Starting phenix.real_space_refine on Tue Dec 31 09:25:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcw_28997/12_2024/8fcw_28997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcw_28997/12_2024/8fcw_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_28997/12_2024/8fcw_28997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcw_28997/12_2024/8fcw_28997.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcw_28997/12_2024/8fcw_28997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcw_28997/12_2024/8fcw_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-5532/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: 9.45, per 1000 atoms: 0.62 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: 4.13 Conformation dependent library (CDL) restraints added in 1.7 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: 5.53 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: 5.05 Time building geometry restraints manager: 4.74 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: 0.860 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:15.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.630 ------------------------------------------------------------------------------- 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= 0.624 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 *********************** 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 : 1.533 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: 1.2383 time to fit residues: 378.4853 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 : 1.811 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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= 0.200 Angle : 0.642 11.593 21407 Z= 0.330 Chirality : 0.041 0.148 2400 Planarity : 0.004 0.046 2515 Dihedral : 19.093 79.174 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 *********************** 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 : 2.019 Fit side-chains REVERT: R 18 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: R 106 TRP cc_start: 0.8767 (m100) cc_final: 0.8269 (m100) REVERT: R 186 GLN cc_start: 0.8547 (mp10) cc_final: 0.8192 (mp10) REVERT: R 248 LEU cc_start: 0.9780 (mt) cc_final: 0.9512 (pp) REVERT: R 318 MET cc_start: 0.8568 (mmt) cc_final: 0.7848 (mmt) REVERT: R 321 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: S 25 ASN cc_start: 0.9000 (m-40) cc_final: 0.8796 (m-40) REVERT: S 71 GLU cc_start: 0.9362 (tt0) cc_final: 0.9135 (tm-30) REVERT: S 103 TYR cc_start: 0.8279 (p90) cc_final: 0.8002 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9253 (t0) cc_final: 0.8989 (t0) REVERT: S 138 PHE cc_start: 0.9206 (m-80) cc_final: 0.8875 (m-80) REVERT: S 146 LYS cc_start: 0.8862 (pttp) cc_final: 0.8489 (pptt) REVERT: S 186 GLN cc_start: 0.8343 (mp10) cc_final: 0.7966 (mp10) REVERT: S 190 ASP cc_start: 0.9304 (m-30) cc_final: 0.9042 (m-30) REVERT: S 234 CYS cc_start: 0.9356 (m) cc_final: 0.9086 (m) REVERT: S 318 MET cc_start: 0.9155 (mtm) cc_final: 0.8822 (mtp) REVERT: S 324 GLU cc_start: 0.8971 (pp20) cc_final: 0.8742 (pp20) REVERT: S 328 GLN cc_start: 0.9186 (mt0) cc_final: 0.8939 (mt0) REVERT: S 337 GLN cc_start: 0.9389 (mm-40) cc_final: 0.8661 (tm-30) REVERT: T 103 TYR cc_start: 0.8596 (p90) cc_final: 0.7941 (p90) REVERT: T 108 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8899 (mm-30) REVERT: T 146 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9164 (mtmm) REVERT: T 164 HIS cc_start: 0.9215 (t-170) cc_final: 0.8716 (t-90) REVERT: T 190 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: T 210 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: U 19 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8556 (mtp85) REVERT: U 108 GLU cc_start: 0.9269 (tp30) cc_final: 0.8884 (tp30) REVERT: U 164 HIS cc_start: 0.8535 (t-90) cc_final: 0.8310 (t-90) REVERT: U 190 ASP cc_start: 0.9133 (m-30) cc_final: 0.8832 (m-30) REVERT: U 321 GLU cc_start: 0.9261 (tp30) cc_final: 0.8812 (mt-10) REVERT: V 51 SER cc_start: 0.9041 (m) cc_final: 0.8805 (p) REVERT: V 121 LEU cc_start: 0.9245 (tt) cc_final: 0.9026 (tm) REVERT: V 158 ASN cc_start: 0.9644 (m-40) cc_final: 0.9370 (m110) REVERT: V 210 GLU cc_start: 0.8974 (mp0) cc_final: 0.8760 (mp0) REVERT: V 321 GLU cc_start: 0.9175 (mp0) cc_final: 0.8883 (mm-30) outliers start: 46 outliers final: 13 residues processed: 189 average time/residue: 1.1663 time to fit residues: 246.0387 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 190 ASP 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 88 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2947 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= 0.197 Angle : 0.604 12.713 21407 Z= 0.309 Chirality : 0.040 0.170 2400 Planarity : 0.004 0.046 2515 Dihedral : 18.663 79.732 2735 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.87 % Favored : 96.72 % Rotamer: Outliers : 3.58 % Allowed : 24.73 % Favored : 71.69 % 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 : -1.15 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 267 HIS 0.004 0.001 HIS R 30 PHE 0.013 0.001 PHE T 138 TYR 0.012 0.001 TYR T 103 ARG 0.005 0.000 ARG U 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 1.796 Fit side-chains REVERT: R 18 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: R 186 GLN cc_start: 0.8529 (mp10) cc_final: 0.8187 (mp10) REVERT: R 193 LYS cc_start: 0.9287 (ttpt) cc_final: 0.9006 (tttt) REVERT: R 248 LEU cc_start: 0.9781 (mt) cc_final: 0.9508 (pp) REVERT: R 293 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8716 (mt) REVERT: S 25 ASN cc_start: 0.9036 (m-40) cc_final: 0.8825 (m-40) REVERT: S 71 GLU cc_start: 0.9341 (tt0) cc_final: 0.9086 (tm-30) REVERT: S 103 TYR cc_start: 0.8338 (p90) cc_final: 0.7933 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9255 (t0) cc_final: 0.8935 (t0) REVERT: S 138 PHE cc_start: 0.9221 (m-80) cc_final: 0.8873 (m-80) REVERT: S 144 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: S 146 LYS cc_start: 0.9072 (pttp) cc_final: 0.8704 (pptt) REVERT: S 190 ASP cc_start: 0.9300 (m-30) cc_final: 0.9076 (m-30) REVERT: S 318 MET cc_start: 0.9152 (mtm) cc_final: 0.8849 (mtp) REVERT: S 337 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8657 (tm-30) REVERT: T 103 TYR cc_start: 0.8775 (p90) cc_final: 0.8004 (p90) REVERT: T 108 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8840 (mm-30) REVERT: T 164 HIS cc_start: 0.9257 (t-170) cc_final: 0.8674 (t-90) REVERT: T 190 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: T 210 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8722 (mp0) REVERT: T 293 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9046 (mm) REVERT: T 321 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8952 (mt-10) REVERT: U 19 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8561 (mtp85) REVERT: U 108 GLU cc_start: 0.9291 (tp30) cc_final: 0.8891 (tp30) REVERT: U 164 HIS cc_start: 0.8502 (t-90) cc_final: 0.8059 (t-90) REVERT: U 190 ASP cc_start: 0.9179 (m-30) cc_final: 0.8825 (m-30) REVERT: U 321 GLU cc_start: 0.9242 (tp30) cc_final: 0.8863 (mt-10) REVERT: V 51 SER cc_start: 0.9154 (m) cc_final: 0.8887 (p) REVERT: V 121 LEU cc_start: 0.9231 (tt) cc_final: 0.8999 (tm) REVERT: V 158 ASN cc_start: 0.9634 (m-40) cc_final: 0.9374 (m110) REVERT: V 210 GLU cc_start: 0.9010 (mp0) cc_final: 0.8775 (mp0) REVERT: V 321 GLU cc_start: 0.9250 (mp0) cc_final: 0.8872 (mm-30) REVERT: V 345 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8558 (mp) outliers start: 53 outliers final: 18 residues processed: 185 average time/residue: 1.1431 time to fit residues: 238.0747 Evaluate side-chains 147 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 S residue 144 GLU Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 128 TYR Chi-restraints excluded: chain T residue 190 ASP 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 158 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** S 197 ASN ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15603 Z= 0.293 Angle : 0.618 11.793 21407 Z= 0.321 Chirality : 0.041 0.154 2400 Planarity : 0.004 0.047 2515 Dihedral : 18.679 84.437 2730 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Rotamer: Outliers : 3.92 % Allowed : 25.14 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.21), residues: 1705 helix: 1.41 (0.17), residues: 1055 sheet: -0.52 (0.45), residues: 140 loop : -1.01 (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 0.002 PHE U 126 TYR 0.019 0.001 TYR R 109 ARG 0.004 0.000 ARG T 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 122 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: R 186 GLN cc_start: 0.8616 (mp10) cc_final: 0.8268 (mp10) REVERT: R 193 LYS cc_start: 0.9338 (ttpt) cc_final: 0.9052 (tttt) REVERT: R 248 LEU cc_start: 0.9795 (mt) cc_final: 0.9509 (pp) REVERT: R 318 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: S 71 GLU cc_start: 0.9370 (tt0) cc_final: 0.9138 (tm-30) REVERT: S 103 TYR cc_start: 0.8312 (p90) cc_final: 0.7901 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9305 (t0) cc_final: 0.8956 (t0) REVERT: S 138 PHE cc_start: 0.9298 (m-80) cc_final: 0.9001 (m-80) REVERT: S 144 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: S 146 LYS cc_start: 0.9360 (pttp) cc_final: 0.8921 (pptt) REVERT: S 318 MET cc_start: 0.9126 (mtm) cc_final: 0.8872 (mtp) REVERT: S 324 GLU cc_start: 0.9050 (pp20) cc_final: 0.8746 (tm-30) REVERT: S 337 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8625 (tm-30) REVERT: T 103 TYR cc_start: 0.8877 (p90) cc_final: 0.7996 (p90) REVERT: T 108 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8930 (mm-30) REVERT: T 164 HIS cc_start: 0.9297 (t-170) cc_final: 0.8664 (t-90) REVERT: T 210 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8721 (mp0) REVERT: T 293 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9127 (mm) REVERT: T 321 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8966 (mt-10) REVERT: U 19 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8562 (mtp85) REVERT: U 128 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: U 164 HIS cc_start: 0.8665 (t-90) cc_final: 0.8087 (t-90) REVERT: U 190 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8901 (m-30) REVERT: U 252 GLN cc_start: 0.9403 (OUTLIER) cc_final: 0.9092 (tt0) REVERT: V 128 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: V 158 ASN cc_start: 0.9624 (m-40) cc_final: 0.9367 (m110) REVERT: V 210 GLU cc_start: 0.9061 (mp0) cc_final: 0.8783 (mp0) REVERT: V 321 GLU cc_start: 0.9292 (mp0) cc_final: 0.8935 (mm-30) REVERT: V 345 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8909 (mp) outliers start: 58 outliers final: 23 residues processed: 169 average time/residue: 1.0869 time to fit residues: 206.7558 Evaluate side-chains 140 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 185 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 145 SER Chi-restraints excluded: chain T residue 160 LEU 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 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 283 ASP Chi-restraints excluded: chain V residue 114 LEU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 192 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 275 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 chunk 57 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15603 Z= 0.164 Angle : 0.595 12.223 21407 Z= 0.301 Chirality : 0.040 0.168 2400 Planarity : 0.004 0.043 2515 Dihedral : 18.389 87.467 2729 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.24 % Allowed : 25.47 % 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: 0.87 (0.21), residues: 1705 helix: 1.41 (0.17), residues: 1065 sheet: -0.45 (0.46), residues: 140 loop : -0.84 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.026 0.001 PHE U 138 TYR 0.020 0.001 TYR R 109 ARG 0.004 0.000 ARG S 112 *********************** 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 178 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 146 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8509 (ttmt) REVERT: R 186 GLN cc_start: 0.8651 (mp10) cc_final: 0.8278 (mp10) REVERT: R 248 LEU cc_start: 0.9770 (mt) cc_final: 0.9499 (pp) REVERT: R 318 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: S 71 GLU cc_start: 0.9352 (tt0) cc_final: 0.9079 (tm-30) REVERT: S 103 TYR cc_start: 0.8251 (p90) cc_final: 0.7871 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9256 (t0) cc_final: 0.8934 (t0) REVERT: S 138 PHE cc_start: 0.9299 (m-80) cc_final: 0.9039 (m-80) REVERT: S 146 LYS cc_start: 0.9327 (pttp) cc_final: 0.8962 (pptt) REVERT: S 190 ASP cc_start: 0.9317 (m-30) cc_final: 0.9088 (m-30) REVERT: S 324 GLU cc_start: 0.8990 (pp20) cc_final: 0.8673 (tm-30) REVERT: S 337 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8637 (tm-30) REVERT: T 108 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8821 (mm-30) REVERT: T 164 HIS cc_start: 0.9257 (t-170) cc_final: 0.8691 (t-90) REVERT: T 190 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.9007 (m-30) REVERT: U 41 MET cc_start: 0.9182 (tpp) cc_final: 0.8853 (mmm) REVERT: U 128 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: U 158 ASN cc_start: 0.9601 (m110) cc_final: 0.9066 (m110) REVERT: U 164 HIS cc_start: 0.8640 (t-90) cc_final: 0.7998 (t-90) REVERT: U 190 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8681 (m-30) REVERT: U 252 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.9142 (tt0) REVERT: V 19 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7967 (mpp80) REVERT: V 51 SER cc_start: 0.9294 (m) cc_final: 0.9040 (p) REVERT: V 103 TYR cc_start: 0.8376 (p90) cc_final: 0.8047 (p90) REVERT: V 128 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: V 158 ASN cc_start: 0.9651 (m-40) cc_final: 0.9347 (m110) REVERT: V 210 GLU cc_start: 0.9120 (mp0) cc_final: 0.8905 (mp0) REVERT: V 321 GLU cc_start: 0.9273 (mp0) cc_final: 0.8897 (mm-30) REVERT: V 345 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8728 (mp) outliers start: 48 outliers final: 18 residues processed: 168 average time/residue: 1.0309 time to fit residues: 196.9320 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 185 LEU 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 R residue 318 MET Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 190 ASP Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- 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 216 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 254 HIS V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15603 Z= 0.469 Angle : 0.701 10.966 21407 Z= 0.364 Chirality : 0.043 0.188 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.620 88.977 2729 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.40 % Favored : 96.19 % Rotamer: Outliers : 4.19 % Allowed : 26.35 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.21), residues: 1705 helix: 1.37 (0.17), residues: 1045 sheet: -0.64 (0.46), residues: 140 loop : -0.88 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 267 HIS 0.004 0.001 HIS V 175 PHE 0.029 0.002 PHE U 138 TYR 0.019 0.002 TYR U 103 ARG 0.006 0.001 ARG S 42 *********************** 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 175 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 113 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: R 146 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8488 (mttt) REVERT: R 186 GLN cc_start: 0.8648 (mp10) cc_final: 0.8294 (mp10) REVERT: R 248 LEU cc_start: 0.9794 (mt) cc_final: 0.9486 (pp) REVERT: S 71 GLU cc_start: 0.9354 (tt0) cc_final: 0.9146 (tm-30) REVERT: S 103 TYR cc_start: 0.8445 (p90) cc_final: 0.7946 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9388 (t0) cc_final: 0.9019 (t0) REVERT: S 138 PHE cc_start: 0.9355 (m-80) cc_final: 0.9112 (m-80) REVERT: S 144 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: S 146 LYS cc_start: 0.9496 (pttp) cc_final: 0.8990 (pptt) REVERT: S 190 ASP cc_start: 0.9450 (m-30) cc_final: 0.9199 (m-30) REVERT: S 321 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: S 324 GLU cc_start: 0.9119 (pp20) cc_final: 0.8785 (tm-30) REVERT: S 337 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8617 (tm-30) REVERT: T 108 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8946 (mm-30) REVERT: T 164 HIS cc_start: 0.9310 (t-170) cc_final: 0.8623 (t-90) REVERT: T 210 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: U 19 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8512 (mtp85) REVERT: U 35 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8430 (pt0) REVERT: U 158 ASN cc_start: 0.9570 (m110) cc_final: 0.9050 (m110) REVERT: U 164 HIS cc_start: 0.8789 (t-90) cc_final: 0.8204 (t-90) REVERT: U 190 ASP cc_start: 0.9379 (OUTLIER) cc_final: 0.9027 (m-30) REVERT: U 252 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9097 (tt0) REVERT: U 321 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9062 (mm-30) REVERT: V 19 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7904 (mpp80) REVERT: V 103 TYR cc_start: 0.8692 (p90) cc_final: 0.8375 (p90) REVERT: V 158 ASN cc_start: 0.9627 (m-40) cc_final: 0.9356 (m110) REVERT: V 210 GLU cc_start: 0.9053 (mp0) cc_final: 0.8757 (mp0) REVERT: V 321 GLU cc_start: 0.9354 (mp0) cc_final: 0.9052 (mm-30) REVERT: V 345 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8990 (mp) outliers start: 62 outliers final: 26 residues processed: 169 average time/residue: 1.1229 time to fit residues: 215.3207 Evaluate side-chains 141 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 189 LEU 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 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 321 GLU Chi-restraints excluded: chain S residue 332 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 35 GLU 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 321 GLU Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 251 PHE Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 301 THR 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 19 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4194 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= 0.183 Angle : 0.615 11.733 21407 Z= 0.312 Chirality : 0.040 0.196 2400 Planarity : 0.004 0.048 2515 Dihedral : 18.235 88.778 2729 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.83 % Rotamer: Outliers : 2.84 % Allowed : 28.31 % Favored : 68.85 % 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: 0.97 (0.21), residues: 1705 helix: 1.56 (0.17), residues: 1045 sheet: -0.62 (0.46), residues: 140 loop : -0.80 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 267 HIS 0.004 0.001 HIS T 254 PHE 0.025 0.001 PHE T 138 TYR 0.029 0.001 TYR T 103 ARG 0.008 0.000 ARG U 215 *********************** 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 156 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 146 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8422 (tttt) REVERT: R 186 GLN cc_start: 0.8623 (mp10) cc_final: 0.8253 (mp10) REVERT: R 248 LEU cc_start: 0.9777 (mt) cc_final: 0.9501 (pp) REVERT: S 71 GLU cc_start: 0.9359 (tt0) cc_final: 0.9112 (tm-30) REVERT: S 103 TYR cc_start: 0.8270 (p90) cc_final: 0.7747 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9307 (t0) cc_final: 0.8939 (t0) REVERT: S 128 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: S 138 PHE cc_start: 0.9393 (m-80) cc_final: 0.9155 (m-80) REVERT: S 190 ASP cc_start: 0.9360 (m-30) cc_final: 0.9143 (m-30) REVERT: S 321 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: S 324 GLU cc_start: 0.9030 (pp20) cc_final: 0.8697 (tm-30) REVERT: S 337 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8647 (tm-30) REVERT: T 89 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9189 (p) REVERT: T 108 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8837 (mm-30) REVERT: T 164 HIS cc_start: 0.9286 (t-170) cc_final: 0.8682 (t-90) REVERT: T 198 MET cc_start: 0.8806 (mtm) cc_final: 0.8526 (mtp) REVERT: T 210 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8767 (mp0) REVERT: U 19 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8939 (mpp80) REVERT: U 41 MET cc_start: 0.9191 (tpp) cc_final: 0.8865 (mmm) REVERT: U 128 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: U 158 ASN cc_start: 0.9596 (m110) cc_final: 0.9026 (m110) REVERT: U 164 HIS cc_start: 0.8836 (t-90) cc_final: 0.8089 (t-90) REVERT: U 190 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: U 252 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.9009 (tt0) REVERT: V 19 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7887 (mpp80) REVERT: V 51 SER cc_start: 0.9375 (m) cc_final: 0.9080 (p) REVERT: V 103 TYR cc_start: 0.8613 (p90) cc_final: 0.8176 (p90) REVERT: V 158 ASN cc_start: 0.9649 (m-40) cc_final: 0.9341 (m110) REVERT: V 210 GLU cc_start: 0.9141 (mp0) cc_final: 0.8914 (mp0) REVERT: V 321 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8988 (mm-30) REVERT: V 345 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8943 (mp) outliers start: 42 outliers final: 19 residues processed: 150 average time/residue: 1.1165 time to fit residues: 189.2449 Evaluate side-chains 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 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 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 321 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 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 332 THR Chi-restraints excluded: chain U residue 19 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 186 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15603 Z= 0.218 Angle : 0.622 11.259 21407 Z= 0.314 Chirality : 0.041 0.223 2400 Planarity : 0.004 0.050 2515 Dihedral : 18.218 88.925 2729 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.70 % Favored : 96.83 % Rotamer: Outliers : 2.91 % Allowed : 29.05 % Favored : 68.04 % 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: 1.03 (0.21), residues: 1705 helix: 1.62 (0.17), residues: 1045 sheet: -0.69 (0.45), residues: 140 loop : -0.80 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.021 0.001 PHE T 138 TYR 0.030 0.001 TYR S 183 ARG 0.007 0.000 ARG U 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 146 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8326 (tttt) REVERT: R 186 GLN cc_start: 0.8648 (mp10) cc_final: 0.8279 (mp10) REVERT: R 248 LEU cc_start: 0.9775 (mt) cc_final: 0.9499 (pp) REVERT: R 318 MET cc_start: 0.8158 (mtt) cc_final: 0.7843 (mtt) REVERT: S 71 GLU cc_start: 0.9372 (tt0) cc_final: 0.9110 (tm-30) REVERT: S 103 TYR cc_start: 0.8295 (p90) cc_final: 0.7772 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9349 (t0) cc_final: 0.8995 (t0) REVERT: S 128 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: S 138 PHE cc_start: 0.9414 (m-80) cc_final: 0.9196 (m-80) REVERT: S 210 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: S 321 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: S 324 GLU cc_start: 0.9045 (pp20) cc_final: 0.8721 (tm-30) REVERT: S 337 GLN cc_start: 0.9332 (mm-40) cc_final: 0.8641 (tm-30) REVERT: T 108 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8878 (mm-30) REVERT: T 164 HIS cc_start: 0.9272 (t-170) cc_final: 0.8629 (t-90) REVERT: T 318 MET cc_start: 0.8957 (mmt) cc_final: 0.8715 (mmm) REVERT: U 19 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8942 (mpp80) REVERT: U 41 MET cc_start: 0.9197 (tpp) cc_final: 0.8890 (mmm) REVERT: U 128 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: U 158 ASN cc_start: 0.9576 (m110) cc_final: 0.8998 (m110) REVERT: U 164 HIS cc_start: 0.8832 (t-90) cc_final: 0.8201 (t-90) REVERT: U 190 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8807 (m-30) REVERT: U 252 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9046 (tt0) REVERT: V 19 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7792 (mpp80) REVERT: V 51 SER cc_start: 0.9413 (m) cc_final: 0.9093 (p) REVERT: V 103 TYR cc_start: 0.8678 (p90) cc_final: 0.8282 (p90) REVERT: V 158 ASN cc_start: 0.9627 (m-40) cc_final: 0.9330 (m110) REVERT: V 210 GLU cc_start: 0.9130 (mp0) cc_final: 0.8890 (mp0) REVERT: V 321 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9057 (mm-30) REVERT: V 345 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8935 (mp) outliers start: 43 outliers final: 24 residues processed: 147 average time/residue: 1.1349 time to fit residues: 187.7329 Evaluate side-chains 143 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 142 ASN Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S 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 123 ASP Chi-restraints excluded: chain T residue 160 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 128 TYR Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 264 VAL Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4417 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= 0.188 Angle : 0.627 10.997 21407 Z= 0.317 Chirality : 0.040 0.186 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.167 89.090 2729 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.76 % Favored : 96.77 % Rotamer: Outliers : 2.30 % Allowed : 29.93 % 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: 1.33 (0.21), residues: 1705 helix: 1.82 (0.17), residues: 1020 sheet: -0.66 (0.45), residues: 140 loop : -0.44 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.019 0.001 PHE T 138 TYR 0.029 0.001 TYR T 103 ARG 0.006 0.000 ARG U 215 *********************** 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 146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 MET cc_start: 0.8840 (mmm) cc_final: 0.8557 (tpt) REVERT: R 186 GLN cc_start: 0.8653 (mp10) cc_final: 0.8306 (mp10) REVERT: R 248 LEU cc_start: 0.9774 (mt) cc_final: 0.9494 (pp) REVERT: R 318 MET cc_start: 0.8071 (mtt) cc_final: 0.7767 (mtt) REVERT: S 71 GLU cc_start: 0.9372 (tt0) cc_final: 0.9103 (tm-30) REVERT: S 103 TYR cc_start: 0.8241 (p90) cc_final: 0.7714 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9346 (t0) cc_final: 0.9011 (t0) REVERT: S 128 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: S 138 PHE cc_start: 0.9412 (m-80) cc_final: 0.9202 (m-80) REVERT: S 189 LEU cc_start: 0.9453 (tp) cc_final: 0.9178 (pt) REVERT: S 324 GLU cc_start: 0.9037 (pp20) cc_final: 0.8687 (tm-30) REVERT: S 337 GLN cc_start: 0.9327 (mm-40) cc_final: 0.8625 (tm-30) REVERT: T 108 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8843 (mm-30) REVERT: T 164 HIS cc_start: 0.9260 (t-170) cc_final: 0.8626 (t-90) REVERT: U 19 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8963 (mpp80) REVERT: U 41 MET cc_start: 0.9178 (tpp) cc_final: 0.8886 (mmm) REVERT: U 158 ASN cc_start: 0.9577 (m110) cc_final: 0.8996 (m110) REVERT: U 164 HIS cc_start: 0.8841 (t-90) cc_final: 0.8331 (t-90) REVERT: U 190 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: U 252 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9054 (tt0) REVERT: V 51 SER cc_start: 0.9407 (m) cc_final: 0.9108 (p) REVERT: V 103 TYR cc_start: 0.8657 (p90) cc_final: 0.8266 (p90) REVERT: V 158 ASN cc_start: 0.9632 (m-40) cc_final: 0.9333 (m110) REVERT: V 210 GLU cc_start: 0.9134 (mp0) cc_final: 0.8910 (mp0) REVERT: V 321 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9068 (mm-30) REVERT: V 345 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8882 (mp) outliers start: 34 outliers final: 22 residues processed: 140 average time/residue: 1.1939 time to fit residues: 191.5398 Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 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 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 308 ARG Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 161 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 chunk 110 optimal weight: 0.0570 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 338 ASN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15603 Z= 0.185 Angle : 0.638 10.871 21407 Z= 0.322 Chirality : 0.040 0.170 2400 Planarity : 0.004 0.049 2515 Dihedral : 18.089 89.065 2729 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Rotamer: Outliers : 2.09 % Allowed : 30.20 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.37 (0.21), residues: 1705 helix: 1.87 (0.17), residues: 1020 sheet: -0.60 (0.46), residues: 140 loop : -0.46 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 267 HIS 0.004 0.001 HIS V 30 PHE 0.022 0.001 PHE V 138 TYR 0.031 0.001 TYR S 183 ARG 0.006 0.000 ARG U 215 ********************** 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 137 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: R 186 GLN cc_start: 0.8654 (mp10) cc_final: 0.8299 (mp10) REVERT: R 248 LEU cc_start: 0.9780 (mt) cc_final: 0.9494 (pp) REVERT: R 318 MET cc_start: 0.8086 (mtt) cc_final: 0.7818 (mtt) REVERT: S 71 GLU cc_start: 0.9371 (tt0) cc_final: 0.9066 (tm-30) REVERT: S 103 TYR cc_start: 0.8253 (p90) cc_final: 0.7720 (OUTLIER) REVERT: S 105 ASN cc_start: 0.9338 (t0) cc_final: 0.9012 (t0) REVERT: S 128 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: S 131 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7938 (mmp80) REVERT: S 138 PHE cc_start: 0.9416 (m-80) cc_final: 0.9212 (m-80) REVERT: S 189 LEU cc_start: 0.9484 (tp) cc_final: 0.9188 (pt) REVERT: S 190 ASP cc_start: 0.9404 (m-30) cc_final: 0.9085 (m-30) REVERT: S 324 GLU cc_start: 0.9027 (pp20) cc_final: 0.8688 (tm-30) REVERT: S 337 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8640 (tm-30) REVERT: T 108 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8856 (mm-30) REVERT: T 164 HIS cc_start: 0.9252 (t-170) cc_final: 0.8624 (t-90) REVERT: T 318 MET cc_start: 0.8976 (mmt) cc_final: 0.8687 (mmm) REVERT: U 19 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8962 (mpp80) REVERT: U 38 GLU cc_start: 0.8383 (pp20) cc_final: 0.8155 (pp20) REVERT: U 41 MET cc_start: 0.9153 (tpp) cc_final: 0.8853 (mmm) REVERT: U 158 ASN cc_start: 0.9579 (m110) cc_final: 0.9002 (m110) REVERT: U 164 HIS cc_start: 0.8852 (t-90) cc_final: 0.8372 (t-90) REVERT: U 190 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8685 (m-30) REVERT: U 252 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9057 (tt0) REVERT: V 51 SER cc_start: 0.9424 (m) cc_final: 0.9135 (p) REVERT: V 103 TYR cc_start: 0.8651 (p90) cc_final: 0.8275 (p90) REVERT: V 158 ASN cc_start: 0.9624 (m-40) cc_final: 0.9327 (m110) REVERT: V 210 GLU cc_start: 0.9132 (mp0) cc_final: 0.8929 (mp0) REVERT: V 318 MET cc_start: 0.9258 (mmm) cc_final: 0.8800 (mpm) REVERT: V 321 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9064 (mm-30) REVERT: V 345 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (mp) outliers start: 31 outliers final: 21 residues processed: 133 average time/residue: 1.1346 time to fit residues: 170.1600 Evaluate side-chains 131 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 203 HIS Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 145 SER Chi-restraints excluded: chain S residue 167 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 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 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 308 ARG Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 321 GLU Chi-restraints excluded: chain V residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 0.0070 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 262 ASN ** V 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.082936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052991 restraints weight = 53142.467| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.96 r_work: 0.2829 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4629 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= 0.184 Angle : 0.637 11.032 21407 Z= 0.322 Chirality : 0.040 0.167 2400 Planarity : 0.004 0.050 2515 Dihedral : 17.998 89.168 2729 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.64 % Favored : 96.95 % Rotamer: Outliers : 2.03 % Allowed : 30.34 % Favored : 67.64 % 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 (0.21), residues: 1705 helix: 1.82 (0.17), residues: 1030 sheet: -0.55 (0.46), residues: 140 loop : -0.63 (0.28), residues: 535 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 0.018 0.001 PHE T 138 TYR 0.031 0.001 TYR R 109 ARG 0.006 0.000 ARG U 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.87 seconds wall clock time: 84 minutes 46.09 seconds (5086.09 seconds total)