Starting phenix.real_space_refine on Sat May 17 01:47:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tah_41135/05_2025/8tah_41135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tah_41135/05_2025/8tah_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_41135/05_2025/8tah_41135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tah_41135/05_2025/8tah_41135.map" model { file = "/net/cci-nas-00/data/ceres_data/8tah_41135/05_2025/8tah_41135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tah_41135/05_2025/8tah_41135.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} 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: 9.04, per 1000 atoms: 0.60 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: 3.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.70 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: 5.17 Time building geometry restraints manager: 4.19 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 - 17.89: 8532 17.89 - 35.78: 534 35.78 - 53.67: 139 53.67 - 71.56: 28 71.56 - 89.45: 6 Dihedral angle restraints: 9239 sinusoidal: 3765 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 9236 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: 1.320 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 35.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.100 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 13.050 89.449 5705 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP C 221 HIS 0.006 0.001 HIS C 224 PHE 0.023 0.002 PHE C 111 TYR 0.016 0.001 TYR D 250 ARG 0.003 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.15935 ( 679) hydrogen bonds : angle 6.78473 ( 1893) covalent geometry : bond 0.00454 (15310) covalent geometry : angle 0.65622 (20736) *********************** 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 : 1.479 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: 0.7564 (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: 0.6322 (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: 0.6869 (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: 0.7574 (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: 1.4846 time to fit residues: 831.0981 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 : 1.834 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3646 r_free = 0.3646 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104106 restraints weight = 20857.786| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.02 r_work: 0.3122 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15310 Z= 0.228 Angle : 0.532 6.222 20736 Z= 0.288 Chirality : 0.045 0.156 2287 Planarity : 0.005 0.061 2666 Dihedral : 8.193 79.075 2184 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 4.03 % Allowed : 13.52 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 1862 helix: -0.03 (0.19), residues: 698 sheet: 0.38 (0.27), residues: 356 loop : -0.87 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 378 HIS 0.006 0.001 HIS F 137 PHE 0.023 0.002 PHE F 101 TYR 0.021 0.002 TYR D 43 ARG 0.004 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 679) hydrogen bonds : angle 4.60842 ( 1893) covalent geometry : bond 0.00540 (15310) covalent geometry : angle 0.53153 (20736) *********************** 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 537 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 472 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 55 VAL cc_start: 0.8356 (p) cc_final: 0.8146 (t) REVERT: A 79 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7441 (mtm-85) REVERT: A 121 GLU cc_start: 0.7732 (mp0) cc_final: 0.7455 (mp0) REVERT: A 241 GLU cc_start: 0.8304 (tp30) cc_final: 0.8023 (mm-30) REVERT: A 251 LYS cc_start: 0.8605 (tttt) cc_final: 0.8375 (ttmm) REVERT: A 298 GLU cc_start: 0.7860 (mp0) cc_final: 0.7469 (mp0) REVERT: A 317 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8220 (ttpp) REVERT: A 329 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7927 (mtm-85) REVERT: A 338 ASP cc_start: 0.8137 (m-30) cc_final: 0.7831 (m-30) REVERT: A 364 ASP cc_start: 0.7785 (p0) cc_final: 0.7532 (p0) REVERT: A 391 TYR cc_start: 0.8543 (m-80) cc_final: 0.8270 (m-80) REVERT: A 414 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: B 127 MET cc_start: 0.6944 (mmt) cc_final: 0.6539 (mmt) REVERT: B 143 VAL cc_start: 0.7876 (m) cc_final: 0.7644 (t) REVERT: B 145 THR cc_start: 0.8494 (m) cc_final: 0.8284 (t) REVERT: B 180 ARG cc_start: 0.8099 (mmt-90) cc_final: 0.7641 (mmp80) REVERT: B 365 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5132 (tmt) REVERT: C 29 ASN cc_start: 0.8431 (p0) cc_final: 0.8216 (p0) REVERT: C 46 HIS cc_start: 0.8502 (m-70) cc_final: 0.8227 (m-70) REVERT: C 65 ASP cc_start: 0.8314 (t70) cc_final: 0.7960 (t0) REVERT: C 131 TRP cc_start: 0.7165 (OUTLIER) cc_final: 0.6599 (p90) REVERT: C 149 ASP cc_start: 0.8006 (t70) cc_final: 0.7778 (t0) REVERT: C 175 GLU cc_start: 0.8305 (mp0) cc_final: 0.7630 (mp0) REVERT: C 176 VAL cc_start: 0.8719 (t) cc_final: 0.8485 (m) REVERT: C 245 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: C 254 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8375 (t80) REVERT: C 290 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5691 (tptp) REVERT: C 361 GLU cc_start: 0.7381 (pp20) cc_final: 0.6956 (pp20) REVERT: D 34 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8602 (p) REVERT: D 75 LEU cc_start: 0.8575 (tt) cc_final: 0.8243 (tp) REVERT: D 77 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8376 (tppp) REVERT: D 79 VAL cc_start: 0.8749 (p) cc_final: 0.8529 (p) REVERT: D 98 ASP cc_start: 0.8296 (t70) cc_final: 0.7967 (t70) REVERT: D 100 GLU cc_start: 0.7873 (mp0) cc_final: 0.7229 (mp0) REVERT: D 213 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7216 (p0) REVERT: D 237 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.8133 (ttp-170) REVERT: D 269 LYS cc_start: 0.8828 (tppt) cc_final: 0.8593 (tptm) REVERT: E 22 LEU cc_start: 0.8348 (mp) cc_final: 0.8032 (mm) REVERT: E 50 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8210 (mttp) REVERT: E 62 ASN cc_start: 0.8074 (t0) cc_final: 0.7650 (t0) REVERT: E 81 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7516 (mmmt) REVERT: F 37 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7686 (mm-30) REVERT: F 57 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: F 156 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8302 (ttm-80) REVERT: F 163 GLU cc_start: 0.8208 (tp30) cc_final: 0.7937 (tp30) REVERT: G 56 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: G 86 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8105 (t80) REVERT: H 24 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7227 (p) outliers start: 65 outliers final: 27 residues processed: 506 average time/residue: 1.4941 time to fit residues: 818.0323 Evaluate side-chains 504 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 464 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 265 LYS 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 293 THR 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 34 THR 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 16 ILE Chi-restraints excluded: chain F residue 20 LEU 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 115 SER 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 180 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3660 r_free = 0.3660 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105186 restraints weight = 20957.623| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.02 r_work: 0.3145 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15310 Z= 0.128 Angle : 0.464 5.812 20736 Z= 0.251 Chirality : 0.043 0.168 2287 Planarity : 0.004 0.056 2666 Dihedral : 7.304 71.212 2150 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 3.91 % Allowed : 16.68 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1862 helix: 0.90 (0.20), residues: 696 sheet: 0.41 (0.26), residues: 367 loop : -0.64 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.014 0.001 PHE A 276 TYR 0.013 0.001 TYR D 43 ARG 0.006 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 679) hydrogen bonds : angle 4.25219 ( 1893) covalent geometry : bond 0.00296 (15310) covalent geometry : angle 0.46398 (20736) *********************** 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 513 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 450 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (pp) REVERT: A 79 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: A 241 GLU cc_start: 0.8257 (tp30) cc_final: 0.8011 (mm-30) REVERT: A 248 ASP cc_start: 0.7829 (t70) cc_final: 0.7569 (t0) REVERT: A 251 LYS cc_start: 0.8495 (tttt) cc_final: 0.8261 (ttmm) REVERT: A 298 GLU cc_start: 0.7858 (mp0) cc_final: 0.7463 (mp0) REVERT: A 317 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8235 (ttpp) REVERT: A 329 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7919 (mtm-85) REVERT: A 338 ASP cc_start: 0.8159 (m-30) cc_final: 0.7934 (m-30) REVERT: A 364 ASP cc_start: 0.7776 (p0) cc_final: 0.7566 (p0) REVERT: A 391 TYR cc_start: 0.8484 (m-80) cc_final: 0.8178 (m-80) REVERT: B 127 MET cc_start: 0.6853 (mmt) cc_final: 0.6614 (mmt) REVERT: B 143 VAL cc_start: 0.7881 (m) cc_final: 0.7675 (t) REVERT: B 180 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7755 (mmt-90) REVERT: B 232 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8447 (ttpp) REVERT: B 365 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5150 (tmt) REVERT: C 29 ASN cc_start: 0.8319 (p0) cc_final: 0.8110 (p0) REVERT: C 49 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8455 (ptpp) REVERT: C 65 ASP cc_start: 0.8229 (t70) cc_final: 0.7880 (t0) REVERT: C 131 TRP cc_start: 0.6865 (OUTLIER) cc_final: 0.6409 (p90) REVERT: C 149 ASP cc_start: 0.8007 (t70) cc_final: 0.7752 (t0) REVERT: C 175 GLU cc_start: 0.8285 (mp0) cc_final: 0.7640 (mp0) REVERT: C 176 VAL cc_start: 0.8711 (t) cc_final: 0.8493 (m) REVERT: C 245 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7755 (pp20) REVERT: C 287 ASP cc_start: 0.7895 (t0) cc_final: 0.7653 (t0) REVERT: C 290 LYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5712 (tptp) REVERT: C 352 MET cc_start: 0.8468 (tmm) cc_final: 0.8190 (tmm) REVERT: C 361 GLU cc_start: 0.7287 (pp20) cc_final: 0.6870 (pp20) REVERT: D 12 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7784 (mm-30) REVERT: D 75 LEU cc_start: 0.8590 (tt) cc_final: 0.8217 (tp) REVERT: D 77 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8377 (tppp) REVERT: D 79 VAL cc_start: 0.8771 (p) cc_final: 0.8535 (p) REVERT: D 98 ASP cc_start: 0.8341 (t70) cc_final: 0.8076 (t70) REVERT: D 100 GLU cc_start: 0.7887 (mp0) cc_final: 0.7267 (mp0) REVERT: D 213 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7099 (p0) REVERT: D 269 LYS cc_start: 0.8830 (tppt) cc_final: 0.8606 (tptt) REVERT: E 22 LEU cc_start: 0.8329 (mp) cc_final: 0.8030 (mm) REVERT: E 57 ASN cc_start: 0.8400 (m-40) cc_final: 0.8109 (m-40) REVERT: E 62 ASN cc_start: 0.7972 (t0) cc_final: 0.7566 (t0) REVERT: E 81 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7505 (mmmt) REVERT: F 57 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: F 163 GLU cc_start: 0.8235 (tp30) cc_final: 0.7740 (tp30) REVERT: F 166 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8209 (ttpt) REVERT: G 56 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6521 (mp10) REVERT: G 86 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8012 (t80) REVERT: H 24 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7153 (p) outliers start: 63 outliers final: 32 residues processed: 480 average time/residue: 1.5026 time to fit residues: 779.9479 Evaluate side-chains 476 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 433 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 206 GLN 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 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 232 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 50 GLU 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 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 109 ILE Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain F residue 30 VAL 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 94 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN B 226 ASN C 30 HIS D 130 GLN F 100 ASN F 125 GLN F 167 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105141 restraints weight = 21041.132| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.00 r_work: 0.3142 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15310 Z= 0.146 Angle : 0.475 5.978 20736 Z= 0.256 Chirality : 0.043 0.151 2287 Planarity : 0.004 0.056 2666 Dihedral : 6.902 71.754 2137 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 4.34 % Allowed : 16.80 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1862 helix: 1.18 (0.20), residues: 706 sheet: 0.37 (0.26), residues: 379 loop : -0.45 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE F 101 TYR 0.016 0.001 TYR D 43 ARG 0.005 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 679) hydrogen bonds : angle 4.15583 ( 1893) covalent geometry : bond 0.00344 (15310) covalent geometry : angle 0.47516 (20736) *********************** 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 513 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 443 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8531 (pp) REVERT: A 79 ARG cc_start: 0.7623 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: A 121 GLU cc_start: 0.7671 (mp0) cc_final: 0.7318 (mp0) REVERT: A 241 GLU cc_start: 0.8261 (tp30) cc_final: 0.8058 (mm-30) REVERT: A 248 ASP cc_start: 0.7810 (t70) cc_final: 0.7559 (t0) REVERT: A 251 LYS cc_start: 0.8432 (tttt) cc_final: 0.8197 (ttmm) REVERT: A 298 GLU cc_start: 0.7855 (mp0) cc_final: 0.7464 (mp0) REVERT: A 317 LYS cc_start: 0.8600 (ttpp) cc_final: 0.8373 (ttpp) REVERT: A 329 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7913 (mtm-85) REVERT: A 338 ASP cc_start: 0.8175 (m-30) cc_final: 0.7969 (m-30) REVERT: A 364 ASP cc_start: 0.7773 (p0) cc_final: 0.7571 (p0) REVERT: A 391 TYR cc_start: 0.8469 (m-80) cc_final: 0.8148 (m-80) REVERT: B 127 MET cc_start: 0.6928 (mmt) cc_final: 0.6700 (mmt) REVERT: B 180 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.7548 (mmp80) REVERT: B 232 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8430 (ttpp) REVERT: B 365 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5168 (tmt) REVERT: C 30 HIS cc_start: 0.8252 (p90) cc_final: 0.7993 (p-80) REVERT: C 65 ASP cc_start: 0.8271 (t70) cc_final: 0.7974 (t0) REVERT: C 131 TRP cc_start: 0.6887 (OUTLIER) cc_final: 0.6437 (p90) REVERT: C 149 ASP cc_start: 0.7985 (t70) cc_final: 0.7727 (t0) REVERT: C 175 GLU cc_start: 0.8265 (mp0) cc_final: 0.7618 (mp0) REVERT: C 245 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7744 (pp20) REVERT: C 287 ASP cc_start: 0.7920 (t0) cc_final: 0.7693 (t0) REVERT: C 290 LYS cc_start: 0.6101 (OUTLIER) cc_final: 0.5690 (tptp) REVERT: C 352 MET cc_start: 0.8467 (tmm) cc_final: 0.8201 (tmm) REVERT: C 361 GLU cc_start: 0.7286 (pp20) cc_final: 0.6864 (pp20) REVERT: D 12 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7837 (mm-30) REVERT: D 34 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8600 (p) REVERT: D 75 LEU cc_start: 0.8584 (tt) cc_final: 0.8209 (tp) REVERT: D 77 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8377 (tppp) REVERT: D 79 VAL cc_start: 0.8746 (p) cc_final: 0.8496 (p) REVERT: D 98 ASP cc_start: 0.8360 (t70) cc_final: 0.8141 (t70) REVERT: D 100 GLU cc_start: 0.7913 (mp0) cc_final: 0.7291 (mp0) REVERT: D 159 ASP cc_start: 0.8770 (p0) cc_final: 0.8548 (p0) REVERT: D 213 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7065 (p0) REVERT: D 269 LYS cc_start: 0.8834 (tppt) cc_final: 0.8614 (tptt) REVERT: E 22 LEU cc_start: 0.8279 (mp) cc_final: 0.7961 (mm) REVERT: E 81 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7487 (mmmt) REVERT: F 57 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: F 163 GLU cc_start: 0.8231 (tp30) cc_final: 0.7952 (tp30) REVERT: G 86 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7994 (t80) REVERT: H 24 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7136 (p) outliers start: 70 outliers final: 41 residues processed: 478 average time/residue: 1.4848 time to fit residues: 767.3634 Evaluate side-chains 490 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 438 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 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 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 232 LYS Chi-restraints excluded: chain B residue 343 ARG 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 50 GLU Chi-restraints excluded: chain C residue 52 ASN 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 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 34 THR Chi-restraints excluded: chain D residue 42 LEU 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 15 LEU Chi-restraints excluded: chain E residue 16 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 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 164 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 181 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 129 ASN 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 = 0.3663 r_free = 0.3663 target = 0.130795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105684 restraints weight = 21231.559| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.01 r_work: 0.3153 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15310 Z= 0.121 Angle : 0.461 7.137 20736 Z= 0.248 Chirality : 0.043 0.148 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.484 70.044 2133 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 4.15 % Allowed : 17.05 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1862 helix: 1.39 (0.20), residues: 707 sheet: 0.39 (0.26), residues: 379 loop : -0.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.016 0.001 PHE A 276 TYR 0.013 0.001 TYR D 43 ARG 0.006 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 679) hydrogen bonds : angle 4.05253 ( 1893) covalent geometry : bond 0.00282 (15310) covalent geometry : angle 0.46097 (20736) *********************** 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 509 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 442 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8540 (pp) REVERT: A 79 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: A 241 GLU cc_start: 0.8291 (tp30) cc_final: 0.8066 (mm-30) REVERT: A 248 ASP cc_start: 0.7780 (t70) cc_final: 0.7566 (t70) REVERT: A 298 GLU cc_start: 0.7850 (mp0) cc_final: 0.7440 (mp0) REVERT: A 317 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8406 (ttpp) REVERT: A 329 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7880 (mtm-85) REVERT: A 338 ASP cc_start: 0.8164 (m-30) cc_final: 0.7945 (m-30) REVERT: A 364 ASP cc_start: 0.7789 (p0) cc_final: 0.7579 (p0) REVERT: A 372 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7381 (mmt) REVERT: A 391 TYR cc_start: 0.8439 (m-80) cc_final: 0.8135 (m-80) REVERT: B 127 MET cc_start: 0.6897 (mmt) cc_final: 0.6684 (mmt) REVERT: B 180 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7752 (mmt-90) REVERT: B 232 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: B 257 GLU cc_start: 0.7942 (mp0) cc_final: 0.7572 (mp0) REVERT: B 365 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5176 (tmt) REVERT: C 65 ASP cc_start: 0.8222 (t70) cc_final: 0.7896 (t0) REVERT: C 149 ASP cc_start: 0.7956 (t70) cc_final: 0.7715 (t0) REVERT: C 175 GLU cc_start: 0.8264 (mp0) cc_final: 0.7638 (mp0) REVERT: C 183 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8032 (t) REVERT: C 245 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7674 (pp20) REVERT: C 287 ASP cc_start: 0.7914 (t0) cc_final: 0.7674 (t0) REVERT: C 290 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5699 (tptp) REVERT: C 352 MET cc_start: 0.8457 (tmm) cc_final: 0.8199 (tmm) REVERT: C 361 GLU cc_start: 0.7303 (pp20) cc_final: 0.6879 (pp20) REVERT: D 34 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8616 (p) REVERT: D 75 LEU cc_start: 0.8595 (tt) cc_final: 0.8220 (tp) REVERT: D 77 LYS cc_start: 0.8594 (mmmt) cc_final: 0.8379 (tppp) REVERT: D 79 VAL cc_start: 0.8761 (p) cc_final: 0.8519 (p) REVERT: D 100 GLU cc_start: 0.7926 (mp0) cc_final: 0.7327 (mp0) REVERT: D 159 ASP cc_start: 0.8761 (p0) cc_final: 0.8551 (p0) REVERT: E 57 ASN cc_start: 0.8442 (m-40) cc_final: 0.8099 (m-40) REVERT: E 62 ASN cc_start: 0.7970 (m-40) cc_final: 0.7664 (t0) REVERT: E 81 LYS cc_start: 0.7855 (mmmt) cc_final: 0.7505 (mmmt) REVERT: E 98 LEU cc_start: 0.8417 (tp) cc_final: 0.8197 (tt) REVERT: E 147 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8453 (ttmm) REVERT: F 57 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: F 92 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7916 (ttp80) REVERT: G 86 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7975 (t80) REVERT: H 24 THR cc_start: 0.7594 (OUTLIER) cc_final: 0.7102 (p) outliers start: 67 outliers final: 45 residues processed: 473 average time/residue: 1.4678 time to fit residues: 750.7259 Evaluate side-chains 482 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 426 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 71 THR 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 293 THR 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 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 232 LYS 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 7 LEU Chi-restraints excluded: chain C residue 13 CYS 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 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 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 73 ASP 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 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 43 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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 168 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 219 GLN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN F 100 ASN 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 = 0.3646 r_free = 0.3646 target = 0.129688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104325 restraints weight = 21027.798| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.01 r_work: 0.3133 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15310 Z= 0.188 Angle : 0.505 7.375 20736 Z= 0.270 Chirality : 0.045 0.153 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.788 73.719 2131 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 4.84 % Allowed : 17.11 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1862 helix: 1.37 (0.20), residues: 707 sheet: 0.37 (0.26), residues: 379 loop : -0.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.020 0.002 PHE F 101 TYR 0.019 0.001 TYR D 43 ARG 0.005 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 679) hydrogen bonds : angle 4.14434 ( 1893) covalent geometry : bond 0.00451 (15310) covalent geometry : angle 0.50526 (20736) *********************** 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 516 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 438 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 75 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (mmtt) REVERT: A 79 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: A 121 GLU cc_start: 0.7735 (mp0) cc_final: 0.7386 (mp0) REVERT: A 241 GLU cc_start: 0.8314 (tp30) cc_final: 0.8080 (mm-30) REVERT: A 248 ASP cc_start: 0.7827 (t70) cc_final: 0.7614 (t70) REVERT: A 298 GLU cc_start: 0.7862 (mp0) cc_final: 0.7490 (mp0) REVERT: A 317 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8391 (ttpp) REVERT: A 329 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7897 (mtm-85) REVERT: A 338 ASP cc_start: 0.8176 (m-30) cc_final: 0.7924 (m-30) REVERT: A 364 ASP cc_start: 0.7765 (p0) cc_final: 0.7525 (p0) REVERT: A 372 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7481 (mmt) REVERT: A 391 TYR cc_start: 0.8481 (m-80) cc_final: 0.8167 (m-80) REVERT: B 127 MET cc_start: 0.6871 (mmt) cc_final: 0.6670 (mmt) REVERT: B 180 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7666 (mmp80) REVERT: B 230 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: B 232 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8471 (ttpp) REVERT: B 257 GLU cc_start: 0.7985 (mp0) cc_final: 0.7653 (mp0) REVERT: B 365 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5205 (tmt) REVERT: C 65 ASP cc_start: 0.8305 (t70) cc_final: 0.7948 (t0) REVERT: C 131 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6498 (p90) REVERT: C 149 ASP cc_start: 0.7988 (t70) cc_final: 0.7749 (t0) REVERT: C 175 GLU cc_start: 0.8281 (mp0) cc_final: 0.7620 (mp0) REVERT: C 183 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8095 (t) REVERT: C 245 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7684 (pp20) REVERT: C 287 ASP cc_start: 0.7937 (t0) cc_final: 0.7678 (t0) REVERT: C 290 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5712 (tptp) REVERT: C 352 MET cc_start: 0.8460 (tmm) cc_final: 0.8190 (tmm) REVERT: C 361 GLU cc_start: 0.7316 (pp20) cc_final: 0.6896 (pp20) REVERT: C 365 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7097 (pp30) REVERT: D 12 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7880 (mm-30) REVERT: D 34 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8605 (p) REVERT: D 54 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (mttp) REVERT: D 75 LEU cc_start: 0.8602 (tt) cc_final: 0.8208 (tp) REVERT: D 77 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8400 (tppp) REVERT: D 79 VAL cc_start: 0.8743 (p) cc_final: 0.8504 (p) REVERT: D 100 GLU cc_start: 0.7980 (mp0) cc_final: 0.7479 (mp0) REVERT: D 213 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7115 (p0) REVERT: E 9 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7453 (tpp) REVERT: E 81 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7520 (mmmt) REVERT: E 147 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8460 (ttmm) REVERT: F 35 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8262 (mttm) REVERT: F 57 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: F 84 LYS cc_start: 0.8300 (tttt) cc_final: 0.8040 (ttpp) REVERT: F 163 GLU cc_start: 0.8201 (tp30) cc_final: 0.7890 (tp30) REVERT: G 16 VAL cc_start: 0.7772 (m) cc_final: 0.7400 (t) REVERT: H 24 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7187 (p) outliers start: 78 outliers final: 46 residues processed: 473 average time/residue: 1.5458 time to fit residues: 788.1526 Evaluate side-chains 499 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 435 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 191 LYS 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 293 THR 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 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 115 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 232 LYS 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 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 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 C residue 365 GLN Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 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 269 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 9 MET 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 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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 F residue 166 LYS 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 24 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 175 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 219 GLN A 243 ASN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 130 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 = 0.3653 r_free = 0.3653 target = 0.130152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104971 restraints weight = 21071.847| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.02 r_work: 0.3142 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15310 Z= 0.150 Angle : 0.491 7.831 20736 Z= 0.261 Chirality : 0.044 0.152 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.653 73.163 2131 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 4.34 % Allowed : 17.85 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1862 helix: 1.44 (0.20), residues: 708 sheet: 0.40 (0.26), residues: 379 loop : -0.30 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.016 0.001 PHE A 276 TYR 0.015 0.001 TYR D 43 ARG 0.005 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 679) hydrogen bonds : angle 4.07893 ( 1893) covalent geometry : bond 0.00357 (15310) covalent geometry : angle 0.49056 (20736) *********************** 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 506 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 436 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8540 (pp) REVERT: A 75 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8178 (mmtt) REVERT: A 79 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: A 121 GLU cc_start: 0.7718 (mp0) cc_final: 0.7341 (mp0) REVERT: A 161 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8330 (mtt-85) REVERT: A 241 GLU cc_start: 0.8312 (tp30) cc_final: 0.8070 (mm-30) REVERT: A 298 GLU cc_start: 0.7852 (mp0) cc_final: 0.7467 (mp0) REVERT: A 317 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8392 (ttpp) REVERT: A 329 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7870 (mtm-85) REVERT: A 338 ASP cc_start: 0.8186 (m-30) cc_final: 0.7859 (m-30) REVERT: A 364 ASP cc_start: 0.7740 (p0) cc_final: 0.7512 (p0) REVERT: A 372 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7428 (mmt) REVERT: B 180 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7777 (mmt-90) REVERT: B 230 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 257 GLU cc_start: 0.7962 (mp0) cc_final: 0.7607 (mp0) REVERT: B 365 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5289 (tmt) REVERT: C 65 ASP cc_start: 0.8272 (t70) cc_final: 0.7923 (t0) REVERT: C 131 TRP cc_start: 0.6858 (OUTLIER) cc_final: 0.6446 (p90) REVERT: C 149 ASP cc_start: 0.7975 (t70) cc_final: 0.7735 (t0) REVERT: C 175 GLU cc_start: 0.8297 (mp0) cc_final: 0.7625 (mp0) REVERT: C 183 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8076 (t) REVERT: C 245 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7665 (pp20) REVERT: C 287 ASP cc_start: 0.7927 (t0) cc_final: 0.7672 (t0) REVERT: C 290 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5661 (tptp) REVERT: C 352 MET cc_start: 0.8451 (tmm) cc_final: 0.8183 (tmm) REVERT: C 361 GLU cc_start: 0.7300 (pp20) cc_final: 0.6902 (pp20) REVERT: D 34 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (p) REVERT: D 54 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8491 (mttm) REVERT: D 75 LEU cc_start: 0.8627 (tt) cc_final: 0.8262 (tp) REVERT: D 77 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8397 (tppp) REVERT: D 79 VAL cc_start: 0.8764 (p) cc_final: 0.8517 (p) REVERT: D 98 ASP cc_start: 0.8614 (t70) cc_final: 0.8312 (t0) REVERT: D 100 GLU cc_start: 0.7995 (mp0) cc_final: 0.7472 (mp0) REVERT: D 213 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7045 (p0) REVERT: E 14 LYS cc_start: 0.8170 (mttp) cc_final: 0.7920 (mttp) REVERT: E 62 ASN cc_start: 0.7927 (m-40) cc_final: 0.7716 (m-40) REVERT: E 81 LYS cc_start: 0.7879 (mmmt) cc_final: 0.7523 (mmmt) REVERT: E 147 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8447 (ttmm) REVERT: F 35 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8252 (mttm) REVERT: F 57 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: F 84 LYS cc_start: 0.8292 (tttt) cc_final: 0.8015 (ttpp) REVERT: F 163 GLU cc_start: 0.8171 (tp30) cc_final: 0.7872 (tp30) REVERT: G 16 VAL cc_start: 0.7757 (m) cc_final: 0.7393 (t) REVERT: H 24 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7169 (p) outliers start: 70 outliers final: 46 residues processed: 468 average time/residue: 1.5370 time to fit residues: 776.1508 Evaluate side-chains 479 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 418 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 75 LYS 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 293 THR Chi-restraints excluded: chain A residue 340 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 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 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL 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 29 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 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 269 LYS 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 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 90 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN 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 119 ASN D 239 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105425 restraints weight = 20906.894| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.01 r_work: 0.3149 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2339 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= 0.131 Angle : 0.483 8.130 20736 Z= 0.258 Chirality : 0.043 0.155 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.494 72.436 2131 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 4.15 % Allowed : 18.47 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1862 helix: 1.52 (0.20), residues: 708 sheet: 0.48 (0.26), residues: 364 loop : -0.25 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 89 HIS 0.004 0.001 HIS F 137 PHE 0.016 0.001 PHE A 276 TYR 0.014 0.001 TYR D 43 ARG 0.006 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 679) hydrogen bonds : angle 4.01862 ( 1893) covalent geometry : bond 0.00309 (15310) covalent geometry : angle 0.48317 (20736) *********************** 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 488 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 421 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8552 (pp) REVERT: A 75 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8180 (mmtt) REVERT: A 79 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7421 (mtm-85) REVERT: A 161 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8338 (mtt-85) REVERT: A 241 GLU cc_start: 0.8341 (tp30) cc_final: 0.8078 (mm-30) REVERT: A 244 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8431 (ptpt) REVERT: A 298 GLU cc_start: 0.7861 (mp0) cc_final: 0.7460 (mp0) REVERT: A 317 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8399 (ttpp) REVERT: A 329 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7876 (mtm-85) REVERT: A 338 ASP cc_start: 0.8185 (m-30) cc_final: 0.7952 (m-30) REVERT: A 364 ASP cc_start: 0.7740 (p0) cc_final: 0.7528 (p0) REVERT: A 372 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (mmt) REVERT: B 127 MET cc_start: 0.6566 (mmt) cc_final: 0.6277 (mmt) REVERT: B 180 ARG cc_start: 0.8042 (mmt-90) cc_final: 0.7765 (mmt-90) REVERT: B 230 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: B 365 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5282 (tmt) REVERT: C 65 ASP cc_start: 0.8283 (t70) cc_final: 0.7953 (t0) REVERT: C 131 TRP cc_start: 0.6793 (OUTLIER) cc_final: 0.6440 (p90) REVERT: C 149 ASP cc_start: 0.7965 (t70) cc_final: 0.7721 (t0) REVERT: C 175 GLU cc_start: 0.8302 (mp0) cc_final: 0.7633 (mp0) REVERT: C 183 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8054 (t) REVERT: C 245 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7661 (pp20) REVERT: C 287 ASP cc_start: 0.7937 (t0) cc_final: 0.7596 (t0) REVERT: C 290 LYS cc_start: 0.6156 (OUTLIER) cc_final: 0.5662 (tptp) REVERT: C 352 MET cc_start: 0.8442 (tmm) cc_final: 0.8180 (tmm) REVERT: C 361 GLU cc_start: 0.7289 (pp20) cc_final: 0.6909 (pp20) REVERT: C 365 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7066 (pp30) REVERT: D 34 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (p) REVERT: D 54 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mttm) REVERT: D 75 LEU cc_start: 0.8611 (tt) cc_final: 0.8239 (tp) REVERT: D 77 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8406 (tppp) REVERT: D 79 VAL cc_start: 0.8763 (p) cc_final: 0.8527 (p) REVERT: D 98 ASP cc_start: 0.8603 (t70) cc_final: 0.8292 (t0) REVERT: D 100 GLU cc_start: 0.7983 (mp0) cc_final: 0.7452 (mp0) REVERT: D 125 PHE cc_start: 0.8361 (m-80) cc_final: 0.8121 (m-80) REVERT: D 213 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7084 (p0) REVERT: E 9 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7493 (tpp) REVERT: E 14 LYS cc_start: 0.8161 (mttp) cc_final: 0.7917 (mttp) REVERT: E 62 ASN cc_start: 0.7949 (m-40) cc_final: 0.7728 (m-40) REVERT: E 81 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7531 (mmmt) REVERT: E 98 LEU cc_start: 0.8418 (tp) cc_final: 0.8197 (tt) REVERT: E 147 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8439 (ttmm) REVERT: F 35 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8257 (mttm) REVERT: F 57 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: F 163 GLU cc_start: 0.8167 (tp30) cc_final: 0.7872 (tp30) REVERT: G 16 VAL cc_start: 0.7769 (m) cc_final: 0.7395 (t) REVERT: H 24 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7246 (p) outliers start: 67 outliers final: 43 residues processed: 451 average time/residue: 1.5760 time to fit residues: 765.6418 Evaluate side-chains 489 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 429 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain A residue 75 LYS 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 340 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 393 VAL Chi-restraints excluded: chain A residue 416 VAL 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 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 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 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL 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 34 THR Chi-restraints excluded: chain D residue 41 VAL 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 179 LYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 172 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 100 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 = 0.3662 r_free = 0.3662 target = 0.130729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105621 restraints weight = 20875.130| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.00 r_work: 0.3142 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15310 Z= 0.135 Angle : 0.494 8.298 20736 Z= 0.261 Chirality : 0.043 0.160 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.459 72.689 2131 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 3.78 % Allowed : 19.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1862 helix: 1.54 (0.20), residues: 708 sheet: 0.45 (0.26), residues: 363 loop : -0.22 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.014 0.001 TYR D 43 ARG 0.009 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 679) hydrogen bonds : angle 4.01060 ( 1893) covalent geometry : bond 0.00320 (15310) covalent geometry : angle 0.49369 (20736) *********************** 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 491 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (pp) REVERT: A 79 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: A 161 ARG cc_start: 0.8559 (mtt-85) cc_final: 0.8332 (mtt-85) REVERT: A 241 GLU cc_start: 0.8322 (tp30) cc_final: 0.8039 (mm-30) REVERT: A 244 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8406 (ptpt) REVERT: A 251 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8126 (ptmm) REVERT: A 298 GLU cc_start: 0.7850 (mp0) cc_final: 0.7444 (mp0) REVERT: A 317 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8382 (ttpp) REVERT: A 329 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7867 (mtm-85) REVERT: A 338 ASP cc_start: 0.8197 (m-30) cc_final: 0.7883 (m-30) REVERT: A 364 ASP cc_start: 0.7736 (p0) cc_final: 0.7516 (p0) REVERT: A 372 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7449 (mmt) REVERT: A 398 LYS cc_start: 0.8119 (tttt) cc_final: 0.7712 (tmtt) REVERT: B 127 MET cc_start: 0.6593 (mmt) cc_final: 0.6301 (mmt) REVERT: B 180 ARG cc_start: 0.8053 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: B 230 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 365 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5287 (tmt) REVERT: C 64 SER cc_start: 0.8560 (m) cc_final: 0.8358 (t) REVERT: C 65 ASP cc_start: 0.8290 (t70) cc_final: 0.7994 (t0) REVERT: C 131 TRP cc_start: 0.6782 (OUTLIER) cc_final: 0.6447 (p90) REVERT: C 149 ASP cc_start: 0.7960 (t70) cc_final: 0.7715 (t0) REVERT: C 175 GLU cc_start: 0.8308 (mp0) cc_final: 0.7638 (mp0) REVERT: C 183 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8048 (t) REVERT: C 245 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: C 287 ASP cc_start: 0.7933 (t0) cc_final: 0.7591 (t0) REVERT: C 290 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5693 (tptp) REVERT: C 361 GLU cc_start: 0.7280 (pp20) cc_final: 0.6916 (pp20) REVERT: C 365 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7086 (pp30) REVERT: D 34 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8620 (p) REVERT: D 54 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8499 (mttm) REVERT: D 75 LEU cc_start: 0.8602 (tt) cc_final: 0.8233 (tp) REVERT: D 77 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8391 (tppp) REVERT: D 79 VAL cc_start: 0.8756 (p) cc_final: 0.8513 (p) REVERT: D 98 ASP cc_start: 0.8597 (t70) cc_final: 0.8293 (t0) REVERT: D 100 GLU cc_start: 0.7994 (mp0) cc_final: 0.7456 (mp0) REVERT: D 213 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7066 (p0) REVERT: E 9 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7480 (tpp) REVERT: E 14 LYS cc_start: 0.8169 (mttp) cc_final: 0.7938 (mttp) REVERT: E 62 ASN cc_start: 0.7955 (m-40) cc_final: 0.7731 (m-40) REVERT: E 81 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7530 (mmmt) REVERT: E 147 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8447 (ttmm) REVERT: F 35 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8256 (mttm) REVERT: F 57 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: F 163 GLU cc_start: 0.8150 (tp30) cc_final: 0.7861 (tp30) REVERT: G 16 VAL cc_start: 0.7761 (m) cc_final: 0.7393 (t) REVERT: H 24 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7283 (p) outliers start: 61 outliers final: 42 residues processed: 456 average time/residue: 1.5856 time to fit residues: 777.3940 Evaluate side-chains 490 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 432 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 293 THR Chi-restraints excluded: chain A residue 340 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 393 VAL Chi-restraints excluded: chain A residue 416 VAL 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 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 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL 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 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 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 269 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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 74 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 162 optimal weight: 0.9980 chunk 153 optimal weight: 0.0870 chunk 149 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 100 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 = 0.3666 r_free = 0.3666 target = 0.131066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105717 restraints weight = 21009.241| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.02 r_work: 0.3157 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2402 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= 0.128 Angle : 0.490 8.401 20736 Z= 0.261 Chirality : 0.043 0.161 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.370 72.651 2131 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 3.66 % Allowed : 19.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1862 helix: 1.58 (0.20), residues: 708 sheet: 0.41 (0.26), residues: 355 loop : -0.18 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS F 137 PHE 0.018 0.001 PHE A 276 TYR 0.014 0.001 TYR D 146 ARG 0.009 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 679) hydrogen bonds : angle 3.98525 ( 1893) covalent geometry : bond 0.00300 (15310) covalent geometry : angle 0.49038 (20736) ********************** 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 494 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 79 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: A 161 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8347 (mtt-85) REVERT: A 241 GLU cc_start: 0.8346 (tp30) cc_final: 0.8044 (mm-30) REVERT: A 244 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8429 (ptpt) REVERT: A 298 GLU cc_start: 0.7843 (mp0) cc_final: 0.7423 (mp0) REVERT: A 317 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8391 (ttpp) REVERT: A 338 ASP cc_start: 0.8189 (m-30) cc_final: 0.7940 (m-30) REVERT: A 364 ASP cc_start: 0.7716 (p0) cc_final: 0.7507 (p0) REVERT: A 372 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7447 (mmt) REVERT: A 398 LYS cc_start: 0.8098 (tttt) cc_final: 0.7705 (tmtt) REVERT: B 127 MET cc_start: 0.6612 (mmt) cc_final: 0.6300 (mmt) REVERT: B 180 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: B 230 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 365 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5306 (tmt) REVERT: C 65 ASP cc_start: 0.8266 (t70) cc_final: 0.7987 (t0) REVERT: C 131 TRP cc_start: 0.6750 (OUTLIER) cc_final: 0.6445 (p90) REVERT: C 149 ASP cc_start: 0.7938 (t70) cc_final: 0.7707 (t0) REVERT: C 175 GLU cc_start: 0.8296 (mp0) cc_final: 0.7631 (mp0) REVERT: C 183 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (t) REVERT: C 245 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: C 257 GLU cc_start: 0.8153 (tp30) cc_final: 0.7932 (tp30) REVERT: C 287 ASP cc_start: 0.7940 (t0) cc_final: 0.7554 (t0) REVERT: C 290 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5721 (tptp) REVERT: C 352 MET cc_start: 0.8431 (tmm) cc_final: 0.8165 (tmm) REVERT: C 361 GLU cc_start: 0.7284 (pp20) cc_final: 0.6941 (pp20) REVERT: C 365 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7063 (pp30) REVERT: D 34 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8616 (p) REVERT: D 54 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (mttm) REVERT: D 75 LEU cc_start: 0.8609 (tt) cc_final: 0.8240 (tp) REVERT: D 77 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8401 (tppp) REVERT: D 79 VAL cc_start: 0.8754 (p) cc_final: 0.8517 (p) REVERT: D 98 ASP cc_start: 0.8614 (t70) cc_final: 0.8304 (t0) REVERT: D 100 GLU cc_start: 0.8001 (mp0) cc_final: 0.7466 (mp0) REVERT: D 125 PHE cc_start: 0.8311 (m-80) cc_final: 0.8073 (m-80) REVERT: D 182 MET cc_start: 0.8446 (mmm) cc_final: 0.8130 (mmm) REVERT: D 213 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7070 (p0) REVERT: E 9 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7488 (tpp) REVERT: E 14 LYS cc_start: 0.8177 (mttp) cc_final: 0.7947 (mttp) REVERT: E 61 LYS cc_start: 0.8145 (ttmp) cc_final: 0.7901 (ttmm) REVERT: E 62 ASN cc_start: 0.7922 (m-40) cc_final: 0.7666 (m-40) REVERT: E 81 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7548 (mmmt) REVERT: E 98 LEU cc_start: 0.8374 (tp) cc_final: 0.8169 (tt) REVERT: E 147 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8456 (ttmm) REVERT: F 35 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8255 (mttm) REVERT: F 57 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: F 163 GLU cc_start: 0.8140 (tp30) cc_final: 0.7861 (tp30) REVERT: H 24 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7459 (p) outliers start: 59 outliers final: 42 residues processed: 464 average time/residue: 1.5871 time to fit residues: 799.1697 Evaluate side-chains 480 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 422 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU 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 293 THR Chi-restraints excluded: chain A residue 340 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 393 VAL Chi-restraints excluded: chain A residue 416 VAL 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 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 245 GLU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 255 VAL 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 34 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 54 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 269 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 9 MET Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 76 VAL 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 28 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 219 ASN F 100 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 = 0.3663 r_free = 0.3663 target = 0.130812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105696 restraints weight = 21095.026| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.01 r_work: 0.3152 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15310 Z= 0.141 Angle : 0.499 8.427 20736 Z= 0.265 Chirality : 0.044 0.165 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.421 73.169 2131 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 3.97 % Allowed : 19.22 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1862 helix: 1.55 (0.20), residues: 708 sheet: 0.44 (0.26), residues: 350 loop : -0.23 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 221 HIS 0.004 0.001 HIS F 137 PHE 0.018 0.001 PHE A 276 TYR 0.015 0.001 TYR D 43 ARG 0.008 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 679) hydrogen bonds : angle 4.00631 ( 1893) covalent geometry : bond 0.00335 (15310) covalent geometry : angle 0.49924 (20736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15635.02 seconds wall clock time: 268 minutes 17.58 seconds (16097.58 seconds total)