Starting phenix.real_space_refine on Fri Jun 27 21:37:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_20420_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_20420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_20420.map" model { file = "/net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_20420_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pp6_20420/06_2025/6pp6_20420_trim.cif" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.82, per 1000 atoms: 0.49 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: 7.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.53 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: 11.77 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 16120 1.06 - 1.28: 2857 1.28 - 1.50: 6187 1.50 - 1.73: 7088 1.73 - 1.95: 59 Bond restraints: 32311 Sorted by residual: bond pdb=" C ILE D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.47e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU F 64 " pdb=" CA LEU F 64 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.70e+00 bond pdb=" C PRO D 223 " pdb=" N PRO D 224 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 2.95e+00 bond pdb=" N UNK S 1 " pdb=" CA UNK S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 58016 2.14 - 4.28: 660 4.28 - 6.42: 87 6.42 - 8.56: 5 8.56 - 10.70: 2 Bond angle restraints: 58770 Sorted by residual: angle pdb=" CA GLY F 206 " pdb=" C GLY F 206 " pdb=" N VAL F 207 " ideal model delta sigma weight residual 116.81 111.26 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" C ASN C 101 " pdb=" N GLY C 102 " pdb=" CA GLY C 102 " ideal model delta sigma weight residual 121.41 132.11 -10.70 1.96e+00 2.60e-01 2.98e+01 angle pdb=" N SER C 105 " pdb=" CA SER C 105 " pdb=" C SER C 105 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" C GLY F 204 " pdb=" N GLU F 205 " pdb=" CA GLU F 205 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLU F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta sigma weight residual 119.94 124.18 -4.24 1.11e+00 8.12e-01 1.46e+01 ... (remaining 58765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13421 17.32 - 34.63: 1152 34.63 - 51.95: 310 51.95 - 69.26: 84 69.26 - 86.58: 11 Dihedral angle restraints: 14978 sinusoidal: 8519 harmonic: 6459 Sorted by residual: dihedral pdb=" CA LYS C 366 " pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " pdb=" CD LYS C 366 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " pdb=" OD1 ASP A 194 " ideal model delta sinusoidal sigma weight residual -30.00 -82.13 52.13 1 2.00e+01 2.50e-03 9.27e+00 dihedral pdb=" N ARG E 370 " pdb=" CA ARG E 370 " pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sinusoidal sigma weight residual -180.00 -129.30 -50.70 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 14975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1961 0.041 - 0.083: 441 0.083 - 0.124: 164 0.124 - 0.166: 31 0.166 - 0.207: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA SER C 105 " pdb=" N SER C 105 " pdb=" C SER C 105 " pdb=" CB SER C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2595 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 370 " 0.090 9.50e-02 1.11e+02 9.25e-02 1.73e+02 pdb=" NE ARG B 370 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 370 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 370 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 370 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 370 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 370 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG B 370 " -0.172 2.00e-02 2.50e+03 pdb="HH22 ARG B 370 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 195 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 328 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO F 329 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 329 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 329 " 0.028 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 141 2.01 - 2.65: 45029 2.65 - 3.30: 91690 3.30 - 3.95: 112076 3.95 - 4.60: 176323 Nonbonded interactions: 425259 Sorted by model distance: nonbonded pdb=" OD1 ASP C 399 " pdb=" HG SER C 401 " model vdw 1.357 2.450 nonbonded pdb=" HZ2 LYS C 112 " pdb=" O SER C 241 " model vdw 1.397 2.450 nonbonded pdb=" OD1 ASP E 144 " pdb=" HG1 THR E 146 " model vdw 1.425 2.450 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.429 2.450 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.434 2.450 ... (remaining 425254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'B' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'C' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'D' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'E' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'F' and (resid 64 through 225 or resid 233 through 259 or (resid 260 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 261 through 413)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.530 Extract box with map and model: 1.130 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 65.470 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16185 Z= 0.166 Angle : 0.713 10.700 21919 Z= 0.392 Chirality : 0.042 0.207 2598 Planarity : 0.004 0.076 2819 Dihedral : 12.431 81.962 6147 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (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 HIS 0.003 0.001 HIS D 95 PHE 0.014 0.001 PHE A 270 TYR 0.010 0.001 TYR E 93 ARG 0.013 0.001 ARG E 261 Details of bonding type rmsd hydrogen bonds : bond 0.30358 ( 607) hydrogen bonds : angle 7.56333 ( 1722) covalent geometry : bond 0.00359 (16185) covalent geometry : angle 0.71290 (21919) *********************** 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 : 2.389 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: 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: B 141 THR cc_start: 0.8912 (t) cc_final: 0.8584 (m) REVERT: B 160 ASN cc_start: 0.9086 (t0) cc_final: 0.8836 (t0) REVERT: B 162 ILE cc_start: 0.9360 (mm) cc_final: 0.9043 (mt) REVERT: B 245 PHE cc_start: 0.8262 (m-80) cc_final: 0.7928 (m-80) REVERT: B 289 GLN cc_start: 0.9303 (mt0) cc_final: 0.9027 (mp10) REVERT: C 205 GLU cc_start: 0.8375 (tt0) cc_final: 0.7573 (tm-30) REVERT: D 363 MET cc_start: 0.9302 (mtm) cc_final: 0.9072 (mmm) REVERT: E 341 PHE cc_start: 0.8935 (m-10) cc_final: 0.8735 (m-10) REVERT: E 366 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8881 (tptp) REVERT: E 384 MET cc_start: 0.8725 (mtm) cc_final: 0.7790 (mtp) REVERT: F 225 GLN cc_start: 0.5795 (tt0) cc_final: 0.5234 (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: 0.6348 time to fit residues: 376.0855 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 : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 225 GLN B 68 HIS B 208 GLN C 95 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.089436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066857 restraints weight = 167372.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070090 restraints weight = 81976.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072263 restraints weight = 50594.023| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16185 Z= 0.214 Angle : 0.622 5.951 21919 Z= 0.335 Chirality : 0.041 0.155 2598 Planarity : 0.004 0.042 2819 Dihedral : 7.528 61.646 2294 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.12 % Allowed : 2.17 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2031 helix: 0.52 (0.16), residues: 867 sheet: -0.12 (0.31), residues: 273 loop : -1.18 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 68 PHE 0.024 0.001 PHE E 298 TYR 0.015 0.001 TYR E 93 ARG 0.007 0.001 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.07261 ( 607) hydrogen bonds : angle 6.31954 ( 1722) covalent geometry : bond 0.00436 (16185) covalent geometry : angle 0.62234 (21919) *********************** 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 278 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 2.608 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: A 137 ASP cc_start: 0.8441 (p0) cc_final: 0.8132 (t0) REVERT: B 245 PHE cc_start: 0.8109 (m-80) cc_final: 0.7803 (m-80) REVERT: B 289 GLN cc_start: 0.9227 (mt0) cc_final: 0.8946 (mp10) REVERT: C 205 GLU cc_start: 0.8178 (tt0) cc_final: 0.7685 (tm-30) REVERT: C 247 CYS cc_start: 0.9045 (m) cc_final: 0.8676 (m) REVERT: D 170 ASP cc_start: 0.9034 (t0) cc_final: 0.8648 (t0) REVERT: D 175 LYS cc_start: 0.9072 (tttt) cc_final: 0.8720 (ttpp) REVERT: E 245 PHE cc_start: 0.8900 (m-80) cc_final: 0.8684 (m-80) REVERT: E 293 GLU cc_start: 0.9190 (pt0) cc_final: 0.8938 (pm20) REVERT: E 366 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9000 (tptp) REVERT: F 209 GLN cc_start: 0.9058 (pt0) cc_final: 0.8561 (pt0) outliers start: 2 outliers final: 2 residues processed: 277 average time/residue: 0.6130 time to fit residues: 254.9716 Evaluate side-chains 207 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 156 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 167 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065578 restraints weight = 169777.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068635 restraints weight = 84052.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.070757 restraints weight = 52377.359| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16185 Z= 0.155 Angle : 0.529 5.664 21919 Z= 0.277 Chirality : 0.039 0.157 2598 Planarity : 0.003 0.031 2819 Dihedral : 7.609 73.698 2294 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2031 helix: 0.57 (0.17), residues: 890 sheet: 0.03 (0.31), residues: 273 loop : -1.18 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.012 0.001 PHE E 298 TYR 0.013 0.001 TYR E 93 ARG 0.004 0.000 ARG F 351 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 607) hydrogen bonds : angle 5.83704 ( 1722) covalent geometry : bond 0.00319 (16185) covalent geometry : angle 0.52893 (21919) *********************** 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 246 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8369 (p0) cc_final: 0.8054 (t0) REVERT: B 142 MET cc_start: 0.7640 (tmm) cc_final: 0.7186 (tmm) REVERT: B 245 PHE cc_start: 0.8192 (m-80) cc_final: 0.7794 (m-80) REVERT: C 247 CYS cc_start: 0.9035 (m) cc_final: 0.8680 (m) REVERT: D 170 ASP cc_start: 0.8995 (t0) cc_final: 0.8639 (t0) REVERT: D 175 LYS cc_start: 0.9037 (tttt) cc_final: 0.8780 (ttpp) REVERT: E 293 GLU cc_start: 0.9145 (pt0) cc_final: 0.8877 (pm20) REVERT: E 366 LYS cc_start: 0.9322 (mmtt) cc_final: 0.9028 (tptp) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.6069 time to fit residues: 232.9482 Evaluate side-chains 196 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 107 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 338 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063893 restraints weight = 171776.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066953 restraints weight = 85051.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069108 restraints weight = 53237.632| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 16185 Z= 0.145 Angle : 0.505 5.708 21919 Z= 0.264 Chirality : 0.039 0.157 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.387 75.103 2294 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2031 helix: 0.63 (0.17), residues: 899 sheet: 0.06 (0.32), residues: 264 loop : -1.01 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 260 PHE 0.015 0.001 PHE E 245 TYR 0.011 0.001 TYR D 93 ARG 0.004 0.000 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 607) hydrogen bonds : angle 5.51519 ( 1722) covalent geometry : bond 0.00309 (16185) covalent geometry : angle 0.50454 (21919) *********************** 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 : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8435 (p0) cc_final: 0.8101 (t0) REVERT: A 148 LEU cc_start: 0.9248 (mt) cc_final: 0.9035 (mt) REVERT: B 118 ILE cc_start: 0.9218 (mt) cc_final: 0.8811 (pt) REVERT: C 247 CYS cc_start: 0.9039 (m) cc_final: 0.8679 (m) REVERT: D 170 ASP cc_start: 0.9041 (t0) cc_final: 0.8608 (t0) REVERT: D 175 LYS cc_start: 0.9051 (tttt) cc_final: 0.8780 (ttpp) REVERT: E 293 GLU cc_start: 0.9174 (pt0) cc_final: 0.8931 (pm20) REVERT: E 366 LYS cc_start: 0.9336 (mmtt) cc_final: 0.9047 (tptp) REVERT: F 94 ASN cc_start: 0.9221 (m-40) cc_final: 0.9008 (m-40) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.5467 time to fit residues: 196.9139 Evaluate side-chains 178 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 169 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 185 GLN B 225 GLN B 260 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN D 225 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064089 restraints weight = 169412.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067118 restraints weight = 83011.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069213 restraints weight = 51572.131| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16185 Z= 0.134 Angle : 0.491 5.473 21919 Z= 0.255 Chirality : 0.039 0.150 2598 Planarity : 0.003 0.042 2819 Dihedral : 7.309 77.191 2294 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2031 helix: 0.64 (0.17), residues: 903 sheet: 0.04 (0.32), residues: 264 loop : -0.96 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS S 3 PHE 0.021 0.001 PHE B 245 TYR 0.014 0.001 TYR B 93 ARG 0.011 0.000 ARG F 307 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 607) hydrogen bonds : angle 5.32367 ( 1722) covalent geometry : bond 0.00284 (16185) covalent geometry : angle 0.49114 (21919) *********************** 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 221 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.939 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: 0.8468 (p0) cc_final: 0.8106 (t0) REVERT: A 148 LEU cc_start: 0.9257 (mt) cc_final: 0.9048 (mt) REVERT: B 118 ILE cc_start: 0.9216 (mt) cc_final: 0.8817 (pt) REVERT: C 247 CYS cc_start: 0.9101 (m) cc_final: 0.8781 (m) REVERT: D 142 MET cc_start: 0.8342 (mmt) cc_final: 0.8116 (mmt) REVERT: D 170 ASP cc_start: 0.9091 (t0) cc_final: 0.8631 (t0) REVERT: D 363 MET cc_start: 0.9110 (tpp) cc_final: 0.8772 (tpp) REVERT: E 293 GLU cc_start: 0.9198 (pt0) cc_final: 0.8966 (pm20) REVERT: E 366 LYS cc_start: 0.9350 (mmtt) cc_final: 0.9041 (tptp) REVERT: F 94 ASN cc_start: 0.9233 (m-40) cc_final: 0.9026 (m-40) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.5654 time to fit residues: 198.7007 Evaluate side-chains 177 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 124 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN C 101 ASN D 167 GLN D 225 GLN E 338 GLN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061142 restraints weight = 172604.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064030 restraints weight = 84954.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066022 restraints weight = 53081.660| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16185 Z= 0.228 Angle : 0.588 6.456 21919 Z= 0.305 Chirality : 0.040 0.180 2598 Planarity : 0.004 0.032 2819 Dihedral : 7.353 82.904 2294 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2031 helix: 0.10 (0.16), residues: 921 sheet: -0.30 (0.32), residues: 250 loop : -1.02 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 73 PHE 0.031 0.002 PHE B 245 TYR 0.019 0.002 TYR D 385 ARG 0.007 0.001 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 607) hydrogen bonds : angle 5.58130 ( 1722) covalent geometry : bond 0.00464 (16185) covalent geometry : angle 0.58837 (21919) *********************** 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 204 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 2.570 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: 0.8546 (p0) cc_final: 0.8215 (t70) REVERT: A 144 ASP cc_start: 0.8432 (m-30) cc_final: 0.7943 (p0) REVERT: A 148 LEU cc_start: 0.9252 (mt) cc_final: 0.9019 (mt) REVERT: B 142 MET cc_start: 0.7659 (tmm) cc_final: 0.7448 (tmm) REVERT: B 162 ILE cc_start: 0.9295 (mm) cc_final: 0.9068 (mt) REVERT: C 202 VAL cc_start: 0.8769 (p) cc_final: 0.8307 (p) REVERT: C 247 CYS cc_start: 0.9119 (m) cc_final: 0.8843 (m) REVERT: D 78 VAL cc_start: 0.7871 (t) cc_final: 0.7535 (m) REVERT: D 142 MET cc_start: 0.8362 (mmt) cc_final: 0.8150 (mmt) REVERT: D 170 ASP cc_start: 0.9110 (t0) cc_final: 0.8691 (t0) REVERT: D 209 GLN cc_start: 0.9057 (mt0) cc_final: 0.8804 (mt0) REVERT: D 363 MET cc_start: 0.9084 (tpp) cc_final: 0.8758 (tpp) REVERT: E 293 GLU cc_start: 0.9218 (pt0) cc_final: 0.8983 (pm20) REVERT: E 366 LYS cc_start: 0.9365 (mmtt) cc_final: 0.9037 (tptp) REVERT: F 225 GLN cc_start: 0.5715 (tt0) cc_final: 0.5420 (tt0) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.5470 time to fit residues: 175.2803 Evaluate side-chains 163 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 260 HIS B 160 ASN C 331 ASN D 167 GLN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN F 114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060533 restraints weight = 171909.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063510 restraints weight = 84397.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065536 restraints weight = 52714.716| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16185 Z= 0.163 Angle : 0.523 6.843 21919 Z= 0.271 Chirality : 0.040 0.150 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.280 83.854 2294 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.06 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2031 helix: 0.19 (0.16), residues: 927 sheet: -0.31 (0.32), residues: 251 loop : -1.06 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 73 PHE 0.033 0.001 PHE B 245 TYR 0.015 0.001 TYR D 385 ARG 0.004 0.000 ARG F 373 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 607) hydrogen bonds : angle 5.35146 ( 1722) covalent geometry : bond 0.00339 (16185) covalent geometry : angle 0.52297 (21919) *********************** 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 204 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 2.650 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: A 137 ASP cc_start: 0.8546 (p0) cc_final: 0.8203 (t70) REVERT: A 144 ASP cc_start: 0.8458 (m-30) cc_final: 0.7938 (p0) REVERT: A 148 LEU cc_start: 0.9254 (mt) cc_final: 0.9024 (mt) REVERT: B 118 ILE cc_start: 0.9268 (mt) cc_final: 0.8906 (pt) REVERT: B 162 ILE cc_start: 0.9322 (mm) cc_final: 0.9083 (mt) REVERT: C 247 CYS cc_start: 0.9133 (m) cc_final: 0.8850 (m) REVERT: D 78 VAL cc_start: 0.8023 (t) cc_final: 0.7588 (m) REVERT: D 170 ASP cc_start: 0.9174 (t0) cc_final: 0.8833 (t0) REVERT: D 209 GLN cc_start: 0.9084 (mt0) cc_final: 0.8820 (mt0) REVERT: D 363 MET cc_start: 0.8932 (tpp) cc_final: 0.8699 (tpp) REVERT: E 142 MET cc_start: 0.8282 (tmm) cc_final: 0.7780 (tmm) REVERT: E 293 GLU cc_start: 0.9194 (pt0) cc_final: 0.8973 (pm20) REVERT: E 366 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9086 (tptp) outliers start: 1 outliers final: 1 residues processed: 203 average time/residue: 0.5412 time to fit residues: 173.5025 Evaluate side-chains 172 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 169 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 152 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN B 160 ASN D 167 GLN ** E 73 HIS ** 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 = 0.3520 r_free = 0.3520 target = 0.082477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059818 restraints weight = 173692.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062714 restraints weight = 86220.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064674 restraints weight = 54370.022| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16185 Z= 0.187 Angle : 0.540 5.994 21919 Z= 0.280 Chirality : 0.040 0.143 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.264 86.719 2294 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2031 helix: 0.12 (0.16), residues: 923 sheet: -0.32 (0.32), residues: 249 loop : -1.08 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 73 PHE 0.021 0.001 PHE E 298 TYR 0.016 0.001 TYR E 93 ARG 0.004 0.000 ARG F 373 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 607) hydrogen bonds : angle 5.37166 ( 1722) covalent geometry : bond 0.00385 (16185) covalent geometry : angle 0.53973 (21919) *********************** 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 196 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.845 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: 0.8460 (p0) cc_final: 0.8189 (t70) REVERT: A 144 ASP cc_start: 0.8497 (m-30) cc_final: 0.8262 (p0) REVERT: B 162 ILE cc_start: 0.9376 (mm) cc_final: 0.9153 (mt) REVERT: D 78 VAL cc_start: 0.8052 (t) cc_final: 0.7694 (m) REVERT: D 170 ASP cc_start: 0.9144 (t0) cc_final: 0.8793 (t0) REVERT: D 363 MET cc_start: 0.8933 (tpp) cc_final: 0.8686 (tpp) REVERT: E 142 MET cc_start: 0.8353 (tmm) cc_final: 0.7800 (tmm) REVERT: E 293 GLU cc_start: 0.9176 (pt0) cc_final: 0.8963 (pm20) REVERT: E 366 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9061 (tptp) REVERT: F 352 ASP cc_start: 0.9092 (p0) cc_final: 0.8864 (p0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.5603 time to fit residues: 173.4904 Evaluate side-chains 166 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 260 HIS B 160 ASN E 95 HIS F 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060359 restraints weight = 171824.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063314 restraints weight = 84040.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065318 restraints weight = 52617.621| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16185 Z= 0.135 Angle : 0.501 6.714 21919 Z= 0.258 Chirality : 0.040 0.166 2598 Planarity : 0.003 0.031 2819 Dihedral : 7.182 87.645 2294 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2031 helix: 0.32 (0.17), residues: 929 sheet: -0.26 (0.32), residues: 249 loop : -1.02 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.022 0.001 PHE B 245 TYR 0.013 0.001 TYR D 385 ARG 0.003 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 607) hydrogen bonds : angle 5.13532 ( 1722) covalent geometry : bond 0.00285 (16185) covalent geometry : angle 0.50125 (21919) *********************** 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 207 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 2.571 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: 0.8454 (p0) cc_final: 0.8181 (t70) REVERT: A 144 ASP cc_start: 0.8519 (m-30) cc_final: 0.8223 (p0) REVERT: B 162 ILE cc_start: 0.9387 (mm) cc_final: 0.9151 (mt) REVERT: C 247 CYS cc_start: 0.9219 (m) cc_final: 0.8961 (m) REVERT: D 78 VAL cc_start: 0.8020 (t) cc_final: 0.7668 (m) REVERT: D 170 ASP cc_start: 0.9136 (t0) cc_final: 0.8783 (t0) REVERT: D 363 MET cc_start: 0.8922 (tpp) cc_final: 0.8682 (tpp) REVERT: E 142 MET cc_start: 0.8282 (tmm) cc_final: 0.7749 (tmm) REVERT: E 293 GLU cc_start: 0.9182 (pt0) cc_final: 0.8978 (pm20) REVERT: E 366 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9070 (tptp) REVERT: F 352 ASP cc_start: 0.9083 (p0) cc_final: 0.8863 (p0) outliers start: 1 outliers final: 1 residues processed: 206 average time/residue: 0.5480 time to fit residues: 178.6413 Evaluate side-chains 173 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 110 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058722 restraints weight = 173267.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061571 restraints weight = 83577.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063565 restraints weight = 52271.412| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16185 Z= 0.238 Angle : 0.580 6.411 21919 Z= 0.302 Chirality : 0.040 0.144 2598 Planarity : 0.003 0.039 2819 Dihedral : 7.332 88.841 2294 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2031 helix: -0.03 (0.16), residues: 926 sheet: -0.46 (0.32), residues: 249 loop : -1.25 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 95 PHE 0.026 0.002 PHE B 245 TYR 0.013 0.002 TYR D 385 ARG 0.004 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 607) hydrogen bonds : angle 5.49505 ( 1722) covalent geometry : bond 0.00485 (16185) covalent geometry : angle 0.57963 (21919) ********************** 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 193 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.921 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: A 137 ASP cc_start: 0.8526 (p0) cc_final: 0.8226 (t70) REVERT: A 363 MET cc_start: 0.8104 (tpp) cc_final: 0.7655 (tpp) REVERT: C 202 VAL cc_start: 0.8900 (m) cc_final: 0.8678 (p) REVERT: D 78 VAL cc_start: 0.8118 (t) cc_final: 0.7788 (m) REVERT: D 170 ASP cc_start: 0.9186 (t0) cc_final: 0.8813 (t0) REVERT: E 142 MET cc_start: 0.8430 (tmm) cc_final: 0.7889 (tmm) REVERT: E 293 GLU cc_start: 0.9283 (pt0) cc_final: 0.9067 (pm20) REVERT: E 366 LYS cc_start: 0.9426 (mmtt) cc_final: 0.9100 (tptp) REVERT: F 352 ASP cc_start: 0.9148 (p0) cc_final: 0.8918 (p0) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.5794 time to fit residues: 177.5000 Evaluate side-chains 163 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 260 HIS B 160 ASN F 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.081683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059037 restraints weight = 172553.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061980 restraints weight = 83013.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063985 restraints weight = 51688.713| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16185 Z= 0.162 Angle : 0.522 6.849 21919 Z= 0.271 Chirality : 0.040 0.146 2598 Planarity : 0.003 0.032 2819 Dihedral : 7.224 88.403 2294 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.06 % Allowed : 0.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2031 helix: 0.20 (0.16), residues: 928 sheet: -0.46 (0.32), residues: 256 loop : -1.15 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 260 PHE 0.024 0.001 PHE B 245 TYR 0.013 0.001 TYR D 385 ARG 0.003 0.000 ARG D 365 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 607) hydrogen bonds : angle 5.23770 ( 1722) covalent geometry : bond 0.00338 (16185) covalent geometry : angle 0.52171 (21919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9309.43 seconds wall clock time: 161 minutes 28.07 seconds (9688.07 seconds total)