Starting phenix.real_space_refine on Mon Sep 14 17:49:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pp6_20420/09_2026/6pp6_20420_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pp6_20420/09_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_20420/09_2026/6pp6_20420_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pp6_20420/09_2026/6pp6_20420_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pp6_20420/09_2026/6pp6_20420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pp6_20420/09_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-2.2.1-6174/lib/python3.11/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: 6.04, per 1000 atoms: 0.19 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: 3.08 Conformation dependent library (CDL) restraints added in 938.7 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: 0.88 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: 8.33 Time building geometry restraints manager: 4.25 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=" O3B AGS D 600 " pdb=" PB AGS D 600 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3B AGS B 600 " pdb=" PB AGS B 600 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O3B AGS C 600 " pdb=" PB AGS C 600 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3B AGS A 600 " pdb=" PB AGS A 600 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3B AGS E 600 " pdb=" PB AGS E 600 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 57919 2.14 - 4.28: 703 4.28 - 6.42: 106 6.42 - 8.56: 27 8.56 - 10.70: 15 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 - 31.74: 14599 31.74 - 63.49: 443 63.49 - 95.23: 16 95.23 - 126.97: 5 126.97 - 158.72: 5 Dihedral angle restraints: 15068 sinusoidal: 8609 harmonic: 6459 Sorted by residual: dihedral pdb=" O1A AGS A 600 " pdb=" O3A AGS A 600 " pdb=" PA AGS A 600 " pdb=" PB AGS A 600 " ideal model delta sinusoidal sigma weight residual 82.37 -76.35 158.72 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" O1A AGS E 600 " pdb=" O3A AGS E 600 " pdb=" PA AGS E 600 " pdb=" PB AGS E 600 " ideal model delta sinusoidal sigma weight residual 82.37 -59.77 142.14 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O1A AGS C 600 " pdb=" O3A AGS C 600 " pdb=" PA AGS C 600 " pdb=" PB AGS C 600 " ideal model delta sinusoidal sigma weight residual 82.37 -53.69 136.06 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2136 0.053 - 0.107: 344 0.107 - 0.160: 102 0.160 - 0.214: 1 0.214 - 0.267: 5 Chirality restraints: 2588 Sorted by residual: chirality pdb=" C3' AGS B 600 " pdb=" C2' AGS B 600 " pdb=" C4' AGS B 600 " pdb=" O3' AGS B 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' AGS A 600 " pdb=" C2' AGS A 600 " pdb=" C4' AGS A 600 " pdb=" O3' AGS A 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' AGS C 600 " pdb=" C2' AGS C 600 " pdb=" C4' AGS C 600 " pdb=" O3' AGS C 600 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2585 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: 0.660 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: 0.200 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.300 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 16185 Z= 0.224 Angle : 0.815 10.700 21919 Z= 0.413 Chirality : 0.044 0.267 2588 Planarity : 0.004 0.076 2819 Dihedral : 13.398 158.715 6237 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/Z covalent geometry : bond 0.00469 / 0.22 (16185) covalent geometry : angle 0.81467 / 0.41 (21919) hydrogen bonds : bond 0.30358 / 20.59 ( 607) hydrogen bonds : angle 7.56333 / 5.36 ( 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 : 0.792 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: 0.2796 time to fit residues: 168.1897 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 : 0.829 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3697 r_free = 0.3697 target = 0.091133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068435 restraints weight = 166464.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071704 restraints weight = 81333.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.073982 restraints weight = 50180.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.075425 restraints weight = 36006.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.076512 restraints weight = 28929.028| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2740 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= 0.150 Angle : 0.565 5.609 21919 Z= 0.299 Chirality : 0.040 0.162 2588 Planarity : 0.004 0.037 2819 Dihedral : 11.345 175.336 2384 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -0.37 (0.17), residues: 2031 helix: 0.62 (0.16), residues: 877 sheet: -0.05 (0.31), residues: 271 loop : -1.15 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 351 TYR 0.014 0.001 TYR E 93 PHE 0.017 0.001 PHE E 298 HIS 0.007 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (16185) covalent geometry : angle 0.56478 / 0.30 (21919) hydrogen bonds : bond 0.06571 / 4.50 ( 607) hydrogen bonds : angle 5.98709 / 4.24 ( 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 286 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.745 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: A 137 ASP cc_start: 0.8277 (p0) cc_final: 0.8040 (t0) REVERT: A 191 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8517 (ttp80) REVERT: A 337 TYR cc_start: 0.8986 (m-80) cc_final: 0.8331 (m-80) REVERT: A 342 ASN cc_start: 0.9286 (m-40) cc_final: 0.9076 (m-40) REVERT: A 356 ASP cc_start: 0.8871 (p0) cc_final: 0.8577 (p0) REVERT: B 245 PHE cc_start: 0.7886 (m-80) cc_final: 0.7682 (m-80) REVERT: B 289 GLN cc_start: 0.9172 (mt0) cc_final: 0.8889 (mp10) REVERT: C 205 GLU cc_start: 0.8117 (tt0) cc_final: 0.7637 (tm-30) REVERT: C 247 CYS cc_start: 0.9008 (m) cc_final: 0.8614 (m) REVERT: D 170 ASP cc_start: 0.8970 (t0) cc_final: 0.8578 (t0) REVERT: D 347 ASP cc_start: 0.8430 (t0) cc_final: 0.8176 (t0) REVERT: E 245 PHE cc_start: 0.8819 (m-80) cc_final: 0.8520 (m-80) REVERT: E 366 LYS cc_start: 0.9382 (mmtt) cc_final: 0.8966 (tptp) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.2652 time to fit residues: 115.2692 Evaluate side-chains 218 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 6.9990 chunk 158 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 167 GLN C 95 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN F 331 ASN F 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064806 restraints weight = 169344.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.067877 restraints weight = 84502.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070040 restraints weight = 53115.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071487 restraints weight = 38612.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072469 restraints weight = 31185.724| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16185 Z= 0.167 Angle : 0.535 7.282 21919 Z= 0.278 Chirality : 0.039 0.151 2588 Planarity : 0.003 0.030 2819 Dihedral : 11.199 176.244 2384 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -0.28 (0.18), residues: 2031 helix: 0.65 (0.17), residues: 905 sheet: 0.06 (0.32), residues: 257 loop : -1.11 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 307 TYR 0.013 0.001 TYR E 93 PHE 0.013 0.001 PHE E 298 HIS 0.012 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (16185) covalent geometry : angle 0.53527 / 0.28 (21919) hydrogen bonds : bond 0.04776 / 3.25 ( 607) hydrogen bonds : angle 5.56940 / 3.95 ( 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 247 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.826 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: A 137 ASP cc_start: 0.8333 (p0) cc_final: 0.8012 (t0) REVERT: A 191 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8438 (ttp80) REVERT: A 337 TYR cc_start: 0.9074 (m-80) cc_final: 0.8822 (m-80) REVERT: A 377 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 142 MET cc_start: 0.7648 (tmm) cc_final: 0.7137 (tmm) REVERT: B 245 PHE cc_start: 0.8214 (m-80) cc_final: 0.7868 (m-80) REVERT: C 247 CYS cc_start: 0.9058 (m) cc_final: 0.8724 (m) REVERT: D 78 VAL cc_start: 0.7595 (t) cc_final: 0.7313 (m) REVERT: D 170 ASP cc_start: 0.8990 (t0) cc_final: 0.8590 (t0) REVERT: D 175 LYS cc_start: 0.9017 (tttt) cc_final: 0.8756 (ttpp) REVERT: D 347 ASP cc_start: 0.8416 (t0) cc_final: 0.8191 (t0) REVERT: E 366 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9053 (tptp) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2460 time to fit residues: 95.1739 Evaluate side-chains 197 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 189 optimal weight: 0.2980 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN B 225 GLN B 260 HIS B 338 GLN C 101 ASN D 225 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063367 restraints weight = 169179.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.066350 restraints weight = 83619.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068420 restraints weight = 52294.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069828 restraints weight = 38009.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070770 restraints weight = 30629.049| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16185 Z= 0.176 Angle : 0.534 6.183 21919 Z= 0.277 Chirality : 0.039 0.149 2588 Planarity : 0.003 0.033 2819 Dihedral : 11.323 179.620 2384 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -0.26 (0.18), residues: 2031 helix: 0.54 (0.17), residues: 905 sheet: 0.10 (0.32), residues: 262 loop : -0.95 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 307 TYR 0.010 0.001 TYR D 182 PHE 0.016 0.001 PHE E 298 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (16185) covalent geometry : angle 0.53352 / 0.28 (21919) hydrogen bonds : bond 0.03892 / 2.64 ( 607) hydrogen bonds : angle 5.47500 / 3.87 ( 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 229 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.982 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: 0.8438 (p0) cc_final: 0.8064 (t0) REVERT: A 148 LEU cc_start: 0.9264 (mt) cc_final: 0.9053 (mt) REVERT: A 182 TYR cc_start: 0.8664 (t80) cc_final: 0.7933 (t80) REVERT: A 377 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 162 ILE cc_start: 0.9251 (mm) cc_final: 0.8984 (mt) REVERT: B 363 MET cc_start: 0.8661 (mtm) cc_final: 0.8457 (mtp) REVERT: C 188 LYS cc_start: 0.9476 (mmpt) cc_final: 0.9251 (mmpt) REVERT: C 247 CYS cc_start: 0.9099 (m) cc_final: 0.8742 (m) REVERT: D 78 VAL cc_start: 0.7699 (t) cc_final: 0.7472 (m) REVERT: D 170 ASP cc_start: 0.8982 (t0) cc_final: 0.8544 (t0) REVERT: D 175 LYS cc_start: 0.9012 (tttt) cc_final: 0.8759 (ttpp) REVERT: D 347 ASP cc_start: 0.8443 (t0) cc_final: 0.8229 (t0) REVERT: D 363 MET cc_start: 0.9075 (tpp) cc_final: 0.8807 (tpp) REVERT: E 366 LYS cc_start: 0.9361 (mmtt) cc_final: 0.9055 (tptp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2513 time to fit residues: 91.9045 Evaluate side-chains 184 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN D 167 GLN D 225 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 = 0.3563 r_free = 0.3563 target = 0.084394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.061556 restraints weight = 171156.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064570 restraints weight = 83643.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066632 restraints weight = 52099.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067971 restraints weight = 38123.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068909 restraints weight = 31102.730| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16185 Z= 0.186 Angle : 0.532 5.985 21919 Z= 0.276 Chirality : 0.039 0.150 2588 Planarity : 0.003 0.045 2819 Dihedral : 11.331 179.171 2384 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -0.35 (0.18), residues: 2031 helix: 0.47 (0.17), residues: 912 sheet: -0.12 (0.32), residues: 248 loop : -0.95 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.009 0.001 TYR E 93 PHE 0.021 0.001 PHE B 245 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (16185) covalent geometry : angle 0.53185 / 0.28 (21919) hydrogen bonds : bond 0.03738 / 2.51 ( 607) hydrogen bonds : angle 5.40873 / 3.82 ( 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 216 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.878 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: A 137 ASP cc_start: 0.8562 (p0) cc_final: 0.8259 (t70) REVERT: A 142 MET cc_start: 0.8965 (mmt) cc_final: 0.8391 (mmt) REVERT: A 182 TYR cc_start: 0.8702 (t80) cc_final: 0.7520 (t80) REVERT: A 377 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 118 ILE cc_start: 0.9234 (mt) cc_final: 0.8815 (pt) REVERT: B 142 MET cc_start: 0.7784 (tmm) cc_final: 0.7273 (tmm) REVERT: B 162 ILE cc_start: 0.9285 (mm) cc_final: 0.9031 (mt) REVERT: C 247 CYS cc_start: 0.9162 (m) cc_final: 0.8863 (m) REVERT: D 78 VAL cc_start: 0.7908 (t) cc_final: 0.7643 (m) REVERT: D 170 ASP cc_start: 0.9101 (t0) cc_final: 0.8654 (t0) REVERT: D 175 LYS cc_start: 0.9147 (tttt) cc_final: 0.8868 (ttpp) REVERT: D 347 ASP cc_start: 0.8594 (t0) cc_final: 0.8296 (t0) REVERT: E 142 MET cc_start: 0.8213 (tmm) cc_final: 0.7610 (tmm) REVERT: E 366 LYS cc_start: 0.9426 (mmtt) cc_final: 0.9100 (tptp) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2484 time to fit residues: 85.2009 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 : 0.862 ------------------------------------------------------------------------------- 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: 0.5980 chunk 128 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 ASN C 331 ASN D 101 ASN D 167 GLN D 260 HIS F 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062592 restraints weight = 167376.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065504 restraints weight = 81850.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067577 restraints weight = 51353.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.068980 restraints weight = 37291.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.069896 restraints weight = 30119.291| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16185 Z= 0.108 Angle : 0.478 5.475 21919 Z= 0.244 Chirality : 0.039 0.146 2588 Planarity : 0.003 0.031 2819 Dihedral : 11.159 177.930 2384 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.13 (0.18), residues: 2031 helix: 0.71 (0.17), residues: 911 sheet: -0.07 (0.32), residues: 249 loop : -0.87 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.015 0.001 TYR D 385 PHE 0.022 0.001 PHE B 245 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16185) covalent geometry : angle 0.47758 / 0.24 (21919) hydrogen bonds : bond 0.03376 / 2.27 ( 607) hydrogen bonds : angle 5.03721 / 3.56 ( 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 221 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.850 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: A 137 ASP cc_start: 0.8463 (p0) cc_final: 0.8132 (t0) REVERT: A 142 MET cc_start: 0.8928 (mmt) cc_final: 0.8357 (mmt) REVERT: A 182 TYR cc_start: 0.8627 (t80) cc_final: 0.7432 (t80) REVERT: A 377 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 118 ILE cc_start: 0.9231 (mt) cc_final: 0.8812 (pt) REVERT: B 162 ILE cc_start: 0.9271 (mm) cc_final: 0.9019 (mt) REVERT: B 390 MET cc_start: 0.7351 (mmp) cc_final: 0.7140 (mmp) REVERT: C 247 CYS cc_start: 0.9130 (m) cc_final: 0.8827 (m) REVERT: D 78 VAL cc_start: 0.7829 (t) cc_final: 0.7492 (m) REVERT: D 170 ASP cc_start: 0.9088 (t0) cc_final: 0.8750 (t0) REVERT: E 142 MET cc_start: 0.8168 (tmm) cc_final: 0.7578 (tmm) REVERT: E 366 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9074 (tptp) REVERT: F 352 ASP cc_start: 0.8959 (p0) cc_final: 0.8754 (p0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2408 time to fit residues: 85.3585 Evaluate side-chains 175 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 8.9990 chunk 147 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 94 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 160 ASN D 167 GLN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN E 342 ASN F 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.082644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060054 restraints weight = 172961.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062905 restraints weight = 86093.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064855 restraints weight = 54477.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066114 restraints weight = 40324.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067018 restraints weight = 33158.240| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16185 Z= 0.212 Angle : 0.562 6.002 21919 Z= 0.291 Chirality : 0.039 0.161 2588 Planarity : 0.003 0.037 2819 Dihedral : 11.306 176.841 2384 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.62 (0.18), residues: 2031 helix: 0.24 (0.16), residues: 927 sheet: -0.28 (0.32), residues: 249 loop : -1.09 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 307 TYR 0.015 0.001 TYR D 385 PHE 0.024 0.001 PHE E 298 HIS 0.008 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (16185) covalent geometry : angle 0.56154 / 0.29 (21919) hydrogen bonds : bond 0.03495 / 2.35 ( 607) hydrogen bonds : angle 5.33505 / 3.76 ( 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 208 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 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: A 137 ASP cc_start: 0.8376 (p0) cc_final: 0.8128 (t70) REVERT: A 144 ASP cc_start: 0.8481 (m-30) cc_final: 0.7992 (p0) REVERT: A 148 LEU cc_start: 0.9241 (mt) cc_final: 0.9018 (mt) REVERT: B 116 LEU cc_start: 0.9583 (tp) cc_final: 0.9365 (tt) REVERT: B 162 ILE cc_start: 0.9362 (mm) cc_final: 0.9115 (mt) REVERT: B 247 CYS cc_start: 0.8564 (m) cc_final: 0.8314 (m) REVERT: C 247 CYS cc_start: 0.9179 (m) cc_final: 0.8927 (m) REVERT: C 384 MET cc_start: 0.9140 (ttm) cc_final: 0.8722 (ttm) REVERT: D 78 VAL cc_start: 0.8095 (t) cc_final: 0.7876 (m) REVERT: D 170 ASP cc_start: 0.9086 (t0) cc_final: 0.8740 (t0) REVERT: E 142 MET cc_start: 0.8416 (tmm) cc_final: 0.7739 (tmm) REVERT: E 366 LYS cc_start: 0.9412 (mmtt) cc_final: 0.9058 (tptp) REVERT: F 352 ASP cc_start: 0.9025 (p0) cc_final: 0.8794 (p0) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2432 time to fit residues: 81.4774 Evaluate side-chains 167 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 200 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN B 160 ASN E 95 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 = 0.3565 r_free = 0.3565 target = 0.084517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061956 restraints weight = 168662.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064949 restraints weight = 82007.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066946 restraints weight = 51183.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068386 restraints weight = 37496.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069287 restraints weight = 30429.717| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16185 Z= 0.091 Angle : 0.473 5.569 21919 Z= 0.241 Chirality : 0.040 0.143 2588 Planarity : 0.003 0.031 2819 Dihedral : 10.920 177.861 2384 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: -0.07 (0.18), residues: 2031 helix: 0.80 (0.17), residues: 909 sheet: -0.26 (0.33), residues: 229 loop : -0.80 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.013 0.001 TYR D 385 PHE 0.010 0.001 PHE E 298 HIS 0.006 0.001 HIS D 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (16185) covalent geometry : angle 0.47349 / 0.24 (21919) hydrogen bonds : bond 0.03107 / 2.10 ( 607) hydrogen bonds : angle 4.78358 / 3.37 ( 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 215 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.671 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: A 137 ASP cc_start: 0.8318 (p0) cc_final: 0.8064 (t70) REVERT: A 144 ASP cc_start: 0.8477 (m-30) cc_final: 0.7871 (p0) REVERT: A 148 LEU cc_start: 0.9244 (mt) cc_final: 0.9016 (mt) REVERT: A 182 TYR cc_start: 0.8681 (t80) cc_final: 0.8430 (t80) REVERT: A 263 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6652 (pp20) REVERT: B 118 ILE cc_start: 0.9254 (mt) cc_final: 0.8785 (pt) REVERT: B 162 ILE cc_start: 0.9337 (mm) cc_final: 0.9057 (mt) REVERT: C 247 CYS cc_start: 0.9201 (m) cc_final: 0.8879 (m) REVERT: D 78 VAL cc_start: 0.7959 (t) cc_final: 0.7738 (m) REVERT: D 170 ASP cc_start: 0.9072 (t0) cc_final: 0.8731 (t0) REVERT: E 142 MET cc_start: 0.8225 (tmm) cc_final: 0.7632 (tmm) REVERT: E 366 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9071 (tptp) REVERT: F 352 ASP cc_start: 0.8992 (p0) cc_final: 0.8748 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2404 time to fit residues: 84.5059 Evaluate side-chains 175 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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: 9.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 94 ASN A 160 ASN B 160 ASN D 167 GLN D 177 GLN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN F 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.058988 restraints weight = 174099.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061787 restraints weight = 86500.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063713 restraints weight = 54809.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065002 restraints weight = 40581.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065796 restraints weight = 33371.599| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16185 Z= 0.243 Angle : 0.598 6.950 21919 Z= 0.310 Chirality : 0.040 0.143 2588 Planarity : 0.004 0.039 2819 Dihedral : 11.199 174.216 2384 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % 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: -0.83 (0.18), residues: 2031 helix: 0.03 (0.16), residues: 949 sheet: -0.41 (0.31), residues: 261 loop : -1.18 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 98 TYR 0.015 0.002 TYR D 385 PHE 0.024 0.002 PHE E 298 HIS 0.006 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.24 (16185) covalent geometry : angle 0.59807 / 0.31 (21919) hydrogen bonds : bond 0.03451 / 2.34 ( 607) hydrogen bonds : angle 5.42431 / 3.82 ( 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 198 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.909 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: A 137 ASP cc_start: 0.8388 (p0) cc_final: 0.8101 (t70) REVERT: A 144 ASP cc_start: 0.8603 (m-30) cc_final: 0.8242 (p0) REVERT: A 182 TYR cc_start: 0.8785 (t80) cc_final: 0.7308 (t80) REVERT: A 193 SER cc_start: 0.7665 (t) cc_final: 0.7445 (t) REVERT: D 78 VAL cc_start: 0.8224 (t) cc_final: 0.8019 (m) REVERT: D 170 ASP cc_start: 0.9059 (t0) cc_final: 0.8729 (t0) REVERT: E 142 MET cc_start: 0.8508 (tmm) cc_final: 0.7807 (tmm) REVERT: E 366 LYS cc_start: 0.9378 (mmtt) cc_final: 0.9036 (tptp) REVERT: F 352 ASP cc_start: 0.9040 (p0) cc_final: 0.8792 (p0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2509 time to fit residues: 80.2466 Evaluate side-chains 168 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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: 3.9990 chunk 142 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 160 ASN B 160 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060491 restraints weight = 170829.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063387 restraints weight = 83783.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065367 restraints weight = 52741.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.066722 restraints weight = 38885.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067594 restraints weight = 31671.986| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16185 Z= 0.107 Angle : 0.488 5.928 21919 Z= 0.249 Chirality : 0.039 0.148 2588 Planarity : 0.003 0.030 2819 Dihedral : 10.836 176.344 2384 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.36 (0.18), residues: 2031 helix: 0.49 (0.17), residues: 931 sheet: -0.27 (0.31), residues: 256 loop : -0.98 (0.21), residues: 844 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 0.015 0.001 PHE B 245 HIS 0.007 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16185) covalent geometry : angle 0.48759 / 0.25 (21919) hydrogen bonds : bond 0.03078 / 2.09 ( 607) hydrogen bonds : angle 4.93787 / 3.48 ( 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 206 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.860 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: 0.8365 (p0) cc_final: 0.7821 (t70) REVERT: A 182 TYR cc_start: 0.8690 (t80) cc_final: 0.7047 (t80) REVERT: A 193 SER cc_start: 0.7603 (t) cc_final: 0.7368 (t) REVERT: B 118 ILE cc_start: 0.9256 (mt) cc_final: 0.8798 (pt) REVERT: B 245 PHE cc_start: 0.8783 (m-10) cc_final: 0.8493 (m-10) REVERT: C 247 CYS cc_start: 0.9195 (m) cc_final: 0.8931 (m) REVERT: C 384 MET cc_start: 0.9174 (ttm) cc_final: 0.8757 (ttm) REVERT: D 78 VAL cc_start: 0.8130 (t) cc_final: 0.7914 (m) REVERT: D 170 ASP cc_start: 0.9076 (t0) cc_final: 0.8722 (t0) REVERT: E 366 LYS cc_start: 0.9404 (mmtt) cc_final: 0.9036 (tptp) REVERT: F 352 ASP cc_start: 0.9110 (p0) cc_final: 0.8864 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2522 time to fit residues: 83.5889 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 : 0.873 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 60 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3534 r_free = 0.3534 target = 0.083059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060550 restraints weight = 170770.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063504 restraints weight = 83392.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065501 restraints weight = 51972.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066893 restraints weight = 38111.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067786 restraints weight = 30940.641| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16185 Z= 0.106 Angle : 0.485 5.741 21919 Z= 0.248 Chirality : 0.039 0.145 2588 Planarity : 0.003 0.030 2819 Dihedral : 10.720 176.382 2384 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.23 (0.18), residues: 2031 helix: 0.63 (0.17), residues: 938 sheet: -0.20 (0.31), residues: 256 loop : -0.95 (0.21), residues: 837 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 0.013 0.001 PHE E 245 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (16185) covalent geometry : angle 0.48500 / 0.25 (21919) hydrogen bonds : bond 0.02967 / 2.02 ( 607) hydrogen bonds : angle 4.83476 / 3.40 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.87 seconds wall clock time: 84 minutes 4.31 seconds (5044.31 seconds total)