Starting phenix.real_space_refine on Fri Jul 3 16:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.map" model { file = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tah_41135/07_2026/8tah_41135.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 6 5.49 5 Mg 2 5.21 5 S 71 5.16 5 C 9529 2.51 5 N 2566 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14978 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3225 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2723 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'TRP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2701 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Chain: "D" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2301 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1415 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1091 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 14978 At special positions: 0 Unit cell: (100.8, 137.76, 140.28, 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 71 16.00 P 6 15.00 Mg 2 11.99 O 2804 8.00 N 2566 7.00 C 9529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 651.2 milliseconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3534 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 22 sheets defined 40.9% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.924A pdb=" N ILE A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.531A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.945A pdb=" N ILE A 190 " --> pdb=" O GLY A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.818A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.627A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.719A pdb=" N ALA A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 330 through 354 removed outlier: 3.935A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.886A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.895A pdb=" N ILE A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS A 408 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.525A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 149 removed outlier: 3.656A pdb=" N GLN B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.548A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.524A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.508A pdb=" N GLU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.504A pdb=" N LEU B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.578A pdb=" N LYS B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.697A pdb=" N MET B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'C' and resid 357 through 364 removed outlier: 3.656A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 removed outlier: 3.513A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.601A pdb=" N GLY D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.513A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.698A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 84 Processing helix chain 'D' and resid 106 through 114 removed outlier: 3.517A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 134 removed outlier: 4.705A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.527A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.727A pdb=" N LYS D 210 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 246 through 279 Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.755A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 82 removed outlier: 4.287A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'E' and resid 122 through 149 removed outlier: 3.905A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.579A pdb=" N ASN E 170 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.700A pdb=" N LEU F 47 " --> pdb=" O LYS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.633A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 167 removed outlier: 4.388A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 68 through 85 removed outlier: 4.198A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 120 through 137 removed outlier: 3.622A pdb=" N VAL G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 removed outlier: 3.550A pdb=" N VAL G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.549A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 395 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.356A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.427A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.373A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.693A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.355A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 55 through 61 removed outlier: 4.241A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 99 through 104 removed outlier: 6.467A pdb=" N GLY C 114 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP C 104 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS C 110 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.702A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.741A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 249 through 254 removed outlier: 6.943A pdb=" N LEU C 271 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 36 Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AC4, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.620A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4776 1.34 - 1.46: 2876 1.46 - 1.58: 7540 1.58 - 1.69: 8 1.69 - 1.81: 110 Bond restraints: 15310 Sorted by residual: bond pdb=" N ALA D 284 " pdb=" CA ALA D 284 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.33e-02 5.65e+03 4.16e+00 bond pdb=" N VAL G 151 " pdb=" CA VAL G 151 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.61e+00 bond pdb=" C LEU B 313 " pdb=" N PRO B 314 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.40e+00 bond pdb=" N GLY E 175 " pdb=" CA GLY E 175 " ideal model delta sigma weight residual 1.451 1.476 -0.025 1.60e-02 3.91e+03 2.36e+00 ... (remaining 15305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 20065 1.58 - 3.16: 552 3.16 - 4.73: 94 4.73 - 6.31: 17 6.31 - 7.89: 8 Bond angle restraints: 20736 Sorted by residual: angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 112.29 108.25 4.04 9.40e-01 1.13e+00 1.85e+01 angle pdb=" C VAL C 335 " pdb=" N ASP C 336 " pdb=" CA ASP C 336 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C SER C 236 " pdb=" N VAL C 237 " pdb=" CA VAL C 237 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 118.44 123.47 -5.03 1.59e+00 3.96e-01 1.00e+01 angle pdb=" C ASN E 153 " pdb=" N ASP E 154 " pdb=" CA ASP E 154 " ideal model delta sigma weight residual 122.40 126.87 -4.47 1.45e+00 4.76e-01 9.50e+00 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 8497 17.58 - 35.16: 518 35.16 - 52.74: 128 52.74 - 70.31: 29 70.31 - 87.89: 5 Dihedral angle restraints: 9177 sinusoidal: 3703 harmonic: 5474 Sorted by residual: dihedral pdb=" CA ASN F 100 " pdb=" C ASN F 100 " pdb=" N PHE F 101 " pdb=" CA PHE F 101 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN E 152 " pdb=" C GLN E 152 " pdb=" N ASN E 153 " pdb=" CA ASN E 153 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP C 336 " pdb=" C ASP C 336 " pdb=" N LYS C 337 " pdb=" CA LYS C 337 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1516 0.042 - 0.084: 523 0.084 - 0.127: 201 0.127 - 0.169: 37 0.169 - 0.211: 10 Chirality restraints: 2287 Sorted by residual: chirality pdb=" CB VAL A 311 " pdb=" CA VAL A 311 " pdb=" CG1 VAL A 311 " pdb=" CG2 VAL A 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL A 55 " pdb=" CA VAL A 55 " pdb=" CG1 VAL A 55 " pdb=" CG2 VAL A 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA LYS C 139 " pdb=" N LYS C 139 " pdb=" C LYS C 139 " pdb=" CB LYS C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 2284 not shown) Planarity restraints: 2666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 228 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 229 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 151 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO C 152 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 313 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A 314 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.035 5.00e-02 4.00e+02 ... (remaining 2663 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 111 2.61 - 3.19: 11400 3.19 - 3.76: 22347 3.76 - 4.33: 32192 4.33 - 4.90: 53732 Nonbonded interactions: 119782 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O2B ATP A 502 " model vdw 2.043 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1G ATP A 502 " model vdw 2.073 2.170 nonbonded pdb="MG MG B 501 " pdb=" O2G ATP B 502 " model vdw 2.282 2.170 nonbonded pdb=" O VAL G 142 " pdb=" OG1 THR G 146 " model vdw 2.326 3.040 nonbonded pdb=" O SER E 157 " pdb=" OG1 THR E 161 " model vdw 2.333 3.040 ... (remaining 119777 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.005 0.054 15310 Z= 0.211 Angle : 0.656 7.888 20736 Z= 0.380 Chirality : 0.050 0.211 2287 Planarity : 0.007 0.083 2666 Dihedral : 12.607 87.893 5643 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.46 % Allowed : 8.62 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.17), residues: 1862 helix: -2.37 (0.14), residues: 692 sheet: 0.21 (0.27), residues: 365 loop : -1.27 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.016 0.001 TYR D 250 PHE 0.023 0.002 PHE C 111 TRP 0.014 0.001 TRP C 221 HIS 0.006 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (15310) covalent geometry : angle 0.65622 / 0.38 (20736) hydrogen bonds : bond 0.15935 / 10.26 ( 679) hydrogen bonds : angle 6.78473 / 4.69 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 470 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7623 (pp) REVERT: A 75 LYS cc_start: 0.7711 (mmtm) cc_final: 0.7370 (mmmm) REVERT: A 106 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 161 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6718 (mtt-85) REVERT: A 182 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 241 GLU cc_start: 0.6904 (tp30) cc_final: 0.6648 (mm-30) REVERT: A 244 LYS cc_start: 0.7136 (mttt) cc_final: 0.6902 (mtpt) REVERT: A 248 ASP cc_start: 0.7299 (t70) cc_final: 0.6755 (t0) REVERT: A 251 LYS cc_start: 0.7712 (tttt) cc_final: 0.7219 (ttpp) REVERT: A 253 ILE cc_start: 0.7716 (mt) cc_final: 0.7492 (OUTLIER) REVERT: A 255 GLN cc_start: 0.7459 (mp10) cc_final: 0.7222 (mp-120) REVERT: A 266 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6276 (mm-30) REVERT: A 298 GLU cc_start: 0.6948 (mp0) cc_final: 0.6344 (mp0) REVERT: A 302 GLU cc_start: 0.7040 (tt0) cc_final: 0.6626 (tt0) REVERT: A 317 LYS cc_start: 0.7477 (ttpp) cc_final: 0.7002 (ttpp) REVERT: A 329 ARG cc_start: 0.7347 (mtp180) cc_final: 0.7034 (mtp180) REVERT: A 333 ARG cc_start: 0.7361 (mtp180) cc_final: 0.7042 (mtp180) REVERT: A 334 ARG cc_start: 0.7146 (ttt180) cc_final: 0.6918 (ttt180) REVERT: A 338 ASP cc_start: 0.6839 (m-30) cc_final: 0.6638 (m-30) REVERT: A 351 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5857 (tp30) REVERT: A 364 ASP cc_start: 0.7394 (p0) cc_final: 0.7136 (p0) REVERT: A 368 ILE cc_start: 0.8148 (mp) cc_final: 0.7818 (mp) REVERT: A 391 TYR cc_start: 0.7712 (m-80) cc_final: 0.7436 (m-80) REVERT: A 393 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7136 (p) REVERT: A 414 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: B 127 MET cc_start: 0.6907 (mmt) cc_final: 0.6604 (mmt) REVERT: B 232 LYS cc_start: 0.7314 (tttt) cc_final: 0.7091 (ttpp) REVERT: B 253 LYS cc_start: 0.7697 (mttt) cc_final: 0.7443 (mtmm) REVERT: B 257 GLU cc_start: 0.7552 (mp0) cc_final: 0.7053 (mp0) REVERT: B 263 GLU cc_start: 0.7224 (tp30) cc_final: 0.6591 (tp30) REVERT: B 292 ASP cc_start: 0.7816 (t0) cc_final: 0.7585 (t0) REVERT: B 327 GLU cc_start: 0.7203 (tt0) cc_final: 0.6938 (tt0) REVERT: B 328 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7333 (mtt180) REVERT: B 345 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: B 346 ASP cc_start: 0.6981 (p0) cc_final: 0.6753 (p0) REVERT: B 365 MET cc_start: 0.5905 (mpt) cc_final: 0.4781 (tmt) REVERT: C 44 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7601 (ttpp) REVERT: C 46 HIS cc_start: 0.7818 (m-70) cc_final: 0.7450 (m-70) REVERT: C 65 ASP cc_start: 0.7633 (t70) cc_final: 0.7344 (t0) REVERT: C 85 VAL cc_start: 0.5929 (t) cc_final: 0.5681 (m) REVERT: C 94 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7883 (mtp180) REVERT: C 118 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7370 (mtm110) REVERT: C 138 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7623 (ptmm) REVERT: C 149 ASP cc_start: 0.7585 (t70) cc_final: 0.7215 (t0) REVERT: C 175 GLU cc_start: 0.7564 (mp0) cc_final: 0.6779 (mp0) REVERT: C 176 VAL cc_start: 0.7787 (t) cc_final: 0.7364 (m) REVERT: C 177 ASP cc_start: 0.7608 (m-30) cc_final: 0.7045 (m-30) REVERT: C 232 ASP cc_start: 0.7750 (t0) cc_final: 0.7392 (t0) REVERT: C 245 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7043 (pp20) REVERT: C 279 CYS cc_start: 0.7628 (t) cc_final: 0.7201 (t) REVERT: C 285 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7662 (mtpt) REVERT: C 290 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5287 (tptp) REVERT: C 361 GLU cc_start: 0.6661 (pp20) cc_final: 0.6408 (pp20) REVERT: D 34 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (p) REVERT: D 54 LYS cc_start: 0.6895 (mmtp) cc_final: 0.6655 (mttm) REVERT: D 62 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8045 (mtmm) REVERT: D 65 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7393 (mmmm) REVERT: D 75 LEU cc_start: 0.6880 (tt) cc_final: 0.6576 (tp) REVERT: D 79 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7318 (p) REVERT: D 98 ASP cc_start: 0.6365 (t70) cc_final: 0.5981 (t70) REVERT: D 100 GLU cc_start: 0.7009 (mp0) cc_final: 0.6281 (mp0) REVERT: D 115 MET cc_start: 0.7024 (mtt) cc_final: 0.6717 (mtm) REVERT: D 179 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6780 (ttmm) REVERT: D 213 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7212 (p0) REVERT: D 249 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (m-30) REVERT: D 267 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7184 (mtt90) REVERT: D 269 LYS cc_start: 0.7220 (tppt) cc_final: 0.6974 (tptm) REVERT: E 22 LEU cc_start: 0.7626 (mp) cc_final: 0.7307 (mp) REVERT: E 50 LYS cc_start: 0.7025 (mtpp) cc_final: 0.6558 (mttp) REVERT: E 57 ASN cc_start: 0.7498 (m-40) cc_final: 0.7250 (m110) REVERT: E 73 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6062 (mt) REVERT: E 81 LYS cc_start: 0.7064 (mmmt) cc_final: 0.6686 (mmmt) REVERT: F 37 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7477 (mm-30) REVERT: F 38 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7261 (p) REVERT: F 53 ILE cc_start: 0.7558 (mp) cc_final: 0.7338 (mt) REVERT: F 91 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6870 (mmt) REVERT: F 96 MET cc_start: 0.7750 (ttp) cc_final: 0.7337 (ttp) REVERT: F 97 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7314 (mtt90) REVERT: F 100 ASN cc_start: 0.7817 (m-40) cc_final: 0.7575 (m-40) REVERT: F 110 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7528 (mt-10) REVERT: F 148 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6654 (mm-30) REVERT: F 163 GLU cc_start: 0.7036 (tp30) cc_final: 0.6535 (tp30) REVERT: G 56 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.4870 (mp10) REVERT: G 146 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7376 (p) REVERT: H 24 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6436 (p) outliers start: 72 outliers final: 23 residues processed: 517 average time/residue: 0.6955 time to fit residues: 390.0848 Evaluate side-chains 477 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 438 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 267 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 153 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 MET Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 ASN B 76 ASN C 30 HIS C 291 GLN D 254 HIS F 125 GLN F 167 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102899 restraints weight = 20871.638| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.99 r_work: 0.3104 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 15310 Z= 0.366 Angle : 0.620 7.415 20736 Z= 0.334 Chirality : 0.050 0.160 2287 Planarity : 0.006 0.067 2666 Dihedral : 7.267 83.389 2122 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 4.59 % Allowed : 13.33 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 1862 helix: -0.17 (0.18), residues: 697 sheet: 0.24 (0.26), residues: 371 loop : -0.91 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 97 TYR 0.028 0.002 TYR D 43 PHE 0.029 0.003 PHE F 101 TRP 0.018 0.002 TRP A 378 HIS 0.008 0.002 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.37 (15310) covalent geometry : angle 0.62015 / 0.33 (20736) hydrogen bonds : bond 0.06360 / 4.16 ( 679) hydrogen bonds : angle 4.81384 / 3.37 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 469 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 VAL cc_start: 0.8466 (p) cc_final: 0.8234 (t) REVERT: A 79 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: A 121 GLU cc_start: 0.7785 (mp0) cc_final: 0.7513 (mp0) REVERT: A 161 ARG cc_start: 0.8400 (mtt90) cc_final: 0.8190 (mtt-85) REVERT: A 241 GLU cc_start: 0.8317 (tp30) cc_final: 0.8025 (mm-30) REVERT: A 251 LYS cc_start: 0.8664 (tttt) cc_final: 0.8407 (ttmm) REVERT: A 298 GLU cc_start: 0.7863 (mp0) cc_final: 0.7493 (mp0) REVERT: A 329 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7943 (mtm-85) REVERT: A 338 ASP cc_start: 0.8168 (m-30) cc_final: 0.7891 (m-30) REVERT: A 364 ASP cc_start: 0.7769 (p0) cc_final: 0.7456 (p0) REVERT: A 391 TYR cc_start: 0.8569 (m-80) cc_final: 0.8235 (m-80) REVERT: A 392 GLN cc_start: 0.7778 (mp10) cc_final: 0.7069 (mp10) REVERT: A 414 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: B 127 MET cc_start: 0.6943 (mmt) cc_final: 0.6532 (mmt) REVERT: B 143 VAL cc_start: 0.7911 (m) cc_final: 0.7692 (t) REVERT: B 180 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7697 (mmp80) REVERT: B 341 LYS cc_start: 0.8245 (mttt) cc_final: 0.7969 (mttt) REVERT: B 365 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5125 (tmt) REVERT: C 46 HIS cc_start: 0.8522 (m-70) cc_final: 0.8245 (m-70) REVERT: C 54 HIS cc_start: 0.8410 (t-90) cc_final: 0.8157 (t-90) REVERT: C 65 ASP cc_start: 0.8371 (t70) cc_final: 0.8029 (t0) REVERT: C 97 ARG cc_start: 0.8933 (mmt-90) cc_final: 0.8610 (mmt-90) REVERT: C 131 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6605 (p90) REVERT: C 149 ASP cc_start: 0.8029 (t70) cc_final: 0.7763 (t0) REVERT: C 175 GLU cc_start: 0.8294 (mp0) cc_final: 0.7606 (mp0) REVERT: C 176 VAL cc_start: 0.8748 (t) cc_final: 0.8524 (m) REVERT: C 245 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: C 287 ASP cc_start: 0.7906 (t0) cc_final: 0.7678 (t0) REVERT: C 290 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5722 (tptp) REVERT: C 361 GLU cc_start: 0.7423 (pp20) cc_final: 0.6987 (pp20) REVERT: D 75 LEU cc_start: 0.8612 (tt) cc_final: 0.8275 (tp) REVERT: D 77 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8385 (tppp) REVERT: D 79 VAL cc_start: 0.8743 (p) cc_final: 0.8530 (p) REVERT: D 98 ASP cc_start: 0.8328 (t70) cc_final: 0.8029 (t70) REVERT: D 100 GLU cc_start: 0.7892 (mp0) cc_final: 0.7223 (mp0) REVERT: D 115 MET cc_start: 0.8600 (mtt) cc_final: 0.8398 (mtp) REVERT: D 131 PHE cc_start: 0.8505 (m-10) cc_final: 0.8282 (m-10) REVERT: D 132 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 213 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7245 (p0) REVERT: D 269 LYS cc_start: 0.8810 (tppt) cc_final: 0.8605 (tptm) REVERT: E 15 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8417 (tt) REVERT: E 22 LEU cc_start: 0.8372 (mp) cc_final: 0.8035 (mm) REVERT: E 78 CYS cc_start: 0.7648 (m) cc_final: 0.7291 (m) REVERT: E 81 LYS cc_start: 0.7890 (mmmt) cc_final: 0.7541 (mmmt) REVERT: F 37 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7731 (mm-30) REVERT: F 57 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: F 163 GLU cc_start: 0.8259 (tp30) cc_final: 0.7899 (tp30) REVERT: F 166 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8212 (ttmt) REVERT: G 56 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: G 86 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8086 (t80) REVERT: H 24 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7317 (p) outliers start: 74 outliers final: 32 residues processed: 508 average time/residue: 0.6834 time to fit residues: 375.7615 Evaluate side-chains 501 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 458 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 28 optimal weight: 0.7980 chunk 184 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN B 226 ASN C 30 HIS C 75 ASN D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105236 restraints weight = 21205.598| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.03 r_work: 0.3146 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15310 Z= 0.118 Angle : 0.469 7.095 20736 Z= 0.253 Chirality : 0.043 0.167 2287 Planarity : 0.004 0.058 2666 Dihedral : 6.345 83.750 2087 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.48 % Rotamer: Outliers : 4.34 % Allowed : 15.56 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1862 helix: 0.79 (0.20), residues: 698 sheet: 0.35 (0.26), residues: 377 loop : -0.67 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.013 0.001 TYR D 43 PHE 0.015 0.001 PHE A 276 TRP 0.013 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15310) covalent geometry : angle 0.46869 / 0.25 (20736) hydrogen bonds : bond 0.04212 / 2.75 ( 679) hydrogen bonds : angle 4.35372 / 3.04 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7617 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: A 241 GLU cc_start: 0.8248 (tp30) cc_final: 0.8006 (mm-30) REVERT: A 248 ASP cc_start: 0.7877 (t70) cc_final: 0.7589 (t0) REVERT: A 251 LYS cc_start: 0.8560 (tttt) cc_final: 0.8288 (ttmm) REVERT: A 298 GLU cc_start: 0.7846 (mp0) cc_final: 0.7446 (mp0) REVERT: A 317 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8376 (ttpp) REVERT: A 338 ASP cc_start: 0.8172 (m-30) cc_final: 0.7917 (m-30) REVERT: A 364 ASP cc_start: 0.7737 (p0) cc_final: 0.7506 (p0) REVERT: A 391 TYR cc_start: 0.8519 (m-80) cc_final: 0.8190 (m-80) REVERT: A 398 LYS cc_start: 0.8182 (tttt) cc_final: 0.7945 (ttpt) REVERT: B 127 MET cc_start: 0.6850 (mmt) cc_final: 0.6450 (mmt) REVERT: B 180 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.7543 (mmp80) REVERT: B 214 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8398 (ttp80) REVERT: B 257 GLU cc_start: 0.7984 (mp0) cc_final: 0.7600 (mp0) REVERT: B 365 MET cc_start: 0.6031 (mpt) cc_final: 0.5151 (tmt) REVERT: C 49 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8492 (ptpp) REVERT: C 65 ASP cc_start: 0.8247 (t70) cc_final: 0.7916 (t0) REVERT: C 131 TRP cc_start: 0.6909 (OUTLIER) cc_final: 0.6449 (p90) REVERT: C 149 ASP cc_start: 0.8119 (t70) cc_final: 0.7864 (t0) REVERT: C 175 GLU cc_start: 0.8276 (mp0) cc_final: 0.7589 (mp0) REVERT: C 176 VAL cc_start: 0.8720 (t) cc_final: 0.8513 (m) REVERT: C 245 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (pp20) REVERT: C 287 ASP cc_start: 0.7900 (t0) cc_final: 0.7641 (t0) REVERT: C 290 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5736 (tptp) REVERT: C 361 GLU cc_start: 0.7274 (pp20) cc_final: 0.6849 (pp20) REVERT: D 12 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7783 (mm-30) REVERT: D 75 LEU cc_start: 0.8602 (tt) cc_final: 0.8219 (tp) REVERT: D 79 VAL cc_start: 0.8756 (p) cc_final: 0.8520 (p) REVERT: D 98 ASP cc_start: 0.8312 (t70) cc_final: 0.8037 (t70) REVERT: D 100 GLU cc_start: 0.7881 (mp0) cc_final: 0.7235 (mp0) REVERT: D 213 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7150 (p0) REVERT: D 269 LYS cc_start: 0.8827 (tppt) cc_final: 0.8622 (tptt) REVERT: E 22 LEU cc_start: 0.8294 (mp) cc_final: 0.7976 (mm) REVERT: E 81 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7499 (mmmt) REVERT: F 57 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: F 92 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7976 (ttp80) REVERT: F 156 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.8431 (ttm-80) REVERT: F 163 GLU cc_start: 0.8262 (tp30) cc_final: 0.7879 (tp30) REVERT: F 166 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8325 (ttpt) REVERT: G 56 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: G 86 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8029 (t80) REVERT: H 24 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7198 (p) outliers start: 70 outliers final: 31 residues processed: 485 average time/residue: 0.7531 time to fit residues: 394.7043 Evaluate side-chains 474 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 435 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN B 226 ASN C 30 HIS C 75 ASN D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103499 restraints weight = 21156.829| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.01 r_work: 0.3114 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15310 Z= 0.264 Angle : 0.551 6.681 20736 Z= 0.296 Chirality : 0.047 0.213 2287 Planarity : 0.005 0.062 2666 Dihedral : 6.134 83.352 2075 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 4.28 % Allowed : 16.43 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1862 helix: 0.97 (0.20), residues: 700 sheet: 0.31 (0.26), residues: 380 loop : -0.65 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 71 TYR 0.024 0.002 TYR D 43 PHE 0.024 0.002 PHE F 101 TRP 0.014 0.002 TRP C 221 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.26 (15310) covalent geometry : angle 0.55082 / 0.30 (20736) hydrogen bonds : bond 0.05236 / 3.43 ( 679) hydrogen bonds : angle 4.43218 / 3.11 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 431 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: A 121 GLU cc_start: 0.7696 (mp0) cc_final: 0.7367 (mp0) REVERT: A 241 GLU cc_start: 0.8307 (tp30) cc_final: 0.8104 (mm-30) REVERT: A 248 ASP cc_start: 0.7864 (t70) cc_final: 0.7569 (t0) REVERT: A 251 LYS cc_start: 0.8555 (tttt) cc_final: 0.8276 (ttmm) REVERT: A 298 GLU cc_start: 0.7869 (mp0) cc_final: 0.7513 (mp0) REVERT: A 317 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8408 (ttpp) REVERT: A 338 ASP cc_start: 0.8106 (m-30) cc_final: 0.7872 (m-30) REVERT: A 364 ASP cc_start: 0.7709 (p0) cc_final: 0.7452 (p0) REVERT: A 392 GLN cc_start: 0.7816 (mp10) cc_final: 0.7087 (mp10) REVERT: A 398 LYS cc_start: 0.8136 (tttt) cc_final: 0.7929 (ttpt) REVERT: B 127 MET cc_start: 0.6907 (mmt) cc_final: 0.6515 (mmt) REVERT: B 180 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7794 (mmt-90) REVERT: B 365 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5215 (tmt) REVERT: C 97 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8589 (mmt-90) REVERT: C 131 TRP cc_start: 0.7201 (OUTLIER) cc_final: 0.6524 (p90) REVERT: C 149 ASP cc_start: 0.8096 (t70) cc_final: 0.7849 (t0) REVERT: C 175 GLU cc_start: 0.8268 (mp0) cc_final: 0.7597 (mp0) REVERT: C 245 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7740 (pp20) REVERT: C 290 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5755 (tptp) REVERT: C 352 MET cc_start: 0.8466 (tmm) cc_final: 0.8194 (tmm) REVERT: C 361 GLU cc_start: 0.7317 (pp20) cc_final: 0.6887 (pp20) REVERT: D 12 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7862 (mm-30) REVERT: D 75 LEU cc_start: 0.8623 (tt) cc_final: 0.8253 (tp) REVERT: D 79 VAL cc_start: 0.8756 (p) cc_final: 0.8518 (p) REVERT: D 100 GLU cc_start: 0.7926 (mp0) cc_final: 0.7283 (mp0) REVERT: D 213 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7114 (p0) REVERT: D 269 LYS cc_start: 0.8823 (tppt) cc_final: 0.8622 (tptm) REVERT: E 9 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7787 (tpt) REVERT: E 22 LEU cc_start: 0.8335 (mp) cc_final: 0.7989 (mm) REVERT: E 81 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7558 (mmmt) REVERT: F 35 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8261 (mttm) REVERT: F 57 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: F 84 LYS cc_start: 0.8294 (tttt) cc_final: 0.8086 (tttp) REVERT: F 163 GLU cc_start: 0.8246 (tp30) cc_final: 0.7955 (tp30) REVERT: F 166 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8411 (ttmt) REVERT: G 56 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6673 (mp10) REVERT: G 86 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8024 (t80) REVERT: H 24 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7166 (p) outliers start: 69 outliers final: 43 residues processed: 465 average time/residue: 0.7705 time to fit residues: 386.1331 Evaluate side-chains 483 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 429 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 0.6980 chunk 148 optimal weight: 0.0770 chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 30 HIS C 129 ASN D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105184 restraints weight = 21263.397| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.01 r_work: 0.3141 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15310 Z= 0.140 Angle : 0.479 7.163 20736 Z= 0.258 Chirality : 0.044 0.177 2287 Planarity : 0.004 0.056 2666 Dihedral : 5.815 82.985 2073 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 3.84 % Allowed : 16.92 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1862 helix: 1.29 (0.20), residues: 699 sheet: 0.32 (0.26), residues: 386 loop : -0.49 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 161 TYR 0.014 0.001 TYR D 43 PHE 0.016 0.001 PHE F 101 TRP 0.013 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15310) covalent geometry : angle 0.47939 / 0.26 (20736) hydrogen bonds : bond 0.04198 / 2.73 ( 679) hydrogen bonds : angle 4.21704 / 2.95 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 429 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8671 (pp) REVERT: A 79 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7429 (mtm-85) REVERT: A 121 GLU cc_start: 0.7682 (mp0) cc_final: 0.7339 (mp0) REVERT: A 241 GLU cc_start: 0.8276 (tp30) cc_final: 0.8035 (mm-30) REVERT: A 248 ASP cc_start: 0.7835 (t70) cc_final: 0.7545 (t0) REVERT: A 251 LYS cc_start: 0.8486 (tttt) cc_final: 0.8224 (ttmm) REVERT: A 298 GLU cc_start: 0.7846 (mp0) cc_final: 0.7460 (mp0) REVERT: A 317 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8402 (ttpp) REVERT: A 338 ASP cc_start: 0.8130 (m-30) cc_final: 0.7909 (m-30) REVERT: A 364 ASP cc_start: 0.7723 (p0) cc_final: 0.7495 (p0) REVERT: A 372 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7396 (mmt) REVERT: B 127 MET cc_start: 0.6873 (mmt) cc_final: 0.6664 (mmt) REVERT: B 180 ARG cc_start: 0.8024 (mmt-90) cc_final: 0.7738 (mmt-90) REVERT: B 230 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: B 365 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5224 (tmt) REVERT: C 49 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (ptpp) REVERT: C 97 ARG cc_start: 0.8870 (mmt-90) cc_final: 0.8583 (mmt-90) REVERT: C 131 TRP cc_start: 0.6888 (OUTLIER) cc_final: 0.6430 (p90) REVERT: C 149 ASP cc_start: 0.8079 (t70) cc_final: 0.7823 (t0) REVERT: C 175 GLU cc_start: 0.8263 (mp0) cc_final: 0.7607 (mp0) REVERT: C 183 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8080 (t) REVERT: C 290 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5682 (tptp) REVERT: C 352 MET cc_start: 0.8444 (tmm) cc_final: 0.8125 (tmm) REVERT: C 361 GLU cc_start: 0.7299 (pp20) cc_final: 0.6869 (pp20) REVERT: D 12 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7834 (mm-30) REVERT: D 75 LEU cc_start: 0.8622 (tt) cc_final: 0.8237 (tp) REVERT: D 79 VAL cc_start: 0.8759 (p) cc_final: 0.8509 (p) REVERT: D 100 GLU cc_start: 0.7948 (mp0) cc_final: 0.7424 (mp0) REVERT: D 125 PHE cc_start: 0.8410 (m-80) cc_final: 0.8205 (m-80) REVERT: D 269 LYS cc_start: 0.8829 (tppt) cc_final: 0.8628 (tptt) REVERT: E 22 LEU cc_start: 0.8286 (mp) cc_final: 0.7948 (mm) REVERT: E 62 ASN cc_start: 0.8041 (m-40) cc_final: 0.7807 (m-40) REVERT: E 81 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7536 (mmmt) REVERT: F 57 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: F 71 ARG cc_start: 0.8653 (ttm110) cc_final: 0.8422 (ttp-170) REVERT: G 16 VAL cc_start: 0.7795 (m) cc_final: 0.7416 (t) REVERT: G 86 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7984 (t80) REVERT: H 24 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.6981 (p) outliers start: 62 outliers final: 35 residues processed: 457 average time/residue: 0.7745 time to fit residues: 381.3049 Evaluate side-chains 465 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 419 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 339 LYS Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 179 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 154 optimal weight: 0.0040 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 30 HIS F 100 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104267 restraints weight = 20868.238| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.00 r_work: 0.3132 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15310 Z= 0.190 Angle : 0.512 7.701 20736 Z= 0.273 Chirality : 0.045 0.197 2287 Planarity : 0.004 0.058 2666 Dihedral : 5.570 82.107 2064 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 4.40 % Allowed : 17.17 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1862 helix: 1.30 (0.20), residues: 706 sheet: 0.37 (0.26), residues: 380 loop : -0.46 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 71 TYR 0.019 0.001 TYR D 43 PHE 0.020 0.001 PHE F 101 TRP 0.012 0.001 TRP C 221 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (15310) covalent geometry : angle 0.51186 / 0.27 (20736) hydrogen bonds : bond 0.04646 / 3.04 ( 679) hydrogen bonds : angle 4.24247 / 2.97 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 424 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7419 (mtm-85) REVERT: A 121 GLU cc_start: 0.7691 (mp0) cc_final: 0.7319 (mp0) REVERT: A 241 GLU cc_start: 0.8301 (tp30) cc_final: 0.8050 (mm-30) REVERT: A 248 ASP cc_start: 0.7850 (t70) cc_final: 0.7575 (t0) REVERT: A 251 LYS cc_start: 0.8501 (tttt) cc_final: 0.8227 (ttmm) REVERT: A 298 GLU cc_start: 0.7861 (mp0) cc_final: 0.7487 (mp0) REVERT: A 317 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8389 (ttpp) REVERT: A 338 ASP cc_start: 0.8138 (m-30) cc_final: 0.7901 (m-30) REVERT: A 364 ASP cc_start: 0.7715 (p0) cc_final: 0.7473 (p0) REVERT: A 372 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7457 (mmt) REVERT: A 414 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: B 180 ARG cc_start: 0.8081 (mmt-90) cc_final: 0.7785 (mmt-90) REVERT: B 230 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: B 365 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5289 (tmt) REVERT: C 97 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8614 (mmt-90) REVERT: C 131 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6537 (p90) REVERT: C 149 ASP cc_start: 0.8070 (t70) cc_final: 0.7822 (t0) REVERT: C 175 GLU cc_start: 0.8278 (mp0) cc_final: 0.7595 (mp0) REVERT: C 290 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5676 (tptp) REVERT: C 352 MET cc_start: 0.8466 (tmm) cc_final: 0.8200 (tmm) REVERT: C 361 GLU cc_start: 0.7310 (pp20) cc_final: 0.6881 (pp20) REVERT: C 365 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7135 (pp30) REVERT: D 12 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7873 (mm-30) REVERT: D 54 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8387 (mttm) REVERT: D 75 LEU cc_start: 0.8635 (tt) cc_final: 0.8260 (tp) REVERT: D 79 VAL cc_start: 0.8751 (p) cc_final: 0.8510 (p) REVERT: D 100 GLU cc_start: 0.7950 (mp0) cc_final: 0.7410 (mp0) REVERT: D 213 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7063 (p0) REVERT: D 269 LYS cc_start: 0.8806 (tppt) cc_final: 0.8598 (tptt) REVERT: E 9 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7728 (tpt) REVERT: E 22 LEU cc_start: 0.8303 (mp) cc_final: 0.7964 (mm) REVERT: E 81 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7556 (mmmt) REVERT: E 147 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8463 (ttmm) REVERT: F 35 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: F 57 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: F 84 LYS cc_start: 0.8281 (tttt) cc_final: 0.8027 (ttpp) REVERT: G 16 VAL cc_start: 0.7789 (m) cc_final: 0.7415 (t) REVERT: G 86 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7969 (t80) REVERT: H 24 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7070 (p) outliers start: 71 outliers final: 44 residues processed: 455 average time/residue: 0.7281 time to fit residues: 357.4643 Evaluate side-chains 487 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 429 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 87 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 243 ASN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 30 HIS F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105361 restraints weight = 20903.591| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.00 r_work: 0.3148 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15310 Z= 0.133 Angle : 0.481 7.891 20736 Z= 0.257 Chirality : 0.043 0.149 2287 Planarity : 0.004 0.056 2666 Dihedral : 5.441 81.714 2064 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 4.03 % Allowed : 18.29 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1862 helix: 1.44 (0.20), residues: 706 sheet: 0.41 (0.26), residues: 380 loop : -0.37 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.014 0.001 TYR D 43 PHE 0.016 0.001 PHE F 101 TRP 0.013 0.001 TRP B 89 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (15310) covalent geometry : angle 0.48092 / 0.26 (20736) hydrogen bonds : bond 0.04116 / 2.68 ( 679) hydrogen bonds : angle 4.13880 / 2.89 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 442 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: A 241 GLU cc_start: 0.8308 (tp30) cc_final: 0.8045 (mm-30) REVERT: A 248 ASP cc_start: 0.7835 (t70) cc_final: 0.7560 (t0) REVERT: A 251 LYS cc_start: 0.8463 (tttt) cc_final: 0.8192 (ttmm) REVERT: A 298 GLU cc_start: 0.7841 (mp0) cc_final: 0.7464 (mp0) REVERT: A 317 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8398 (ttpp) REVERT: A 338 ASP cc_start: 0.8159 (m-30) cc_final: 0.7910 (m-30) REVERT: A 364 ASP cc_start: 0.7717 (p0) cc_final: 0.7488 (p0) REVERT: A 372 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7391 (mmt) REVERT: A 414 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: B 127 MET cc_start: 0.6576 (mmt) cc_final: 0.6296 (mmt) REVERT: B 180 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7755 (mmt-90) REVERT: B 230 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: B 365 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5285 (tmt) REVERT: C 49 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (ptpp) REVERT: C 97 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8578 (mmt-90) REVERT: C 131 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6473 (p90) REVERT: C 149 ASP cc_start: 0.8041 (t70) cc_final: 0.7785 (t0) REVERT: C 175 GLU cc_start: 0.8279 (mp0) cc_final: 0.7615 (mp0) REVERT: C 183 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8067 (t) REVERT: C 290 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5682 (tptp) REVERT: C 361 GLU cc_start: 0.7304 (pp20) cc_final: 0.6869 (pp20) REVERT: C 365 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7099 (pp30) REVERT: D 75 LEU cc_start: 0.8623 (tt) cc_final: 0.8248 (tp) REVERT: D 79 VAL cc_start: 0.8771 (p) cc_final: 0.8529 (p) REVERT: D 100 GLU cc_start: 0.7969 (mp0) cc_final: 0.7442 (mp0) REVERT: D 213 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7076 (p0) REVERT: E 14 LYS cc_start: 0.8182 (mttp) cc_final: 0.7944 (mttp) REVERT: E 57 ASN cc_start: 0.8458 (m-40) cc_final: 0.8257 (m-40) REVERT: E 62 ASN cc_start: 0.7942 (m-40) cc_final: 0.7701 (m-40) REVERT: E 81 LYS cc_start: 0.7916 (mmmt) cc_final: 0.7567 (mmmt) REVERT: E 98 LEU cc_start: 0.8391 (tp) cc_final: 0.8178 (tt) REVERT: E 147 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8459 (ttmm) REVERT: F 35 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8254 (mttm) REVERT: F 57 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: G 16 VAL cc_start: 0.7771 (m) cc_final: 0.7398 (t) REVERT: G 86 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (t80) REVERT: H 24 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.6973 (p) outliers start: 65 outliers final: 40 residues processed: 471 average time/residue: 0.6551 time to fit residues: 333.5326 Evaluate side-chains 484 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 430 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 161 optimal weight: 0.7980 chunk 153 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 352 HIS D 8 ASN D 140 ASN D 239 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105673 restraints weight = 20952.652| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.01 r_work: 0.3157 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15310 Z= 0.122 Angle : 0.485 7.541 20736 Z= 0.257 Chirality : 0.043 0.151 2287 Planarity : 0.004 0.055 2666 Dihedral : 5.367 80.334 2064 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 18.72 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1862 helix: 1.58 (0.21), residues: 702 sheet: 0.43 (0.26), residues: 378 loop : -0.31 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 161 TYR 0.013 0.001 TYR D 43 PHE 0.016 0.001 PHE A 276 TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (15310) covalent geometry : angle 0.48479 / 0.26 (20736) hydrogen bonds : bond 0.03982 / 2.60 ( 679) hydrogen bonds : angle 4.06905 / 2.84 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 445 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: A 241 GLU cc_start: 0.8313 (tp30) cc_final: 0.8031 (mm-30) REVERT: A 244 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8462 (mtmt) REVERT: A 248 ASP cc_start: 0.7801 (t70) cc_final: 0.7534 (t0) REVERT: A 251 LYS cc_start: 0.8422 (tttt) cc_final: 0.8197 (ttmm) REVERT: A 298 GLU cc_start: 0.7849 (mp0) cc_final: 0.7433 (mp0) REVERT: A 338 ASP cc_start: 0.8165 (m-30) cc_final: 0.7852 (m-30) REVERT: A 364 ASP cc_start: 0.7718 (p0) cc_final: 0.7493 (p0) REVERT: A 372 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: A 414 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: B 74 MET cc_start: 0.5389 (mmm) cc_final: 0.4908 (mmm) REVERT: B 127 MET cc_start: 0.6632 (mmt) cc_final: 0.6331 (mmt) REVERT: B 180 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7764 (mmt-90) REVERT: B 230 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 365 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5285 (tmt) REVERT: C 49 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8434 (ptpp) REVERT: C 65 ASP cc_start: 0.8264 (t70) cc_final: 0.7925 (t0) REVERT: C 97 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8555 (mmt-90) REVERT: C 131 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.6455 (p90) REVERT: C 149 ASP cc_start: 0.8011 (t70) cc_final: 0.7740 (t0) REVERT: C 175 GLU cc_start: 0.8289 (mp0) cc_final: 0.7618 (mp0) REVERT: C 183 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8047 (t) REVERT: C 287 ASP cc_start: 0.7923 (t0) cc_final: 0.7542 (t0) REVERT: C 290 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5669 (tptp) REVERT: C 361 GLU cc_start: 0.7308 (pp20) cc_final: 0.6898 (pp20) REVERT: C 365 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7117 (pp30) REVERT: D 75 LEU cc_start: 0.8618 (tt) cc_final: 0.8231 (tp) REVERT: D 79 VAL cc_start: 0.8771 (p) cc_final: 0.8532 (p) REVERT: D 100 GLU cc_start: 0.7982 (mp0) cc_final: 0.7445 (mp0) REVERT: D 213 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7071 (p0) REVERT: E 14 LYS cc_start: 0.8191 (mttp) cc_final: 0.7961 (mttp) REVERT: E 62 ASN cc_start: 0.7908 (m-40) cc_final: 0.7651 (m-40) REVERT: E 81 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7594 (mmmt) REVERT: E 98 LEU cc_start: 0.8361 (tp) cc_final: 0.8143 (tt) REVERT: E 147 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8461 (ttmm) REVERT: F 35 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: F 57 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: F 156 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8327 (ttm-80) REVERT: G 16 VAL cc_start: 0.7764 (m) cc_final: 0.7395 (t) REVERT: G 86 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7897 (t80) REVERT: H 24 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.6911 (p) outliers start: 59 outliers final: 40 residues processed: 472 average time/residue: 0.6440 time to fit residues: 328.9587 Evaluate side-chains 501 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 447 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105501 restraints weight = 20948.042| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.01 r_work: 0.3149 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15310 Z= 0.140 Angle : 0.497 8.287 20736 Z= 0.263 Chirality : 0.044 0.151 2287 Planarity : 0.004 0.056 2666 Dihedral : 5.371 79.129 2064 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.84 % Allowed : 18.85 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1862 helix: 1.59 (0.21), residues: 704 sheet: 0.42 (0.26), residues: 366 loop : -0.29 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.015 0.001 TYR D 43 PHE 0.018 0.001 PHE A 276 TRP 0.012 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (15310) covalent geometry : angle 0.49702 / 0.26 (20736) hydrogen bonds : bond 0.04118 / 2.69 ( 679) hydrogen bonds : angle 4.06469 / 2.84 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 439 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7431 (mtm-85) REVERT: A 241 GLU cc_start: 0.8322 (tp30) cc_final: 0.8033 (mm-30) REVERT: A 244 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8464 (mtmt) REVERT: A 248 ASP cc_start: 0.7816 (t70) cc_final: 0.7554 (t0) REVERT: A 251 LYS cc_start: 0.8410 (tttt) cc_final: 0.8187 (ttmm) REVERT: A 298 GLU cc_start: 0.7848 (mp0) cc_final: 0.7437 (mp0) REVERT: A 338 ASP cc_start: 0.8174 (m-30) cc_final: 0.7927 (m-30) REVERT: A 364 ASP cc_start: 0.7709 (p0) cc_final: 0.7483 (p0) REVERT: A 372 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: A 414 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5640 (m-80) REVERT: B 74 MET cc_start: 0.5372 (mmm) cc_final: 0.4929 (mmm) REVERT: B 127 MET cc_start: 0.6581 (mmt) cc_final: 0.6290 (mmt) REVERT: B 140 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7725 (mm) REVERT: B 180 ARG cc_start: 0.8082 (mmt-90) cc_final: 0.7790 (mmt-90) REVERT: B 230 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: B 365 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5313 (tmt) REVERT: C 49 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8445 (ptpp) REVERT: C 65 ASP cc_start: 0.8275 (t70) cc_final: 0.7924 (t0) REVERT: C 97 ARG cc_start: 0.8835 (mmt-90) cc_final: 0.8564 (mmt-90) REVERT: C 175 GLU cc_start: 0.8285 (mp0) cc_final: 0.7612 (mp0) REVERT: C 183 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8054 (t) REVERT: C 287 ASP cc_start: 0.7949 (t0) cc_final: 0.7563 (t0) REVERT: C 290 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5667 (tptp) REVERT: C 361 GLU cc_start: 0.7305 (pp20) cc_final: 0.6947 (pp20) REVERT: C 365 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7090 (pp30) REVERT: D 75 LEU cc_start: 0.8623 (tt) cc_final: 0.8249 (tp) REVERT: D 79 VAL cc_start: 0.8775 (p) cc_final: 0.8537 (p) REVERT: D 100 GLU cc_start: 0.8005 (mp0) cc_final: 0.7461 (mp0) REVERT: D 125 PHE cc_start: 0.8377 (m-80) cc_final: 0.8155 (m-80) REVERT: D 213 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7065 (p0) REVERT: E 14 LYS cc_start: 0.8190 (mttp) cc_final: 0.7959 (mttp) REVERT: E 62 ASN cc_start: 0.7949 (m-40) cc_final: 0.7705 (m-40) REVERT: E 81 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7649 (mmmt) REVERT: E 98 LEU cc_start: 0.8336 (tp) cc_final: 0.8131 (tt) REVERT: E 147 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8454 (ttmm) REVERT: F 35 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (mttm) REVERT: F 57 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: G 16 VAL cc_start: 0.7751 (m) cc_final: 0.7386 (t) REVERT: H 24 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.6943 (p) outliers start: 62 outliers final: 43 residues processed: 468 average time/residue: 0.6833 time to fit residues: 345.7128 Evaluate side-chains 492 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 436 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 125 GLN F 167 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105527 restraints weight = 20976.921| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.01 r_work: 0.3148 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15310 Z= 0.143 Angle : 0.508 8.458 20736 Z= 0.267 Chirality : 0.044 0.159 2287 Planarity : 0.004 0.056 2666 Dihedral : 5.373 79.073 2064 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 3.53 % Allowed : 19.53 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1862 helix: 1.60 (0.21), residues: 704 sheet: 0.42 (0.26), residues: 361 loop : -0.25 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 161 TYR 0.015 0.001 TYR D 43 PHE 0.018 0.001 PHE A 276 TRP 0.011 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (15310) covalent geometry : angle 0.50789 / 0.27 (20736) hydrogen bonds : bond 0.04147 / 2.71 ( 679) hydrogen bonds : angle 4.06420 / 2.84 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 427 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: A 241 GLU cc_start: 0.8331 (tp30) cc_final: 0.8055 (mm-30) REVERT: A 244 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8380 (mtmt) REVERT: A 248 ASP cc_start: 0.7806 (t70) cc_final: 0.7539 (t0) REVERT: A 251 LYS cc_start: 0.8393 (tttt) cc_final: 0.8179 (ttmm) REVERT: A 298 GLU cc_start: 0.7844 (mp0) cc_final: 0.7442 (mp0) REVERT: A 338 ASP cc_start: 0.8170 (m-30) cc_final: 0.7873 (m-30) REVERT: A 364 ASP cc_start: 0.7701 (p0) cc_final: 0.7472 (p0) REVERT: A 372 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7296 (mmt) REVERT: A 391 TYR cc_start: 0.8428 (m-80) cc_final: 0.8092 (m-80) REVERT: B 74 MET cc_start: 0.5377 (mmm) cc_final: 0.4942 (mmm) REVERT: B 127 MET cc_start: 0.6616 (mmt) cc_final: 0.6309 (mmt) REVERT: B 140 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7728 (mm) REVERT: B 180 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7778 (mmt-90) REVERT: B 230 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: B 365 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5318 (tmt) REVERT: C 49 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8450 (ptpp) REVERT: C 97 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8557 (mmt-90) REVERT: C 131 TRP cc_start: 0.6816 (OUTLIER) cc_final: 0.6491 (p90) REVERT: C 175 GLU cc_start: 0.8294 (mp0) cc_final: 0.7623 (mp0) REVERT: C 183 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8054 (t) REVERT: C 290 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5673 (tptp) REVERT: C 361 GLU cc_start: 0.7274 (pp20) cc_final: 0.6927 (pp20) REVERT: C 365 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7092 (pp30) REVERT: D 75 LEU cc_start: 0.8627 (tt) cc_final: 0.8244 (tp) REVERT: D 79 VAL cc_start: 0.8771 (p) cc_final: 0.8535 (p) REVERT: D 100 GLU cc_start: 0.8002 (mp0) cc_final: 0.7427 (mp0) REVERT: D 213 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7061 (p0) REVERT: E 14 LYS cc_start: 0.8200 (mttp) cc_final: 0.7968 (mttp) REVERT: E 62 ASN cc_start: 0.7961 (m-40) cc_final: 0.7708 (m-40) REVERT: E 81 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7680 (mmmt) REVERT: E 147 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8436 (ttmm) REVERT: F 35 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8267 (mttm) REVERT: F 57 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: G 16 VAL cc_start: 0.7740 (m) cc_final: 0.7366 (t) REVERT: H 24 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7174 (p) outliers start: 57 outliers final: 41 residues processed: 452 average time/residue: 0.7043 time to fit residues: 343.3408 Evaluate side-chains 483 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 429 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 27 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104819 restraints weight = 20832.845| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.01 r_work: 0.3142 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15310 Z= 0.178 Angle : 0.527 8.018 20736 Z= 0.277 Chirality : 0.045 0.155 2287 Planarity : 0.004 0.057 2666 Dihedral : 5.451 79.920 2064 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 3.72 % Allowed : 19.34 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1862 helix: 1.55 (0.21), residues: 706 sheet: 0.43 (0.26), residues: 361 loop : -0.27 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 161 TYR 0.018 0.001 TYR D 43 PHE 0.019 0.001 PHE A 276 TRP 0.011 0.001 TRP C 221 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (15310) covalent geometry : angle 0.52750 / 0.28 (20736) hydrogen bonds : bond 0.04476 / 2.93 ( 679) hydrogen bonds : angle 4.13278 / 2.89 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7242.56 seconds wall clock time: 123 minutes 41.40 seconds (7421.40 seconds total)