 371.3776 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 : 1.618 ------------------------------------------------------------------------------- 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 148 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.086315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055716 restraints weight = 52118.099| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.95 r_work: 0.2894 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15603 Z= 0.141 Angle : 0.642 11.593 21407 Z= 0.330 Chirality : 0.041 0.148 2400 Planarity : 0.004 0.046 2515 Dihedral : 19.093 79.177 2740 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.76 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 26.22 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.020 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.022 0.001 PHE U 138 TYR 0.019 0.002 TYR U 103 ARG 0.010 0.000 ARG U 102 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 833) hydrogen bonds : angle 4.19182 ( 2259) covalent geometry : bond 0.00310 (15603) covalent geometry : angle 0.64234 (21407) *********************** 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 196 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.796 Fit side-chains REVERT: R 18 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: R 186 GLN cc_start: 0.8819 (mp10) cc_final: 0.8589 (mp10) REVERT: R 248 LEU cc_start: 0.9816 (mt) cc_final: 0.9519 (pp) REVERT: R 318 MET cc_start: 0.8515 (mmt) cc_final: 0.7836 (mmt) REVERT: R 321 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8760 (pp20) REVERT: S 71 GLU cc_start: 0.9567 (tt0) cc_final: 0.9268 (tm-30) REVERT: S 103 TYR cc_start: 0.9086 (p90) cc_final: 0.8786 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9278 (t0) cc_final: 0.9001 (t0) REVERT: S 138 PHE cc_start: 0.9222 (m-80) cc_final: 0.8895 (m-80) REVERT: S 146 LYS cc_start: 0.8723 (pttp) cc_final: 0.8348 (pptt) REVERT: S 186 GLN cc_start: 0.8581 (mp10) cc_final: 0.8243 (mp10) REVERT: S 190 ASP cc_start: 0.9408 (m-30) cc_final: 0.9189 (m-30) REVERT: S 318 MET cc_start: 0.9384 (mtm) cc_final: 0.9075 (mtp) REVERT: S 328 GLN cc_start: 0.9352 (mt0) cc_final: 0.9140 (mt0) REVERT: S 337 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8629 (tm-30) REVERT: T 103 TYR cc_start: 0.8738 (p90) cc_final: 0.8095 (p90) REVERT: T 108 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9193 (mm-30) REVERT: T 164 HIS cc_start: 0.9391 (t-170) cc_final: 0.8910 (t-90) REVERT: T 210 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: U 19 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8741 (mtp85) REVERT: U 108 GLU cc_start: 0.9457 (tp30) cc_final: 0.9083 (tp30) REVERT: U 190 ASP cc_start: 0.9258 (m-30) cc_final: 0.9004 (m-30) REVERT: U 321 GLU cc_start: 0.9534 (tp30) cc_final: 0.9160 (mt-10) REVERT: V 121 LEU cc_start: 0.9261 (tt) cc_final: 0.9031 (tm) REVERT: V 158 ASN cc_start: 0.9674 (m-40) cc_final: 0.9415 (m110) REVERT: V 321 GLU cc_start: 0.9443 (mp0) cc_final: 0.9172 (mm-30) outliers start: 46 outliers final: 13 residues processed: 189 average time/residue: 1.1680 time to fit residues: 246.6533 Evaluate side-chains 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 175 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054745 restraints weight = 52824.697| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.98 r_work: 0.2866 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15603 Z= 0.133 Angle : 0.607 12.899 21407 Z= 0.310 Chirality : 0.040 0.169 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.652 79.606 2735 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Rotamer: Outliers : 3.31 % Allowed : 25.41 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1705 helix: 1.31 (0.17), residues: 1060 sheet: -0.47 (0.46), residues: 140 loop : -1.16 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 267 HIS 0.004 0.001 HIS R 30 PHE 0.014 0.001 PHE T 138 TYR 0.012 0.001 TYR T 103 ARG 0.006 0.000 ARG U 102 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 833) hydrogen bonds : angle 3.88521 ( 2259) covalent geometry : bond 0.00294 (15603) covalent geometry : angle 0.60712 (21407) *********************** 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 186 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: R 186 GLN cc_start: 0.8915 (mp10) cc_final: 0.8677 (mp10) REVERT: R 248 LEU cc_start: 0.9818 (mt) cc_final: 0.9514 (pp) REVERT: R 293 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8645 (mt) REVERT: S 71 GLU cc_start: 0.9569 (tt0) cc_final: 0.9242 (tm-30) REVERT: S 103 TYR cc_start: 0.9130 (p90) cc_final: 0.8737 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9289 (t0) cc_final: 0.8949 (t0) REVERT: S 138 PHE cc_start: 0.9224 (m-80) cc_final: 0.8865 (m-80) REVERT: S 185 LEU cc_start: 0.9257 (tp) cc_final: 0.9048 (pt) REVERT: S 318 MET cc_start: 0.9360 (mtm) cc_final: 0.9070 (mtp) REVERT: S 337 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8618 (tm-30) REVERT: T 103 TYR cc_start: 0.8903 (p90) cc_final: 0.8169 (p90) REVERT: T 108 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9151 (mm-30) REVERT: T 164 HIS cc_start: 0.9442 (t-170) cc_final: 0.8894 (t-90) REVERT: T 210 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8939 (mp0) REVERT: T 293 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9166 (mm) REVERT: T 321 GLU cc_start: 0.9537 (mt-10) cc_final: 0.9254 (mt-10) REVERT: U 19 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8756 (mtp85) REVERT: U 108 GLU cc_start: 0.9460 (tp30) cc_final: 0.9073 (tp30) REVERT: U 164 HIS cc_start: 0.8714 (t-90) cc_final: 0.8501 (t-90) REVERT: U 190 ASP cc_start: 0.9280 (m-30) cc_final: 0.8981 (m-30) REVERT: U 321 GLU cc_start: 0.9522 (tp30) cc_final: 0.9191 (mt-10) REVERT: V 121 LEU cc_start: 0.9278 (tt) cc_final: 0.9031 (tm) REVERT: V 158 ASN cc_start: 0.9667 (m-40) cc_final: 0.9430 (m110) REVERT: V 210 GLU cc_start: 0.9291 (mp0) cc_final: 0.9088 (mp0) REVERT: V 321 GLU cc_start: 0.9497 (mp0) cc_final: 0.9161 (mm-30) REVERT: V 345 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8754 (mp) outliers start: 49 outliers final: 18 residues processed: 178 average time/residue: 1.0597 time to fit residues: 213.0312 Evaluate side-chains 146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 293 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 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 283 ASP Chi-restraints excluded: chain V residue 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 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 129 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 GLN ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3759 r_free = 0.3759 target = 0.084007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053518 restraints weight = 52607.033| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.91 r_work: 0.2832 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15603 Z= 0.143 Angle : 0.587 11.100 21407 Z= 0.304 Chirality : 0.040 0.152 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.544 83.631 2730 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.87 % Favored : 96.77 % Rotamer: Outliers : 4.12 % Allowed : 24.86 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1705 helix: 1.44 (0.17), residues: 1055 sheet: -0.51 (0.46), residues: 140 loop : -1.03 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.033 0.001 PHE U 126 TYR 0.019 0.001 TYR U 103 ARG 0.004 0.000 ARG U 102 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 833) hydrogen bonds : angle 3.80392 ( 2259) covalent geometry : bond 0.00317 (15603) covalent geometry : angle 0.58713 (21407) *********************** 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 189 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 128 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: R 186 GLN cc_start: 0.8788 (mp10) cc_final: 0.8532 (mp10) REVERT: R 193 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8778 (mttt) REVERT: R 248 LEU cc_start: 0.9818 (mt) cc_final: 0.9520 (pp) REVERT: S 71 GLU cc_start: 0.9565 (tt0) cc_final: 0.9265 (tm-30) REVERT: S 103 TYR cc_start: 0.9088 (p90) cc_final: 0.8672 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9319 (t0) cc_final: 0.8958 (t0) REVERT: S 138 PHE cc_start: 0.9276 (m-80) cc_final: 0.8955 (m-80) REVERT: S 144 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: S 146 LYS cc_start: 0.9228 (pttp) cc_final: 0.8799 (pptt) REVERT: S 185 LEU cc_start: 0.9221 (tp) cc_final: 0.8965 (pt) REVERT: S 337 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8607 (tm-30) REVERT: T 103 TYR cc_start: 0.8971 (p90) cc_final: 0.8187 (p90) REVERT: T 164 HIS cc_start: 0.9483 (t-170) cc_final: 0.8877 (t-90) REVERT: T 210 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8939 (mp0) REVERT: T 293 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9174 (mm) REVERT: T 321 GLU cc_start: 0.9551 (OUTLIER) cc_final: 0.9274 (mt-10) REVERT: U 19 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9088 (mpp80) REVERT: U 128 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: U 164 HIS cc_start: 0.8828 (t-90) cc_final: 0.8431 (t-90) REVERT: U 190 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: U 252 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9386 (tt0) REVERT: V 128 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: V 158 ASN cc_start: 0.9672 (m-40) cc_final: 0.9428 (m110) REVERT: V 210 GLU cc_start: 0.9336 (mp0) cc_final: 0.9134 (mp0) REVERT: V 321 GLU cc_start: 0.9527 (mp0) cc_final: 0.9171 (mm-30) REVERT: V 345 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8862 (mp) outliers start: 61 outliers final: 21 residues processed: 175 average time/residue: 1.0674 time to fit residues: 211.0791 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 : 1.810 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 293 LEU 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 114 LEU 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 252 GLN Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 315 CYS 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 30 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.3738 r_free = 0.3738 target = 0.083082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052582 restraints weight = 53421.796| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.95 r_work: 0.2807 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15603 Z= 0.158 Angle : 0.596 11.807 21407 Z= 0.307 Chirality : 0.040 0.189 2400 Planarity : 0.004 0.045 2515 Dihedral : 18.480 86.740 2729 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.46 % Favored : 97.13 % Rotamer: Outliers : 3.45 % Allowed : 26.15 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1705 helix: 1.75 (0.17), residues: 1020 sheet: -0.51 (0.46), residues: 140 loop : -0.57 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 267 HIS 0.005 0.001 HIS R 229 PHE 0.025 0.001 PHE U 138 TYR 0.027 0.001 TYR S 183 ARG 0.004 0.000 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 833) hydrogen bonds : angle 3.80155 ( 2259) covalent geometry : bond 0.00355 (15603) covalent geometry : angle 0.59566 (21407) *********************** 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 177 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 186 GLN cc_start: 0.8814 (mp10) cc_final: 0.8513 (mp10) REVERT: R 193 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8628 (tptt) REVERT: R 248 LEU cc_start: 0.9806 (mt) cc_final: 0.9510 (pp) REVERT: S 71 GLU cc_start: 0.9589 (tt0) cc_final: 0.9257 (tm-30) REVERT: S 103 TYR cc_start: 0.9133 (p90) cc_final: 0.8743 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9358 (t0) cc_final: 0.8993 (t0) REVERT: S 138 PHE cc_start: 0.9318 (m-80) cc_final: 0.9043 (m-80) REVERT: S 144 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8790 (mp0) REVERT: S 146 LYS cc_start: 0.9369 (pttp) cc_final: 0.8897 (pptt) REVERT: S 185 LEU cc_start: 0.9243 (tp) cc_final: 0.9011 (pt) REVERT: S 337 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8587 (tm-30) REVERT: T 118 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8268 (tm-30) REVERT: T 164 HIS cc_start: 0.9464 (t-170) cc_final: 0.8839 (t-90) REVERT: T 210 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8957 (mp0) REVERT: T 321 GLU cc_start: 0.9559 (OUTLIER) cc_final: 0.9288 (mt-10) REVERT: U 19 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.9108 (mpp80) REVERT: U 158 ASN cc_start: 0.9690 (m110) cc_final: 0.9269 (m110) REVERT: U 164 HIS cc_start: 0.8878 (t-90) cc_final: 0.8357 (t-90) REVERT: U 190 ASP cc_start: 0.9345 (OUTLIER) cc_final: 0.8990 (m-30) REVERT: V 103 TYR cc_start: 0.8666 (p90) cc_final: 0.8348 (p90) REVERT: V 128 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: V 158 ASN cc_start: 0.9683 (m-40) cc_final: 0.9441 (m110) REVERT: V 210 GLU cc_start: 0.9336 (mp0) cc_final: 0.9115 (mp0) REVERT: V 321 GLU cc_start: 0.9548 (mp0) cc_final: 0.9200 (mm-30) REVERT: V 345 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9063 (mp) outliers start: 51 outliers final: 27 residues processed: 167 average time/residue: 1.1030 time to fit residues: 208.4043 Evaluate side-chains 150 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 275 LEU 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 11 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 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 = 0.3718 r_free = 0.3718 target = 0.081927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051627 restraints weight = 52858.168| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.88 r_work: 0.2783 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15603 Z= 0.182 Angle : 0.614 11.814 21407 Z= 0.316 Chirality : 0.041 0.165 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.308 88.166 2729 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.45 % Allowed : 27.36 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1705 helix: 1.80 (0.17), residues: 1020 sheet: -0.59 (0.46), residues: 140 loop : -0.75 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 267 HIS 0.004 0.001 HIS R 229 PHE 0.021 0.002 PHE U 126 TYR 0.020 0.001 TYR U 103 ARG 0.007 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 833) hydrogen bonds : angle 3.79482 ( 2259) covalent geometry : bond 0.00407 (15603) covalent geometry : angle 0.61438 (21407) *********************** 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 171 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: R 186 GLN cc_start: 0.8893 (mp10) cc_final: 0.8656 (mp10) REVERT: R 248 LEU cc_start: 0.9808 (mt) cc_final: 0.9506 (pp) REVERT: S 71 GLU cc_start: 0.9574 (tt0) cc_final: 0.9264 (tm-30) REVERT: S 103 TYR cc_start: 0.9164 (p90) cc_final: 0.8724 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9373 (t0) cc_final: 0.8989 (t0) REVERT: S 138 PHE cc_start: 0.9343 (m-80) cc_final: 0.9087 (m-80) REVERT: S 144 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8714 (mp0) REVERT: S 146 LYS cc_start: 0.9501 (pttp) cc_final: 0.8993 (pptt) REVERT: S 337 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8561 (tm-30) REVERT: T 164 HIS cc_start: 0.9482 (t-170) cc_final: 0.8859 (t-90) REVERT: T 210 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8975 (mp0) REVERT: T 321 GLU cc_start: 0.9560 (OUTLIER) cc_final: 0.9287 (mt-10) REVERT: U 19 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.9053 (mpp80) REVERT: U 128 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: U 158 ASN cc_start: 0.9695 (m110) cc_final: 0.9205 (m110) REVERT: U 164 HIS cc_start: 0.8979 (t-90) cc_final: 0.8398 (t-90) REVERT: U 190 ASP cc_start: 0.9410 (OUTLIER) cc_final: 0.9081 (m-30) REVERT: U 252 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.9265 (tt0) REVERT: U 305 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9283 (mm) REVERT: U 321 GLU cc_start: 0.9541 (tp30) cc_final: 0.9290 (mm-30) REVERT: V 19 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7890 (mpp80) REVERT: V 103 TYR cc_start: 0.8785 (p90) cc_final: 0.8440 (p90) REVERT: V 128 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: V 158 ASN cc_start: 0.9679 (m-40) cc_final: 0.9420 (m110) REVERT: V 210 GLU cc_start: 0.9355 (mp0) cc_final: 0.9098 (mp0) REVERT: V 321 GLU cc_start: 0.9562 (mp0) cc_final: 0.9225 (mm-30) REVERT: V 345 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9089 (mp) outliers start: 51 outliers final: 24 residues processed: 163 average time/residue: 1.0295 time to fit residues: 188.9156 Evaluate side-chains 145 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 192 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 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP 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 61 VAL Chi-restraints excluded: chain V residue 114 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 275 LEU 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 165 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 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** U 254 HIS V 142 ASN V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050669 restraints weight = 53632.379| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.90 r_work: 0.2757 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15603 Z= 0.216 Angle : 0.637 11.708 21407 Z= 0.327 Chirality : 0.041 0.206 2400 Planarity : 0.004 0.050 2515 Dihedral : 18.297 89.349 2729 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.99 % Favored : 96.60 % Rotamer: Outliers : 3.85 % Allowed : 27.36 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1705 helix: 1.78 (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 TRP 0.030 0.002 TRP R 267 HIS 0.005 0.001 HIS V 124 PHE 0.031 0.002 PHE U 138 TYR 0.029 0.002 TYR T 103 ARG 0.007 0.000 ARG U 215 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 833) hydrogen bonds : angle 3.84741 ( 2259) covalent geometry : bond 0.00480 (15603) covalent geometry : angle 0.63737 (21407) *********************** 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 166 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 186 GLN cc_start: 0.8866 (mp10) cc_final: 0.8629 (mp10) REVERT: R 248 LEU cc_start: 0.9806 (mt) cc_final: 0.9512 (pp) REVERT: S 71 GLU cc_start: 0.9576 (tt0) cc_final: 0.9269 (tm-30) REVERT: S 103 TYR cc_start: 0.9198 (p90) cc_final: 0.8740 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9404 (t0) cc_final: 0.9011 (t0) REVERT: S 138 PHE cc_start: 0.9457 (m-80) cc_final: 0.9234 (m-80) REVERT: S 144 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8736 (mp0) REVERT: S 146 LYS cc_start: 0.9546 (pttp) cc_final: 0.9011 (pptt) REVERT: S 337 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8592 (tm-30) REVERT: T 89 VAL cc_start: 0.9546 (OUTLIER) cc_final: 0.9278 (p) REVERT: T 164 HIS cc_start: 0.9482 (t-170) cc_final: 0.8821 (t-90) REVERT: T 210 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: T 321 GLU cc_start: 0.9538 (OUTLIER) cc_final: 0.9099 (mt-10) REVERT: U 19 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8843 (mtp85) REVERT: U 41 MET cc_start: 0.9402 (tpp) cc_final: 0.9154 (mmm) REVERT: U 158 ASN cc_start: 0.9691 (m110) cc_final: 0.9260 (m110) REVERT: U 164 HIS cc_start: 0.9056 (t-90) cc_final: 0.8457 (t-90) REVERT: U 190 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.9110 (m-30) REVERT: U 252 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.9271 (tt0) REVERT: U 305 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9283 (mm) REVERT: U 321 GLU cc_start: 0.9541 (tp30) cc_final: 0.9325 (mm-30) REVERT: V 103 TYR cc_start: 0.8927 (p90) cc_final: 0.8556 (p90) REVERT: V 158 ASN cc_start: 0.9676 (m-40) cc_final: 0.9400 (m110) REVERT: V 210 GLU cc_start: 0.9342 (mp0) cc_final: 0.9057 (mp0) REVERT: V 321 GLU cc_start: 0.9572 (mp0) cc_final: 0.9243 (mm-30) REVERT: V 345 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9107 (mp) outliers start: 57 outliers final: 31 residues processed: 156 average time/residue: 1.0358 time to fit residues: 182.9974 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 263 LEU 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 208 THR Chi-restraints excluded: chain S residue 324 GLU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 114 LEU Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 190 ASP 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 114 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS 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 158 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 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 = 0.3730 r_free = 0.3730 target = 0.082418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052052 restraints weight = 52706.069| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.90 r_work: 0.2799 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4348 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= 0.136 Angle : 0.620 11.806 21407 Z= 0.315 Chirality : 0.040 0.212 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.133 89.331 2729 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.87 % Favored : 96.72 % Rotamer: Outliers : 2.70 % Allowed : 29.32 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1705 helix: 1.79 (0.17), residues: 1030 sheet: -0.59 (0.46), residues: 140 loop : -0.55 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.024 0.001 PHE U 138 TYR 0.027 0.001 TYR R 109 ARG 0.006 0.000 ARG U 215 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 833) hydrogen bonds : angle 3.73454 ( 2259) covalent geometry : bond 0.00303 (15603) covalent geometry : angle 0.62015 (21407) *********************** 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 158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: R 186 GLN cc_start: 0.8829 (mp10) cc_final: 0.8587 (mp10) REVERT: R 248 LEU cc_start: 0.9805 (mt) cc_final: 0.9510 (pp) REVERT: R 318 MET cc_start: 0.8435 (mtt) cc_final: 0.8214 (mtt) REVERT: S 71 GLU cc_start: 0.9577 (tt0) cc_final: 0.9254 (tm-30) REVERT: S 103 TYR cc_start: 0.9188 (p90) cc_final: 0.8722 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9384 (t0) cc_final: 0.9003 (t0) REVERT: S 138 PHE cc_start: 0.9445 (m-80) cc_final: 0.9216 (m-80) REVERT: S 144 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8779 (mp0) REVERT: S 146 LYS cc_start: 0.9560 (pttp) cc_final: 0.9046 (pptt) REVERT: S 337 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8583 (tm-30) REVERT: T 164 HIS cc_start: 0.9474 (t-170) cc_final: 0.8859 (t-90) REVERT: T 210 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: T 321 GLU cc_start: 0.9544 (OUTLIER) cc_final: 0.9267 (mt-10) REVERT: U 41 MET cc_start: 0.9360 (tpp) cc_final: 0.9115 (mmm) REVERT: U 158 ASN cc_start: 0.9699 (m110) cc_final: 0.9209 (m110) REVERT: U 164 HIS cc_start: 0.9051 (t-90) cc_final: 0.8382 (t-90) REVERT: U 190 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8943 (m-30) REVERT: U 252 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9220 (tt0) REVERT: U 305 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9261 (mm) REVERT: V 95 GLU cc_start: 0.8363 (pp20) cc_final: 0.8108 (tm-30) REVERT: V 103 TYR cc_start: 0.8898 (p90) cc_final: 0.8515 (p90) REVERT: V 158 ASN cc_start: 0.9695 (m-40) cc_final: 0.9415 (m110) REVERT: V 210 GLU cc_start: 0.9396 (mp0) cc_final: 0.9155 (mp0) REVERT: V 321 GLU cc_start: 0.9565 (OUTLIER) cc_final: 0.9248 (mm-30) REVERT: V 345 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9089 (mp) outliers start: 40 outliers final: 21 residues processed: 150 average time/residue: 1.0864 time to fit residues: 184.2449 Evaluate side-chains 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 192 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 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 321 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 190 ASP 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 226 VAL Chi-restraints excluded: chain V residue 264 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 116 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 57 optimal weight: 0.4980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 S 216 ASN T 105 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.083599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053377 restraints weight = 52151.644| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.93 r_work: 0.2835 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15603 Z= 0.123 Angle : 0.645 12.973 21407 Z= 0.326 Chirality : 0.040 0.203 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.015 89.059 2729 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 2.03 % Allowed : 30.27 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1705 helix: 1.83 (0.17), residues: 1025 sheet: -0.56 (0.46), residues: 140 loop : -0.52 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.023 0.001 PHE U 138 TYR 0.028 0.001 TYR T 103 ARG 0.008 0.000 ARG S 131 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 833) hydrogen bonds : angle 3.70853 ( 2259) covalent geometry : bond 0.00271 (15603) covalent geometry : angle 0.64466 (21407) *********************** 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 144 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: R 41 MET cc_start: 0.8619 (mmm) cc_final: 0.8392 (tpt) REVERT: R 186 GLN cc_start: 0.8802 (mp10) cc_final: 0.8548 (mp10) REVERT: R 248 LEU cc_start: 0.9796 (mt) cc_final: 0.9501 (pp) REVERT: R 318 MET cc_start: 0.8352 (mtt) cc_final: 0.8117 (mtt) REVERT: S 71 GLU cc_start: 0.9589 (tt0) cc_final: 0.9262 (tm-30) REVERT: S 103 TYR cc_start: 0.9161 (p90) cc_final: 0.8679 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9371 (t0) cc_final: 0.9020 (t0) REVERT: S 138 PHE cc_start: 0.9435 (m-80) cc_final: 0.9218 (m-80) REVERT: S 337 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8561 (tm-30) REVERT: T 164 HIS cc_start: 0.9459 (t-170) cc_final: 0.8878 (t-90) REVERT: U 19 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.9145 (mpp80) REVERT: U 38 GLU cc_start: 0.8698 (pp20) cc_final: 0.8482 (pp20) REVERT: U 41 MET cc_start: 0.9330 (tpp) cc_final: 0.9108 (mmm) REVERT: U 158 ASN cc_start: 0.9693 (m110) cc_final: 0.9199 (m110) REVERT: U 164 HIS cc_start: 0.9059 (t-90) cc_final: 0.8376 (t-90) REVERT: U 190 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8853 (m-30) REVERT: U 252 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9251 (tt0) REVERT: U 305 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9257 (mm) REVERT: V 19 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7834 (mpp80) REVERT: V 95 GLU cc_start: 0.8256 (pp20) cc_final: 0.7896 (tm-30) REVERT: V 103 TYR cc_start: 0.8844 (p90) cc_final: 0.8488 (p90) REVERT: V 158 ASN cc_start: 0.9690 (m-40) cc_final: 0.9408 (m110) REVERT: V 210 GLU cc_start: 0.9403 (mp0) cc_final: 0.9194 (mp0) REVERT: V 321 GLU cc_start: 0.9553 (OUTLIER) cc_final: 0.9230 (mm-30) REVERT: V 345 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9069 (mp) outliers start: 30 outliers final: 16 residues processed: 137 average time/residue: 1.0341 time to fit residues: 160.4902 Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 192 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 167 VAL Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 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 190 ASP 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 226 VAL Chi-restraints excluded: chain V residue 264 VAL 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 113 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 338 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.083359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053233 restraints weight = 52627.054| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.92 r_work: 0.2832 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4566 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= 0.127 Angle : 0.646 12.833 21407 Z= 0.328 Chirality : 0.040 0.177 2400 Planarity : 0.004 0.048 2515 Dihedral : 17.921 89.173 2729 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.58 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 30.61 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1705 helix: 1.88 (0.17), residues: 1025 sheet: -0.56 (0.46), residues: 140 loop : -0.52 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.023 0.001 PHE U 138 TYR 0.029 0.001 TYR R 109 ARG 0.006 0.000 ARG S 131 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 833) hydrogen bonds : angle 3.70257 ( 2259) covalent geometry : bond 0.00282 (15603) covalent geometry : angle 0.64601 (21407) ********************** 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 136 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8629 (mp0) REVERT: R 186 GLN cc_start: 0.8812 (mp10) cc_final: 0.8563 (mp10) REVERT: R 248 LEU cc_start: 0.9789 (mt) cc_final: 0.9488 (pp) REVERT: R 318 MET cc_start: 0.8333 (mtt) cc_final: 0.8106 (mtt) REVERT: S 71 GLU cc_start: 0.9593 (tt0) cc_final: 0.9264 (tm-30) REVERT: S 103 TYR cc_start: 0.9153 (p90) cc_final: 0.8655 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9374 (t0) cc_final: 0.9027 (t0) REVERT: S 138 PHE cc_start: 0.9431 (m-80) cc_final: 0.9210 (m-80) REVERT: S 337 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8535 (tm-30) REVERT: T 164 HIS cc_start: 0.9466 (t-170) cc_final: 0.8867 (t-90) REVERT: U 19 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.9147 (mpp80) REVERT: U 41 MET cc_start: 0.9333 (tpp) cc_final: 0.9103 (mmm) REVERT: U 158 ASN cc_start: 0.9691 (m110) cc_final: 0.9201 (m110) REVERT: U 164 HIS cc_start: 0.9074 (t-90) cc_final: 0.8387 (t-90) REVERT: U 190 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8869 (m-30) REVERT: U 252 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9210 (tt0) REVERT: U 305 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9263 (mm) REVERT: V 95 GLU cc_start: 0.8244 (pp20) cc_final: 0.7808 (tm-30) REVERT: V 103 TYR cc_start: 0.8827 (p90) cc_final: 0.8477 (p90) REVERT: V 158 ASN cc_start: 0.9680 (m-40) cc_final: 0.9410 (m110) REVERT: V 210 GLU cc_start: 0.9416 (mp0) cc_final: 0.9205 (mp0) REVERT: V 318 MET cc_start: 0.9381 (mmm) cc_final: 0.8928 (mpm) REVERT: V 321 GLU cc_start: 0.9557 (OUTLIER) cc_final: 0.9231 (mm-30) REVERT: V 345 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9021 (mp) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 1.0985 time to fit residues: 162.1280 Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.702 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 183 TYR Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 189 LEU 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 252 GLN Chi-restraints excluded: chain U residue 305 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL 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 161 optimal weight: 0.0970 chunk 98 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 143 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 142 ASN ** R 203 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 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 = 0.3751 r_free = 0.3751 target = 0.083136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053151 restraints weight = 52733.667| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.93 r_work: 0.2832 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.379 15603 Z= 0.298 Angle : 1.067 61.600 21407 Z= 0.585 Chirality : 0.045 0.706 2400 Planarity : 0.005 0.173 2515 Dihedral : 17.950 89.172 2729 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.64 % Favored : 96.77 % Rotamer: Outliers : 1.96 % Allowed : 30.34 % Favored : 67.70 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1705 helix: 1.86 (0.17), residues: 1025 sheet: -0.56 (0.46), residues: 140 loop : -0.52 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.022 0.001 PHE U 138 TYR 0.329 0.003 TYR S 183 ARG 0.005 0.000 ARG U 215 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 833) hydrogen bonds : angle 3.75572 ( 2259) covalent geometry : bond 0.00611 (15603) covalent geometry : angle 1.06702 (21407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12358.83 seconds wall clock time: 216 minutes 38.76 seconds (12998.76 seconds total)