Starting phenix.real_space_refine on Mon Jun 16 20:59:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pto_17876/06_2025/8pto_17876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pto_17876/06_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_17876/06_2025/8pto_17876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pto_17876/06_2025/8pto_17876.map" model { file = "/net/cci-nas-00/data/ceres_data/8pto_17876/06_2025/8pto_17876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pto_17876/06_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-5710/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: 12.36, per 1000 atoms: 0.65 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: 4.89 Conformation dependent library (CDL) restraints added in 2.4 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: 2.58 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: 6.60 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: 0.04 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.860 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.300 ------------------------------------------------------------------------------- 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 : 2.113 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: 1.5651 time to fit residues: 607.2732 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 : 2.325 ------------------------------------------------------------------------------- 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 = 60)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.069042 restraints weight = 42621.848| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.83 r_work: 0.2907 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 2.227 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: 0.9200 (mmm) cc_final: 0.8764 (mmm) REVERT: A 188 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9104 (mm) REVERT: A 333 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 348 LYS cc_start: 0.8975 (ptmm) cc_final: 0.8774 (ptmm) REVERT: A 415 MET cc_start: 0.8740 (tmm) cc_final: 0.8507 (tmm) REVERT: B 134 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8481 (mp0) REVERT: B 362 ARG cc_start: 0.9178 (mtp85) cc_final: 0.8941 (ttm-80) REVERT: B 374 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7494 (tp-100) REVERT: B 378 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8415 (mm110) REVERT: C 378 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8710 (mm-40) REVERT: D 58 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 244 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8479 (mm-30) REVERT: D 329 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8273 (mm-30) REVERT: D 341 MET cc_start: 0.8443 (tmt) cc_final: 0.8113 (tmt) REVERT: E 42 HIS cc_start: 0.8277 (t70) cc_final: 0.7944 (t70) REVERT: E 211 GLU cc_start: 0.8452 (tp30) cc_final: 0.8088 (tp30) REVERT: E 234 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: E 244 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 332 TYR cc_start: 0.9298 (t80) cc_final: 0.9012 (t80) REVERT: E 336 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8550 (mmmm) REVERT: E 341 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6814 (tmm) REVERT: E 388 HIS cc_start: 0.9144 (t-90) cc_final: 0.8628 (t-90) REVERT: b 25 MET cc_start: 0.8311 (tpp) cc_final: 0.7896 (tpp) REVERT: b 46 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8230 (mtm-85) REVERT: b 50 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8205 (mt-10) REVERT: b 51 TYR cc_start: 0.8175 (m-80) cc_final: 0.7911 (m-80) REVERT: b 73 HIS cc_start: 0.7902 (t-90) cc_final: 0.7283 (t-90) REVERT: b 79 VAL cc_start: 0.8505 (t) cc_final: 0.8270 (m) REVERT: d 47 LYS cc_start: 0.9011 (mptp) cc_final: 0.8593 (tptp) REVERT: a 25 MET cc_start: 0.6506 (tmt) cc_final: 0.6238 (tpt) outliers start: 54 outliers final: 16 residues processed: 305 average time/residue: 1.7089 time to fit residues: 584.1921 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 : 2.674 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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 b 23 HIS d 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067411 restraints weight = 42909.945| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.84 r_work: 0.2876 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19407 Z= 0.181 Angle : 0.578 9.643 26168 Z= 0.283 Chirality : 0.042 0.147 2992 Planarity : 0.004 0.044 3402 Dihedral : 6.209 94.978 2670 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.73 % Allowed : 11.41 % Favored : 85.86 % 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: 1.41 (0.17), residues: 2400 helix: 1.80 (0.17), residues: 1009 sheet: 0.33 (0.26), residues: 436 loop : 0.42 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.013 0.001 HIS A 42 PHE 0.013 0.001 PHE A 398 TYR 0.024 0.001 TYR a 51 ARG 0.006 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 892) hydrogen bonds : angle 4.77907 ( 2538) covalent geometry : bond 0.00423 (19407) covalent geometry : angle 0.57764 (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: 57 poor density : 267 time to evaluate : 2.078 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: 0.9225 (mmm) cc_final: 0.8835 (mmm) REVERT: A 188 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 415 MET cc_start: 0.8665 (tmm) cc_final: 0.8455 (tmm) REVERT: B 1 MET cc_start: 0.8187 (pmm) cc_final: 0.7924 (pmm) REVERT: B 32 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8816 (mp10) REVERT: B 134 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8480 (mp0) REVERT: B 244 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 362 ARG cc_start: 0.9239 (mtp85) cc_final: 0.8994 (ttp-110) REVERT: B 374 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7385 (tp-100) REVERT: B 378 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8359 (mm110) REVERT: C 193 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8490 (mp10) REVERT: C 378 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8662 (mm-40) REVERT: D 58 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8538 (mm) REVERT: D 234 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: D 244 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 329 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8240 (mm-30) REVERT: D 341 MET cc_start: 0.8538 (tmt) cc_final: 0.8239 (tmt) REVERT: E 211 GLU cc_start: 0.8510 (tp30) cc_final: 0.8180 (tp30) REVERT: E 234 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: E 244 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8251 (mm-30) REVERT: E 332 TYR cc_start: 0.9266 (t80) cc_final: 0.8861 (t80) REVERT: E 336 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8561 (mmmm) REVERT: E 341 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6897 (tmm) REVERT: b 25 MET cc_start: 0.8340 (tpp) cc_final: 0.7999 (tpp) REVERT: b 46 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8450 (mtm-85) REVERT: b 50 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8166 (mt-10) REVERT: b 73 HIS cc_start: 0.7856 (t-90) cc_final: 0.7164 (t-90) REVERT: b 79 VAL cc_start: 0.8459 (t) cc_final: 0.8201 (m) REVERT: d 46 ARG cc_start: 0.8532 (tpp80) cc_final: 0.7837 (mmt90) REVERT: d 47 LYS cc_start: 0.9036 (mptp) cc_final: 0.8470 (tptp) REVERT: d 64 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6861 (mtm180) outliers start: 57 outliers final: 21 residues processed: 301 average time/residue: 1.5944 time to fit residues: 535.0684 Evaluate side-chains 283 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 147 MET 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: 8.9990 chunk 122 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.0670 chunk 221 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 185 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068693 restraints weight = 42590.408| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.85 r_work: 0.2903 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19407 Z= 0.117 Angle : 0.562 10.454 26168 Z= 0.272 Chirality : 0.041 0.133 2992 Planarity : 0.003 0.045 3402 Dihedral : 6.081 95.233 2670 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.59 % Allowed : 12.61 % Favored : 84.80 % 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: 1.47 (0.18), residues: 2400 helix: 1.95 (0.17), residues: 1009 sheet: 0.26 (0.25), residues: 436 loop : 0.41 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 381 HIS 0.004 0.001 HIS E 140 PHE 0.015 0.001 PHE A 398 TYR 0.020 0.001 TYR E 197 ARG 0.006 0.000 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 892) hydrogen bonds : angle 4.46845 ( 2538) covalent geometry : bond 0.00269 (19407) covalent geometry : angle 0.56189 (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 321 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 2.079 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: 0.9212 (mmm) cc_final: 0.8829 (mmm) REVERT: A 188 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9141 (mm) REVERT: A 329 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8061 (mp0) REVERT: A 342 GLU cc_start: 0.8544 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 1 MET cc_start: 0.8194 (pmm) cc_final: 0.7873 (pmm) REVERT: B 32 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8731 (mp10) REVERT: B 134 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8474 (mp0) REVERT: B 244 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 374 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7265 (tp-100) REVERT: B 378 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8369 (mm110) REVERT: C 58 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 193 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: C 326 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8613 (mmmm) REVERT: C 378 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8622 (mm-40) REVERT: D 58 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8526 (mm) REVERT: D 234 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: D 244 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8479 (mm-30) REVERT: D 329 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8158 (mm-30) REVERT: D 405 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8657 (mtm) REVERT: E 21 MET cc_start: 0.8488 (mtp) cc_final: 0.7880 (ttt) REVERT: E 193 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: E 211 GLU cc_start: 0.8463 (tp30) cc_final: 0.8150 (tp30) REVERT: E 244 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 332 TYR cc_start: 0.9239 (t80) cc_final: 0.8816 (t80) REVERT: E 336 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8576 (mmmm) REVERT: E 341 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6864 (tmm) REVERT: E 416 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6838 (ttp) REVERT: b 25 MET cc_start: 0.8475 (tpp) cc_final: 0.8186 (tpp) REVERT: b 46 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8395 (mtm-85) REVERT: b 50 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8164 (mt-10) REVERT: b 73 HIS cc_start: 0.7793 (t-90) cc_final: 0.7158 (t-90) REVERT: b 79 VAL cc_start: 0.8450 (t) cc_final: 0.8196 (m) REVERT: d 46 ARG cc_start: 0.8584 (tpp80) cc_final: 0.7928 (mmt90) REVERT: d 47 LYS cc_start: 0.9060 (mptp) cc_final: 0.8481 (tptp) outliers start: 54 outliers final: 18 residues processed: 302 average time/residue: 1.3921 time to fit residues: 469.5003 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 : 2.129 ------------------------------------------------------------------------------- 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 390 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 193 GLN 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 D residue 416 MET 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 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 80 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: 2.9990 chunk 121 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 193 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 = 0.3627 r_free = 0.3627 target = 0.097755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066505 restraints weight = 42774.452| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.79 r_work: 0.2845 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19407 Z= 0.234 Angle : 0.605 9.766 26168 Z= 0.295 Chirality : 0.043 0.190 2992 Planarity : 0.004 0.045 3402 Dihedral : 6.108 97.231 2667 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.78 % Allowed : 13.23 % 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: 1.33 (0.17), residues: 2400 helix: 1.84 (0.17), residues: 1003 sheet: 0.27 (0.25), residues: 423 loop : 0.27 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 381 HIS 0.005 0.001 HIS A 42 PHE 0.012 0.001 PHE D 89 TYR 0.021 0.001 TYR E 197 ARG 0.008 0.000 ARG B 362 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 892) hydrogen bonds : angle 4.57603 ( 2538) covalent geometry : bond 0.00549 (19407) covalent geometry : angle 0.60511 (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 308 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 2.029 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: 0.9208 (mmm) cc_final: 0.8828 (mmm) REVERT: A 188 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9175 (mm) REVERT: A 329 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8178 (mp0) REVERT: B 1 MET cc_start: 0.8304 (pmm) cc_final: 0.7914 (pmm) REVERT: B 32 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8823 (mp10) REVERT: B 134 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8540 (mp0) REVERT: B 408 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 58 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8775 (mm) REVERT: C 87 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8626 (ttp80) REVERT: C 193 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: C 378 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8665 (mm-40) REVERT: D 58 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8621 (mm) REVERT: D 234 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: D 244 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8512 (mm-30) REVERT: D 329 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8164 (mm-30) REVERT: D 341 MET cc_start: 0.8587 (tmt) cc_final: 0.8345 (tmt) REVERT: D 405 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: E 193 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: E 211 GLU cc_start: 0.8533 (tp30) cc_final: 0.8232 (tp30) REVERT: E 244 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8319 (mm-30) REVERT: E 332 TYR cc_start: 0.9272 (t80) cc_final: 0.8848 (t80) REVERT: E 336 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8588 (mmmm) REVERT: E 341 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6937 (tmm) REVERT: E 416 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6745 (ttp) REVERT: b 16 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (mp) REVERT: b 25 MET cc_start: 0.8412 (tpp) cc_final: 0.8120 (tpp) REVERT: b 46 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8558 (mtm-85) REVERT: b 50 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8106 (mt-10) REVERT: b 73 HIS cc_start: 0.7788 (t-90) cc_final: 0.7121 (t-90) REVERT: b 79 VAL cc_start: 0.8488 (t) cc_final: 0.8213 (m) REVERT: d 46 ARG cc_start: 0.8596 (tpp80) cc_final: 0.7924 (mmt90) REVERT: d 47 LYS cc_start: 0.9065 (mptp) cc_final: 0.8508 (tptp) outliers start: 58 outliers final: 24 residues processed: 287 average time/residue: 1.4181 time to fit residues: 454.5562 Evaluate side-chains 275 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 A residue 341 MET Chi-restraints excluded: chain A residue 390 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 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 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 b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 73 HIS 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: 8.9990 chunk 32 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 GLN E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067991 restraints weight = 42738.678| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.78 r_work: 0.2871 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19407 Z= 0.136 Angle : 0.583 11.003 26168 Z= 0.281 Chirality : 0.041 0.170 2992 Planarity : 0.004 0.046 3402 Dihedral : 6.001 96.821 2667 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 1.38 (0.17), residues: 2400 helix: 1.91 (0.17), residues: 1003 sheet: 0.28 (0.26), residues: 423 loop : 0.28 (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 A 42 PHE 0.013 0.001 PHE A 398 TYR 0.023 0.001 TYR E 197 ARG 0.009 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 892) hydrogen bonds : angle 4.40756 ( 2538) covalent geometry : bond 0.00320 (19407) covalent geometry : angle 0.58271 (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 290 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 2.458 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: 0.9185 (mmm) cc_final: 0.8866 (mmm) REVERT: A 188 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9161 (mm) REVERT: A 329 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8188 (mp0) REVERT: A 342 GLU cc_start: 0.8481 (tt0) cc_final: 0.7568 (tm-30) REVERT: B 1 MET cc_start: 0.8360 (pmm) cc_final: 0.7970 (pmm) REVERT: B 32 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: B 134 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8491 (mp0) REVERT: B 374 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7295 (tp-100) REVERT: B 378 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8409 (mm110) REVERT: B 408 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8540 (t) REVERT: C 58 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8789 (mm) REVERT: C 193 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: C 378 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8635 (mm-40) REVERT: D 58 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8635 (mm) REVERT: D 234 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: D 244 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8491 (mm-30) REVERT: D 289 VAL cc_start: 0.9031 (t) cc_final: 0.8705 (m) REVERT: D 329 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8333 (mm-30) REVERT: D 341 MET cc_start: 0.8555 (tmt) cc_final: 0.8292 (tmt) REVERT: D 374 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8351 (tp40) REVERT: D 405 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: E 193 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: E 211 GLU cc_start: 0.8494 (tp30) cc_final: 0.8200 (tp30) REVERT: E 244 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8302 (mm-30) REVERT: E 332 TYR cc_start: 0.9265 (t80) cc_final: 0.8855 (t80) REVERT: E 336 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8572 (mmmm) REVERT: E 341 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6953 (tmm) REVERT: E 416 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6690 (ttp) REVERT: b 16 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (mp) REVERT: b 25 MET cc_start: 0.8520 (tpp) cc_final: 0.8231 (tpp) REVERT: b 46 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8508 (mtm-85) REVERT: b 50 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8085 (mt-10) REVERT: b 73 HIS cc_start: 0.7704 (t-90) cc_final: 0.7077 (t-90) REVERT: b 79 VAL cc_start: 0.8487 (t) cc_final: 0.8215 (m) REVERT: d 46 ARG cc_start: 0.8623 (tpp80) cc_final: 0.7986 (mmt90) REVERT: d 47 LYS cc_start: 0.9088 (mptp) cc_final: 0.8532 (tptp) outliers start: 47 outliers final: 22 residues processed: 274 average time/residue: 1.5856 time to fit residues: 489.2836 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 : 2.309 ------------------------------------------------------------------------------- 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 390 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 408 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU 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 D residue 416 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 185 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 E 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069106 restraints weight = 42324.508| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.76 r_work: 0.2896 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19407 Z= 0.111 Angle : 0.579 11.243 26168 Z= 0.276 Chirality : 0.041 0.139 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.887 96.282 2667 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.06 % Allowed : 15.05 % Favored : 82.89 % 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: 1.99 (0.17), residues: 1003 sheet: 0.31 (0.26), residues: 423 loop : 0.29 (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 239 PHE 0.014 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 0.03125 ( 892) hydrogen bonds : angle 4.29424 ( 2538) covalent geometry : bond 0.00258 (19407) covalent geometry : angle 0.57859 (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 290 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 2.796 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: 0.9209 (pm20) cc_final: 0.8956 (pm20) REVERT: A 186 MET cc_start: 0.9192 (mmm) cc_final: 0.8804 (mmm) REVERT: A 188 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9166 (mm) REVERT: A 244 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8083 (mp0) REVERT: A 329 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8288 (mp0) REVERT: A 342 GLU cc_start: 0.8458 (tt0) cc_final: 0.7582 (tm-30) REVERT: B 32 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8727 (mp10) REVERT: B 134 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8488 (mp0) REVERT: B 244 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8363 (mm-30) REVERT: C 87 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8305 (ttp80) REVERT: C 193 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: C 244 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8349 (mm-30) REVERT: C 378 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8638 (mm-40) REVERT: D 234 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: D 244 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8469 (mm-30) REVERT: D 289 VAL cc_start: 0.9034 (t) cc_final: 0.8746 (m) REVERT: D 329 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8296 (mm-30) REVERT: D 341 MET cc_start: 0.8554 (tmt) cc_final: 0.8345 (tmt) REVERT: D 405 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8628 (mtm) REVERT: E 193 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: E 211 GLU cc_start: 0.8452 (tp30) cc_final: 0.8144 (tp30) REVERT: E 244 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 332 TYR cc_start: 0.9250 (t80) cc_final: 0.8832 (t80) REVERT: E 336 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8562 (mmmm) REVERT: E 341 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6890 (tmm) REVERT: E 416 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6649 (ttp) REVERT: b 16 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8300 (mp) REVERT: b 25 MET cc_start: 0.8479 (tpp) cc_final: 0.8195 (tpp) REVERT: b 46 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: b 50 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8042 (mt-10) REVERT: b 73 HIS cc_start: 0.7637 (t-90) cc_final: 0.6995 (t-90) REVERT: b 79 VAL cc_start: 0.8501 (t) cc_final: 0.8248 (m) REVERT: d 46 ARG cc_start: 0.8633 (tpp80) cc_final: 0.7967 (mmt90) REVERT: d 47 LYS cc_start: 0.9069 (mptp) cc_final: 0.8523 (tptp) outliers start: 43 outliers final: 19 residues processed: 276 average time/residue: 1.6179 time to fit residues: 499.9705 Evaluate side-chains 272 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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 390 MET Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 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 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: 0.8980 chunk 43 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 180 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068005 restraints weight = 42628.272| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.78 r_work: 0.2874 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19407 Z= 0.161 Angle : 0.609 11.178 26168 Z= 0.293 Chirality : 0.042 0.156 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.904 96.800 2667 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.97 % Allowed : 15.58 % Favored : 82.45 % 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: 1.41 (0.17), residues: 2400 helix: 1.95 (0.17), residues: 1003 sheet: 0.30 (0.26), residues: 423 loop : 0.27 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 381 HIS 0.005 0.001 HIS E 388 PHE 0.012 0.001 PHE A 398 TYR 0.024 0.001 TYR E 197 ARG 0.008 0.000 ARG c 46 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 892) hydrogen bonds : angle 4.33316 ( 2538) covalent geometry : bond 0.00381 (19407) covalent geometry : angle 0.60925 (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 286 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 2.287 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: 0.9201 (mmm) cc_final: 0.8806 (mmm) REVERT: A 188 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 244 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8043 (mp0) REVERT: A 329 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8295 (mp0) REVERT: A 342 GLU cc_start: 0.8540 (tt0) cc_final: 0.7791 (tm-30) REVERT: B 1 MET cc_start: 0.8269 (pmm) cc_final: 0.7990 (pmm) REVERT: B 32 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: B 134 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8484 (mp0) REVERT: B 244 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 374 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7146 (tp-100) REVERT: B 378 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8420 (mp10) REVERT: C 87 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8339 (ttp80) REVERT: C 193 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8510 (mp10) REVERT: C 244 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8317 (mm-30) REVERT: C 378 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8644 (mm-40) REVERT: D 234 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: D 244 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8491 (mm-30) REVERT: D 289 VAL cc_start: 0.9036 (t) cc_final: 0.8752 (m) REVERT: D 329 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 374 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8362 (tp40) REVERT: D 405 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8643 (mtm) REVERT: E 193 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: E 211 GLU cc_start: 0.8507 (tp30) cc_final: 0.8189 (tp30) REVERT: E 244 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 332 TYR cc_start: 0.9258 (t80) cc_final: 0.8844 (t80) REVERT: E 336 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8569 (mmmm) REVERT: E 341 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6909 (tmm) REVERT: E 380 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8220 (tmm) REVERT: E 384 ARG cc_start: 0.9061 (tmt-80) cc_final: 0.8777 (tmm160) REVERT: E 416 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6667 (ttp) REVERT: b 16 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (mp) REVERT: b 25 MET cc_start: 0.8447 (tpp) cc_final: 0.8157 (tpp) REVERT: b 46 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8366 (mtm-85) REVERT: b 50 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8011 (mt-10) REVERT: b 73 HIS cc_start: 0.7609 (t-90) cc_final: 0.6941 (t-90) REVERT: b 79 VAL cc_start: 0.8472 (t) cc_final: 0.8206 (m) REVERT: d 46 ARG cc_start: 0.8661 (tpp80) cc_final: 0.7997 (mmt90) REVERT: d 47 LYS cc_start: 0.9072 (mptp) cc_final: 0.8537 (tptp) outliers start: 41 outliers final: 21 residues processed: 271 average time/residue: 1.8357 time to fit residues: 556.8901 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 : 2.186 ------------------------------------------------------------------------------- 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 390 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 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: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 32 GLN 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 = 0.3651 r_free = 0.3651 target = 0.099125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068119 restraints weight = 42514.956| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.79 r_work: 0.2878 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2220 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= 0.145 Angle : 0.608 11.383 26168 Z= 0.290 Chirality : 0.041 0.185 2992 Planarity : 0.003 0.045 3402 Dihedral : 5.882 96.828 2667 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.21 % Allowed : 15.48 % Favored : 82.31 % 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: 1.40 (0.18), residues: 2400 helix: 1.95 (0.17), residues: 1002 sheet: 0.31 (0.26), residues: 423 loop : 0.25 (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 388 PHE 0.013 0.001 PHE A 398 TYR 0.025 0.001 TYR E 197 ARG 0.008 0.000 ARG c 46 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 892) hydrogen bonds : angle 4.30719 ( 2538) covalent geometry : bond 0.00344 (19407) covalent geometry : angle 0.60783 (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 293 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9195 (pm20) cc_final: 0.8965 (pm20) REVERT: A 186 MET cc_start: 0.9186 (mmm) cc_final: 0.8788 (mmm) REVERT: A 188 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9171 (mm) REVERT: A 329 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8311 (mp0) REVERT: A 342 GLU cc_start: 0.8539 (tt0) cc_final: 0.7608 (tm-30) REVERT: B 1 MET cc_start: 0.8248 (pmm) cc_final: 0.7983 (pmm) REVERT: B 32 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8713 (mp10) REVERT: B 134 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8479 (mp0) REVERT: B 244 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 374 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7137 (tp-100) REVERT: B 378 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8422 (mp10) REVERT: C 87 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8358 (ttp80) REVERT: C 193 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: C 244 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8304 (mm-30) REVERT: C 378 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8636 (mm-40) REVERT: D 58 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 234 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: D 244 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8496 (mm-30) REVERT: D 289 VAL cc_start: 0.9025 (t) cc_final: 0.8749 (m) REVERT: D 329 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 342 GLU cc_start: 0.8430 (tt0) cc_final: 0.8226 (tm-30) REVERT: D 374 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8346 (tp40) REVERT: D 405 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: E 193 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: E 211 GLU cc_start: 0.8511 (tp30) cc_final: 0.8193 (tp30) REVERT: E 244 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 326 LYS cc_start: 0.9412 (tppp) cc_final: 0.8881 (tmtt) REVERT: E 332 TYR cc_start: 0.9262 (t80) cc_final: 0.8852 (t80) REVERT: E 336 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8558 (mmmm) REVERT: E 341 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6958 (tmm) REVERT: E 384 ARG cc_start: 0.9097 (tmt-80) cc_final: 0.8752 (tmm160) REVERT: E 416 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6748 (ttp) REVERT: b 16 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (mp) REVERT: b 25 MET cc_start: 0.8480 (tpp) cc_final: 0.8197 (tpp) REVERT: b 46 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8368 (mtm-85) REVERT: b 50 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8040 (mt-10) REVERT: b 73 HIS cc_start: 0.7600 (t-90) cc_final: 0.6932 (t-90) REVERT: b 79 VAL cc_start: 0.8497 (t) cc_final: 0.8240 (m) REVERT: d 46 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8024 (mmt90) REVERT: d 47 LYS cc_start: 0.9098 (mptp) cc_final: 0.8545 (tptp) REVERT: d 73 HIS cc_start: 0.8062 (t-170) cc_final: 0.7592 (t70) outliers start: 46 outliers final: 20 residues processed: 276 average time/residue: 1.8468 time to fit residues: 566.2772 Evaluate side-chains 274 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 390 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 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 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 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: 1.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.099149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068357 restraints weight = 42595.512| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.78 r_work: 0.2879 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19407 Z= 0.146 Angle : 0.619 11.472 26168 Z= 0.296 Chirality : 0.041 0.131 2992 Planarity : 0.003 0.045 3402 Dihedral : 5.842 96.576 2665 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.63 % Allowed : 16.40 % Favored : 81.98 % 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 (0.18), residues: 2400 helix: 1.93 (0.17), residues: 1002 sheet: 0.20 (0.26), residues: 431 loop : 0.27 (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 0.024 0.001 TYR E 197 ARG 0.009 0.000 ARG B 296 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 892) hydrogen bonds : angle 4.29641 ( 2538) covalent geometry : bond 0.00346 (19407) covalent geometry : angle 0.61916 (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 281 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8195 (pmm) cc_final: 0.7771 (ppp) REVERT: A 32 GLN cc_start: 0.9187 (pm20) cc_final: 0.8956 (pm20) REVERT: A 186 MET cc_start: 0.9196 (mmm) cc_final: 0.8793 (mmm) REVERT: A 188 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 329 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8304 (mp0) REVERT: A 342 GLU cc_start: 0.8527 (tt0) cc_final: 0.7598 (tm-30) REVERT: B 1 MET cc_start: 0.8272 (pmm) cc_final: 0.8011 (pmm) REVERT: B 32 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8713 (mp10) REVERT: B 134 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8483 (mp0) REVERT: B 244 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 347 ARG cc_start: 0.8717 (tpt-90) cc_final: 0.8347 (tpp80) REVERT: B 374 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7204 (tp-100) REVERT: B 378 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8463 (mp10) REVERT: C 87 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8374 (ttp80) REVERT: C 193 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: C 244 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8291 (mm-30) REVERT: C 378 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8643 (mm-40) REVERT: D 58 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8743 (mm) REVERT: D 234 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: D 244 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8492 (mm-30) REVERT: D 289 VAL cc_start: 0.9026 (t) cc_final: 0.8742 (m) REVERT: D 329 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8310 (mm-30) REVERT: D 374 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8341 (tp40) REVERT: D 405 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: E 21 MET cc_start: 0.8908 (mtp) cc_final: 0.8189 (ttt) REVERT: E 193 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8349 (pm20) REVERT: E 211 GLU cc_start: 0.8492 (tp30) cc_final: 0.8157 (tp30) REVERT: E 244 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8319 (mm-30) REVERT: E 332 TYR cc_start: 0.9252 (t80) cc_final: 0.8845 (t80) REVERT: E 336 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8553 (mmmm) REVERT: E 341 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6919 (tmm) REVERT: E 416 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6770 (ttp) REVERT: b 16 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8322 (mp) REVERT: b 25 MET cc_start: 0.8471 (tpp) cc_final: 0.8187 (tpp) REVERT: b 46 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: b 50 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8021 (mt-10) REVERT: b 73 HIS cc_start: 0.7486 (t-90) cc_final: 0.6877 (t-90) REVERT: b 79 VAL cc_start: 0.8419 (t) cc_final: 0.8165 (m) REVERT: d 46 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8013 (mmt90) REVERT: d 47 LYS cc_start: 0.9105 (mptp) cc_final: 0.8549 (tptp) REVERT: d 73 HIS cc_start: 0.8026 (t-170) cc_final: 0.7620 (t70) outliers start: 34 outliers final: 20 residues processed: 268 average time/residue: 1.4465 time to fit residues: 431.2557 Evaluate side-chains 270 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 390 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 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 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 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7338 > 50: distance: 19 - 53: 27.962 distance: 42 - 44: 30.427 distance: 44 - 45: 50.920 distance: 45 - 46: 57.050 distance: 45 - 48: 63.137 distance: 46 - 47: 55.972 distance: 46 - 53: 42.080 distance: 47 - 163: 30.912 distance: 48 - 49: 44.691 distance: 49 - 50: 5.275 distance: 50 - 51: 18.751 distance: 51 - 52: 31.604 distance: 53 - 54: 56.914 distance: 54 - 55: 49.297 distance: 54 - 57: 58.512 distance: 55 - 56: 49.235 distance: 55 - 61: 47.375 distance: 57 - 58: 42.425 distance: 57 - 59: 28.944 distance: 58 - 60: 34.722 distance: 61 - 62: 6.752 distance: 61 - 154: 32.360 distance: 62 - 63: 47.637 distance: 62 - 65: 63.941 distance: 63 - 64: 42.777 distance: 63 - 72: 34.728 distance: 64 - 151: 26.355 distance: 65 - 66: 40.325 distance: 67 - 68: 57.081 distance: 68 - 69: 60.630 distance: 69 - 70: 43.429 distance: 69 - 71: 27.398 distance: 72 - 73: 46.613 distance: 72 - 78: 34.026 distance: 73 - 74: 50.148 distance: 73 - 76: 52.885 distance: 74 - 79: 41.322 distance: 76 - 77: 5.545 distance: 77 - 78: 35.959 distance: 79 - 80: 33.738 distance: 79 - 85: 42.768 distance: 80 - 81: 35.722 distance: 80 - 83: 39.575 distance: 81 - 82: 29.630 distance: 81 - 86: 48.677 distance: 83 - 84: 16.984 distance: 84 - 85: 38.862 distance: 86 - 87: 39.093 distance: 87 - 88: 44.898 distance: 87 - 90: 53.146 distance: 88 - 89: 24.590 distance: 88 - 95: 57.263 distance: 90 - 91: 14.695 distance: 91 - 92: 13.213 distance: 92 - 93: 19.967 distance: 93 - 94: 40.578 distance: 95 - 96: 66.959 distance: 96 - 97: 65.919 distance: 96 - 99: 49.743 distance: 97 - 98: 56.090 distance: 97 - 104: 51.482 distance: 99 - 100: 32.611 distance: 100 - 101: 52.705 distance: 101 - 102: 48.280 distance: 101 - 103: 43.671 distance: 104 - 105: 55.686 distance: 105 - 106: 40.245 distance: 106 - 107: 40.549 distance: 106 - 108: 49.839 distance: 108 - 109: 4.156 distance: 109 - 110: 29.248 distance: 109 - 112: 41.313 distance: 110 - 111: 31.472 distance: 110 - 117: 32.499 distance: 112 - 113: 40.974 distance: 113 - 114: 54.684 distance: 114 - 115: 23.031 distance: 114 - 116: 52.226 distance: 117 - 118: 37.605 distance: 118 - 119: 11.229 distance: 118 - 121: 11.567 distance: 119 - 128: 29.858 distance: 121 - 122: 24.699 distance: 122 - 123: 6.199 distance: 124 - 125: 9.192 distance: 125 - 126: 37.418 distance: 125 - 127: 40.403