Starting phenix.real_space_refine on Fri Mar 6 15:44:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pp6_20420/03_2026/6pp6_20420.map" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10050 2.51 5 N 2691 2.21 5 O 3187 1.98 5 H 16126 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32106 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5330 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "D" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5380 Classifications: {'peptide': 349} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5336 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5125 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" 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: 5.82, per 1000 atoms: 0.18 Number of scatterers: 32106 At special positions: 0 Unit cell: (147.32, 140.36, 104.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 17 15.00 O 3187 8.00 N 2691 7.00 C 10050 6.00 H 16126 1.00 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: 2.79 Conformation dependent library (CDL) restraints added in 950.6 milliseconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 19 sheets defined 53.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.813A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 101 removed outlier: 3.909A pdb=" N LYS A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.549A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 4.231A pdb=" N GLY A 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.684A pdb=" N GLY A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.681A pdb=" N GLY A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.772A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.505A pdb=" N LEU A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 380 removed outlier: 4.282A pdb=" N ILE A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.947A pdb=" N ILE A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.810A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.886A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.570A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 4.056A pdb=" N ILE B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.572A pdb=" N LEU B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.847A pdb=" N VAL B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.685A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.612A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.903A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.727A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.968A pdb=" N ILE B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.694A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.685A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.860A pdb=" N LYS C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.704A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 4.382A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 204 through 217 removed outlier: 3.583A pdb=" N GLN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.699A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.774A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.530A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 removed outlier: 4.006A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.834A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.922A pdb=" N ILE C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N THR C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.953A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.751A pdb=" N TYR D 77 " --> pdb=" O HIS D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.983A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.617A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.328A pdb=" N GLN D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 227 removed outlier: 4.175A pdb=" N GLY D 226 " --> pdb=" O PRO D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.579A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.593A pdb=" N LEU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.670A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.703A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.623A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 removed outlier: 3.505A pdb=" N ASP D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.663A pdb=" N ILE D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP D 382 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.624A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.637A pdb=" N HIS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 removed outlier: 3.520A pdb=" N LYS E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.551A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.563A pdb=" N GLN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 204 through 217 removed outlier: 3.792A pdb=" N GLN E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 264 Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.758A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.730A pdb=" N LEU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 320 through 328 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.963A pdb=" N GLU E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 Processing helix chain 'E' and resid 368 through 370 No H-bonds generated for 'chain 'E' and resid 368 through 370' Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.898A pdb=" N ILE E 375 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'E' and resid 399 through 405 Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.792A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 102 removed outlier: 3.652A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.742A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 3.656A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.630A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 227 removed outlier: 3.741A pdb=" N GLY F 227 " --> pdb=" O PRO F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.673A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 removed outlier: 3.511A pdb=" N LEU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 removed outlier: 3.658A pdb=" N LEU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.795A pdb=" N ARG F 307 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.558A pdb=" N LEU F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 Processing helix chain 'F' and resid 351 through 366 removed outlier: 3.530A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 387 removed outlier: 4.082A pdb=" N ILE F 375 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 removed outlier: 4.122A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 3.831A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 182 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 184 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 181 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLY A 248 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE A 183 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 249 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.744A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.595A pdb=" N ASP A 347 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 398 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU A 349 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 397 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 410 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.690A pdb=" N GLY B 248 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 222 removed outlier: 4.066A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.345A pdb=" N ASP B 347 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 398 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.671A pdb=" N LEU C 116 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.616A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 395 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AB2, first strand: chain 'D' and resid 143 through 144 removed outlier: 6.936A pdb=" N VAL D 181 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY D 248 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE D 183 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 222 removed outlier: 3.989A pdb=" N ALA D 220 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D 238 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 222 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.518A pdb=" N ILE D 398 " --> pdb=" O GLU D 349 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS D 395 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 144 removed outlier: 3.548A pdb=" N ALA E 143 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP E 184 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 219 through 222 removed outlier: 4.036A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.416A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE E 398 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU E 349 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AB9, first strand: chain 'F' and resid 219 through 222 removed outlier: 4.112A pdb=" N ALA F 220 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL F 238 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 236 " --> pdb=" O VAL F 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 347 through 350 removed outlier: 6.747A pdb=" N ASP F 347 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE F 398 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU F 349 " --> pdb=" O ILE F 398 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1722 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: 6.87 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 16120 1.06 - 1.28: 2857 1.28 - 1.50: 6187 1.50 - 1.73: 7088 1.73 - 1.95: 59 Bond restraints: 32311 Sorted by residual: bond pdb=" C ILE D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.47e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU F 64 " pdb=" CA LEU F 64 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.70e+00 bond pdb=" C PRO D 223 " pdb=" N PRO D 224 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 2.95e+00 bond pdb=" N UNK S 1 " pdb=" CA UNK S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 58016 2.14 - 4.28: 660 4.28 - 6.42: 87 6.42 - 8.56: 5 8.56 - 10.70: 2 Bond angle restraints: 58770 Sorted by residual: angle pdb=" CA GLY F 206 " pdb=" C GLY F 206 " pdb=" N VAL F 207 " ideal model delta sigma weight residual 116.81 111.26 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" C ASN C 101 " pdb=" N GLY C 102 " pdb=" CA GLY C 102 " ideal model delta sigma weight residual 121.41 132.11 -10.70 1.96e+00 2.60e-01 2.98e+01 angle pdb=" N SER C 105 " pdb=" CA SER C 105 " pdb=" C SER C 105 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" C GLY F 204 " pdb=" N GLU F 205 " pdb=" CA GLU F 205 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLU F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta sigma weight residual 119.94 124.18 -4.24 1.11e+00 8.12e-01 1.46e+01 ... (remaining 58765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13421 17.32 - 34.63: 1152 34.63 - 51.95: 310 51.95 - 69.26: 84 69.26 - 86.58: 11 Dihedral angle restraints: 14978 sinusoidal: 8519 harmonic: 6459 Sorted by residual: dihedral pdb=" CA LYS C 366 " pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " pdb=" CD LYS C 366 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " pdb=" OD1 ASP A 194 " ideal model delta sinusoidal sigma weight residual -30.00 -82.13 52.13 1 2.00e+01 2.50e-03 9.27e+00 dihedral pdb=" N ARG E 370 " pdb=" CA ARG E 370 " pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sinusoidal sigma weight residual -180.00 -129.30 -50.70 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 14975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1961 0.041 - 0.083: 441 0.083 - 0.124: 164 0.124 - 0.166: 31 0.166 - 0.207: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA SER C 105 " pdb=" N SER C 105 " pdb=" C SER C 105 " pdb=" CB SER C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2595 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 370 " 0.090 9.50e-02 1.11e+02 9.25e-02 1.73e+02 pdb=" NE ARG B 370 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 370 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 370 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 370 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 370 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 370 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG B 370 " -0.172 2.00e-02 2.50e+03 pdb="HH22 ARG B 370 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 195 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 328 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO F 329 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 329 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 329 " 0.028 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 141 2.01 - 2.65: 45029 2.65 - 3.30: 91690 3.30 - 3.95: 112076 3.95 - 4.60: 176323 Nonbonded interactions: 425259 Sorted by model distance: nonbonded pdb=" OD1 ASP C 399 " pdb=" HG SER C 401 " model vdw 1.357 2.450 nonbonded pdb=" HZ2 LYS C 112 " pdb=" O SER C 241 " model vdw 1.397 2.450 nonbonded pdb=" OD1 ASP E 144 " pdb=" HG1 THR E 146 " model vdw 1.425 2.450 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.429 2.450 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.434 2.450 ... (remaining 425254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'B' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'C' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'D' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'E' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'F' and (resid 64 through 225 or resid 233 through 259 or (resid 260 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 261 through 413)) } 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 group one per residue 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: 0.410 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: 0.140 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.780 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.004 0.040 16185 Z= 0.166 Angle : 0.713 10.700 21919 Z= 0.392 Chirality : 0.042 0.207 2598 Planarity : 0.004 0.076 2819 Dihedral : 12.431 81.962 6147 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2031 helix: -0.21 (0.16), residues: 770 sheet: -0.40 (0.30), residues: 272 loop : -1.23 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 261 TYR 0.010 0.001 TYR E 93 PHE 0.014 0.001 PHE A 270 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00359 (16185) covalent geometry : angle 0.71290 (21919) hydrogen bonds : bond 0.30358 ( 607) hydrogen bonds : angle 7.56333 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.768 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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 137 ASP cc_start: 0.8301 (p0) cc_final: 0.8074 (t0) REVERT: A 342 ASN cc_start: 0.9335 (m-40) cc_final: 0.9120 (m-40) REVERT: B 141 THR cc_start: 0.8912 (t) cc_final: 0.8618 (m) REVERT: B 160 ASN cc_start: 0.9086 (t0) cc_final: 0.8840 (t0) REVERT: B 162 ILE cc_start: 0.9360 (mm) cc_final: 0.9029 (mt) REVERT: B 245 PHE cc_start: 0.8262 (m-80) cc_final: 0.7925 (m-80) REVERT: B 289 GLN cc_start: 0.9303 (mt0) cc_final: 0.9024 (mp10) REVERT: C 205 GLU cc_start: 0.8375 (tt0) cc_final: 0.7574 (tm-30) REVERT: D 175 LYS cc_start: 0.9035 (tttt) cc_final: 0.8718 (ttpp) REVERT: D 363 MET cc_start: 0.9302 (mtm) cc_final: 0.9071 (mmm) REVERT: E 366 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8883 (tptp) REVERT: F 225 GLN cc_start: 0.5795 (tt0) cc_final: 0.5235 (tt0) REVERT: F 381 LEU cc_start: 0.9518 (tp) cc_final: 0.9237 (pp) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2828 time to fit residues: 167.5519 Evaluate side-chains 243 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 225 GLN B 68 HIS B 208 GLN C 101 ASN D 260 HIS F 114 ASN F 237 GLN F 331 ASN F 336 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.090363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067815 restraints weight = 167658.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071083 restraints weight = 81589.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073310 restraints weight = 50218.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074829 restraints weight = 36046.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.075705 restraints weight = 28802.022| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16185 Z= 0.178 Angle : 0.596 6.346 21919 Z= 0.322 Chirality : 0.041 0.167 2598 Planarity : 0.004 0.039 2819 Dihedral : 7.504 60.945 2294 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2031 helix: 0.60 (0.16), residues: 867 sheet: -0.09 (0.31), residues: 271 loop : -1.16 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 351 TYR 0.017 0.001 TYR E 93 PHE 0.019 0.001 PHE E 298 HIS 0.006 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00355 (16185) covalent geometry : angle 0.59616 (21919) hydrogen bonds : bond 0.07102 ( 607) hydrogen bonds : angle 6.21362 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.916 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8319 (p0) cc_final: 0.8088 (t0) REVERT: A 342 ASN cc_start: 0.9303 (m-40) cc_final: 0.9095 (m-40) REVERT: B 116 LEU cc_start: 0.9515 (tp) cc_final: 0.9315 (tt) REVERT: B 245 PHE cc_start: 0.7988 (m-80) cc_final: 0.7751 (m-80) REVERT: B 289 GLN cc_start: 0.9183 (mt0) cc_final: 0.8915 (mp10) REVERT: C 205 GLU cc_start: 0.8094 (tt0) cc_final: 0.7630 (tm-30) REVERT: C 247 CYS cc_start: 0.9052 (m) cc_final: 0.8756 (m) REVERT: D 170 ASP cc_start: 0.8954 (t0) cc_final: 0.8573 (t0) REVERT: D 347 ASP cc_start: 0.8448 (t0) cc_final: 0.8198 (t0) REVERT: E 245 PHE cc_start: 0.8862 (m-80) cc_final: 0.8600 (m-80) REVERT: E 366 LYS cc_start: 0.9363 (mmtt) cc_final: 0.8973 (tptp) REVERT: F 225 GLN cc_start: 0.5470 (tt0) cc_final: 0.5268 (tt0) outliers start: 1 outliers final: 1 residues processed: 279 average time/residue: 0.2913 time to fit residues: 121.9936 Evaluate side-chains 212 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 159 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 chunk 196 optimal weight: 9.9990 chunk 88 optimal weight: 0.0070 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 167 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 336 GLN 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 = 0.089587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067481 restraints weight = 165468.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070694 restraints weight = 81904.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072911 restraints weight = 50639.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074405 restraints weight = 36247.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075423 restraints weight = 28910.476| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16185 Z= 0.119 Angle : 0.506 5.522 21919 Z= 0.264 Chirality : 0.040 0.161 2598 Planarity : 0.003 0.030 2819 Dihedral : 7.377 61.832 2294 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2031 helix: 0.73 (0.17), residues: 888 sheet: 0.08 (0.31), residues: 271 loop : -1.13 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 307 TYR 0.020 0.001 TYR A 182 PHE 0.009 0.001 PHE E 298 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00247 (16185) covalent geometry : angle 0.50608 (21919) hydrogen bonds : bond 0.05731 ( 607) hydrogen bonds : angle 5.72782 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.871 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8201 (p0) cc_final: 0.7982 (t0) REVERT: A 182 TYR cc_start: 0.8191 (t80) cc_final: 0.7603 (t80) REVERT: A 283 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7104 (pm20) REVERT: A 342 ASN cc_start: 0.9236 (m-40) cc_final: 0.9018 (m-40) REVERT: A 356 ASP cc_start: 0.8785 (p0) cc_final: 0.8516 (p0) REVERT: A 377 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8307 (mm-30) REVERT: B 142 MET cc_start: 0.7512 (tmm) cc_final: 0.7272 (tmm) REVERT: B 245 PHE cc_start: 0.7998 (m-80) cc_final: 0.7642 (m-80) REVERT: C 205 GLU cc_start: 0.8164 (tt0) cc_final: 0.7681 (tm-30) REVERT: C 247 CYS cc_start: 0.9018 (m) cc_final: 0.8663 (m) REVERT: D 142 MET cc_start: 0.8350 (mmm) cc_final: 0.7982 (tpp) REVERT: D 170 ASP cc_start: 0.8935 (t0) cc_final: 0.8552 (t0) REVERT: D 175 LYS cc_start: 0.8943 (tttt) cc_final: 0.8695 (ttpp) REVERT: E 245 PHE cc_start: 0.8808 (m-80) cc_final: 0.8557 (m-80) REVERT: E 366 LYS cc_start: 0.9357 (mmtt) cc_final: 0.8958 (tptp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2556 time to fit residues: 102.6951 Evaluate side-chains 200 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 150 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN C 95 HIS C 101 ASN D 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064541 restraints weight = 169889.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067695 restraints weight = 83173.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069888 restraints weight = 51634.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.071354 restraints weight = 37419.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072277 restraints weight = 30134.752| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16185 Z= 0.162 Angle : 0.527 5.620 21919 Z= 0.275 Chirality : 0.039 0.153 2598 Planarity : 0.003 0.043 2819 Dihedral : 7.308 64.659 2294 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2031 helix: 0.67 (0.17), residues: 900 sheet: 0.14 (0.32), residues: 262 loop : -1.04 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 307 TYR 0.013 0.001 TYR B 93 PHE 0.016 0.001 PHE E 298 HIS 0.010 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00334 (16185) covalent geometry : angle 0.52727 (21919) hydrogen bonds : bond 0.04493 ( 607) hydrogen bonds : angle 5.57643 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.870 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8374 (p0) cc_final: 0.8061 (t0) REVERT: A 142 MET cc_start: 0.8777 (mmt) cc_final: 0.8331 (mmt) REVERT: A 182 TYR cc_start: 0.8536 (t80) cc_final: 0.7368 (t80) REVERT: A 342 ASN cc_start: 0.9291 (m-40) cc_final: 0.9061 (m-40) REVERT: B 142 MET cc_start: 0.7698 (tmm) cc_final: 0.7227 (tmm) REVERT: B 289 GLN cc_start: 0.9112 (mt0) cc_final: 0.8912 (mt0) REVERT: C 247 CYS cc_start: 0.9070 (m) cc_final: 0.8693 (m) REVERT: D 78 VAL cc_start: 0.7636 (t) cc_final: 0.7335 (m) REVERT: D 170 ASP cc_start: 0.9040 (t0) cc_final: 0.8597 (t0) REVERT: D 175 LYS cc_start: 0.9018 (tttt) cc_final: 0.8731 (ttpp) REVERT: D 347 ASP cc_start: 0.8400 (t0) cc_final: 0.8186 (t0) REVERT: E 366 LYS cc_start: 0.9361 (mmtt) cc_final: 0.9056 (tptp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2411 time to fit residues: 85.5228 Evaluate side-chains 186 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 167 GLN F 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.086585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064543 restraints weight = 169898.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067618 restraints weight = 83500.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.069743 restraints weight = 51736.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071154 restraints weight = 37393.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072122 restraints weight = 30073.917| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16185 Z= 0.141 Angle : 0.502 7.686 21919 Z= 0.261 Chirality : 0.039 0.150 2598 Planarity : 0.003 0.062 2819 Dihedral : 7.238 65.791 2294 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2031 helix: 0.69 (0.17), residues: 902 sheet: 0.14 (0.32), residues: 262 loop : -0.98 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 307 TYR 0.012 0.001 TYR D 182 PHE 0.018 0.001 PHE B 245 HIS 0.013 0.001 HIS S 3 Details of bonding type rmsd covalent geometry : bond 0.00302 (16185) covalent geometry : angle 0.50203 (21919) hydrogen bonds : bond 0.04047 ( 607) hydrogen bonds : angle 5.36765 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.783 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8393 (p0) cc_final: 0.8089 (t0) REVERT: A 142 MET cc_start: 0.8762 (mmt) cc_final: 0.8540 (mmt) REVERT: A 182 TYR cc_start: 0.8577 (t80) cc_final: 0.7607 (t80) REVERT: B 142 MET cc_start: 0.7767 (tmm) cc_final: 0.7330 (tmm) REVERT: B 144 ASP cc_start: 0.7727 (p0) cc_final: 0.7359 (p0) REVERT: C 247 CYS cc_start: 0.9093 (m) cc_final: 0.8731 (m) REVERT: D 170 ASP cc_start: 0.9012 (t0) cc_final: 0.8546 (t0) REVERT: D 175 LYS cc_start: 0.9007 (tttt) cc_final: 0.8745 (ttpp) REVERT: D 347 ASP cc_start: 0.8357 (t0) cc_final: 0.8137 (t0) REVERT: D 363 MET cc_start: 0.9124 (tpp) cc_final: 0.8803 (tpp) REVERT: E 366 LYS cc_start: 0.9350 (mmtt) cc_final: 0.9063 (tptp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2408 time to fit residues: 85.3119 Evaluate side-chains 183 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 0.0050 chunk 162 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 182 optimal weight: 30.0000 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 167 GLN D 260 HIS F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.087388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.065189 restraints weight = 167381.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068336 restraints weight = 82318.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070489 restraints weight = 50945.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.071933 restraints weight = 36740.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072839 restraints weight = 29465.185| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16185 Z= 0.098 Angle : 0.473 5.528 21919 Z= 0.243 Chirality : 0.040 0.150 2598 Planarity : 0.003 0.032 2819 Dihedral : 7.135 64.074 2294 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2031 helix: 0.92 (0.17), residues: 900 sheet: 0.02 (0.33), residues: 243 loop : -0.83 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.012 0.001 TYR D 385 PHE 0.024 0.001 PHE B 245 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00213 (16185) covalent geometry : angle 0.47286 (21919) hydrogen bonds : bond 0.03682 ( 607) hydrogen bonds : angle 5.03256 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.897 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8426 (p0) cc_final: 0.8120 (t0) REVERT: A 142 MET cc_start: 0.8744 (mmt) cc_final: 0.8519 (mmt) REVERT: A 148 LEU cc_start: 0.9249 (mt) cc_final: 0.9024 (mt) REVERT: A 182 TYR cc_start: 0.8610 (t80) cc_final: 0.7617 (t80) REVERT: C 247 CYS cc_start: 0.9119 (m) cc_final: 0.8802 (m) REVERT: D 170 ASP cc_start: 0.8984 (t0) cc_final: 0.8500 (t0) REVERT: D 175 LYS cc_start: 0.9013 (tttt) cc_final: 0.8777 (ttpp) REVERT: D 347 ASP cc_start: 0.8339 (t0) cc_final: 0.8101 (t0) REVERT: D 363 MET cc_start: 0.9077 (tpp) cc_final: 0.8795 (tpp) REVERT: E 316 GLU cc_start: 0.8320 (tp30) cc_final: 0.8111 (tp30) REVERT: E 366 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9022 (tptp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2418 time to fit residues: 85.7996 Evaluate side-chains 180 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 225 GLN D 167 GLN F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.087320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064345 restraints weight = 170785.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067438 restraints weight = 84468.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069588 restraints weight = 53061.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071041 restraints weight = 38802.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.071993 restraints weight = 31421.396| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16185 Z= 0.102 Angle : 0.474 5.486 21919 Z= 0.242 Chirality : 0.039 0.152 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.111 63.841 2294 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2031 helix: 0.90 (0.17), residues: 905 sheet: 0.02 (0.33), residues: 243 loop : -0.80 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.014 0.001 TYR A 337 PHE 0.017 0.001 PHE E 245 HIS 0.008 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00224 (16185) covalent geometry : angle 0.47365 (21919) hydrogen bonds : bond 0.03454 ( 607) hydrogen bonds : angle 4.91161 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.926 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8429 (p0) cc_final: 0.8115 (t0) REVERT: A 142 MET cc_start: 0.8758 (mmt) cc_final: 0.8524 (mmt) REVERT: A 148 LEU cc_start: 0.9230 (mt) cc_final: 0.9023 (mt) REVERT: A 182 TYR cc_start: 0.8646 (t80) cc_final: 0.7610 (t80) REVERT: B 142 MET cc_start: 0.7613 (tmm) cc_final: 0.7123 (tmm) REVERT: C 247 CYS cc_start: 0.9126 (m) cc_final: 0.8797 (m) REVERT: D 170 ASP cc_start: 0.9001 (t0) cc_final: 0.8528 (t0) REVERT: D 347 ASP cc_start: 0.8338 (t0) cc_final: 0.8069 (t0) REVERT: D 363 MET cc_start: 0.9066 (tpp) cc_final: 0.8765 (tpp) REVERT: E 316 GLU cc_start: 0.8303 (tp30) cc_final: 0.8095 (tp30) REVERT: E 366 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9020 (tptp) REVERT: F 94 ASN cc_start: 0.9364 (m-40) cc_final: 0.9087 (m-40) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2380 time to fit residues: 80.5749 Evaluate side-chains 170 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 184 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 157 optimal weight: 0.1980 chunk 200 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 167 GLN F 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.087655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065381 restraints weight = 166888.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068467 restraints weight = 81698.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070606 restraints weight = 50768.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072051 restraints weight = 36709.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073011 restraints weight = 29439.140| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16185 Z= 0.087 Angle : 0.466 5.520 21919 Z= 0.236 Chirality : 0.040 0.142 2598 Planarity : 0.003 0.031 2819 Dihedral : 7.062 62.509 2294 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 2031 helix: 1.11 (0.17), residues: 901 sheet: 0.09 (0.33), residues: 243 loop : -0.76 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.012 0.001 TYR D 385 PHE 0.028 0.001 PHE B 245 HIS 0.009 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00195 (16185) covalent geometry : angle 0.46570 (21919) hydrogen bonds : bond 0.03282 ( 607) hydrogen bonds : angle 4.72042 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.880 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: 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 137 ASP cc_start: 0.8460 (p0) cc_final: 0.8143 (t0) REVERT: A 148 LEU cc_start: 0.9245 (mt) cc_final: 0.9039 (mt) REVERT: B 142 MET cc_start: 0.7786 (tmm) cc_final: 0.7261 (tmm) REVERT: C 247 CYS cc_start: 0.9172 (m) cc_final: 0.8819 (m) REVERT: D 170 ASP cc_start: 0.9070 (t0) cc_final: 0.8580 (t0) REVERT: D 347 ASP cc_start: 0.8382 (t0) cc_final: 0.8094 (t0) REVERT: D 363 MET cc_start: 0.9120 (tpp) cc_final: 0.8776 (tpp) REVERT: E 366 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9019 (tptp) REVERT: F 94 ASN cc_start: 0.9346 (m-40) cc_final: 0.9111 (m-40) REVERT: F 209 GLN cc_start: 0.9109 (pt0) cc_final: 0.8884 (pp30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2519 time to fit residues: 84.4163 Evaluate side-chains 173 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 139 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN D 101 ASN D 167 GLN D 225 GLN D 406 GLN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063637 restraints weight = 168967.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066628 restraints weight = 83379.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.068708 restraints weight = 52001.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070099 restraints weight = 37755.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070960 restraints weight = 30482.309| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16185 Z= 0.155 Angle : 0.515 7.327 21919 Z= 0.265 Chirality : 0.039 0.143 2598 Planarity : 0.003 0.039 2819 Dihedral : 7.194 64.039 2294 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2031 helix: 0.93 (0.17), residues: 914 sheet: 0.02 (0.32), residues: 248 loop : -0.89 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.013 0.001 TYR C 182 PHE 0.026 0.001 PHE B 245 HIS 0.010 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00325 (16185) covalent geometry : angle 0.51465 (21919) hydrogen bonds : bond 0.03277 ( 607) hydrogen bonds : angle 4.93890 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.777 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8461 (p0) cc_final: 0.8073 (t0) REVERT: A 148 LEU cc_start: 0.9247 (mt) cc_final: 0.9040 (mt) REVERT: A 300 LEU cc_start: 0.8577 (mm) cc_final: 0.8210 (mm) REVERT: B 142 MET cc_start: 0.7848 (tmm) cc_final: 0.7305 (tmm) REVERT: B 162 ILE cc_start: 0.9266 (mm) cc_final: 0.9022 (mt) REVERT: C 188 LYS cc_start: 0.9501 (mmpt) cc_final: 0.9204 (mmmm) REVERT: C 247 CYS cc_start: 0.9138 (m) cc_final: 0.8811 (m) REVERT: D 170 ASP cc_start: 0.9032 (t0) cc_final: 0.8557 (t0) REVERT: D 363 MET cc_start: 0.9068 (tpp) cc_final: 0.8753 (tpp) REVERT: E 366 LYS cc_start: 0.9396 (mmtt) cc_final: 0.9060 (tptp) REVERT: F 209 GLN cc_start: 0.9163 (pt0) cc_final: 0.8907 (pp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2534 time to fit residues: 81.5845 Evaluate side-chains 169 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 208 GLN B 160 ASN D 167 GLN D 225 GLN E 95 HIS F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.086106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063992 restraints weight = 167914.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066989 restraints weight = 81514.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069110 restraints weight = 50534.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070521 restraints weight = 36448.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071448 restraints weight = 29285.108| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16185 Z= 0.103 Angle : 0.479 7.547 21919 Z= 0.245 Chirality : 0.039 0.150 2598 Planarity : 0.003 0.032 2819 Dihedral : 7.096 63.451 2294 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2031 helix: 1.04 (0.17), residues: 911 sheet: 0.02 (0.32), residues: 249 loop : -0.84 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 98 TYR 0.012 0.001 TYR D 385 PHE 0.018 0.001 PHE A 304 HIS 0.010 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00230 (16185) covalent geometry : angle 0.47858 (21919) hydrogen bonds : bond 0.03103 ( 607) hydrogen bonds : angle 4.75708 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.841 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8471 (p0) cc_final: 0.8118 (t0) REVERT: A 144 ASP cc_start: 0.8527 (m-30) cc_final: 0.7875 (p0) REVERT: A 148 LEU cc_start: 0.9246 (mt) cc_final: 0.8995 (mt) REVERT: B 162 ILE cc_start: 0.9257 (mm) cc_final: 0.9022 (mt) REVERT: C 247 CYS cc_start: 0.9148 (m) cc_final: 0.8830 (m) REVERT: D 170 ASP cc_start: 0.9037 (t0) cc_final: 0.8561 (t0) REVERT: D 175 LYS cc_start: 0.8993 (tttt) cc_final: 0.8728 (ttpp) REVERT: D 363 MET cc_start: 0.9078 (tpp) cc_final: 0.8722 (tpp) REVERT: E 142 MET cc_start: 0.8037 (tmm) cc_final: 0.7645 (tmm) REVERT: E 366 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9042 (tptp) REVERT: F 94 ASN cc_start: 0.9496 (m-40) cc_final: 0.9207 (m-40) REVERT: F 209 GLN cc_start: 0.9152 (pt0) cc_final: 0.8903 (pp30) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2461 time to fit residues: 81.1215 Evaluate side-chains 171 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 84 optimal weight: 0.2980 chunk 169 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN D 167 GLN F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.064427 restraints weight = 167132.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067525 restraints weight = 81404.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069630 restraints weight = 50222.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071050 restraints weight = 36281.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071922 restraints weight = 29135.468| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16185 Z= 0.088 Angle : 0.473 6.913 21919 Z= 0.241 Chirality : 0.040 0.146 2598 Planarity : 0.003 0.031 2819 Dihedral : 6.931 62.102 2294 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2031 helix: 1.26 (0.17), residues: 901 sheet: 0.08 (0.32), residues: 244 loop : -0.74 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.012 0.001 TYR D 171 PHE 0.020 0.001 PHE A 304 HIS 0.007 0.001 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00203 (16185) covalent geometry : angle 0.47308 (21919) hydrogen bonds : bond 0.02975 ( 607) hydrogen bonds : angle 4.59410 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.53 seconds wall clock time: 83 minutes 39.74 seconds (5019.74 seconds total)