Starting phenix.real_space_refine on Fri Jun 13 14:41:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tah_41135/06_2025/8tah_41135.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tah_41135/06_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_41135/06_2025/8tah_41135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tah_41135/06_2025/8tah_41135.map" model { file = "/net/cci-nas-00/data/ceres_data/8tah_41135/06_2025/8tah_41135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tah_41135/06_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-5710/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: 3.23 Conformation dependent library (CDL) restraints added in 1.9 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: 1.89 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: 4.93 Time building geometry restraints manager: 3.91 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.420 ------------------------------------------------------------------------------- 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 : 1.609 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: 1.4994 time to fit residues: 837.4457 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 : 1.624 ------------------------------------------------------------------------------- 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 = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104105 restraints weight = 20857.835| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.02 r_work: 0.3122 rms_B_bonded: 2.56 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: 0.8020 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 79.072 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 0.05277 ( 679) hydrogen bonds : angle 4.60839 ( 1893) covalent geometry : bond 0.00540 (15310) covalent geometry : angle 0.53154 (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 : 1.670 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: 0.7456 (mp0) REVERT: A 241 GLU cc_start: 0.8303 (tp30) cc_final: 0.8022 (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: 0.7468 (mp0) REVERT: A 317 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8221 (ttpp) REVERT: A 329 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7928 (mtm-85) REVERT: A 338 ASP cc_start: 0.8137 (m-30) cc_final: 0.7830 (m-30) REVERT: A 364 ASP cc_start: 0.7784 (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: 0.6540 (mmt) REVERT: B 143 VAL cc_start: 0.7876 (m) cc_final: 0.7644 (t) REVERT: B 145 THR cc_start: 0.8495 (m) cc_final: 0.8284 (t) REVERT: B 180 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7641 (mmp80) REVERT: B 365 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5131 (tmt) REVERT: C 29 ASN cc_start: 0.8432 (p0) cc_final: 0.8216 (p0) REVERT: C 46 HIS cc_start: 0.8502 (m-70) cc_final: 0.8226 (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: 0.8005 (t70) cc_final: 0.7778 (t0) REVERT: C 175 GLU cc_start: 0.8304 (mp0) cc_final: 0.7628 (mp0) REVERT: C 176 VAL cc_start: 0.8718 (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: 0.6096 (OUTLIER) cc_final: 0.5686 (tptp) REVERT: C 361 GLU cc_start: 0.7380 (pp20) cc_final: 0.6955 (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: 0.8244 (tp) REVERT: D 77 LYS cc_start: 0.8611 (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: 0.8297 (t70) cc_final: 0.7968 (t70) REVERT: D 100 GLU cc_start: 0.7873 (mp0) cc_final: 0.7229 (mp0) REVERT: D 213 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7215 (p0) REVERT: D 237 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.8134 (ttp-170) REVERT: D 269 LYS cc_start: 0.8828 (tppt) cc_final: 0.8593 (tptm) REVERT: E 22 LEU cc_start: 0.8347 (mp) cc_final: 0.8032 (mm) REVERT: E 50 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8209 (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: 0.7937 (mm-30) cc_final: 0.7684 (mm-30) REVERT: F 57 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: F 156 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8302 (ttm-80) REVERT: F 163 GLU cc_start: 0.8209 (tp30) cc_final: 0.7939 (tp30) REVERT: G 56 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6603 (mp10) REVERT: G 86 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8106 (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: 1.4834 time to fit residues: 811.9801 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 : 1.670 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104465 restraints weight = 20941.861| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.01 r_work: 0.3134 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15310 Z= 0.162 Angle : 0.488 6.023 20736 Z= 0.264 Chirality : 0.044 0.169 2287 Planarity : 0.004 0.058 2666 Dihedral : 7.539 74.451 2150 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 4.22 % Allowed : 16.37 % 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: 0.10 (0.19), residues: 1862 helix: 0.82 (0.20), residues: 696 sheet: 0.41 (0.26), residues: 367 loop : -0.69 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 221 HIS 0.005 0.001 HIS D 254 PHE 0.018 0.001 PHE F 101 TYR 0.016 0.001 TYR D 43 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 679) hydrogen bonds : angle 4.34659 ( 1893) covalent geometry : bond 0.00382 (15310) covalent geometry : angle 0.48761 (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 515 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 447 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8558 (pp) REVERT: A 79 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: A 121 GLU cc_start: 0.7655 (mp0) cc_final: 0.7351 (mp0) REVERT: A 241 GLU cc_start: 0.8261 (tp30) cc_final: 0.8038 (mm-30) REVERT: A 298 GLU cc_start: 0.7860 (mp0) cc_final: 0.7473 (mp0) REVERT: A 317 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8236 (ttpp) REVERT: A 329 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7942 (mtm-85) REVERT: A 338 ASP cc_start: 0.8147 (m-30) cc_final: 0.7921 (m-30) REVERT: A 364 ASP cc_start: 0.7763 (p0) cc_final: 0.7540 (p0) REVERT: A 391 TYR cc_start: 0.8529 (m-80) cc_final: 0.8185 (m-80) REVERT: B 127 MET cc_start: 0.6876 (mmt) cc_final: 0.6490 (mmt) REVERT: B 143 VAL cc_start: 0.7885 (m) cc_final: 0.7671 (t) REVERT: B 145 THR cc_start: 0.8533 (m) cc_final: 0.8319 (t) REVERT: B 180 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7558 (mmp80) REVERT: B 214 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8435 (ttp80) REVERT: B 232 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8433 (ttpp) REVERT: B 365 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5152 (tmt) REVERT: C 29 ASN cc_start: 0.8341 (p0) cc_final: 0.8127 (p0) REVERT: C 46 HIS cc_start: 0.8437 (m-70) cc_final: 0.8175 (m-70) REVERT: C 49 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8473 (ptpp) REVERT: C 65 ASP cc_start: 0.8258 (t70) cc_final: 0.7912 (t0) REVERT: C 131 TRP cc_start: 0.7023 (OUTLIER) cc_final: 0.6483 (p90) REVERT: C 149 ASP cc_start: 0.8029 (t70) cc_final: 0.7787 (t0) REVERT: C 175 GLU cc_start: 0.8286 (mp0) cc_final: 0.7615 (mp0) REVERT: C 176 VAL cc_start: 0.8719 (t) cc_final: 0.8498 (m) REVERT: C 245 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7782 (pp20) REVERT: C 287 ASP cc_start: 0.7912 (t0) cc_final: 0.7670 (t0) REVERT: C 290 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5723 (tptp) REVERT: C 352 MET cc_start: 0.8465 (tmm) cc_final: 0.8187 (tmm) REVERT: C 361 GLU cc_start: 0.7298 (pp20) cc_final: 0.6880 (pp20) REVERT: D 12 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7799 (mm-30) REVERT: D 75 LEU cc_start: 0.8594 (tt) cc_final: 0.8220 (tp) REVERT: D 77 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8380 (tppp) REVERT: D 79 VAL cc_start: 0.8751 (p) cc_final: 0.8510 (p) REVERT: D 98 ASP cc_start: 0.8332 (t70) cc_final: 0.8070 (t70) REVERT: D 100 GLU cc_start: 0.7893 (mp0) cc_final: 0.7250 (mp0) REVERT: D 213 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7132 (p0) REVERT: D 269 LYS cc_start: 0.8826 (tppt) cc_final: 0.8613 (tptm) REVERT: E 22 LEU cc_start: 0.8325 (mp) cc_final: 0.8019 (mm) REVERT: E 81 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7512 (mmmt) REVERT: F 57 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: F 156 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8318 (ttm-80) REVERT: F 163 GLU cc_start: 0.8242 (tp30) cc_final: 0.7791 (tp30) REVERT: F 166 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8262 (ttpt) REVERT: G 56 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: G 86 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8038 (t80) REVERT: H 24 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7209 (p) outliers start: 68 outliers final: 35 residues processed: 478 average time/residue: 1.6289 time to fit residues: 842.0204 Evaluate side-chains 477 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 431 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 259 ILE Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 375 TYR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 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 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 243 LEU 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 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 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: 0.5980 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 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 219 GLN A 255 GLN B 226 ASN C 30 HIS D 130 GLN D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105204 restraints weight = 20913.413| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.01 r_work: 0.3146 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1968 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= 0.134 Angle : 0.468 6.032 20736 Z= 0.253 Chirality : 0.043 0.149 2287 Planarity : 0.004 0.055 2666 Dihedral : 6.995 71.623 2139 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.53 % Rotamer: Outliers : 4.15 % Allowed : 17.23 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.19), residues: 1862 helix: 1.24 (0.20), residues: 699 sheet: 0.36 (0.26), residues: 379 loop : -0.48 (0.22), residues: 784 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 F 101 TYR 0.014 0.001 TYR D 43 ARG 0.005 0.000 ARG F 71 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 679) hydrogen bonds : angle 4.16268 ( 1893) covalent geometry : bond 0.00313 (15310) covalent geometry : angle 0.46800 (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 510 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 443 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (pp) REVERT: A 79 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: A 121 GLU cc_start: 0.7669 (mp0) cc_final: 0.7325 (mp0) REVERT: A 241 GLU cc_start: 0.8256 (tp30) cc_final: 0.8037 (mm-30) REVERT: A 248 ASP cc_start: 0.7808 (t70) cc_final: 0.7544 (t0) REVERT: A 298 GLU cc_start: 0.7858 (mp0) cc_final: 0.7469 (mp0) REVERT: A 317 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8374 (ttpp) REVERT: A 329 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7912 (mtm-85) REVERT: A 338 ASP cc_start: 0.8150 (m-30) cc_final: 0.7936 (m-30) REVERT: A 391 TYR cc_start: 0.8466 (m-80) cc_final: 0.8135 (m-80) REVERT: B 127 MET cc_start: 0.6910 (mmt) cc_final: 0.6681 (mmt) REVERT: B 143 VAL cc_start: 0.7882 (m) cc_final: 0.7681 (t) REVERT: B 180 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7752 (mmt-90) REVERT: B 214 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8411 (ttp80) REVERT: B 232 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: B 365 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5168 (tmt) REVERT: C 29 ASN cc_start: 0.8308 (p0) cc_final: 0.8098 (p0) REVERT: C 30 HIS cc_start: 0.8259 (p90) cc_final: 0.8033 (p-80) REVERT: C 65 ASP cc_start: 0.8272 (t70) cc_final: 0.7978 (t0) REVERT: C 131 TRP cc_start: 0.6851 (OUTLIER) cc_final: 0.6430 (p90) REVERT: C 149 ASP cc_start: 0.7976 (t70) cc_final: 0.7711 (t0) REVERT: C 175 GLU cc_start: 0.8269 (mp0) cc_final: 0.7630 (mp0) REVERT: C 176 VAL cc_start: 0.8705 (t) cc_final: 0.8502 (m) REVERT: C 245 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7730 (pp20) REVERT: C 287 ASP cc_start: 0.7922 (t0) cc_final: 0.7690 (t0) REVERT: C 290 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5716 (tptp) REVERT: C 352 MET cc_start: 0.8470 (tmm) cc_final: 0.8206 (tmm) REVERT: C 361 GLU cc_start: 0.7284 (pp20) cc_final: 0.6865 (pp20) REVERT: D 12 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7826 (mm-30) REVERT: D 34 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (p) REVERT: D 75 LEU cc_start: 0.8585 (tt) cc_final: 0.8213 (tp) REVERT: D 77 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8376 (tppp) REVERT: D 79 VAL cc_start: 0.8762 (p) cc_final: 0.8519 (p) REVERT: D 100 GLU cc_start: 0.7911 (mp0) cc_final: 0.7282 (mp0) REVERT: D 159 ASP cc_start: 0.8758 (p0) cc_final: 0.8531 (p0) REVERT: D 213 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7091 (p0) REVERT: D 269 LYS cc_start: 0.8833 (tppt) cc_final: 0.8616 (tptt) REVERT: E 22 LEU cc_start: 0.8276 (mp) cc_final: 0.7958 (mm) REVERT: E 57 ASN cc_start: 0.8449 (m-40) cc_final: 0.8145 (m-40) REVERT: E 62 ASN cc_start: 0.7952 (t0) cc_final: 0.7646 (t0) REVERT: E 81 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7486 (mmmt) REVERT: F 57 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: F 163 GLU cc_start: 0.8244 (tp30) cc_final: 0.7858 (tp30) REVERT: F 166 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8361 (ttpt) REVERT: G 86 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8018 (t80) REVERT: H 24 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7142 (p) outliers start: 67 outliers final: 40 residues processed: 476 average time/residue: 1.5040 time to fit residues: 774.4889 Evaluate side-chains 471 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 420 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 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 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 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 20 LEU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 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: 0.7980 chunk 157 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 D 197 GLN F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104838 restraints weight = 21203.878| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.01 r_work: 0.3139 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15310 Z= 0.166 Angle : 0.488 6.405 20736 Z= 0.263 Chirality : 0.044 0.152 2287 Planarity : 0.004 0.056 2666 Dihedral : 6.789 73.629 2133 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 4.34 % Allowed : 17.23 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.20), residues: 1862 helix: 1.29 (0.20), residues: 707 sheet: 0.38 (0.26), residues: 379 loop : -0.41 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.005 0.001 HIS F 137 PHE 0.017 0.001 PHE F 101 TYR 0.017 0.001 TYR D 43 ARG 0.006 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 679) hydrogen bonds : angle 4.16129 ( 1893) covalent geometry : bond 0.00393 (15310) covalent geometry : angle 0.48806 (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 494 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 424 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 79 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7437 (mtm-85) REVERT: A 121 GLU cc_start: 0.7716 (mp0) cc_final: 0.7372 (mp0) REVERT: A 241 GLU cc_start: 0.8280 (tp30) cc_final: 0.8029 (mm-30) REVERT: A 248 ASP cc_start: 0.7775 (t70) cc_final: 0.7466 (t70) REVERT: A 298 GLU cc_start: 0.7853 (mp0) cc_final: 0.7470 (mp0) REVERT: A 317 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8367 (ttpp) REVERT: A 329 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7903 (mtm-85) REVERT: A 338 ASP cc_start: 0.8173 (m-30) cc_final: 0.7964 (m-30) REVERT: A 340 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (ttmm) REVERT: A 372 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: A 391 TYR cc_start: 0.8480 (m-80) cc_final: 0.8174 (m-80) REVERT: B 127 MET cc_start: 0.6889 (mmt) cc_final: 0.6681 (mmt) REVERT: B 180 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7773 (mmt-90) REVERT: B 232 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8443 (ttpp) REVERT: B 257 GLU cc_start: 0.7987 (mp0) cc_final: 0.7623 (mp0) REVERT: B 365 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.5210 (tmt) REVERT: C 29 ASN cc_start: 0.8317 (p0) cc_final: 0.8113 (p0) REVERT: C 65 ASP cc_start: 0.8247 (t70) cc_final: 0.7921 (t0) REVERT: C 131 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6494 (p90) REVERT: C 149 ASP cc_start: 0.7976 (t70) cc_final: 0.7660 (t0) REVERT: C 175 GLU cc_start: 0.8259 (mp0) cc_final: 0.7572 (mp0) REVERT: C 183 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (t) REVERT: C 245 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: C 287 ASP cc_start: 0.7934 (t0) cc_final: 0.7696 (t0) REVERT: C 290 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5701 (tptp) REVERT: C 352 MET cc_start: 0.8456 (tmm) cc_final: 0.8198 (tmm) REVERT: C 361 GLU cc_start: 0.7313 (pp20) cc_final: 0.6885 (pp20) REVERT: D 12 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7849 (mm-30) REVERT: D 34 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (p) REVERT: D 75 LEU cc_start: 0.8606 (tt) cc_final: 0.8231 (tp) REVERT: D 77 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8383 (tppp) REVERT: D 79 VAL cc_start: 0.8745 (p) cc_final: 0.8498 (p) REVERT: D 100 GLU cc_start: 0.7952 (mp0) cc_final: 0.7439 (mp0) REVERT: D 159 ASP cc_start: 0.8765 (p0) cc_final: 0.8545 (p0) REVERT: D 269 LYS cc_start: 0.8823 (tppt) cc_final: 0.8613 (tptt) REVERT: E 22 LEU cc_start: 0.8272 (mp) cc_final: 0.7953 (mm) REVERT: E 81 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7491 (mmmt) REVERT: F 57 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: F 84 LYS cc_start: 0.8283 (tttt) cc_final: 0.7964 (ttpp) REVERT: F 163 GLU cc_start: 0.8249 (tp30) cc_final: 0.7886 (tp30) REVERT: F 166 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8396 (ttpt) REVERT: G 16 VAL cc_start: 0.7783 (m) cc_final: 0.7415 (t) REVERT: G 86 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7974 (t80) REVERT: H 24 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7148 (p) outliers start: 70 outliers final: 42 residues processed: 458 average time/residue: 1.5894 time to fit residues: 784.5309 Evaluate side-chains 474 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 419 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 340 LYS 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 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 42 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 SER 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 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 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: 0.9990 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 166 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 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 243 ASN A 255 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 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 = 0.3662 r_free = 0.3662 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105729 restraints weight = 21091.396| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.00 r_work: 0.3154 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15310 Z= 0.123 Angle : 0.469 7.395 20736 Z= 0.252 Chirality : 0.043 0.149 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.552 71.522 2131 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 4.34 % Allowed : 17.48 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.20), residues: 707 sheet: 0.38 (0.26), residues: 379 loop : -0.31 (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 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 679) hydrogen bonds : angle 4.06891 ( 1893) covalent geometry : bond 0.00287 (15310) covalent geometry : angle 0.46914 (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 493 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 423 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 75 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (mmtt) REVERT: A 79 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: A 241 GLU cc_start: 0.8293 (tp30) cc_final: 0.8066 (mm-30) REVERT: A 248 ASP cc_start: 0.7759 (t70) cc_final: 0.7464 (t70) REVERT: A 298 GLU cc_start: 0.7853 (mp0) cc_final: 0.7443 (mp0) REVERT: A 317 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8376 (ttpp) REVERT: A 329 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7887 (mtm-85) REVERT: A 338 ASP cc_start: 0.8182 (m-30) cc_final: 0.7943 (m-30) REVERT: A 340 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: A 372 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7446 (mmt) REVERT: A 391 TYR cc_start: 0.8450 (m-80) cc_final: 0.8122 (m-80) REVERT: B 127 MET cc_start: 0.6870 (mmt) cc_final: 0.6668 (mmt) REVERT: B 180 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7758 (mmt-90) REVERT: B 230 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 257 GLU cc_start: 0.7955 (mp0) cc_final: 0.7606 (mp0) REVERT: B 365 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5193 (tmt) REVERT: C 29 ASN cc_start: 0.8306 (p0) cc_final: 0.8096 (p0) REVERT: C 30 HIS cc_start: 0.8253 (p90) cc_final: 0.8025 (p-80) REVERT: C 65 ASP cc_start: 0.8280 (t70) cc_final: 0.7959 (t0) REVERT: C 131 TRP cc_start: 0.6792 (OUTLIER) cc_final: 0.6420 (p90) REVERT: C 149 ASP cc_start: 0.8039 (t70) cc_final: 0.7796 (t0) REVERT: C 175 GLU cc_start: 0.8268 (mp0) cc_final: 0.7610 (mp0) REVERT: C 183 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8039 (t) REVERT: C 245 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7656 (pp20) REVERT: C 287 ASP cc_start: 0.7915 (t0) cc_final: 0.7662 (t0) REVERT: C 290 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5718 (tptp) REVERT: C 352 MET cc_start: 0.8464 (tmm) cc_final: 0.8207 (tmm) REVERT: C 361 GLU cc_start: 0.7294 (pp20) cc_final: 0.6870 (pp20) REVERT: D 34 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8606 (p) REVERT: D 54 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (mttp) REVERT: D 75 LEU cc_start: 0.8614 (tt) cc_final: 0.8235 (tp) REVERT: D 79 VAL cc_start: 0.8762 (p) cc_final: 0.8521 (p) REVERT: D 100 GLU cc_start: 0.7966 (mp0) cc_final: 0.7480 (mp0) REVERT: D 213 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7117 (p0) REVERT: E 22 LEU cc_start: 0.8244 (mp) cc_final: 0.7937 (mm) REVERT: E 62 ASN cc_start: 0.7946 (m-40) cc_final: 0.7630 (m-40) REVERT: E 81 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7509 (mmmt) REVERT: E 147 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8448 (ttmm) REVERT: F 35 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8257 (mttm) REVERT: F 57 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: F 92 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7946 (mtp85) REVERT: F 163 GLU cc_start: 0.8212 (tp30) cc_final: 0.7846 (tp30) REVERT: F 166 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8400 (ttpt) REVERT: G 86 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (t80) REVERT: H 24 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7115 (p) outliers start: 70 outliers final: 42 residues processed: 453 average time/residue: 1.6805 time to fit residues: 817.9574 Evaluate side-chains 480 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 421 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 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 A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 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 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 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 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 245 HIS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 20 LEU 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 G residue 86 PHE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 175 optimal weight: 1.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 D 130 GLN 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 = 0.3658 r_free = 0.3658 target = 0.130543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105122 restraints weight = 20977.250| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.02 r_work: 0.3148 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15310 Z= 0.145 Angle : 0.483 7.788 20736 Z= 0.258 Chirality : 0.043 0.151 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.578 72.647 2131 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 4.34 % Allowed : 18.29 % 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: 0.78 (0.20), residues: 1862 helix: 1.51 (0.20), residues: 708 sheet: 0.40 (0.26), residues: 379 loop : -0.28 (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 0.017 0.001 PHE F 101 TYR 0.016 0.001 TYR D 43 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 679) hydrogen bonds : angle 4.04503 ( 1893) covalent geometry : bond 0.00344 (15310) covalent geometry : angle 0.48266 (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 501 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 431 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8551 (pp) REVERT: A 75 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8189 (mmtt) REVERT: A 79 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: A 121 GLU cc_start: 0.7681 (mp0) cc_final: 0.7309 (mp0) REVERT: A 161 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8358 (mtt-85) REVERT: A 241 GLU cc_start: 0.8301 (tp30) cc_final: 0.8073 (mm-30) REVERT: A 248 ASP cc_start: 0.7767 (t70) cc_final: 0.7432 (t70) REVERT: A 298 GLU cc_start: 0.7848 (mp0) cc_final: 0.7449 (mp0) REVERT: A 329 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7878 (mtm-85) REVERT: A 338 ASP cc_start: 0.8172 (m-30) cc_final: 0.7859 (m-30) REVERT: A 340 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8264 (mtmm) REVERT: A 372 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: A 373 GLN cc_start: 0.8503 (tt0) cc_final: 0.8275 (tt0) REVERT: B 180 ARG cc_start: 0.8043 (mmt-90) cc_final: 0.7780 (mmt-90) REVERT: B 230 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 257 GLU cc_start: 0.7966 (mp0) cc_final: 0.7610 (mp0) REVERT: B 365 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5182 (tmt) REVERT: C 29 ASN cc_start: 0.8312 (p0) cc_final: 0.8102 (p0) REVERT: C 65 ASP cc_start: 0.8294 (t70) cc_final: 0.7943 (t0) REVERT: C 131 TRP cc_start: 0.6862 (OUTLIER) cc_final: 0.6425 (p90) REVERT: C 149 ASP cc_start: 0.8018 (t70) cc_final: 0.7760 (t0) REVERT: C 175 GLU cc_start: 0.8282 (mp0) cc_final: 0.7613 (mp0) REVERT: C 183 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8057 (t) REVERT: C 245 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: C 287 ASP cc_start: 0.7950 (t0) cc_final: 0.7586 (t0) REVERT: C 290 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5673 (tptp) REVERT: C 352 MET cc_start: 0.8455 (tmm) cc_final: 0.8194 (tmm) REVERT: C 361 GLU cc_start: 0.7298 (pp20) cc_final: 0.6874 (pp20) REVERT: C 365 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7077 (pp30) REVERT: D 34 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8618 (p) REVERT: D 75 LEU cc_start: 0.8648 (tt) cc_final: 0.8273 (tp) REVERT: D 79 VAL cc_start: 0.8777 (p) cc_final: 0.8529 (p) REVERT: D 100 GLU cc_start: 0.7991 (mp0) cc_final: 0.7488 (mp0) REVERT: D 213 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7131 (p0) REVERT: E 22 LEU cc_start: 0.8261 (mp) cc_final: 0.7957 (mm) REVERT: E 62 ASN cc_start: 0.7997 (m-40) cc_final: 0.7699 (m-40) REVERT: E 81 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7529 (mmmt) REVERT: E 147 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8463 (ttmm) REVERT: F 35 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8253 (mttm) REVERT: F 57 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: F 163 GLU cc_start: 0.8207 (tp30) cc_final: 0.7840 (tp30) REVERT: F 166 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8418 (ttpt) REVERT: H 24 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7141 (p) outliers start: 70 outliers final: 42 residues processed: 466 average time/residue: 1.5698 time to fit residues: 788.8461 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 : 1.661 ------------------------------------------------------------------------------- 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 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 A residue 417 MET Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 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 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 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 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 271 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 20 LEU 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 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: 2.9990 chunk 72 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.130423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105230 restraints weight = 21011.329| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.00 r_work: 0.3145 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15310 Z= 0.159 Angle : 0.500 8.138 20736 Z= 0.266 Chirality : 0.044 0.156 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.639 73.892 2131 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 4.34 % Allowed : 18.54 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1862 helix: 1.49 (0.20), residues: 708 sheet: 0.42 (0.26), residues: 374 loop : -0.25 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS F 137 PHE 0.018 0.001 PHE F 101 TYR 0.016 0.001 TYR D 43 ARG 0.008 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 679) hydrogen bonds : angle 4.06718 ( 1893) covalent geometry : bond 0.00379 (15310) covalent geometry : angle 0.49951 (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 490 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8540 (pp) REVERT: A 75 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8182 (mmtt) REVERT: A 79 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: A 121 GLU cc_start: 0.7695 (mp0) cc_final: 0.7320 (mp0) REVERT: A 161 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8328 (mtt-85) REVERT: A 241 GLU cc_start: 0.8332 (tp30) cc_final: 0.8050 (mm-30) REVERT: A 244 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8417 (ptpt) REVERT: A 248 ASP cc_start: 0.7811 (t70) cc_final: 0.7545 (t70) REVERT: A 298 GLU cc_start: 0.7849 (mp0) cc_final: 0.7449 (mp0) REVERT: A 329 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7880 (mtm-85) REVERT: A 338 ASP cc_start: 0.8181 (m-30) cc_final: 0.7865 (m-30) REVERT: A 340 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8264 (mtmm) REVERT: A 372 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7511 (mmt) REVERT: A 373 GLN cc_start: 0.8502 (tt0) cc_final: 0.8275 (tt0) REVERT: B 127 MET cc_start: 0.6541 (mmt) cc_final: 0.6256 (mmt) REVERT: B 180 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7772 (mmt-90) REVERT: B 230 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 257 GLU cc_start: 0.7948 (mp0) cc_final: 0.7579 (mp0) REVERT: B 365 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5284 (tmt) REVERT: C 65 ASP cc_start: 0.8283 (t70) cc_final: 0.7946 (t0) REVERT: C 131 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.6452 (p90) REVERT: C 149 ASP cc_start: 0.8022 (t70) cc_final: 0.7767 (t0) REVERT: C 175 GLU cc_start: 0.8294 (mp0) cc_final: 0.7610 (mp0) REVERT: C 183 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8065 (t) REVERT: C 245 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7675 (pp20) REVERT: C 257 GLU cc_start: 0.8155 (tp30) cc_final: 0.7869 (tp30) REVERT: C 287 ASP cc_start: 0.7936 (t0) cc_final: 0.7582 (t0) REVERT: C 290 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5686 (tptp) REVERT: C 352 MET cc_start: 0.8447 (tmm) cc_final: 0.8187 (tmm) REVERT: C 361 GLU cc_start: 0.7285 (pp20) cc_final: 0.6902 (pp20) REVERT: C 365 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7087 (pp30) REVERT: D 34 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (p) REVERT: D 75 LEU cc_start: 0.8639 (tt) cc_final: 0.8315 (tp) REVERT: D 79 VAL cc_start: 0.8765 (p) cc_final: 0.8513 (p) REVERT: D 98 ASP cc_start: 0.8710 (t0) cc_final: 0.8472 (t0) REVERT: D 100 GLU cc_start: 0.8013 (mp0) cc_final: 0.7503 (mp0) REVERT: D 213 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7105 (p0) REVERT: E 22 LEU cc_start: 0.8207 (mp) cc_final: 0.7901 (mm) REVERT: E 62 ASN cc_start: 0.8045 (m-40) cc_final: 0.7787 (m-40) REVERT: E 81 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7530 (mmmt) REVERT: E 147 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8456 (ttmm) REVERT: F 35 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (mttm) REVERT: F 57 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: F 84 LYS cc_start: 0.8290 (tttt) cc_final: 0.7972 (ttpp) REVERT: F 163 GLU cc_start: 0.8218 (tp30) cc_final: 0.7907 (tp30) REVERT: G 16 VAL cc_start: 0.7755 (m) cc_final: 0.7388 (t) REVERT: H 24 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7245 (p) outliers start: 70 outliers final: 46 residues processed: 453 average time/residue: 1.5725 time to fit residues: 767.3008 Evaluate side-chains 489 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 427 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 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 31 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 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 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 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 20 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 114 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 172 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105428 restraints weight = 20749.169| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.00 r_work: 0.3152 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15310 Z= 0.142 Angle : 0.498 8.208 20736 Z= 0.264 Chirality : 0.044 0.159 2287 Planarity : 0.004 0.053 2666 Dihedral : 6.542 72.604 2131 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.15 % 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: 0.85 (0.20), residues: 1862 helix: 1.56 (0.20), residues: 708 sheet: 0.44 (0.26), residues: 368 loop : -0.22 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS F 137 PHE 0.017 0.001 PHE A 276 TYR 0.015 0.001 TYR D 43 ARG 0.009 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 679) hydrogen bonds : angle 4.02962 ( 1893) covalent geometry : bond 0.00339 (15310) covalent geometry : angle 0.49775 (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 475 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 416 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8534 (pp) REVERT: A 75 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8188 (mmtt) REVERT: A 79 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: A 161 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8348 (mtt-85) REVERT: A 241 GLU cc_start: 0.8322 (tp30) cc_final: 0.8062 (mm-30) REVERT: A 244 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8418 (ptpt) REVERT: A 248 ASP cc_start: 0.7761 (t70) cc_final: 0.7434 (t0) REVERT: A 298 GLU cc_start: 0.7852 (mp0) cc_final: 0.7452 (mp0) REVERT: A 329 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7882 (mtm-85) REVERT: A 338 ASP cc_start: 0.8193 (m-30) cc_final: 0.7957 (m-30) REVERT: A 340 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: A 372 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7498 (mmt) REVERT: A 373 GLN cc_start: 0.8496 (tt0) cc_final: 0.8281 (tt0) REVERT: B 127 MET cc_start: 0.6577 (mmt) cc_final: 0.6271 (mmt) REVERT: B 180 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7768 (mmt-90) REVERT: B 230 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: B 365 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5300 (tmt) REVERT: C 65 ASP cc_start: 0.8271 (t70) cc_final: 0.7939 (t0) REVERT: C 131 TRP cc_start: 0.6823 (OUTLIER) cc_final: 0.6459 (p90) REVERT: C 175 GLU cc_start: 0.8286 (mp0) cc_final: 0.7609 (mp0) REVERT: C 183 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8043 (t) REVERT: C 245 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7646 (pp20) REVERT: C 257 GLU cc_start: 0.8167 (tp30) cc_final: 0.7879 (tp30) REVERT: C 287 ASP cc_start: 0.7949 (t0) cc_final: 0.7679 (t0) REVERT: C 290 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5688 (tptp) REVERT: C 352 MET cc_start: 0.8431 (tmm) cc_final: 0.8171 (tmm) REVERT: C 361 GLU cc_start: 0.7292 (pp20) cc_final: 0.6927 (pp20) REVERT: C 365 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7079 (pp30) REVERT: D 34 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8603 (p) REVERT: D 75 LEU cc_start: 0.8630 (tt) cc_final: 0.8266 (tp) REVERT: D 79 VAL cc_start: 0.8767 (p) cc_final: 0.8518 (p) REVERT: D 100 GLU cc_start: 0.8005 (mp0) cc_final: 0.7500 (mp0) REVERT: D 213 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7101 (p0) REVERT: E 22 LEU cc_start: 0.8175 (mp) cc_final: 0.7871 (mm) REVERT: E 62 ASN cc_start: 0.8039 (m-40) cc_final: 0.7795 (m-40) REVERT: E 81 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7525 (mmmt) REVERT: E 147 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8450 (ttmm) REVERT: F 35 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: F 57 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: F 163 GLU cc_start: 0.8174 (tp30) cc_final: 0.7832 (tp30) REVERT: F 166 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8381 (ttpt) REVERT: G 16 VAL cc_start: 0.7750 (m) cc_final: 0.7381 (t) REVERT: H 24 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7247 (p) outliers start: 59 outliers final: 42 residues processed: 447 average time/residue: 1.5826 time to fit residues: 762.6470 Evaluate side-chains 469 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 411 time to evaluate : 3.025 ------------------------------------------------------------------------------- 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 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 31 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 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 34 THR Chi-restraints excluded: chain D residue 41 VAL 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 271 SER Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 20 LEU 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: 2.9990 chunk 171 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105138 restraints weight = 21034.064| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3146 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15310 Z= 0.159 Angle : 0.507 8.294 20736 Z= 0.270 Chirality : 0.044 0.164 2287 Planarity : 0.004 0.054 2666 Dihedral : 6.619 73.184 2131 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 3.47 % Allowed : 19.65 % Favored : 76.88 % 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: 1.53 (0.20), residues: 709 sheet: 0.44 (0.26), residues: 361 loop : -0.23 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS F 137 PHE 0.018 0.001 PHE F 101 TYR 0.017 0.001 TYR D 43 ARG 0.009 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 679) hydrogen bonds : angle 4.05107 ( 1893) covalent geometry : bond 0.00382 (15310) covalent geometry : angle 0.50741 (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 467 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 411 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8536 (pp) REVERT: A 75 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8198 (mmtt) REVERT: A 79 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7431 (mtm-85) REVERT: A 121 GLU cc_start: 0.7710 (mp0) cc_final: 0.7335 (mp0) REVERT: A 161 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8330 (mtt-85) REVERT: A 241 GLU cc_start: 0.8336 (tp30) cc_final: 0.8078 (mm-30) REVERT: A 248 ASP cc_start: 0.7783 (t70) cc_final: 0.7460 (t0) REVERT: A 298 GLU cc_start: 0.7850 (mp0) cc_final: 0.7453 (mp0) REVERT: A 338 ASP cc_start: 0.8194 (m-30) cc_final: 0.7960 (m-30) REVERT: A 340 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: A 372 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7543 (mmt) REVERT: B 127 MET cc_start: 0.6600 (mmt) cc_final: 0.6287 (mmt) REVERT: B 180 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7802 (mmt-90) REVERT: B 230 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: B 365 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5305 (tmt) REVERT: C 64 SER cc_start: 0.8592 (m) cc_final: 0.8390 (t) REVERT: C 131 TRP cc_start: 0.6864 (OUTLIER) cc_final: 0.6499 (p90) REVERT: C 175 GLU cc_start: 0.8295 (mp0) cc_final: 0.7621 (mp0) REVERT: C 183 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8058 (t) REVERT: C 245 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7643 (pp20) REVERT: C 257 GLU cc_start: 0.8149 (tp30) cc_final: 0.7861 (tp30) REVERT: C 290 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5680 (tptp) REVERT: C 361 GLU cc_start: 0.7286 (pp20) cc_final: 0.6937 (pp20) REVERT: C 365 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7091 (pp30) REVERT: D 12 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7890 (mm-30) REVERT: D 34 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8610 (p) REVERT: D 75 LEU cc_start: 0.8631 (tt) cc_final: 0.8303 (tp) REVERT: D 79 VAL cc_start: 0.8761 (p) cc_final: 0.8511 (p) REVERT: D 100 GLU cc_start: 0.8025 (mp0) cc_final: 0.7465 (mp0) REVERT: D 213 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7100 (p0) REVERT: E 22 LEU cc_start: 0.8187 (mp) cc_final: 0.7881 (mm) REVERT: E 62 ASN cc_start: 0.8066 (m-40) cc_final: 0.7826 (m-40) REVERT: E 81 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7534 (mmmt) REVERT: E 147 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8460 (ttmm) REVERT: F 35 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8274 (mttm) REVERT: F 57 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: F 163 GLU cc_start: 0.8173 (tp30) cc_final: 0.7841 (tp30) REVERT: F 166 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8401 (ttpt) REVERT: G 16 VAL cc_start: 0.7761 (m) cc_final: 0.7393 (t) REVERT: H 24 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7220 (p) outliers start: 56 outliers final: 40 residues processed: 440 average time/residue: 1.7217 time to fit residues: 824.8883 Evaluate side-chains 475 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 419 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 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 31 ILE Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 13 CYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 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 34 THR Chi-restraints excluded: chain D residue 41 VAL 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 271 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 20 LEU 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 110 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain H residue 24 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 28 optimal weight: 0.8980 chunk 139 optimal weight: 0.0070 chunk 138 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 D 219 ASN F 100 ASN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106188 restraints weight = 20991.069| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.02 r_work: 0.3165 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15310 Z= 0.113 Angle : 0.487 8.545 20736 Z= 0.257 Chirality : 0.043 0.158 2287 Planarity : 0.004 0.052 2666 Dihedral : 6.316 72.205 2131 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 3.29 % Allowed : 19.96 % Favored : 76.75 % 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: 0.93 (0.20), residues: 1862 helix: 1.69 (0.20), residues: 704 sheet: 0.41 (0.26), residues: 355 loop : -0.17 (0.22), residues: 803 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 0.019 0.001 PHE A 276 TYR 0.014 0.001 TYR D 146 ARG 0.008 0.000 ARG D 281 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 679) hydrogen bonds : angle 3.95158 ( 1893) covalent geometry : bond 0.00263 (15310) covalent geometry : angle 0.48737 (20736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16614.80 seconds wall clock time: 284 minutes 12.98 seconds (17052.98 seconds total)