Starting phenix.real_space_refine on Sun Aug 24 09:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptp_17877/08_2025/8ptp_17877_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11959 2.51 5 N 3357 2.21 5 O 3626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19039 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Time building chain proxies: 5.28, per 1000 atoms: 0.28 Number of scatterers: 19039 At special positions: 0 Unit cell: (116.48, 133.12, 164.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3626 8.00 N 3357 7.00 C 11959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 865.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4522 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 43.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.776A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.549A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.503A pdb=" N ASN A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 removed outlier: 4.164A pdb=" N THR A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.816A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.134A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.685A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.733A pdb=" N LYS B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.625A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.566A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.690A pdb=" N VAL B 289 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.547A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.777A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.114A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.337A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.557A pdb=" N ALA C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.844A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.840A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.623A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.777A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.504A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.012A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.506A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.512A pdb=" N ALA D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.611A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 4.019A pdb=" N MET D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 45 Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.531A pdb=" N HIS E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.701A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 346 through 352 removed outlier: 4.138A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.866A pdb=" N LEU E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.528A pdb=" N LEU E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 399 removed outlier: 3.907A pdb=" N LEU E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 417 removed outlier: 3.964A pdb=" N PHE E 412 " --> pdb=" O THR E 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 23 removed outlier: 3.567A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'c' and resid 9 through 22 Processing helix chain 'd' and resid 9 through 22 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 7.416A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.850A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP A 265 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 207 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.850A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 203 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU A 263 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ASP A 265 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 207 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 345 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 177 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N GLU A 342 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ASN A 361 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N HIS A 344 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.886A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 6.387A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.754A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.517A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.451A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU B 345 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 177 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLU B 342 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASN B 361 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS B 344 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 4.014A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.499A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.448A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.930A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.639A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 364 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.596A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 231 removed outlier: 4.088A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 206 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU E 342 " --> pdb=" O GLY E 364 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 364 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 26 through 29 Processing sheet with id=AB8, first strand: chain 'a' and resid 40 through 46 removed outlier: 5.325A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 35 through 37 removed outlier: 3.500A pdb=" N GLU b 29 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER b 70 " --> pdb=" O GLU b 29 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS b 73 " --> pdb=" O GLY b 77 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY b 77 " --> pdb=" O HIS b 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 39 through 42 removed outlier: 7.554A pdb=" N VAL b 53 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 39 through 42 removed outlier: 7.554A pdb=" N VAL b 53 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 61 through 64 removed outlier: 4.097A pdb=" N ASP c 42 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU c 55 " --> pdb=" O ALA c 40 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA c 40 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR c 69 " --> pdb=" O VAL c 80 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL c 80 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE c 71 " --> pdb=" O THR c 78 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR c 78 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS c 73 " --> pdb=" O ILE c 76 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 25 through 29 removed outlier: 6.853A pdb=" N VAL d 53 " --> pdb=" O SER d 41 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU d 43 " --> pdb=" O TYR d 51 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR d 51 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER d 45 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL d 49 " --> pdb=" O SER d 45 " (cutoff:3.500A) 873 hydrogen bonds defined for protein. 2529 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: 3.71 Time building geometry restraints manager: 2.22 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: 6500 1.34 - 1.46: 3654 1.46 - 1.58: 8981 1.58 - 1.70: 0 1.70 - 1.82: 181 Bond restraints: 19316 Sorted by residual: bond pdb=" CB GLN D 59 " pdb=" CG GLN D 59 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB LYS c 35 " pdb=" CG LYS c 35 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CB LYS b 47 " pdb=" CG LYS b 47 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CG MET E 396 " pdb=" SD MET E 396 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB PRO A 10 " pdb=" CG PRO A 10 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.28e+00 ... (remaining 19311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 25615 2.19 - 4.38: 334 4.38 - 6.57: 58 6.57 - 8.75: 11 8.75 - 10.94: 7 Bond angle restraints: 26025 Sorted by residual: angle pdb=" CA MET E 396 " pdb=" CB MET E 396 " pdb=" CG MET E 396 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 angle pdb=" CB LYS c 35 " pdb=" CG LYS c 35 " pdb=" CD LYS c 35 " ideal model delta sigma weight residual 111.30 120.28 -8.98 2.30e+00 1.89e-01 1.52e+01 angle pdb=" CB MET A 341 " pdb=" CG MET A 341 " pdb=" SD MET A 341 " ideal model delta sigma weight residual 112.70 123.64 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA GLU C 329 " pdb=" CB GLU C 329 " pdb=" CG GLU C 329 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB MET A 415 " pdb=" CG MET A 415 " pdb=" SD MET A 415 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.19e+01 ... (remaining 26020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10296 17.98 - 35.97: 1304 35.97 - 53.95: 319 53.95 - 71.93: 51 71.93 - 89.92: 21 Dihedral angle restraints: 11991 sinusoidal: 5013 harmonic: 6978 Sorted by residual: dihedral pdb=" CA HIS E 344 " pdb=" C HIS E 344 " pdb=" N LEU E 345 " pdb=" CA LEU E 345 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET c 25 " pdb=" C MET c 25 " pdb=" N LEU c 26 " pdb=" CA LEU c 26 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PRO A 10 " pdb=" C PRO A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta harmonic sigma weight residual 180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 11988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1920 0.033 - 0.066: 689 0.066 - 0.099: 241 0.099 - 0.133: 127 0.133 - 0.166: 3 Chirality restraints: 2980 Sorted by residual: chirality pdb=" CA MET E 396 " pdb=" N MET E 396 " pdb=" C MET E 396 " pdb=" CB MET E 396 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CG LEU c 28 " pdb=" CB LEU c 28 " pdb=" CD1 LEU c 28 " pdb=" CD2 LEU c 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA GLU A 334 " pdb=" N GLU A 334 " pdb=" C GLU A 334 " pdb=" CB GLU A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2977 not shown) Planarity restraints: 3395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 178 " 0.060 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO E 179 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS b 73 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO b 74 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 210 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ASP D 210 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP D 210 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU D 211 " -0.012 2.00e-02 2.50e+03 ... (remaining 3392 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 552 2.70 - 3.25: 19215 3.25 - 3.80: 30920 3.80 - 4.35: 39162 4.35 - 4.90: 64663 Nonbonded interactions: 154512 Sorted by model distance: nonbonded pdb=" OG SER C 84 " pdb=" OD1 ASP c 14 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR E 408 " pdb=" OD1 ASP E 410 " model vdw 2.155 3.040 nonbonded pdb=" O GLU c 29 " pdb=" OG1 THR c 69 " model vdw 2.179 3.040 nonbonded pdb=" ND1 HIS d 73 " pdb=" OE1 GLU d 75 " model vdw 2.180 3.120 nonbonded pdb=" OG1 THR D 158 " pdb=" OD1 ASN D 190 " model vdw 2.184 3.040 ... (remaining 154507 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.600 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.003 0.056 19316 Z= 0.148 Angle : 0.642 10.942 26025 Z= 0.333 Chirality : 0.042 0.166 2980 Planarity : 0.004 0.092 3395 Dihedral : 16.707 89.917 7469 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.14 % Allowed : 25.79 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2400 helix: 1.41 (0.17), residues: 991 sheet: 0.12 (0.26), residues: 425 loop : 0.23 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 296 TYR 0.011 0.001 TYR C 332 PHE 0.029 0.001 PHE E 301 TRP 0.011 0.002 TRP C 381 HIS 0.014 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00330 (19316) covalent geometry : angle 0.64178 (26025) hydrogen bonds : bond 0.14864 ( 864) hydrogen bonds : angle 5.54953 ( 2529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5664 (ppp) cc_final: 0.4691 (pmm) REVERT: E 193 GLN cc_start: 0.9203 (mt0) cc_final: 0.8997 (mt0) REVERT: E 244 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 416 MET cc_start: 0.8362 (ppp) cc_final: 0.7772 (pmt) REVERT: b 17 GLU cc_start: 0.8954 (tp30) cc_final: 0.8337 (tm-30) REVERT: b 66 ASP cc_start: 0.7697 (t0) cc_final: 0.7449 (t0) REVERT: d 48 ASN cc_start: 0.6448 (t0) cc_final: 0.6125 (t0) outliers start: 3 outliers final: 5 residues processed: 351 average time/residue: 0.7461 time to fit residues: 290.6440 Evaluate side-chains 303 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 298 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain b residue 24 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.105432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075018 restraints weight = 50055.575| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.37 r_work: 0.3083 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19316 Z= 0.151 Angle : 0.635 10.147 26025 Z= 0.317 Chirality : 0.043 0.209 2980 Planarity : 0.004 0.062 3395 Dihedral : 4.561 83.647 2629 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.64 % Allowed : 26.85 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2400 helix: 1.52 (0.17), residues: 991 sheet: 0.07 (0.26), residues: 429 loop : 0.27 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 347 TYR 0.020 0.001 TYR c 5 PHE 0.017 0.001 PHE E 301 TRP 0.008 0.001 TRP A 381 HIS 0.013 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00347 (19316) covalent geometry : angle 0.63538 (26025) hydrogen bonds : bond 0.04119 ( 864) hydrogen bonds : angle 4.47053 ( 2529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6680 (ppp) cc_final: 0.5550 (pmm) REVERT: A 60 ASP cc_start: 0.8830 (t0) cc_final: 0.8374 (p0) REVERT: A 238 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6977 (tpt170) REVERT: A 248 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 274 TYR cc_start: 0.9053 (m-80) cc_final: 0.8789 (m-80) REVERT: A 341 MET cc_start: 0.8760 (tmm) cc_final: 0.8400 (tmm) REVERT: A 353 ARG cc_start: 0.8362 (tmm160) cc_final: 0.8007 (tmm160) REVERT: A 355 PHE cc_start: 0.8777 (m-10) cc_final: 0.8419 (m-10) REVERT: C 56 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: C 181 LYS cc_start: 0.8856 (pptt) cc_final: 0.7866 (pptt) REVERT: C 193 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: C 347 ARG cc_start: 0.7817 (tpt-90) cc_final: 0.7450 (tpt-90) REVERT: C 362 ARG cc_start: 0.9186 (ttm-80) cc_final: 0.8932 (ttm110) REVERT: D 193 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7456 (mp-120) REVERT: D 210 ASP cc_start: 0.8053 (t0) cc_final: 0.7505 (t0) REVERT: D 244 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8145 (mm-30) REVERT: D 290 ASP cc_start: 0.7716 (t0) cc_final: 0.7394 (t0) REVERT: E 175 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8018 (tm) REVERT: E 244 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7847 (mm-30) REVERT: E 272 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7753 (ttm110) REVERT: E 328 ASP cc_start: 0.8741 (m-30) cc_final: 0.8393 (m-30) REVERT: E 342 GLU cc_start: 0.8660 (pm20) cc_final: 0.8051 (tm-30) REVERT: b 6 GLN cc_start: 0.8721 (pm20) cc_final: 0.8513 (pm20) REVERT: b 17 GLU cc_start: 0.9280 (tp30) cc_final: 0.8596 (tm-30) REVERT: b 50 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7857 (mt-10) REVERT: c 25 MET cc_start: 0.8475 (tpt) cc_final: 0.8259 (tpt) REVERT: d 28 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7611 (mm) REVERT: d 48 ASN cc_start: 0.7697 (t0) cc_final: 0.6993 (t0) REVERT: d 51 TYR cc_start: 0.8297 (m-80) cc_final: 0.7861 (m-80) REVERT: d 66 ASP cc_start: 0.8415 (p0) cc_final: 0.8114 (p0) outliers start: 55 outliers final: 15 residues processed: 363 average time/residue: 0.7824 time to fit residues: 313.6281 Evaluate side-chains 331 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 344 HIS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 73 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 218 optimal weight: 0.2980 chunk 113 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 193 GLN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 140 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.105942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075504 restraints weight = 50383.607| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.41 r_work: 0.3096 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19316 Z= 0.126 Angle : 0.630 13.012 26025 Z= 0.309 Chirality : 0.042 0.148 2980 Planarity : 0.004 0.063 3395 Dihedral : 4.464 97.404 2622 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.16 % Allowed : 27.52 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.17), residues: 2400 helix: 1.60 (0.17), residues: 988 sheet: -0.04 (0.27), residues: 400 loop : 0.18 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 30 TYR 0.020 0.001 TYR E 197 PHE 0.010 0.001 PHE B 398 TRP 0.008 0.001 TRP A 381 HIS 0.010 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00291 (19316) covalent geometry : angle 0.63028 (26025) hydrogen bonds : bond 0.03500 ( 864) hydrogen bonds : angle 4.31704 ( 2529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6645 (ppp) cc_final: 0.5551 (pmm) REVERT: A 33 ASP cc_start: 0.8250 (m-30) cc_final: 0.8014 (m-30) REVERT: A 60 ASP cc_start: 0.8772 (t0) cc_final: 0.8364 (p0) REVERT: A 238 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6938 (tpm170) REVERT: A 248 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 274 TYR cc_start: 0.9028 (m-80) cc_final: 0.8760 (m-80) REVERT: A 341 MET cc_start: 0.8767 (tmm) cc_final: 0.8308 (tmm) REVERT: A 353 ARG cc_start: 0.8374 (tmm160) cc_final: 0.7371 (tmm160) REVERT: A 355 PHE cc_start: 0.8803 (m-10) cc_final: 0.8524 (m-80) REVERT: B 244 GLU cc_start: 0.8105 (pp20) cc_final: 0.7697 (pp20) REVERT: B 396 MET cc_start: 0.8194 (tpp) cc_final: 0.7948 (tpt) REVERT: C 56 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: C 181 LYS cc_start: 0.8881 (pptt) cc_final: 0.8098 (pptt) REVERT: C 347 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7583 (tpt-90) REVERT: C 418 ARG cc_start: 0.7661 (mpp80) cc_final: 0.7261 (mpp80) REVERT: D 85 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8473 (mm-40) REVERT: D 193 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7441 (mp-120) REVERT: D 210 ASP cc_start: 0.8074 (t0) cc_final: 0.7680 (t0) REVERT: D 290 ASP cc_start: 0.7816 (t0) cc_final: 0.7466 (t0) REVERT: D 342 GLU cc_start: 0.8840 (pt0) cc_final: 0.8129 (pp20) REVERT: E 1 MET cc_start: 0.7849 (mpp) cc_final: 0.7422 (mmm) REVERT: E 175 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8017 (tm) REVERT: E 244 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7991 (mm-30) REVERT: E 265 ASP cc_start: 0.8161 (t0) cc_final: 0.7924 (t0) REVERT: E 328 ASP cc_start: 0.8737 (m-30) cc_final: 0.8481 (m-30) REVERT: E 342 GLU cc_start: 0.8677 (pm20) cc_final: 0.7986 (tm-30) REVERT: b 10 CYS cc_start: 0.8259 (m) cc_final: 0.7548 (m) REVERT: b 17 GLU cc_start: 0.9297 (tp30) cc_final: 0.8641 (tm-30) REVERT: b 50 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7956 (mt-10) REVERT: c 21 GLN cc_start: 0.8223 (pp30) cc_final: 0.7682 (pp30) REVERT: c 22 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8400 (m90) REVERT: c 25 MET cc_start: 0.8418 (tpt) cc_final: 0.8191 (tpt) REVERT: d 14 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: d 48 ASN cc_start: 0.7688 (t0) cc_final: 0.6984 (t0) REVERT: d 51 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.8067 (m-80) outliers start: 66 outliers final: 21 residues processed: 365 average time/residue: 0.7493 time to fit residues: 303.3071 Evaluate side-chains 332 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 14 ASP Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 73 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 138 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN C 344 HIS E 42 HIS E 140 HIS E 172 GLN E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.105752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075612 restraints weight = 50127.692| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.39 r_work: 0.3099 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19316 Z= 0.124 Angle : 0.622 10.829 26025 Z= 0.304 Chirality : 0.042 0.146 2980 Planarity : 0.004 0.063 3395 Dihedral : 4.470 101.905 2622 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.74 % Allowed : 27.85 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2400 helix: 1.65 (0.17), residues: 989 sheet: 0.01 (0.27), residues: 385 loop : 0.15 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 362 TYR 0.021 0.001 TYR E 197 PHE 0.009 0.001 PHE B 398 TRP 0.007 0.001 TRP A 381 HIS 0.007 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00289 (19316) covalent geometry : angle 0.62221 (26025) hydrogen bonds : bond 0.03252 ( 864) hydrogen bonds : angle 4.25147 ( 2529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6657 (ppp) cc_final: 0.5603 (pmm) REVERT: A 33 ASP cc_start: 0.8274 (m-30) cc_final: 0.8033 (m-30) REVERT: A 60 ASP cc_start: 0.8699 (t0) cc_final: 0.8304 (p0) REVERT: A 193 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8674 (tp-100) REVERT: A 238 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6933 (tpm170) REVERT: A 248 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 274 TYR cc_start: 0.9038 (m-80) cc_final: 0.8792 (m-80) REVERT: A 299 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8373 (mtp85) REVERT: A 333 GLU cc_start: 0.8357 (pp20) cc_final: 0.8146 (pp20) REVERT: A 334 GLU cc_start: 0.8741 (tt0) cc_final: 0.8473 (mt-10) REVERT: A 341 MET cc_start: 0.8773 (tmm) cc_final: 0.8314 (tmm) REVERT: A 353 ARG cc_start: 0.8402 (tmm160) cc_final: 0.7263 (tmm160) REVERT: A 355 PHE cc_start: 0.8792 (m-10) cc_final: 0.8436 (m-80) REVERT: B 215 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 353 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8466 (ttp-170) REVERT: B 396 MET cc_start: 0.8130 (tpp) cc_final: 0.7920 (tpp) REVERT: C 56 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: C 181 LYS cc_start: 0.8856 (pptt) cc_final: 0.8079 (pptt) REVERT: C 226 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 347 ARG cc_start: 0.7918 (tpt-90) cc_final: 0.7535 (tpt-90) REVERT: C 418 ARG cc_start: 0.7699 (mpp80) cc_final: 0.7476 (mpp80) REVERT: D 193 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7397 (mp-120) REVERT: D 210 ASP cc_start: 0.8027 (t0) cc_final: 0.7708 (t0) REVERT: D 290 ASP cc_start: 0.7857 (t70) cc_final: 0.7486 (t0) REVERT: D 342 GLU cc_start: 0.8819 (pt0) cc_final: 0.8020 (pp20) REVERT: E 175 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8165 (tm) REVERT: E 193 GLN cc_start: 0.9338 (mt0) cc_final: 0.9061 (mt0) REVERT: E 244 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: E 328 ASP cc_start: 0.8759 (m-30) cc_final: 0.8491 (m-30) REVERT: E 336 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8906 (mtpp) REVERT: b 10 CYS cc_start: 0.8333 (m) cc_final: 0.7580 (m) REVERT: b 17 GLU cc_start: 0.9317 (tp30) cc_final: 0.8672 (tm-30) REVERT: b 50 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7865 (mt-10) REVERT: b 70 SER cc_start: 0.9276 (p) cc_final: 0.8824 (m) REVERT: b 80 VAL cc_start: 0.9651 (t) cc_final: 0.9346 (t) REVERT: c 21 GLN cc_start: 0.8267 (pp30) cc_final: 0.7829 (pp30) REVERT: c 22 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8416 (m90) REVERT: c 25 MET cc_start: 0.8414 (tpt) cc_final: 0.8201 (tpt) REVERT: d 14 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: d 48 ASN cc_start: 0.7887 (t0) cc_final: 0.7252 (t0) outliers start: 78 outliers final: 32 residues processed: 371 average time/residue: 0.7313 time to fit residues: 301.7220 Evaluate side-chains 344 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 14 ASP Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 138 optimal weight: 0.0040 chunk 174 optimal weight: 0.0970 chunk 142 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 181 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN E 42 HIS E 172 GLN E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.106338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076126 restraints weight = 50032.756| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.40 r_work: 0.3116 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19316 Z= 0.118 Angle : 0.656 11.619 26025 Z= 0.316 Chirality : 0.043 0.268 2980 Planarity : 0.004 0.063 3395 Dihedral : 4.419 101.280 2620 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.40 % Allowed : 28.86 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2400 helix: 1.67 (0.17), residues: 989 sheet: -0.01 (0.27), residues: 394 loop : 0.14 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 30 TYR 0.023 0.001 TYR b 13 PHE 0.009 0.001 PHE B 398 TRP 0.007 0.001 TRP A 381 HIS 0.013 0.001 HIS d 73 Details of bonding type rmsd covalent geometry : bond 0.00270 (19316) covalent geometry : angle 0.65593 (26025) hydrogen bonds : bond 0.03063 ( 864) hydrogen bonds : angle 4.17917 ( 2529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 330 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6697 (ppp) cc_final: 0.5762 (pmm) REVERT: A 33 ASP cc_start: 0.8285 (m-30) cc_final: 0.8042 (m-30) REVERT: A 60 ASP cc_start: 0.8645 (t0) cc_final: 0.8405 (p0) REVERT: A 193 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8671 (tp-100) REVERT: A 238 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6925 (tpm170) REVERT: A 248 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 274 TYR cc_start: 0.9022 (m-80) cc_final: 0.8809 (m-80) REVERT: A 333 GLU cc_start: 0.8407 (pp20) cc_final: 0.8143 (pp20) REVERT: A 334 GLU cc_start: 0.8765 (tt0) cc_final: 0.8496 (mt-10) REVERT: A 341 MET cc_start: 0.8769 (tmm) cc_final: 0.8022 (tmm) REVERT: A 353 ARG cc_start: 0.8440 (tmm160) cc_final: 0.7287 (tmm160) REVERT: A 355 PHE cc_start: 0.8742 (m-10) cc_final: 0.8419 (m-80) REVERT: A 396 MET cc_start: 0.8859 (mmt) cc_final: 0.8344 (mmm) REVERT: B 215 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8289 (mm-30) REVERT: B 244 GLU cc_start: 0.8058 (pp20) cc_final: 0.7651 (pp20) REVERT: B 396 MET cc_start: 0.8102 (tpp) cc_final: 0.7810 (tpp) REVERT: C 56 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: C 181 LYS cc_start: 0.8875 (pptt) cc_final: 0.8211 (pptt) REVERT: C 347 ARG cc_start: 0.7878 (tpt-90) cc_final: 0.7529 (tpt-90) REVERT: D 85 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8449 (mm-40) REVERT: D 193 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7545 (mp-120) REVERT: D 210 ASP cc_start: 0.8012 (t0) cc_final: 0.7674 (t0) REVERT: D 290 ASP cc_start: 0.7945 (t70) cc_final: 0.7517 (t0) REVERT: D 342 GLU cc_start: 0.8763 (pt0) cc_final: 0.7968 (pp20) REVERT: E 175 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8009 (tm) REVERT: E 189 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8193 (mm-40) REVERT: E 193 GLN cc_start: 0.9338 (mt0) cc_final: 0.8988 (mt0) REVERT: E 219 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8903 (mmm) REVERT: E 244 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7918 (mm-30) REVERT: E 328 ASP cc_start: 0.8797 (m-30) cc_final: 0.8528 (m-30) REVERT: E 336 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8928 (mtpp) REVERT: E 342 GLU cc_start: 0.8608 (pm20) cc_final: 0.7894 (tm-30) REVERT: b 10 CYS cc_start: 0.8351 (m) cc_final: 0.7608 (m) REVERT: b 17 GLU cc_start: 0.9304 (tp30) cc_final: 0.8632 (tm-30) REVERT: b 50 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7937 (mt-10) REVERT: b 70 SER cc_start: 0.9252 (p) cc_final: 0.8749 (m) REVERT: b 80 VAL cc_start: 0.9652 (t) cc_final: 0.9331 (t) REVERT: c 21 GLN cc_start: 0.8294 (pp30) cc_final: 0.7859 (pp30) REVERT: c 22 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (m90) REVERT: d 14 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: d 48 ASN cc_start: 0.7964 (t0) cc_final: 0.7381 (t0) outliers start: 71 outliers final: 30 residues processed: 377 average time/residue: 0.7327 time to fit residues: 307.1027 Evaluate side-chains 343 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 306 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 14 ASP Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN C 193 GLN C 292 ASN D 189 GLN E 42 HIS E 172 GLN E 241 GLN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.105263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074810 restraints weight = 50307.864| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.39 r_work: 0.3080 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19316 Z= 0.163 Angle : 0.674 11.655 26025 Z= 0.326 Chirality : 0.043 0.150 2980 Planarity : 0.005 0.086 3395 Dihedral : 4.479 99.553 2620 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.98 % Allowed : 28.86 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2400 helix: 1.63 (0.17), residues: 989 sheet: -0.14 (0.27), residues: 390 loop : 0.17 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 30 TYR 0.026 0.002 TYR b 13 PHE 0.020 0.001 PHE E 121 TRP 0.007 0.001 TRP A 381 HIS 0.007 0.001 HIS d 73 Details of bonding type rmsd covalent geometry : bond 0.00382 (19316) covalent geometry : angle 0.67423 (26025) hydrogen bonds : bond 0.03349 ( 864) hydrogen bonds : angle 4.18773 ( 2529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 312 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6939 (ppp) cc_final: 0.5819 (pmm) REVERT: A 33 ASP cc_start: 0.8286 (m-30) cc_final: 0.8034 (m-30) REVERT: A 58 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7975 (mm) REVERT: A 60 ASP cc_start: 0.8638 (t0) cc_final: 0.8369 (p0) REVERT: A 193 GLN cc_start: 0.8933 (tp-100) cc_final: 0.8673 (tp-100) REVERT: A 238 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6952 (tpt170) REVERT: A 248 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 274 TYR cc_start: 0.9042 (m-80) cc_final: 0.8817 (m-80) REVERT: A 333 GLU cc_start: 0.8450 (pp20) cc_final: 0.8168 (pp20) REVERT: A 334 GLU cc_start: 0.8792 (tt0) cc_final: 0.8496 (mt-10) REVERT: A 341 MET cc_start: 0.8814 (tmm) cc_final: 0.8349 (tmm) REVERT: A 353 ARG cc_start: 0.8436 (tmm160) cc_final: 0.8003 (tmm160) REVERT: A 355 PHE cc_start: 0.8784 (m-10) cc_final: 0.8334 (m-10) REVERT: A 390 MET cc_start: 0.8516 (ppp) cc_final: 0.8218 (ppp) REVERT: A 396 MET cc_start: 0.9079 (mmt) cc_final: 0.8449 (mmm) REVERT: B 215 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 266 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8771 (t) REVERT: B 353 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8488 (ttp-170) REVERT: C 56 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7831 (tp30) REVERT: C 181 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8165 (pptt) REVERT: C 193 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8334 (mp10) REVERT: C 347 ARG cc_start: 0.7884 (tpt-90) cc_final: 0.7536 (tpt-90) REVERT: C 373 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8028 (p) REVERT: D 193 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7547 (mp-120) REVERT: D 210 ASP cc_start: 0.8099 (t0) cc_final: 0.7780 (t0) REVERT: D 244 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8147 (mm-30) REVERT: D 290 ASP cc_start: 0.7896 (t70) cc_final: 0.7451 (t0) REVERT: D 342 GLU cc_start: 0.8775 (pt0) cc_final: 0.7995 (pp20) REVERT: E 5 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: E 175 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8077 (tm) REVERT: E 193 GLN cc_start: 0.9336 (mt0) cc_final: 0.9028 (mt0) REVERT: E 211 GLU cc_start: 0.8213 (tp30) cc_final: 0.7855 (tp30) REVERT: E 219 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8992 (mmm) REVERT: E 244 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: E 328 ASP cc_start: 0.8877 (m-30) cc_final: 0.8624 (m-30) REVERT: E 336 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8958 (mtpp) REVERT: E 342 GLU cc_start: 0.8688 (pm20) cc_final: 0.8146 (pp20) REVERT: b 17 GLU cc_start: 0.9324 (tp30) cc_final: 0.8700 (tm-30) REVERT: b 50 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7869 (mt-10) REVERT: b 70 SER cc_start: 0.9306 (p) cc_final: 0.8743 (m) REVERT: b 80 VAL cc_start: 0.9623 (t) cc_final: 0.9280 (t) REVERT: c 21 GLN cc_start: 0.8270 (pp30) cc_final: 0.7883 (pp30) REVERT: c 22 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8403 (m90) REVERT: d 28 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7310 (mp) REVERT: d 48 ASN cc_start: 0.8022 (t0) cc_final: 0.7457 (t0) outliers start: 83 outliers final: 35 residues processed: 366 average time/residue: 0.6905 time to fit residues: 281.6389 Evaluate side-chains 349 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 84 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN E 42 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.106078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075730 restraints weight = 50216.055| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.40 r_work: 0.3088 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19316 Z= 0.131 Angle : 0.698 15.365 26025 Z= 0.334 Chirality : 0.043 0.272 2980 Planarity : 0.004 0.093 3395 Dihedral : 4.494 102.851 2620 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.69 % Allowed : 30.01 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.17), residues: 2400 helix: 1.63 (0.17), residues: 989 sheet: -0.25 (0.26), residues: 400 loop : 0.16 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 30 TYR 0.025 0.001 TYR b 13 PHE 0.015 0.001 PHE b 71 TRP 0.007 0.001 TRP A 381 HIS 0.006 0.001 HIS d 73 Details of bonding type rmsd covalent geometry : bond 0.00307 (19316) covalent geometry : angle 0.69821 (26025) hydrogen bonds : bond 0.03140 ( 864) hydrogen bonds : angle 4.18489 ( 2529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 323 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6744 (ppp) cc_final: 0.5974 (pmm) REVERT: A 29 MET cc_start: 0.3798 (tpt) cc_final: 0.2889 (tpp) REVERT: A 33 ASP cc_start: 0.8320 (m-30) cc_final: 0.8070 (m-30) REVERT: A 58 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7953 (mm) REVERT: A 60 ASP cc_start: 0.8627 (t0) cc_final: 0.8348 (p0) REVERT: A 193 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8685 (tp-100) REVERT: A 238 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6926 (tpm170) REVERT: A 248 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 274 TYR cc_start: 0.9028 (m-80) cc_final: 0.8827 (m-80) REVERT: A 333 GLU cc_start: 0.8450 (pp20) cc_final: 0.8247 (pp20) REVERT: A 341 MET cc_start: 0.8811 (tmm) cc_final: 0.8364 (tmm) REVERT: A 353 ARG cc_start: 0.8428 (tmm160) cc_final: 0.7314 (tmm160) REVERT: A 355 PHE cc_start: 0.8796 (m-10) cc_final: 0.8435 (m-80) REVERT: A 396 MET cc_start: 0.8834 (mmt) cc_final: 0.8312 (mmm) REVERT: B 215 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8328 (mm-30) REVERT: B 244 GLU cc_start: 0.7964 (pp20) cc_final: 0.7577 (pp20) REVERT: B 245 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7574 (mmm) REVERT: B 266 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8750 (t) REVERT: B 353 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8484 (ttp-170) REVERT: B 396 MET cc_start: 0.8300 (tpp) cc_final: 0.8015 (tpp) REVERT: C 56 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: C 181 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8200 (pptt) REVERT: C 347 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7532 (tpt-90) REVERT: C 373 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7961 (p) REVERT: D 193 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7550 (mp-120) REVERT: D 210 ASP cc_start: 0.8056 (t0) cc_final: 0.7730 (t0) REVERT: D 244 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8220 (mm-30) REVERT: D 290 ASP cc_start: 0.7889 (t70) cc_final: 0.7439 (t0) REVERT: D 342 GLU cc_start: 0.8738 (pt0) cc_final: 0.7991 (pp20) REVERT: E 5 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: E 175 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8024 (tm) REVERT: E 189 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8108 (mm-40) REVERT: E 193 GLN cc_start: 0.9334 (mt0) cc_final: 0.9029 (mt0) REVERT: E 219 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8915 (mmm) REVERT: E 244 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: E 328 ASP cc_start: 0.8864 (m-30) cc_final: 0.8575 (m-30) REVERT: E 336 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8911 (mmtt) REVERT: E 342 GLU cc_start: 0.8684 (pm20) cc_final: 0.8157 (pp20) REVERT: b 17 GLU cc_start: 0.9312 (tp30) cc_final: 0.8702 (tm-30) REVERT: b 25 MET cc_start: 0.8002 (tpp) cc_final: 0.7675 (tpp) REVERT: b 50 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7877 (mt-10) REVERT: b 70 SER cc_start: 0.9333 (p) cc_final: 0.8764 (m) REVERT: b 71 PHE cc_start: 0.8440 (p90) cc_final: 0.8231 (p90) REVERT: b 80 VAL cc_start: 0.9619 (t) cc_final: 0.9271 (t) REVERT: c 21 GLN cc_start: 0.8269 (pp30) cc_final: 0.7995 (pp30) REVERT: c 22 HIS cc_start: 0.8723 (OUTLIER) cc_final: 0.8416 (m-70) REVERT: d 28 LEU cc_start: 0.8163 (tm) cc_final: 0.7291 (mm) REVERT: d 48 ASN cc_start: 0.7999 (t0) cc_final: 0.7500 (t0) REVERT: d 62 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6291 (tm-30) outliers start: 77 outliers final: 36 residues processed: 375 average time/residue: 0.6851 time to fit residues: 286.9328 Evaluate side-chains 359 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 274 TYR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 164 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 182 optimal weight: 0.4980 chunk 214 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN E 42 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.105010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074459 restraints weight = 50332.373| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.41 r_work: 0.3074 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19316 Z= 0.178 Angle : 0.726 17.047 26025 Z= 0.349 Chirality : 0.044 0.199 2980 Planarity : 0.004 0.062 3395 Dihedral : 4.582 104.196 2620 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.31 % Allowed : 31.11 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2400 helix: 1.58 (0.17), residues: 989 sheet: -0.35 (0.27), residues: 396 loop : 0.18 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 30 TYR 0.027 0.002 TYR b 13 PHE 0.012 0.001 PHE b 71 TRP 0.006 0.001 TRP A 381 HIS 0.006 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00418 (19316) covalent geometry : angle 0.72569 (26025) hydrogen bonds : bond 0.03399 ( 864) hydrogen bonds : angle 4.24076 ( 2529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6763 (ppp) cc_final: 0.6027 (pmm) REVERT: A 29 MET cc_start: 0.3797 (tpt) cc_final: 0.2925 (tpp) REVERT: A 33 ASP cc_start: 0.8281 (m-30) cc_final: 0.8012 (m-30) REVERT: A 58 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7984 (mm) REVERT: A 60 ASP cc_start: 0.8637 (t0) cc_final: 0.8334 (p0) REVERT: A 193 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8709 (tp-100) REVERT: A 238 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6970 (tpt170) REVERT: A 248 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 274 TYR cc_start: 0.9086 (m-80) cc_final: 0.8836 (m-80) REVERT: A 333 GLU cc_start: 0.8477 (pp20) cc_final: 0.8263 (pp20) REVERT: A 341 MET cc_start: 0.8823 (tmm) cc_final: 0.8409 (tmm) REVERT: A 353 ARG cc_start: 0.8458 (tmm160) cc_final: 0.8040 (tmm160) REVERT: A 355 PHE cc_start: 0.8810 (m-10) cc_final: 0.8360 (m-10) REVERT: A 396 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8398 (mmm) REVERT: B 215 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 266 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8771 (t) REVERT: B 351 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8444 (mm-30) REVERT: B 416 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8288 (mpp) REVERT: C 56 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: C 181 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8180 (pptt) REVERT: C 347 ARG cc_start: 0.7922 (tpt-90) cc_final: 0.7562 (tpt-90) REVERT: C 373 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8054 (p) REVERT: D 193 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7568 (mp-120) REVERT: D 210 ASP cc_start: 0.8123 (t0) cc_final: 0.7798 (t0) REVERT: D 244 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8182 (mm-30) REVERT: D 290 ASP cc_start: 0.7896 (t70) cc_final: 0.7442 (t0) REVERT: D 342 GLU cc_start: 0.8754 (pt0) cc_final: 0.7971 (pp20) REVERT: E 5 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: E 175 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8012 (tm) REVERT: E 189 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8206 (mm-40) REVERT: E 193 GLN cc_start: 0.9350 (mt0) cc_final: 0.8977 (mt0) REVERT: E 219 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8967 (mmm) REVERT: E 244 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: E 272 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7729 (mtp-110) REVERT: E 328 ASP cc_start: 0.8825 (m-30) cc_final: 0.8574 (m-30) REVERT: E 336 LYS cc_start: 0.9187 (mtmm) cc_final: 0.8975 (mtpp) REVERT: b 17 GLU cc_start: 0.9309 (tp30) cc_final: 0.8694 (tm-30) REVERT: b 50 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7890 (mt-10) REVERT: c 21 GLN cc_start: 0.8327 (pp30) cc_final: 0.8067 (pp30) REVERT: c 22 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8444 (m-70) REVERT: d 28 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7296 (mp) REVERT: d 48 ASN cc_start: 0.7955 (t0) cc_final: 0.7472 (t0) REVERT: d 53 VAL cc_start: 0.8508 (m) cc_final: 0.8178 (m) REVERT: d 62 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6162 (tm-30) outliers start: 69 outliers final: 39 residues processed: 350 average time/residue: 0.7147 time to fit residues: 278.9176 Evaluate side-chains 352 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 22 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 92 optimal weight: 0.1980 chunk 212 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 234 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN E 42 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075577 restraints weight = 49783.695| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.38 r_work: 0.3082 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19316 Z= 0.139 Angle : 0.745 17.375 26025 Z= 0.356 Chirality : 0.043 0.182 2980 Planarity : 0.004 0.061 3395 Dihedral : 4.080 20.671 2618 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.31 % Allowed : 31.16 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.17), residues: 2400 helix: 1.58 (0.17), residues: 989 sheet: -0.16 (0.27), residues: 375 loop : 0.10 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 30 TYR 0.024 0.001 TYR E 197 PHE 0.010 0.001 PHE E 412 TRP 0.007 0.001 TRP E 381 HIS 0.005 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00330 (19316) covalent geometry : angle 0.74548 (26025) hydrogen bonds : bond 0.03209 ( 864) hydrogen bonds : angle 4.18433 ( 2529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.3727 (tpt) cc_final: 0.2860 (tpp) REVERT: A 33 ASP cc_start: 0.8285 (m-30) cc_final: 0.8015 (m-30) REVERT: A 58 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 60 ASP cc_start: 0.8649 (t0) cc_final: 0.8256 (p0) REVERT: A 193 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8705 (tp-100) REVERT: A 205 MET cc_start: 0.7703 (mtm) cc_final: 0.7439 (mtp) REVERT: A 238 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6960 (tpm170) REVERT: A 248 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 333 GLU cc_start: 0.8468 (pp20) cc_final: 0.8239 (pp20) REVERT: A 341 MET cc_start: 0.8807 (tmm) cc_final: 0.8385 (tmm) REVERT: A 353 ARG cc_start: 0.8446 (tmm160) cc_final: 0.8046 (tmm160) REVERT: A 355 PHE cc_start: 0.8823 (m-10) cc_final: 0.8382 (m-10) REVERT: A 390 MET cc_start: 0.8507 (ppp) cc_final: 0.8224 (ppp) REVERT: A 396 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: B 215 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 244 GLU cc_start: 0.7896 (pp20) cc_final: 0.7594 (pp20) REVERT: B 266 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8746 (t) REVERT: B 351 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 416 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: C 56 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: C 373 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8008 (p) REVERT: D 4 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8240 (p) REVERT: D 52 ASP cc_start: 0.8356 (p0) cc_final: 0.8079 (p0) REVERT: D 193 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7514 (mp-120) REVERT: D 210 ASP cc_start: 0.8092 (t0) cc_final: 0.7761 (t0) REVERT: D 244 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8408 (mm-30) REVERT: D 342 GLU cc_start: 0.8694 (pt0) cc_final: 0.8005 (pp20) REVERT: E 5 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: E 175 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7956 (tm) REVERT: E 189 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8271 (mm-40) REVERT: E 193 GLN cc_start: 0.9340 (mt0) cc_final: 0.8965 (mt0) REVERT: E 244 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: E 272 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7654 (mtp-110) REVERT: E 336 LYS cc_start: 0.9210 (mtmm) cc_final: 0.9005 (mtpp) REVERT: E 342 GLU cc_start: 0.8607 (pm20) cc_final: 0.8325 (pp20) REVERT: b 11 ASP cc_start: 0.7902 (m-30) cc_final: 0.7666 (p0) REVERT: b 17 GLU cc_start: 0.9328 (tp30) cc_final: 0.8728 (tm-30) REVERT: b 50 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7854 (mt-10) REVERT: b 70 SER cc_start: 0.9184 (p) cc_final: 0.8642 (m) REVERT: c 21 GLN cc_start: 0.8318 (pp30) cc_final: 0.7943 (pp30) REVERT: c 22 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8494 (m90) REVERT: d 28 LEU cc_start: 0.8161 (tm) cc_final: 0.7367 (mp) REVERT: d 48 ASN cc_start: 0.7908 (t0) cc_final: 0.7465 (t0) REVERT: d 53 VAL cc_start: 0.8518 (m) cc_final: 0.8179 (m) REVERT: d 62 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6144 (tm-30) outliers start: 69 outliers final: 39 residues processed: 352 average time/residue: 0.7017 time to fit residues: 276.1326 Evaluate side-chains 352 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 274 TYR Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 59 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 292 ASN E 42 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.105980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075623 restraints weight = 50061.274| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.39 r_work: 0.3084 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19316 Z= 0.141 Angle : 0.760 17.555 26025 Z= 0.363 Chirality : 0.044 0.265 2980 Planarity : 0.004 0.065 3395 Dihedral : 4.090 20.584 2618 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 31.59 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2400 helix: 1.55 (0.17), residues: 989 sheet: -0.27 (0.27), residues: 388 loop : 0.12 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 30 TYR 0.026 0.001 TYR b 13 PHE 0.022 0.001 PHE E 121 TRP 0.008 0.001 TRP E 381 HIS 0.004 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00336 (19316) covalent geometry : angle 0.76042 (26025) hydrogen bonds : bond 0.03207 ( 864) hydrogen bonds : angle 4.20125 ( 2529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 308 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6741 (ptm) cc_final: 0.5926 (pmm) REVERT: A 29 MET cc_start: 0.3727 (tpt) cc_final: 0.2862 (tpp) REVERT: A 33 ASP cc_start: 0.8312 (m-30) cc_final: 0.8043 (m-30) REVERT: A 58 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (mm) REVERT: A 60 ASP cc_start: 0.8649 (t0) cc_final: 0.8252 (p0) REVERT: A 193 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8702 (tp-100) REVERT: A 205 MET cc_start: 0.7726 (mtm) cc_final: 0.7458 (mtp) REVERT: A 238 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6913 (tpm170) REVERT: A 248 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 274 TYR cc_start: 0.9042 (m-80) cc_final: 0.8783 (m-80) REVERT: A 333 GLU cc_start: 0.8489 (pp20) cc_final: 0.8277 (pp20) REVERT: A 341 MET cc_start: 0.8807 (tmm) cc_final: 0.8384 (tmm) REVERT: A 353 ARG cc_start: 0.8442 (tmm160) cc_final: 0.8076 (tmm160) REVERT: A 355 PHE cc_start: 0.8816 (m-10) cc_final: 0.8388 (m-10) REVERT: A 390 MET cc_start: 0.8518 (ppp) cc_final: 0.8226 (ppp) REVERT: A 396 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8473 (mmm) REVERT: B 215 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 244 GLU cc_start: 0.7948 (pp20) cc_final: 0.7519 (pp20) REVERT: B 266 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8754 (t) REVERT: B 416 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8267 (mpp) REVERT: C 56 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: C 373 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8000 (p) REVERT: D 4 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8257 (p) REVERT: D 52 ASP cc_start: 0.8325 (p0) cc_final: 0.8046 (p0) REVERT: D 186 MET cc_start: 0.8813 (tpp) cc_final: 0.8595 (mmm) REVERT: D 193 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7524 (mp-120) REVERT: D 210 ASP cc_start: 0.8104 (t0) cc_final: 0.7759 (t0) REVERT: D 290 ASP cc_start: 0.7914 (t70) cc_final: 0.7433 (t0) REVERT: D 342 GLU cc_start: 0.8668 (pt0) cc_final: 0.7869 (pp20) REVERT: E 5 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: E 175 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7897 (tm) REVERT: E 193 GLN cc_start: 0.9345 (mt0) cc_final: 0.8965 (mt0) REVERT: E 244 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: E 272 ARG cc_start: 0.8149 (mtp-110) cc_final: 0.7672 (mtp-110) REVERT: b 17 GLU cc_start: 0.9317 (tp30) cc_final: 0.8706 (tm-30) REVERT: b 50 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7964 (mt-10) REVERT: b 70 SER cc_start: 0.9287 (p) cc_final: 0.8785 (m) REVERT: c 21 GLN cc_start: 0.8301 (pp30) cc_final: 0.7941 (pp30) REVERT: c 22 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (m90) REVERT: d 28 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7365 (mp) REVERT: d 48 ASN cc_start: 0.7937 (t0) cc_final: 0.7490 (t0) REVERT: d 53 VAL cc_start: 0.8599 (m) cc_final: 0.8245 (m) REVERT: d 62 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6393 (tm-30) outliers start: 63 outliers final: 41 residues processed: 350 average time/residue: 0.6795 time to fit residues: 265.0240 Evaluate side-chains 353 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 298 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 341 MET Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 142 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 274 TYR Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 163 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 0.0020 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN E 42 HIS E 172 GLN E 241 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 ASN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.076251 restraints weight = 49911.673| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.40 r_work: 0.3115 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19316 Z= 0.135 Angle : 0.774 17.421 26025 Z= 0.370 Chirality : 0.044 0.297 2980 Planarity : 0.004 0.064 3395 Dihedral : 4.070 21.495 2618 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.78 % Allowed : 31.98 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.17), residues: 2400 helix: 1.56 (0.17), residues: 989 sheet: -0.20 (0.27), residues: 382 loop : 0.09 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 30 TYR 0.024 0.001 TYR E 197 PHE 0.013 0.001 PHE b 71 TRP 0.007 0.001 TRP A 381 HIS 0.005 0.001 HIS b 73 Details of bonding type rmsd covalent geometry : bond 0.00320 (19316) covalent geometry : angle 0.77385 (26025) hydrogen bonds : bond 0.03131 ( 864) hydrogen bonds : angle 4.19384 ( 2529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8299.66 seconds wall clock time: 142 minutes 5.99 seconds (8525.99 seconds total)