Starting phenix.real_space_refine on Mon May 19 22:34:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.map" model { file = "/net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pto_17876/05_2025/8pto_17876.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 97 5.16 5 C 11989 2.51 5 N 3372 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19124 Number of models: 1 Model: "" Number of chains: 12 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: "b" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "a" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.88, per 1000 atoms: 0.62 Number of scatterers: 19124 At special positions: 0 Unit cell: (118.144, 134.784, 161.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 6 15.00 O 3660 8.00 N 3372 7.00 C 11989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 106 helices and 23 sheets defined 46.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.630A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.655A pdb=" N ASN A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.893A 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: 3.676A 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 285 through 289 removed outlier: 4.197A pdb=" N VAL A 289 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.043A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 removed outlier: 4.277A pdb=" N GLY A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.146A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.623A pdb=" N GLN A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.588A pdb=" N MET A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.684A pdb=" N LEU B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.744A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.280A 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 255 removed outlier: 3.504A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 336 through 339 removed outlier: 4.495A pdb=" N GLY B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.260A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.518A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.563A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) 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 44 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.803A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.114A 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 removed outlier: 3.566A pdb=" N THR C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 334 through 339 removed outlier: 5.369A pdb=" N GLY C 337 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 338 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 339' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.305A pdb=" N LEU C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.597A pdb=" N MET C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.565A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.297A 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 removed outlier: 3.611A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.968A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.531A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.653A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.276A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.872A 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 2 through 8 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.735A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.532A pdb=" N PHE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.997A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 removed outlier: 3.597A pdb=" N THR E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) 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: 4.223A 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 326 through 335 removed outlier: 3.674A pdb=" N VAL E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.559A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.742A pdb=" N GLN E 378 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.534A pdb=" N GLU E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'b' and resid 56 through 59 Processing helix chain 'c' and resid 9 through 22 removed outlier: 3.677A pdb=" N HIS c 22 " --> pdb=" O LEU c 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'a' and resid 9 through 22 removed outlier: 3.707A pdb=" N HIS a 22 " --> pdb=" O LEU a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 7.793A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 341 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.540A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.536A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.302A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.882A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP C 265 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 207 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.790A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.863A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.323A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.381A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.374A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.876A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.579A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.613A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 35 through 37 removed outlier: 6.550A pdb=" N THR b 27 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE b 71 " --> pdb=" O THR b 27 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU b 29 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 40 through 46 removed outlier: 4.072A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL b 53 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 61 through 64 removed outlier: 6.041A pdb=" N VAL c 49 " --> pdb=" O SER c 45 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER c 45 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR c 51 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU c 43 " --> pdb=" O TYR c 51 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL c 53 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS c 39 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR c 27 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE c 71 " --> pdb=" O THR c 27 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU c 29 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE c 71 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL c 79 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.679A pdb=" N VAL d 53 " --> pdb=" O ASP d 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR d 27 " --> pdb=" O SER d 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER d 72 " --> pdb=" O THR d 27 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE d 71 " --> pdb=" O VAL d 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 35 through 38 removed outlier: 3.593A pdb=" N ALA a 38 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU a 26 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR a 27 " --> pdb=" O PHE a 71 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE a 71 " --> pdb=" O THR a 27 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU a 29 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 40 through 46 removed outlier: 4.369A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2538 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: 6.76 Time building geometry restraints manager: 5.75 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: 6505 1.34 - 1.46: 2616 1.46 - 1.57: 10096 1.57 - 1.69: 9 1.69 - 1.81: 181 Bond restraints: 19407 Sorted by residual: bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.87e-01 bond pdb=" C4 ADP C1000 " pdb=" C5 ADP C1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.56e-01 bond pdb=" C4 ADP D1000 " pdb=" C5 ADP D1000 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.18e-01 bond pdb=" CB THR C 365 " pdb=" CG2 THR C 365 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.18e-01 bond pdb=" CB VAL C 260 " pdb=" CG2 VAL C 260 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.98e-01 ... (remaining 19402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 25734 1.18 - 2.36: 273 2.36 - 3.53: 114 3.53 - 4.71: 24 4.71 - 5.89: 23 Bond angle restraints: 26168 Sorted by residual: angle pdb=" O1B ADP D1000 " pdb=" PB ADP D1000 " pdb=" O3B ADP D1000 " ideal model delta sigma weight residual 119.90 114.01 5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O3B ADP B1000 " ideal model delta sigma weight residual 119.90 114.08 5.82 3.00e+00 1.11e-01 3.76e+00 angle pdb=" C ILE E 321 " pdb=" N ASP E 322 " pdb=" CA ASP E 322 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.60e+00 angle pdb=" C ASP C 265 " pdb=" N SER C 266 " pdb=" CA SER C 266 " ideal model delta sigma weight residual 121.70 125.08 -3.38 1.80e+00 3.09e-01 3.52e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O2B ADP B1000 " ideal model delta sigma weight residual 119.90 114.29 5.61 3.00e+00 1.11e-01 3.50e+00 ... (remaining 26163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 11653 23.18 - 46.37: 353 46.37 - 69.55: 16 69.55 - 92.73: 2 92.73 - 115.91: 4 Dihedral angle restraints: 12028 sinusoidal: 5050 harmonic: 6978 Sorted by residual: dihedral pdb=" O1B ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " pdb=" PA ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.92 115.91 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.28 110.28 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 -162.91 102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 12025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1709 0.025 - 0.049: 743 0.049 - 0.074: 294 0.074 - 0.098: 127 0.098 - 0.123: 119 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE C 261 " pdb=" N ILE C 261 " pdb=" C ILE C 261 " pdb=" CB ILE C 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 2989 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS b 73 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO b 74 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 179 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO B 180 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 179 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 180 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.017 5.00e-02 4.00e+02 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2326 2.75 - 3.29: 19334 3.29 - 3.82: 30739 3.82 - 4.36: 38377 4.36 - 4.90: 65013 Nonbonded interactions: 155789 Sorted by model distance: nonbonded pdb=" OG1 THR E 323 " pdb=" OD2 ASP E 328 " model vdw 2.212 3.040 nonbonded pdb=" NH1 ARG E 66 " pdb=" OD2 ASP E 78 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR D 408 " pdb=" OD1 ASP D 410 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG D 66 " pdb=" OD2 ASP D 78 " model vdw 2.240 3.120 nonbonded pdb=" OG SER D 84 " pdb=" OD1 ASP d 14 " model vdw 2.245 3.040 ... (remaining 155784 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 418) selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) 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: 2.370 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: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 44.960 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 0.032 19407 Z= 0.125 Angle : 0.432 5.890 26168 Z= 0.206 Chirality : 0.039 0.123 2992 Planarity : 0.003 0.035 3402 Dihedral : 10.473 115.914 7506 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 5.90 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.17), residues: 2400 helix: 1.31 (0.17), residues: 962 sheet: 0.59 (0.27), residues: 451 loop : 0.77 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 381 HIS 0.003 0.001 HIS c 73 PHE 0.008 0.001 PHE D 89 TYR 0.005 0.001 TYR B 110 ARG 0.003 0.000 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.24513 ( 892) hydrogen bonds : angle 7.04464 ( 2538) covalent geometry : bond 0.00289 (19407) covalent geometry : angle 0.43183 (26168) *********************** 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 361 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 2.153 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 32 GLN cc_start: 0.8988 (pm20) cc_final: 0.8653 (pm20) REVERT: A 42 HIS cc_start: 0.8557 (m-70) cc_final: 0.8283 (m-70) REVERT: A 333 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 415 MET cc_start: 0.8737 (tmm) cc_final: 0.8495 (tmm) REVERT: B 134 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8457 (mp0) REVERT: B 378 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8235 (mm110) REVERT: C 334 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8173 (mp0) REVERT: C 378 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8703 (mm-40) REVERT: D 244 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 284 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8734 (t) REVERT: D 285 LEU cc_start: 0.9159 (mt) cc_final: 0.8930 (mp) REVERT: D 329 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 42 HIS cc_start: 0.8273 (t70) cc_final: 0.7964 (t70) REVERT: E 211 GLU cc_start: 0.8606 (tp30) cc_final: 0.8295 (tp30) REVERT: E 341 MET cc_start: 0.7341 (tpt) cc_final: 0.6460 (tmm) REVERT: b 5 TYR cc_start: 0.8469 (t80) cc_final: 0.8130 (t80) REVERT: b 12 ASP cc_start: 0.8753 (m-30) cc_final: 0.8533 (m-30) REVERT: b 46 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: b 73 HIS cc_start: 0.8193 (t-90) cc_final: 0.7443 (t70) REVERT: b 79 VAL cc_start: 0.9003 (t) cc_final: 0.8767 (m) REVERT: b 82 SER cc_start: 0.8805 (p) cc_final: 0.8533 (p) REVERT: d 47 LYS cc_start: 0.8900 (mptp) cc_final: 0.8627 (tptp) REVERT: d 65 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8677 (mm) outliers start: 50 outliers final: 14 residues processed: 350 average time/residue: 1.4736 time to fit residues: 571.6120 Evaluate side-chains 271 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 185 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 2 ASN D 41 GLN D 85 GLN D 193 GLN D 241 GLN E 2 ASN E 140 HIS E 199 HIS E 275 ASN d 6 GLN d 9 ASN d 21 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069044 restraints weight = 42621.850| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.84 r_work: 0.2906 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19407 Z= 0.126 Angle : 0.590 10.456 26168 Z= 0.294 Chirality : 0.042 0.180 2992 Planarity : 0.004 0.041 3402 Dihedral : 6.312 96.618 2678 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.59 % Allowed : 10.83 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2400 helix: 1.71 (0.17), residues: 1007 sheet: 0.61 (0.26), residues: 420 loop : 0.46 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 381 HIS 0.005 0.001 HIS E 140 PHE 0.017 0.001 PHE A 398 TYR 0.019 0.001 TYR E 197 ARG 0.008 0.001 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 892) hydrogen bonds : angle 5.02982 ( 2538) covalent geometry : bond 0.00274 (19407) covalent geometry : angle 0.58982 (26168) *********************** 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 326 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 2.223 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 186 MET cc_start: 0.9202 (mmm) cc_final: 0.8768 (mmm) REVERT: A 188 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9111 (mm) REVERT: A 333 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 348 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8772 (ptmm) REVERT: A 415 MET cc_start: 0.8739 (tmm) cc_final: 0.8505 (tmm) REVERT: B 134 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8479 (mp0) REVERT: B 362 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8948 (ttm-80) REVERT: B 374 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7497 (tp-100) REVERT: B 378 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8417 (mm110) REVERT: C 378 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8710 (mm-40) REVERT: D 58 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8477 (mm) REVERT: D 244 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8484 (mm-30) REVERT: D 329 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8266 (mm-30) REVERT: D 341 MET cc_start: 0.8449 (tmt) cc_final: 0.8119 (tmt) REVERT: E 42 HIS cc_start: 0.8280 (t70) cc_final: 0.7948 (t70) REVERT: E 211 GLU cc_start: 0.8451 (tp30) cc_final: 0.8088 (tp30) REVERT: E 234 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: E 244 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8259 (mm-30) REVERT: E 332 TYR cc_start: 0.9296 (t80) cc_final: 0.9011 (t80) REVERT: E 336 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8548 (mmmm) REVERT: E 341 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6803 (tmm) REVERT: E 388 HIS cc_start: 0.9143 (t-90) cc_final: 0.8632 (t-90) REVERT: b 25 MET cc_start: 0.8316 (tpp) cc_final: 0.7901 (tpp) REVERT: b 46 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: b 50 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8188 (mt-10) REVERT: b 51 TYR cc_start: 0.8158 (m-80) cc_final: 0.7892 (m-80) REVERT: b 73 HIS cc_start: 0.7902 (t-90) cc_final: 0.7280 (t-90) REVERT: b 79 VAL cc_start: 0.8491 (t) cc_final: 0.8256 (m) REVERT: d 47 LYS cc_start: 0.9011 (mptp) cc_final: 0.8590 (tptp) REVERT: a 25 MET cc_start: 0.6510 (tmt) cc_final: 0.6243 (tpt) outliers start: 54 outliers final: 16 residues processed: 305 average time/residue: 1.4485 time to fit residues: 492.0634 Evaluate side-chains 271 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 32 GLN E 140 HIS d 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067618 restraints weight = 42858.885| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.84 r_work: 0.2880 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19407 Z= 0.165 Angle : 0.571 9.683 26168 Z= 0.279 Chirality : 0.042 0.134 2992 Planarity : 0.004 0.043 3402 Dihedral : 6.180 94.908 2670 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.68 % Allowed : 11.36 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2400 helix: 1.83 (0.17), residues: 1009 sheet: 0.35 (0.26), residues: 436 loop : 0.43 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.010 0.001 HIS A 42 PHE 0.014 0.001 PHE A 398 TYR 0.019 0.001 TYR E 197 ARG 0.007 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 892) hydrogen bonds : angle 4.73832 ( 2538) covalent geometry : bond 0.00382 (19407) covalent geometry : angle 0.57149 (26168) *********************** 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 324 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 2.076 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 186 MET cc_start: 0.9227 (mmm) cc_final: 0.8836 (mmm) REVERT: A 188 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9143 (mm) REVERT: B 1 MET cc_start: 0.8174 (pmm) cc_final: 0.7922 (pmm) REVERT: B 32 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8818 (mp10) REVERT: B 134 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8482 (mp0) REVERT: B 244 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 362 ARG cc_start: 0.9249 (mtp85) cc_final: 0.9009 (ttp-110) REVERT: B 374 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7401 (tp-100) REVERT: B 378 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8355 (mm110) REVERT: C 193 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: C 378 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8697 (mm-40) REVERT: D 58 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8566 (mm) REVERT: D 234 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: D 329 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 341 MET cc_start: 0.8552 (tmt) cc_final: 0.8242 (tmt) REVERT: E 41 GLN cc_start: 0.8649 (tp40) cc_final: 0.8185 (tm-30) REVERT: E 211 GLU cc_start: 0.8513 (tp30) cc_final: 0.8192 (tp30) REVERT: E 234 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: E 244 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8278 (mm-30) REVERT: E 332 TYR cc_start: 0.9267 (t80) cc_final: 0.8863 (t80) REVERT: E 336 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8563 (mmmm) REVERT: E 341 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6906 (tmm) REVERT: b 25 MET cc_start: 0.8378 (tpp) cc_final: 0.8042 (tpp) REVERT: b 46 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8433 (mtm-85) REVERT: b 50 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8148 (mt-10) REVERT: b 73 HIS cc_start: 0.7868 (t-90) cc_final: 0.7162 (t-90) REVERT: b 79 VAL cc_start: 0.8424 (t) cc_final: 0.8170 (m) REVERT: d 46 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7799 (mmt90) REVERT: d 47 LYS cc_start: 0.9038 (mptp) cc_final: 0.8466 (tptp) REVERT: d 64 ARG cc_start: 0.7319 (mtp85) cc_final: 0.6799 (mtm180) outliers start: 56 outliers final: 20 residues processed: 302 average time/residue: 1.3937 time to fit residues: 469.3954 Evaluate side-chains 280 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 9 ASN Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 192 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 140 HIS E 193 GLN E 374 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.098381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067372 restraints weight = 42507.520| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.76 r_work: 0.2854 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19407 Z= 0.193 Angle : 0.587 9.992 26168 Z= 0.286 Chirality : 0.042 0.142 2992 Planarity : 0.004 0.044 3402 Dihedral : 6.201 97.079 2670 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.92 % Allowed : 12.46 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2400 helix: 1.81 (0.17), residues: 1013 sheet: 0.21 (0.26), residues: 431 loop : 0.37 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 381 HIS 0.004 0.001 HIS A 42 PHE 0.012 0.001 PHE A 398 TYR 0.020 0.001 TYR E 197 ARG 0.006 0.000 ARG c 46 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 892) hydrogen bonds : angle 4.58830 ( 2538) covalent geometry : bond 0.00453 (19407) covalent geometry : angle 0.58680 (26168) *********************** 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 322 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 2.319 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 186 MET cc_start: 0.9216 (mmm) cc_final: 0.8821 (mmm) REVERT: A 188 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9161 (mm) REVERT: A 342 GLU cc_start: 0.8540 (tt0) cc_final: 0.7686 (tm-30) REVERT: B 1 MET cc_start: 0.8256 (pmm) cc_final: 0.7996 (pmm) REVERT: B 32 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8787 (mp10) REVERT: B 134 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8504 (mp0) REVERT: B 374 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7402 (tp-100) REVERT: B 378 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8411 (mm110) REVERT: B 408 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8581 (t) REVERT: C 58 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8770 (mm) REVERT: C 87 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8624 (ttp80) REVERT: C 193 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: C 326 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8663 (mmmm) REVERT: C 378 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8673 (mm-40) REVERT: D 58 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 234 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: D 329 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8213 (mm-30) REVERT: D 341 MET cc_start: 0.8555 (tmt) cc_final: 0.8325 (tmt) REVERT: D 405 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8688 (mtm) REVERT: E 193 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: E 211 GLU cc_start: 0.8504 (tp30) cc_final: 0.8211 (tp30) REVERT: E 244 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8340 (mm-30) REVERT: E 332 TYR cc_start: 0.9270 (t80) cc_final: 0.8861 (t80) REVERT: E 336 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8578 (mmmm) REVERT: E 341 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6924 (tmm) REVERT: E 416 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6705 (ttp) REVERT: b 25 MET cc_start: 0.8414 (tpp) cc_final: 0.8108 (tpp) REVERT: b 46 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: b 50 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8143 (mt-10) REVERT: b 73 HIS cc_start: 0.7799 (t-90) cc_final: 0.7146 (t-90) REVERT: b 79 VAL cc_start: 0.8373 (t) cc_final: 0.8078 (m) REVERT: d 46 ARG cc_start: 0.8571 (tpp80) cc_final: 0.7865 (mmt90) REVERT: d 47 LYS cc_start: 0.9066 (mptp) cc_final: 0.8492 (tptp) outliers start: 61 outliers final: 21 residues processed: 300 average time/residue: 1.3477 time to fit residues: 452.2216 Evaluate side-chains 273 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 230 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 32 GLN E 140 HIS E 189 GLN E 193 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067321 restraints weight = 42645.071| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.79 r_work: 0.2860 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19407 Z= 0.167 Angle : 0.582 10.475 26168 Z= 0.282 Chirality : 0.042 0.170 2992 Planarity : 0.003 0.045 3402 Dihedral : 6.065 97.388 2667 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.59 % Allowed : 13.42 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.17), residues: 2400 helix: 1.89 (0.17), residues: 1003 sheet: 0.14 (0.25), residues: 436 loop : 0.34 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 381 HIS 0.006 0.001 HIS A 42 PHE 0.013 0.001 PHE A 398 TYR 0.021 0.001 TYR E 197 ARG 0.008 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 892) hydrogen bonds : angle 4.49753 ( 2538) covalent geometry : bond 0.00393 (19407) covalent geometry : angle 0.58190 (26168) *********************** 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 306 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 2.119 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 186 MET cc_start: 0.9217 (mmm) cc_final: 0.8843 (mmm) REVERT: A 188 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 329 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8163 (mp0) REVERT: A 342 GLU cc_start: 0.8591 (tt0) cc_final: 0.7771 (tm-30) REVERT: B 1 MET cc_start: 0.8308 (pmm) cc_final: 0.7958 (pmm) REVERT: B 32 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8713 (mp10) REVERT: B 134 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8525 (mp0) REVERT: B 374 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7360 (tp-100) REVERT: B 378 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8397 (mm110) REVERT: C 58 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8778 (mm) REVERT: C 87 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8616 (ttp80) REVERT: C 193 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: C 326 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8541 (mmmm) REVERT: C 378 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8653 (mm-40) REVERT: D 58 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8610 (mm) REVERT: D 234 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: D 289 VAL cc_start: 0.9014 (t) cc_final: 0.8619 (m) REVERT: D 329 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8311 (mm-30) REVERT: D 341 MET cc_start: 0.8543 (tmt) cc_final: 0.8308 (tmt) REVERT: D 405 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (mtm) REVERT: E 21 MET cc_start: 0.8530 (mtp) cc_final: 0.7880 (ttt) REVERT: E 41 GLN cc_start: 0.8659 (tp40) cc_final: 0.8439 (tp40) REVERT: E 189 GLN cc_start: 0.8920 (mt0) cc_final: 0.8581 (mt0) REVERT: E 193 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: E 211 GLU cc_start: 0.8514 (tp30) cc_final: 0.8203 (tp30) REVERT: E 244 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8312 (mm-30) REVERT: E 332 TYR cc_start: 0.9265 (t80) cc_final: 0.8850 (t80) REVERT: E 336 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8571 (mmmm) REVERT: E 341 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6912 (tmm) REVERT: E 416 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6740 (ttp) REVERT: b 16 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8226 (mp) REVERT: b 25 MET cc_start: 0.8435 (tpp) cc_final: 0.8151 (tpp) REVERT: b 46 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: b 50 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8109 (mt-10) REVERT: b 73 HIS cc_start: 0.7777 (t-90) cc_final: 0.7107 (t-90) REVERT: b 79 VAL cc_start: 0.8453 (t) cc_final: 0.8180 (m) REVERT: d 46 ARG cc_start: 0.8578 (tpp80) cc_final: 0.7917 (mmt90) REVERT: d 47 LYS cc_start: 0.9060 (mptp) cc_final: 0.8492 (tptp) outliers start: 54 outliers final: 22 residues processed: 286 average time/residue: 1.3454 time to fit residues: 429.7656 Evaluate side-chains 268 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 228 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 186 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN E 140 HIS E 193 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068521 restraints weight = 42759.055| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.78 r_work: 0.2886 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19407 Z= 0.118 Angle : 0.571 10.807 26168 Z= 0.275 Chirality : 0.041 0.134 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.956 96.754 2667 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.49 % Allowed : 14.09 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2400 helix: 1.97 (0.17), residues: 1003 sheet: 0.29 (0.25), residues: 428 loop : 0.33 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.004 0.001 HIS A 42 PHE 0.014 0.001 PHE A 398 TYR 0.022 0.001 TYR E 197 ARG 0.010 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 892) hydrogen bonds : angle 4.34621 ( 2538) covalent geometry : bond 0.00273 (19407) covalent geometry : angle 0.57064 (26168) *********************** 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 294 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 2.348 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 186 MET cc_start: 0.9198 (mmm) cc_final: 0.8814 (mmm) REVERT: A 188 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 244 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8070 (mp0) REVERT: A 329 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8273 (mp0) REVERT: A 342 GLU cc_start: 0.8569 (tt0) cc_final: 0.7815 (tm-30) REVERT: B 1 MET cc_start: 0.8361 (pmm) cc_final: 0.7995 (pmm) REVERT: B 32 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: B 134 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8475 (mp0) REVERT: B 244 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8359 (mm-30) REVERT: B 408 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (t) REVERT: C 87 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8626 (ttp80) REVERT: C 193 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: C 378 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8637 (mm-40) REVERT: D 234 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: D 289 VAL cc_start: 0.9033 (t) cc_final: 0.8656 (m) REVERT: D 329 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 341 MET cc_start: 0.8564 (tmt) cc_final: 0.8307 (tmt) REVERT: D 405 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: E 41 GLN cc_start: 0.8684 (tp40) cc_final: 0.8184 (tm-30) REVERT: E 193 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: E 211 GLU cc_start: 0.8492 (tp30) cc_final: 0.8179 (tp30) REVERT: E 244 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8305 (mm-30) REVERT: E 332 TYR cc_start: 0.9252 (t80) cc_final: 0.8838 (t80) REVERT: E 336 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8561 (mmmm) REVERT: E 341 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6888 (tmm) REVERT: E 416 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6721 (ttp) REVERT: b 16 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8248 (mp) REVERT: b 25 MET cc_start: 0.8495 (tpp) cc_final: 0.8228 (tpp) REVERT: b 46 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8497 (mtm-85) REVERT: b 50 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8103 (mt-10) REVERT: b 73 HIS cc_start: 0.7641 (t-90) cc_final: 0.7038 (t-90) REVERT: b 79 VAL cc_start: 0.8505 (t) cc_final: 0.8247 (m) REVERT: d 46 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8011 (mmt90) REVERT: d 47 LYS cc_start: 0.9077 (mptp) cc_final: 0.8531 (tptp) outliers start: 52 outliers final: 22 residues processed: 279 average time/residue: 1.3750 time to fit residues: 430.5352 Evaluate side-chains 277 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN E 140 HIS E 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068379 restraints weight = 42414.086| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.77 r_work: 0.2883 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19407 Z= 0.136 Angle : 0.590 11.111 26168 Z= 0.283 Chirality : 0.041 0.157 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.913 96.914 2667 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.25 % Allowed : 14.72 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2400 helix: 1.98 (0.17), residues: 1003 sheet: 0.29 (0.25), residues: 428 loop : 0.32 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 PHE 0.013 0.001 PHE A 398 TYR 0.023 0.001 TYR E 197 ARG 0.009 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 892) hydrogen bonds : angle 4.31470 ( 2538) covalent geometry : bond 0.00319 (19407) covalent geometry : angle 0.59003 (26168) *********************** 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 300 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 2.205 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 32 GLN cc_start: 0.9202 (pm20) cc_final: 0.8947 (pm20) REVERT: A 186 MET cc_start: 0.9198 (mmm) cc_final: 0.8811 (mmm) REVERT: A 188 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9167 (mm) REVERT: A 244 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7999 (mp0) REVERT: A 329 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8294 (mp0) REVERT: B 32 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: B 134 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8496 (mp0) REVERT: B 244 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 374 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7218 (tp-100) REVERT: B 378 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8352 (mm110) REVERT: C 87 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8623 (ttp80) REVERT: C 193 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8490 (mp10) REVERT: C 244 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 378 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8642 (mm-40) REVERT: D 58 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8651 (mm) REVERT: D 234 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: D 244 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8416 (mm-30) REVERT: D 289 VAL cc_start: 0.9025 (t) cc_final: 0.8657 (m) REVERT: D 329 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8310 (mm-30) REVERT: D 341 MET cc_start: 0.8579 (tmt) cc_final: 0.8315 (tmt) REVERT: D 374 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8301 (tp40) REVERT: D 405 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8620 (mtm) REVERT: E 21 MET cc_start: 0.8481 (mtp) cc_final: 0.7972 (ttt) REVERT: E 193 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: E 211 GLU cc_start: 0.8500 (tp30) cc_final: 0.8182 (tp30) REVERT: E 244 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8314 (mm-30) REVERT: E 332 TYR cc_start: 0.9253 (t80) cc_final: 0.8838 (t80) REVERT: E 336 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8569 (mmmm) REVERT: E 341 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6902 (tmm) REVERT: E 416 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6741 (ttp) REVERT: b 16 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8297 (mp) REVERT: b 25 MET cc_start: 0.8466 (tpp) cc_final: 0.8176 (tpp) REVERT: b 46 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8491 (mtm-85) REVERT: b 50 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8053 (mt-10) REVERT: b 73 HIS cc_start: 0.7662 (t-90) cc_final: 0.7009 (t-90) REVERT: b 79 VAL cc_start: 0.8502 (t) cc_final: 0.8246 (m) REVERT: d 46 ARG cc_start: 0.8645 (tpp80) cc_final: 0.7956 (mmt90) REVERT: d 47 LYS cc_start: 0.9073 (mptp) cc_final: 0.8532 (tptp) outliers start: 47 outliers final: 22 residues processed: 286 average time/residue: 1.4150 time to fit residues: 451.5572 Evaluate side-chains 273 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 124 optimal weight: 0.0570 chunk 180 optimal weight: 1.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.099221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068412 restraints weight = 42611.695| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.77 r_work: 0.2881 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19407 Z= 0.141 Angle : 0.607 11.291 26168 Z= 0.291 Chirality : 0.041 0.156 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.896 96.942 2667 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.16 % Allowed : 15.24 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2400 helix: 1.96 (0.17), residues: 1003 sheet: 0.31 (0.26), residues: 423 loop : 0.30 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS E 42 PHE 0.013 0.001 PHE A 398 TYR 0.024 0.001 TYR E 197 ARG 0.009 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 892) hydrogen bonds : angle 4.30484 ( 2538) covalent geometry : bond 0.00333 (19407) covalent geometry : angle 0.60715 (26168) *********************** 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 288 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 2.093 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 32 GLN cc_start: 0.9175 (pm20) cc_final: 0.8945 (pm20) REVERT: A 186 MET cc_start: 0.9192 (mmm) cc_final: 0.8799 (mmm) REVERT: A 188 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9164 (mm) REVERT: A 244 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7968 (mp0) REVERT: A 329 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8286 (mp0) REVERT: A 342 GLU cc_start: 0.8489 (tt0) cc_final: 0.7746 (tm-30) REVERT: B 1 MET cc_start: 0.8257 (pmm) cc_final: 0.7949 (pmm) REVERT: B 32 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8711 (mp10) REVERT: B 134 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8496 (mp0) REVERT: B 244 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8292 (mm-30) REVERT: C 193 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: C 244 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 378 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8636 (mm-40) REVERT: D 58 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8702 (mm) REVERT: D 234 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: D 289 VAL cc_start: 0.9005 (t) cc_final: 0.8631 (m) REVERT: D 329 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 405 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8616 (mtm) REVERT: E 21 MET cc_start: 0.8667 (mtp) cc_final: 0.7459 (ttt) REVERT: E 41 GLN cc_start: 0.8483 (tp40) cc_final: 0.8010 (tm-30) REVERT: E 193 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8337 (pm20) REVERT: E 211 GLU cc_start: 0.8482 (tp30) cc_final: 0.8159 (tp30) REVERT: E 244 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8320 (mm-30) REVERT: E 336 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8602 (mtpp) REVERT: E 341 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6920 (tmm) REVERT: E 380 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: E 384 ARG cc_start: 0.9057 (tmt-80) cc_final: 0.8747 (tmm160) REVERT: E 416 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6743 (ttp) REVERT: b 16 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8290 (mp) REVERT: b 25 MET cc_start: 0.8477 (tpp) cc_final: 0.8189 (tpp) REVERT: b 46 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8402 (mtm-85) REVERT: b 50 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8033 (mt-10) REVERT: b 73 HIS cc_start: 0.7647 (t-90) cc_final: 0.6983 (t-90) REVERT: b 79 VAL cc_start: 0.8465 (t) cc_final: 0.8210 (m) REVERT: d 46 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8006 (mmt90) REVERT: d 47 LYS cc_start: 0.9085 (mptp) cc_final: 0.8541 (tptp) outliers start: 45 outliers final: 22 residues processed: 272 average time/residue: 1.3806 time to fit residues: 419.5031 Evaluate side-chains 276 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 140 HIS E 193 GLN E 198 ASN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067851 restraints weight = 42707.670| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.78 r_work: 0.2869 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19407 Z= 0.171 Angle : 0.626 11.335 26168 Z= 0.301 Chirality : 0.042 0.186 2992 Planarity : 0.004 0.045 3402 Dihedral : 5.924 97.422 2667 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.06 % Allowed : 15.53 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2400 helix: 1.91 (0.17), residues: 1002 sheet: 0.29 (0.26), residues: 423 loop : 0.27 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS E 42 PHE 0.012 0.001 PHE A 398 TYR 0.025 0.001 TYR E 332 ARG 0.011 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 892) hydrogen bonds : angle 4.34848 ( 2538) covalent geometry : bond 0.00405 (19407) covalent geometry : angle 0.62567 (26168) *********************** 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 292 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9189 (pm20) cc_final: 0.8958 (pm20) REVERT: A 186 MET cc_start: 0.9198 (mmm) cc_final: 0.8869 (mmm) REVERT: A 188 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 244 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8026 (mp0) REVERT: A 329 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8338 (mp0) REVERT: A 342 GLU cc_start: 0.8472 (tt0) cc_final: 0.7751 (tm-30) REVERT: B 1 MET cc_start: 0.8237 (pmm) cc_final: 0.7905 (pmm) REVERT: B 32 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8774 (mp10) REVERT: B 134 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8495 (mp0) REVERT: B 244 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 374 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7150 (tp-100) REVERT: B 378 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8433 (mp10) REVERT: C 193 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8518 (mp10) REVERT: C 244 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 378 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8647 (mm-40) REVERT: D 58 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8723 (mm) REVERT: D 234 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: D 244 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8464 (mm-30) REVERT: D 289 VAL cc_start: 0.9017 (t) cc_final: 0.8639 (m) REVERT: D 329 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 374 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8382 (tp40) REVERT: D 405 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8629 (mtm) REVERT: E 193 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: E 211 GLU cc_start: 0.8494 (tp30) cc_final: 0.8178 (tp30) REVERT: E 244 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 326 LYS cc_start: 0.9407 (tppp) cc_final: 0.8880 (tmtt) REVERT: E 332 TYR cc_start: 0.9146 (t80) cc_final: 0.8836 (t80) REVERT: E 336 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8559 (mmmm) REVERT: E 341 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6948 (tmm) REVERT: E 384 ARG cc_start: 0.9099 (tmt-80) cc_final: 0.8747 (tmm160) REVERT: E 416 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6757 (ttp) REVERT: b 16 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8288 (mp) REVERT: b 25 MET cc_start: 0.8490 (tpp) cc_final: 0.8209 (tpp) REVERT: b 46 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8373 (mtm-85) REVERT: b 50 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8039 (mt-10) REVERT: b 73 HIS cc_start: 0.7652 (t-90) cc_final: 0.6971 (t-90) REVERT: b 79 VAL cc_start: 0.8407 (t) cc_final: 0.8145 (m) REVERT: d 46 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8025 (mmt90) REVERT: d 47 LYS cc_start: 0.9102 (mptp) cc_final: 0.8546 (tptp) REVERT: d 73 HIS cc_start: 0.8087 (t-170) cc_final: 0.7549 (t70) outliers start: 43 outliers final: 22 residues processed: 277 average time/residue: 1.4168 time to fit residues: 437.3257 Evaluate side-chains 271 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 149 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 0.0370 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 344 HIS E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068695 restraints weight = 42613.863| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.78 r_work: 0.2887 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19407 Z= 0.124 Angle : 0.622 11.748 26168 Z= 0.297 Chirality : 0.041 0.131 2992 Planarity : 0.004 0.051 3402 Dihedral : 5.829 96.961 2665 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.63 % Allowed : 16.30 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2400 helix: 1.95 (0.17), residues: 1002 sheet: 0.32 (0.26), residues: 423 loop : 0.29 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.004 0.001 HIS E 388 PHE 0.013 0.001 PHE A 398 TYR 0.024 0.001 TYR E 197 ARG 0.013 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 892) hydrogen bonds : angle 4.25851 ( 2538) covalent geometry : bond 0.00294 (19407) covalent geometry : angle 0.62204 (26168) ********************** 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 282 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9192 (pm20) cc_final: 0.8957 (pm20) REVERT: A 186 MET cc_start: 0.9189 (mmm) cc_final: 0.8786 (mmm) REVERT: A 188 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9168 (mm) REVERT: A 244 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8007 (mp0) REVERT: A 329 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8315 (mp0) REVERT: A 342 GLU cc_start: 0.8476 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 1 MET cc_start: 0.8218 (pmm) cc_final: 0.7946 (pmm) REVERT: B 32 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8718 (mp10) REVERT: B 134 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8487 (mp0) REVERT: B 244 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 347 ARG cc_start: 0.8586 (tpt-90) cc_final: 0.8243 (tpp80) REVERT: B 374 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7279 (tp-100) REVERT: B 378 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8387 (mm110) REVERT: C 193 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8465 (mp10) REVERT: C 244 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 378 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8633 (mm-40) REVERT: D 58 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 234 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: D 244 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8449 (mm-30) REVERT: D 289 VAL cc_start: 0.9021 (t) cc_final: 0.8653 (m) REVERT: D 329 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7913 (mm-30) REVERT: D 333 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8279 (mm-30) REVERT: D 374 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8387 (tp40) REVERT: D 405 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (mtm) REVERT: E 21 MET cc_start: 0.8893 (mtp) cc_final: 0.8125 (ttt) REVERT: E 193 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: E 211 GLU cc_start: 0.8455 (tp30) cc_final: 0.8125 (tp30) REVERT: E 244 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8306 (mm-30) REVERT: E 332 TYR cc_start: 0.9108 (t80) cc_final: 0.8861 (t80) REVERT: E 336 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8580 (mmmm) REVERT: E 341 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6908 (tmm) REVERT: E 384 ARG cc_start: 0.9112 (tmt-80) cc_final: 0.8712 (tmm160) REVERT: E 416 MET cc_start: 0.6995 (ttt) cc_final: 0.6743 (ttp) REVERT: b 16 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (mp) REVERT: b 25 MET cc_start: 0.8459 (tpp) cc_final: 0.8172 (tpp) REVERT: b 46 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8350 (mtm-85) REVERT: b 50 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8061 (mt-10) REVERT: b 73 HIS cc_start: 0.7451 (t-90) cc_final: 0.6846 (t-90) REVERT: b 79 VAL cc_start: 0.8439 (t) cc_final: 0.8196 (m) REVERT: d 46 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8022 (mmt90) REVERT: d 47 LYS cc_start: 0.9098 (mptp) cc_final: 0.8550 (tptp) REVERT: d 73 HIS cc_start: 0.8038 (t-170) cc_final: 0.7599 (t70) outliers start: 34 outliers final: 19 residues processed: 271 average time/residue: 1.4670 time to fit residues: 442.1782 Evaluate side-chains 269 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 11 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 227 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN D 344 HIS E 32 GLN E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.099195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068366 restraints weight = 42681.101| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.78 r_work: 0.2875 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19407 Z= 0.144 Angle : 0.626 11.785 26168 Z= 0.298 Chirality : 0.041 0.131 2992 Planarity : 0.003 0.045 3402 Dihedral : 5.818 96.878 2665 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.53 % Allowed : 16.73 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2400 helix: 1.91 (0.17), residues: 1002 sheet: 0.21 (0.26), residues: 431 loop : 0.30 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 PHE 0.013 0.001 PHE A 398 TYR 0.025 0.001 TYR E 197 ARG 0.010 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 892) hydrogen bonds : angle 4.26719 ( 2538) covalent geometry : bond 0.00343 (19407) covalent geometry : angle 0.62628 (26168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14251.72 seconds wall clock time: 245 minutes 55.83 seconds (14755.83 seconds total)