Starting phenix.real_space_refine on Fri Jan 24 09:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300.map" model { file = "/net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c88_45300/01_2025/9c88_45300_trim.cif" } resolution = 2.6 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= 0.001 sd= 0.032 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 198 5.16 5 C 23202 2.51 5 N 6300 2.21 5 O 7107 1.98 5 H 37082 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 73908 Number of models: 1 Model: "" Number of chains: 27 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5125 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "B" Number of atoms: 5331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5331 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 5373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5373 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "D" Number of atoms: 5366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5366 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain breaks: 1 Chain: "E" Number of atoms: 5152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5152 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 5111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5111 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain breaks: 2 Chain: "h" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "i" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "j" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "k" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "l" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3014 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "m" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "n" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "p" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "q" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "r" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "s" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "t" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "u" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "v" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 28.61, per 1000 atoms: 0.39 Number of scatterers: 73908 At special positions: 0 Unit cell: (147.47, 138.533, 186.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 198 16.00 P 15 15.00 Mg 4 11.99 O 7107 8.00 N 6300 7.00 C 23202 6.00 H 37082 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: 15.65 Conformation dependent library (CDL) restraints added in 4.4 seconds 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8704 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 65 sheets defined 51.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 Creating SS restraints... Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.717A pdb=" N ARG A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.719A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.560A pdb=" N ILE A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.706A pdb=" N GLN A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.534A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.555A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.925A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 removed outlier: 3.905A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.518A pdb=" N ASP A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.050A pdb=" N SER A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.932A pdb=" N TYR B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.654A pdb=" N LYS B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.673A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.544A 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 158 through 169 removed outlier: 4.239A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.563A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.523A 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 300 removed outlier: 3.917A pdb=" N LEU B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.610A pdb=" N ARG B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.606A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 387 removed outlier: 4.191A pdb=" N ARG B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.809A pdb=" N ILE B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.922A pdb=" N TYR C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 101 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.617A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 204 through 217 removed outlier: 4.676A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.570A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 289 removed outlier: 3.511A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.536A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.781A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.523A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.613A pdb=" N ALA C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 387 removed outlier: 4.089A pdb=" N ARG C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.501A pdb=" N ILE C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.531A pdb=" N HIS D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.547A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.531A pdb=" N GLN D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 186 through 189 removed outlier: 3.647A pdb=" N ILE D 189 " --> pdb=" O ILE D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 189' Processing helix chain 'D' and resid 204 through 217 removed outlier: 4.549A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.711A pdb=" N VAL D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 289 removed outlier: 3.965A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.515A pdb=" N GLY D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 removed outlier: 3.530A pdb=" N ARG D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.727A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.975A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 365 Processing helix chain 'D' and resid 368 through 387 removed outlier: 3.675A pdb=" N LEU D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP D 382 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 387 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.646A pdb=" N ILE D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 81 through 101 Processing helix chain 'E' and resid 124 through 136 removed outlier: 3.529A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 4.084A pdb=" N ILE E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.633A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 Processing helix chain 'E' and resid 279 through 289 removed outlier: 4.582A pdb=" N GLU E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 Processing helix chain 'E' and resid 301 through 308 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'E' and resid 332 through 343 Processing helix chain 'E' and resid 351 through 366 removed outlier: 3.616A pdb=" N ASP E 356 " --> pdb=" O ASP E 352 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 387 removed outlier: 3.681A pdb=" N LEU E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG E 373 " --> pdb=" O ALA E 369 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP E 382 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR E 383 " --> pdb=" O ALA E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 399 through 405 Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.728A pdb=" N HIS F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 101 removed outlier: 3.637A pdb=" N ARG F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 136 Processing helix chain 'F' and resid 159 through 169 removed outlier: 3.644A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 204 through 216 removed outlier: 3.678A pdb=" N GLN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 262 Processing helix chain 'F' and resid 282 through 289 removed outlier: 3.588A pdb=" N LEU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 299 Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.523A pdb=" N LEU F 308 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 removed outlier: 3.585A pdb=" N ILE F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 345 Processing helix chain 'F' and resid 351 through 366 removed outlier: 3.540A pdb=" N ASP F 356 " --> pdb=" O ASP F 352 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 380 removed outlier: 3.601A pdb=" N LEU F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 399 through 405 removed outlier: 4.227A pdb=" N ILE F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.851A pdb=" N GLU h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 54 Processing helix chain 'h' and resid 69 through 83 removed outlier: 3.675A pdb=" N ILE h 76 " --> pdb=" O ALA h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 105 Processing helix chain 'h' and resid 132 through 158 Processing helix chain 'h' and resid 160 through 169 Processing helix chain 'h' and resid 176 through 183 Processing helix chain 'i' and resid 19 through 26 removed outlier: 3.502A pdb=" N LYS i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU i 26 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 54 Processing helix chain 'i' and resid 69 through 83 removed outlier: 3.696A pdb=" N ILE i 76 " --> pdb=" O ALA i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 105 Processing helix chain 'i' and resid 132 through 158 Processing helix chain 'i' and resid 160 through 169 Processing helix chain 'i' and resid 175 through 183 removed outlier: 3.500A pdb=" N VAL i 180 " --> pdb=" O ALA i 176 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 25 Processing helix chain 'j' and resid 36 through 54 Processing helix chain 'j' and resid 69 through 83 removed outlier: 3.571A pdb=" N ILE j 76 " --> pdb=" O ALA j 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR j 79 " --> pdb=" O SER j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 105 Processing helix chain 'j' and resid 132 through 158 Processing helix chain 'j' and resid 160 through 169 Processing helix chain 'j' and resid 176 through 182 removed outlier: 3.581A pdb=" N GLU j 181 " --> pdb=" O PRO j 177 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 26 removed outlier: 4.127A pdb=" N GLU k 26 " --> pdb=" O ARG k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 54 Processing helix chain 'k' and resid 69 through 83 removed outlier: 3.716A pdb=" N ILE k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 105 Processing helix chain 'k' and resid 132 through 158 removed outlier: 3.712A pdb=" N LEU k 143 " --> pdb=" O ALA k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 160 through 169 Processing helix chain 'k' and resid 176 through 182 Processing helix chain 'l' and resid 19 through 25 Processing helix chain 'l' and resid 36 through 54 Processing helix chain 'l' and resid 69 through 83 removed outlier: 3.744A pdb=" N ILE l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 96 through 105 Processing helix chain 'l' and resid 132 through 158 Processing helix chain 'l' and resid 160 through 169 Processing helix chain 'l' and resid 176 through 183 Processing helix chain 'm' and resid 19 through 26 removed outlier: 3.859A pdb=" N GLU m 26 " --> pdb=" O ARG m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 54 Processing helix chain 'm' and resid 69 through 83 removed outlier: 3.668A pdb=" N ILE m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 105 Processing helix chain 'm' and resid 132 through 158 Processing helix chain 'm' and resid 160 through 168 Processing helix chain 'm' and resid 176 through 183 Processing helix chain 'n' and resid 19 through 26 removed outlier: 3.967A pdb=" N GLU n 26 " --> pdb=" O ARG n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 36 through 54 Processing helix chain 'n' and resid 69 through 83 Processing helix chain 'n' and resid 96 through 105 Processing helix chain 'n' and resid 132 through 158 Processing helix chain 'n' and resid 160 through 170 removed outlier: 4.634A pdb=" N ARG n 170 " --> pdb=" O ARG n 166 " (cutoff:3.500A) Processing helix chain 'n' and resid 176 through 183 Processing helix chain 'p' and resid 19 through 26 removed outlier: 3.633A pdb=" N GLU p 26 " --> pdb=" O ARG p 22 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 54 Processing helix chain 'p' and resid 69 through 83 removed outlier: 3.507A pdb=" N GLY p 73 " --> pdb=" O VAL p 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 105 Processing helix chain 'p' and resid 132 through 158 Processing helix chain 'p' and resid 160 through 169 Processing helix chain 'p' and resid 176 through 182 Processing helix chain 'q' and resid 19 through 25 Processing helix chain 'q' and resid 36 through 54 Processing helix chain 'q' and resid 69 through 83 removed outlier: 3.516A pdb=" N ILE q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 105 Processing helix chain 'q' and resid 132 through 158 Processing helix chain 'q' and resid 160 through 169 Processing helix chain 'q' and resid 176 through 182 Processing helix chain 'r' and resid 19 through 26 removed outlier: 3.604A pdb=" N GLU r 26 " --> pdb=" O ARG r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 36 through 54 Processing helix chain 'r' and resid 69 through 83 removed outlier: 3.548A pdb=" N GLY r 73 " --> pdb=" O VAL r 69 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE r 76 " --> pdb=" O ALA r 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 96 through 105 Processing helix chain 'r' and resid 132 through 158 Processing helix chain 'r' and resid 160 through 169 Processing helix chain 'r' and resid 176 through 182 Processing helix chain 's' and resid 19 through 25 Processing helix chain 's' and resid 36 through 54 Processing helix chain 's' and resid 69 through 83 removed outlier: 3.548A pdb=" N GLY s 73 " --> pdb=" O VAL s 69 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE s 76 " --> pdb=" O ALA s 72 " (cutoff:3.500A) Processing helix chain 's' and resid 96 through 105 Processing helix chain 's' and resid 132 through 158 Processing helix chain 's' and resid 160 through 169 Processing helix chain 's' and resid 176 through 182 Processing helix chain 't' and resid 19 through 26 removed outlier: 3.636A pdb=" N GLU t 26 " --> pdb=" O ARG t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 36 through 54 Processing helix chain 't' and resid 69 through 83 removed outlier: 3.530A pdb=" N GLY t 73 " --> pdb=" O VAL t 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) Processing helix chain 't' and resid 96 through 105 Processing helix chain 't' and resid 132 through 158 Processing helix chain 't' and resid 160 through 169 Processing helix chain 't' and resid 176 through 182 Processing helix chain 'u' and resid 19 through 25 Processing helix chain 'u' and resid 36 through 54 Processing helix chain 'u' and resid 69 through 83 Processing helix chain 'u' and resid 96 through 105 Processing helix chain 'u' and resid 132 through 158 Processing helix chain 'u' and resid 160 through 169 Processing helix chain 'u' and resid 176 through 182 Processing helix chain 'v' and resid 19 through 25 Processing helix chain 'v' and resid 36 through 54 Processing helix chain 'v' and resid 69 through 83 removed outlier: 3.558A pdb=" N GLY v 73 " --> pdb=" O VAL v 69 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE v 76 " --> pdb=" O ALA v 72 " (cutoff:3.500A) Processing helix chain 'v' and resid 96 through 105 Processing helix chain 'v' and resid 132 through 158 Processing helix chain 'v' and resid 160 through 169 Processing helix chain 'v' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 144 removed outlier: 3.541A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 115 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.623A pdb=" N ASP A 347 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 396 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 412 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL A 396 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 410 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.503A pdb=" N THR B 141 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 184 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 143 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 116 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 222 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.592A pdb=" N ASP B 347 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 398 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU B 349 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 144 removed outlier: 6.506A pdb=" N THR C 141 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP C 184 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 143 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 181 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY C 248 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 183 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 222 Processing sheet with id=AA9, first strand: chain 'C' and resid 347 through 350 Processing sheet with id=AB1, first strand: chain 'D' and resid 140 through 144 removed outlier: 6.989A pdb=" N THR D 141 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP D 184 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA D 143 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 115 " --> pdb=" O PHE D 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 219 through 222 Processing sheet with id=AB3, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.701A pdb=" N VAL D 396 " --> pdb=" O ASP D 347 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 349 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 398 " --> pdb=" O GLU D 349 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL D 396 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 410 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 144 removed outlier: 6.362A pdb=" N THR E 141 " --> pdb=" O TYR E 182 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP E 184 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA E 143 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 181 " --> pdb=" O ILE E 246 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY E 248 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE E 183 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU E 116 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.272A pdb=" N ASP E 347 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ILE E 398 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU E 349 " --> pdb=" O ILE E 398 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 395 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.346A pdb=" N THR F 141 " --> pdb=" O TYR F 182 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP F 184 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA F 143 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 115 " --> pdb=" O CYS F 247 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY F 249 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 117 " --> pdb=" O GLY F 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 347 through 349 removed outlier: 3.880A pdb=" N LYS F 395 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.727A pdb=" N ILE h 29 " --> pdb=" O TYR h 62 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN h 64 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU h 31 " --> pdb=" O ASN h 64 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG h 118 " --> pdb=" O CYS h 91 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY h 93 " --> pdb=" O ARG h 118 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET h 120 " --> pdb=" O GLY h 93 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA h 95 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 28 through 32 removed outlier: 6.727A pdb=" N ILE h 29 " --> pdb=" O TYR h 62 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN h 64 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU h 31 " --> pdb=" O ASN h 64 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE h 59 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE h 90 " --> pdb=" O ILE h 59 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU h 61 " --> pdb=" O ILE h 90 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET h 92 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE h 63 " --> pdb=" O MET h 92 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN h 94 " --> pdb=" O ILE h 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER h 65 " --> pdb=" O GLN h 94 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE h 112 " --> pdb=" O VAL h 87 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR h 89 " --> pdb=" O PHE h 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'i' and resid 5 through 8 Processing sheet with id=AC4, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.126A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER i 65 " --> pdb=" O GLN i 94 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N VAL i 87 " --> pdb=" O PHE i 112 " (cutoff:3.500A) removed outlier: 14.054A pdb=" N LEU i 114 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 12.902A pdb=" N THR i 89 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 12.996A pdb=" N ASN i 116 " --> pdb=" O THR i 89 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N CYS i 91 " --> pdb=" O ASN i 116 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'i' and resid 28 through 32 removed outlier: 6.126A pdb=" N ILE i 59 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE i 90 " --> pdb=" O ILE i 59 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU i 61 " --> pdb=" O ILE i 90 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET i 92 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE i 63 " --> pdb=" O MET i 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN i 94 " --> pdb=" O ILE i 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER i 65 " --> pdb=" O GLN i 94 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N VAL i 87 " --> pdb=" O PHE i 112 " (cutoff:3.500A) removed outlier: 14.054A pdb=" N LEU i 114 " --> pdb=" O VAL i 87 " (cutoff:3.500A) removed outlier: 12.902A pdb=" N THR i 89 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 12.996A pdb=" N ASN i 116 " --> pdb=" O THR i 89 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N CYS i 91 " --> pdb=" O ASN i 116 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG i 118 " --> pdb=" O CYS i 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY i 93 " --> pdb=" O ARG i 118 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N MET i 120 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA i 95 " --> pdb=" O MET i 120 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER i 187 " --> pdb=" O ARG i 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'i' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'j' and resid 5 through 9 removed outlier: 3.524A pdb=" N ARG j 15 " --> pdb=" O GLU j 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.693A pdb=" N ILE j 29 " --> pdb=" O TYR j 62 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASN j 64 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU j 31 " --> pdb=" O ASN j 64 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER j 65 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN j 94 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG j 118 " --> pdb=" O CYS j 91 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY j 93 " --> pdb=" O ARG j 118 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N MET j 120 " --> pdb=" O GLY j 93 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA j 95 " --> pdb=" O MET j 120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'j' and resid 28 through 32 removed outlier: 6.693A pdb=" N ILE j 29 " --> pdb=" O TYR j 62 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASN j 64 " --> pdb=" O ILE j 29 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU j 31 " --> pdb=" O ASN j 64 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N SER j 65 " --> pdb=" O MET j 92 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN j 94 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE j 112 " --> pdb=" O VAL j 87 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR j 89 " --> pdb=" O PHE j 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'j' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'k' and resid 5 through 9 Processing sheet with id=AD3, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.285A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG k 118 " --> pdb=" O CYS k 91 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY k 93 " --> pdb=" O ARG k 118 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET k 120 " --> pdb=" O GLY k 93 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA k 95 " --> pdb=" O MET k 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 28 through 32 removed outlier: 6.285A pdb=" N ILE k 59 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE k 90 " --> pdb=" O ILE k 59 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU k 61 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET k 92 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE k 63 " --> pdb=" O MET k 92 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN k 94 " --> pdb=" O ILE k 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER k 65 " --> pdb=" O GLN k 94 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE k 112 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR k 89 " --> pdb=" O PHE k 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 125 through 131 Processing sheet with id=AD6, first strand: chain 'l' and resid 5 through 8 Processing sheet with id=AD7, first strand: chain 'l' and resid 28 through 32 removed outlier: 6.835A pdb=" N ILE l 29 " --> pdb=" O TYR l 62 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN l 64 " --> pdb=" O ILE l 29 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU l 31 " --> pdb=" O ASN l 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE l 59 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE l 90 " --> pdb=" O ILE l 59 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU l 61 " --> pdb=" O ILE l 90 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N PHE l 112 " --> pdb=" O VAL l 87 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N THR l 89 " --> pdb=" O PHE l 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 94 through 95 removed outlier: 6.246A pdb=" N ALA l 95 " --> pdb=" O MET l 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 125 through 131 Processing sheet with id=AE1, first strand: chain 'm' and resid 5 through 9 Processing sheet with id=AE2, first strand: chain 'm' and resid 28 through 32 removed outlier: 6.197A pdb=" N ILE m 59 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE m 90 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU m 61 " --> pdb=" O ILE m 90 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE m 112 " --> pdb=" O VAL m 87 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR m 89 " --> pdb=" O PHE m 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 94 through 95 removed outlier: 6.185A pdb=" N ALA m 95 " --> pdb=" O MET m 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'm' and resid 125 through 131 Processing sheet with id=AE5, first strand: chain 'n' and resid 5 through 10 Processing sheet with id=AE6, first strand: chain 'n' and resid 28 through 32 removed outlier: 5.518A pdb=" N SER n 65 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN n 94 " --> pdb=" O SER n 65 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N VAL n 87 " --> pdb=" O PHE n 112 " (cutoff:3.500A) removed outlier: 14.101A pdb=" N LEU n 114 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 13.007A pdb=" N THR n 89 " --> pdb=" O LEU n 114 " (cutoff:3.500A) removed outlier: 13.221A pdb=" N ASN n 116 " --> pdb=" O THR n 89 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N CYS n 91 " --> pdb=" O ASN n 116 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'n' and resid 28 through 32 removed outlier: 5.518A pdb=" N SER n 65 " --> pdb=" O MET n 92 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN n 94 " --> pdb=" O SER n 65 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N VAL n 87 " --> pdb=" O PHE n 112 " (cutoff:3.500A) removed outlier: 14.101A pdb=" N LEU n 114 " --> pdb=" O VAL n 87 " (cutoff:3.500A) removed outlier: 13.007A pdb=" N THR n 89 " --> pdb=" O LEU n 114 " (cutoff:3.500A) removed outlier: 13.221A pdb=" N ASN n 116 " --> pdb=" O THR n 89 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N CYS n 91 " --> pdb=" O ASN n 116 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG n 118 " --> pdb=" O CYS n 91 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY n 93 " --> pdb=" O ARG n 118 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N MET n 120 " --> pdb=" O GLY n 93 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA n 95 " --> pdb=" O MET n 120 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'n' and resid 125 through 131 Processing sheet with id=AE9, first strand: chain 'p' and resid 5 through 9 Processing sheet with id=AF1, first strand: chain 'p' and resid 28 through 32 removed outlier: 6.268A pdb=" N ILE p 59 " --> pdb=" O SER p 88 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE p 90 " --> pdb=" O ILE p 59 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU p 61 " --> pdb=" O ILE p 90 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET p 92 " --> pdb=" O LEU p 61 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE p 63 " --> pdb=" O MET p 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN p 94 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p 65 " --> pdb=" O GLN p 94 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG p 118 " --> pdb=" O CYS p 91 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY p 93 " --> pdb=" O ARG p 118 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N MET p 120 " --> pdb=" O GLY p 93 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA p 95 " --> pdb=" O MET p 120 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'p' and resid 28 through 32 removed outlier: 6.268A pdb=" N ILE p 59 " --> pdb=" O SER p 88 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE p 90 " --> pdb=" O ILE p 59 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU p 61 " --> pdb=" O ILE p 90 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N MET p 92 " --> pdb=" O LEU p 61 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE p 63 " --> pdb=" O MET p 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN p 94 " --> pdb=" O ILE p 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p 65 " --> pdb=" O GLN p 94 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE p 112 " --> pdb=" O VAL p 87 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR p 89 " --> pdb=" O PHE p 112 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'q' and resid 5 through 9 Processing sheet with id=AF4, first strand: chain 'q' and resid 28 through 32 removed outlier: 6.666A pdb=" N ILE q 29 " --> pdb=" O TYR q 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN q 64 " --> pdb=" O ILE q 29 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU q 31 " --> pdb=" O ASN q 64 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE q 59 " --> pdb=" O SER q 88 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE q 90 " --> pdb=" O ILE q 59 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU q 61 " --> pdb=" O ILE q 90 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET q 92 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE q 63 " --> pdb=" O MET q 92 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN q 94 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER q 65 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG q 118 " --> pdb=" O CYS q 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY q 93 " --> pdb=" O ARG q 118 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N MET q 120 " --> pdb=" O GLY q 93 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA q 95 " --> pdb=" O MET q 120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'q' and resid 28 through 32 removed outlier: 6.666A pdb=" N ILE q 29 " --> pdb=" O TYR q 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASN q 64 " --> pdb=" O ILE q 29 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU q 31 " --> pdb=" O ASN q 64 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE q 59 " --> pdb=" O SER q 88 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE q 90 " --> pdb=" O ILE q 59 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU q 61 " --> pdb=" O ILE q 90 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET q 92 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE q 63 " --> pdb=" O MET q 92 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN q 94 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER q 65 " --> pdb=" O GLN q 94 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE q 112 " --> pdb=" O VAL q 87 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR q 89 " --> pdb=" O PHE q 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'r' and resid 5 through 9 Processing sheet with id=AF7, first strand: chain 'r' and resid 28 through 32 removed outlier: 6.249A pdb=" N ILE r 59 " --> pdb=" O SER r 88 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE r 90 " --> pdb=" O ILE r 59 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU r 61 " --> pdb=" O ILE r 90 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N MET r 92 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE r 63 " --> pdb=" O MET r 92 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN r 94 " --> pdb=" O ILE r 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER r 65 " --> pdb=" O GLN r 94 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG r 118 " --> pdb=" O CYS r 91 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY r 93 " --> pdb=" O ARG r 118 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N MET r 120 " --> pdb=" O GLY r 93 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA r 95 " --> pdb=" O MET r 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'r' and resid 28 through 32 removed outlier: 6.249A pdb=" N ILE r 59 " --> pdb=" O SER r 88 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE r 90 " --> pdb=" O ILE r 59 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU r 61 " --> pdb=" O ILE r 90 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N MET r 92 " --> pdb=" O LEU r 61 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE r 63 " --> pdb=" O MET r 92 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN r 94 " --> pdb=" O ILE r 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER r 65 " --> pdb=" O GLN r 94 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE r 112 " --> pdb=" O VAL r 87 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR r 89 " --> pdb=" O PHE r 112 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 's' and resid 5 through 9 Processing sheet with id=AG1, first strand: chain 's' and resid 28 through 32 removed outlier: 6.235A pdb=" N ILE s 59 " --> pdb=" O SER s 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE s 90 " --> pdb=" O ILE s 59 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU s 61 " --> pdb=" O ILE s 90 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET s 92 " --> pdb=" O LEU s 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE s 63 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN s 94 " --> pdb=" O ILE s 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER s 65 " --> pdb=" O GLN s 94 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG s 118 " --> pdb=" O CYS s 91 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY s 93 " --> pdb=" O ARG s 118 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N MET s 120 " --> pdb=" O GLY s 93 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA s 95 " --> pdb=" O MET s 120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 's' and resid 28 through 32 removed outlier: 6.235A pdb=" N ILE s 59 " --> pdb=" O SER s 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE s 90 " --> pdb=" O ILE s 59 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU s 61 " --> pdb=" O ILE s 90 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET s 92 " --> pdb=" O LEU s 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE s 63 " --> pdb=" O MET s 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN s 94 " --> pdb=" O ILE s 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER s 65 " --> pdb=" O GLN s 94 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE s 112 " --> pdb=" O VAL s 87 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR s 89 " --> pdb=" O PHE s 112 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 't' and resid 5 through 9 Processing sheet with id=AG4, first strand: chain 't' and resid 28 through 32 removed outlier: 6.242A pdb=" N ILE t 59 " --> pdb=" O SER t 88 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE t 90 " --> pdb=" O ILE t 59 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU t 61 " --> pdb=" O ILE t 90 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET t 92 " --> pdb=" O LEU t 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE t 63 " --> pdb=" O MET t 92 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN t 94 " --> pdb=" O ILE t 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER t 65 " --> pdb=" O GLN t 94 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG t 118 " --> pdb=" O CYS t 91 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY t 93 " --> pdb=" O ARG t 118 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N MET t 120 " --> pdb=" O GLY t 93 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA t 95 " --> pdb=" O MET t 120 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 't' and resid 28 through 32 removed outlier: 6.242A pdb=" N ILE t 59 " --> pdb=" O SER t 88 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE t 90 " --> pdb=" O ILE t 59 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU t 61 " --> pdb=" O ILE t 90 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N MET t 92 " --> pdb=" O LEU t 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE t 63 " --> pdb=" O MET t 92 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN t 94 " --> pdb=" O ILE t 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER t 65 " --> pdb=" O GLN t 94 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE t 112 " --> pdb=" O VAL t 87 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR t 89 " --> pdb=" O PHE t 112 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'u' and resid 5 through 9 Processing sheet with id=AG7, first strand: chain 'u' and resid 28 through 32 removed outlier: 6.261A pdb=" N ILE u 59 " --> pdb=" O SER u 88 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE u 90 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU u 61 " --> pdb=" O ILE u 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET u 92 " --> pdb=" O LEU u 61 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE u 63 " --> pdb=" O MET u 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN u 94 " --> pdb=" O ILE u 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER u 65 " --> pdb=" O GLN u 94 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG u 118 " --> pdb=" O CYS u 91 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY u 93 " --> pdb=" O ARG u 118 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N MET u 120 " --> pdb=" O GLY u 93 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA u 95 " --> pdb=" O MET u 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'u' and resid 28 through 32 removed outlier: 6.261A pdb=" N ILE u 59 " --> pdb=" O SER u 88 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE u 90 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU u 61 " --> pdb=" O ILE u 90 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N MET u 92 " --> pdb=" O LEU u 61 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE u 63 " --> pdb=" O MET u 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN u 94 " --> pdb=" O ILE u 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER u 65 " --> pdb=" O GLN u 94 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE u 112 " --> pdb=" O VAL u 87 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR u 89 " --> pdb=" O PHE u 112 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'v' and resid 5 through 9 Processing sheet with id=AH1, first strand: chain 'v' and resid 28 through 32 removed outlier: 6.260A pdb=" N ILE v 59 " --> pdb=" O SER v 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE v 90 " --> pdb=" O ILE v 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU v 61 " --> pdb=" O ILE v 90 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET v 92 " --> pdb=" O LEU v 61 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE v 63 " --> pdb=" O MET v 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN v 94 " --> pdb=" O ILE v 63 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER v 65 " --> pdb=" O GLN v 94 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG v 118 " --> pdb=" O CYS v 91 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY v 93 " --> pdb=" O ARG v 118 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N MET v 120 " --> pdb=" O GLY v 93 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA v 95 " --> pdb=" O MET v 120 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'v' and resid 28 through 32 removed outlier: 6.260A pdb=" N ILE v 59 " --> pdb=" O SER v 88 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE v 90 " --> pdb=" O ILE v 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU v 61 " --> pdb=" O ILE v 90 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET v 92 " --> pdb=" O LEU v 61 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE v 63 " --> pdb=" O MET v 92 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLN v 94 " --> pdb=" O ILE v 63 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER v 65 " --> pdb=" O GLN v 94 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE v 112 " --> pdb=" O VAL v 87 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR v 89 " --> pdb=" O PHE v 112 " (cutoff:3.500A) 1872 hydrogen bonds defined for protein. 5499 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: 29.67 Time building geometry restraints manager: 18.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37048 1.03 - 1.23: 35 1.23 - 1.42: 14876 1.42 - 1.62: 22120 1.62 - 1.81: 362 Bond restraints: 74441 Sorted by residual: bond pdb=" N GLU C 328 " pdb=" CA GLU C 328 " ideal model delta sigma weight residual 1.462 1.491 -0.030 9.50e-03 1.11e+04 9.89e+00 bond pdb=" N VAL E 262 " pdb=" CA VAL E 262 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.37e-02 5.33e+03 7.83e+00 bond pdb=" N ASP A 157 " pdb=" CA ASP A 157 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.71e+00 bond pdb=" N VAL A 154 " pdb=" CA VAL A 154 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.98e+00 bond pdb=" N LYS C 327 " pdb=" CA LYS C 327 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.57e+00 ... (remaining 74436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 132637 1.46 - 2.91: 2099 2.91 - 4.37: 205 4.37 - 5.82: 45 5.82 - 7.28: 5 Bond angle restraints: 134991 Sorted by residual: angle pdb=" CA ASP F 184 " pdb=" C ASP F 184 " pdb=" O ASP F 184 " ideal model delta sigma weight residual 121.94 117.49 4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA THR C 334 " pdb=" C THR C 334 " pdb=" O THR C 334 " ideal model delta sigma weight residual 120.55 116.54 4.01 1.06e+00 8.90e-01 1.43e+01 angle pdb=" CA ASP C 184 " pdb=" C ASP C 184 " pdb=" O ASP C 184 " ideal model delta sigma weight residual 121.81 117.38 4.43 1.18e+00 7.18e-01 1.41e+01 angle pdb=" N VAL E 262 " pdb=" CA VAL E 262 " pdb=" CB VAL E 262 " ideal model delta sigma weight residual 112.08 105.86 6.22 1.68e+00 3.54e-01 1.37e+01 angle pdb=" CA GLY A 155 " pdb=" C GLY A 155 " pdb=" O GLY A 155 " ideal model delta sigma weight residual 122.82 118.05 4.77 1.29e+00 6.01e-01 1.37e+01 ... (remaining 134986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 32598 17.67 - 35.33: 1321 35.33 - 53.00: 566 53.00 - 70.66: 155 70.66 - 88.33: 14 Dihedral angle restraints: 34654 sinusoidal: 19516 harmonic: 15138 Sorted by residual: dihedral pdb=" CD ARG q 192 " pdb=" NE ARG q 192 " pdb=" CZ ARG q 192 " pdb=" NH1 ARG q 192 " ideal model delta sinusoidal sigma weight residual 0.00 45.37 -45.37 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CD ARG s 118 " pdb=" NE ARG s 118 " pdb=" CZ ARG s 118 " pdb=" NH1 ARG s 118 " ideal model delta sinusoidal sigma weight residual 0.00 43.76 -43.76 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CD ARG q 118 " pdb=" NE ARG q 118 " pdb=" CZ ARG q 118 " pdb=" NH1 ARG q 118 " ideal model delta sinusoidal sigma weight residual 0.00 42.13 -42.13 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 34651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4831 0.052 - 0.104: 739 0.104 - 0.156: 237 0.156 - 0.208: 5 0.208 - 0.260: 9 Chirality restraints: 5821 Sorted by residual: chirality pdb=" C2' ATP C 500 " pdb=" C1' ATP C 500 " pdb=" C3' ATP C 500 " pdb=" O2' ATP C 500 " both_signs ideal model delta sigma weight residual False -2.68 -2.94 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C2' ATP B 500 " pdb=" C1' ATP B 500 " pdb=" C3' ATP B 500 " pdb=" O2' ATP B 500 " both_signs ideal model delta sigma weight residual False -2.68 -2.93 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C4' ATP C 500 " pdb=" C3' ATP C 500 " pdb=" C5' ATP C 500 " pdb=" O4' ATP C 500 " both_signs ideal model delta sigma weight residual False -2.49 -2.74 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 5818 not shown) Planarity restraints: 11048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 373 " -0.297 9.50e-02 1.11e+02 2.39e-01 1.08e+03 pdb=" NE ARG D 373 " 0.174 2.00e-02 2.50e+03 pdb=" CZ ARG D 373 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG D 373 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 373 " -0.054 2.00e-02 2.50e+03 pdb="HH11 ARG D 373 " -0.426 2.00e-02 2.50e+03 pdb="HH12 ARG D 373 " 0.429 2.00e-02 2.50e+03 pdb="HH21 ARG D 373 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG D 373 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 307 " 0.675 9.50e-02 1.11e+02 2.86e-01 7.49e+02 pdb=" NE ARG B 307 " 0.162 2.00e-02 2.50e+03 pdb=" CZ ARG B 307 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 307 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 307 " -0.041 2.00e-02 2.50e+03 pdb="HH11 ARG B 307 " -0.369 2.00e-02 2.50e+03 pdb="HH12 ARG B 307 " 0.318 2.00e-02 2.50e+03 pdb="HH21 ARG B 307 " -0.110 2.00e-02 2.50e+03 pdb="HH22 ARG B 307 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG k 192 " -0.105 9.50e-02 1.11e+02 1.52e-01 4.92e+02 pdb=" NE ARG k 192 " -0.105 2.00e-02 2.50e+03 pdb=" CZ ARG k 192 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG k 192 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG k 192 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG k 192 " 0.286 2.00e-02 2.50e+03 pdb="HH12 ARG k 192 " -0.292 2.00e-02 2.50e+03 pdb="HH21 ARG k 192 " -0.005 2.00e-02 2.50e+03 pdb="HH22 ARG k 192 " 0.125 2.00e-02 2.50e+03 ... (remaining 11045 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1421 2.11 - 2.73: 134813 2.73 - 3.35: 220438 3.35 - 3.98: 284137 3.98 - 4.60: 450670 Nonbonded interactions: 1091479 Sorted by model distance: nonbonded pdb=" HG SER B 190 " pdb=" O GLY B 299 " model vdw 1.482 2.450 nonbonded pdb=" HG1 THR E 218 " pdb=" OG1 THR E 240 " model vdw 1.515 2.450 nonbonded pdb=" O MET v 153 " pdb=" HG1 THR v 157 " model vdw 1.515 2.450 nonbonded pdb=" H THR F 126 " pdb=" O1A ADP F 500 " model vdw 1.544 2.450 nonbonded pdb=" O MET u 153 " pdb=" HG1 THR u 157 " model vdw 1.547 2.450 ... (remaining 1091474 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 192 or (resid 204 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 205 through 214 or (resid 215 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA or nam \ e HB )) or resid 216 through 223 or (resid 235 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1 or name HE2 or name HZ )) or resid 236 through 413)) selection = (chain 'B' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 101 or (resid 110 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name H \ B3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 o \ r name HD23)) or resid 111 through 192 or (resid 204 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 205 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB or name H or name HA or n \ ame HB )) or resid 216 through 223 or (resid 235 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1 or name HE2 or name HZ )) or resid 236 through 413)) selection = (chain 'C' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 101 or (resid 110 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name H \ B3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 o \ r name HD23)) or resid 111 through 192 or (resid 204 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 205 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB or name H or name HA or n \ ame HB )) or resid 216 through 223 or (resid 235 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1 or name HE2 or name HZ )) or resid 236 through 413)) selection = (chain 'D' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 101 or (resid 110 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or name H \ B3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 o \ r name HD23)) or resid 111 through 192 or (resid 204 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 205 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB or name H or name HA or n \ ame HB )) or resid 216 through 223 or (resid 235 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1 or name HE2 or name HZ )) or resid 236 through 413)) selection = (chain 'E' and (resid 64 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name H or name \ HA or name HB or name HG21 or name HG22 or name HG23)) or resid 127 through 223 \ or (resid 235 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or name HB \ 2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) or r \ esid 236 through 413)) selection = (chain 'F' and (resid 64 through 101 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 111 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name H or name \ HA or name HB or name HG21 or name HG22 or name HG23)) or resid 127 through 192 \ or (resid 204 and (name N or name CA or name C or name O or name HA2 or name HA \ 3)) or resid 205 through 214 or (resid 215 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA or name HB )) or resid 216 through 413)) } ncs_group { reference = (chain 'h' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'i' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'j' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'k' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = chain 'l' selection = (chain 'm' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'n' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'p' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'r' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 's' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 't' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'u' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) selection = (chain 'v' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2 or name HH )) or (resid 61 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name \ HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 62 through 193)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.950 Extract box with map and model: 2.370 Check model and map are aligned: 0.520 Set scattering table: 0.650 Process input model: 124.760 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.002 0.038 37359 Z= 0.165 Angle : 0.501 7.279 50447 Z= 0.292 Chirality : 0.042 0.260 5821 Planarity : 0.017 0.339 6529 Dihedral : 9.784 88.328 14221 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.03 % Allowed : 0.98 % Favored : 98.99 % 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: 0.74 (0.12), residues: 4663 helix: 1.59 (0.11), residues: 2291 sheet: -0.45 (0.18), residues: 741 loop : -0.55 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 38 PHE 0.012 0.001 PHE k 17 TYR 0.016 0.001 TYR F 96 ARG 0.009 0.001 ARG j 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 746 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 745 time to evaluate : 4.409 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: A 163 GLN cc_start: 0.8793 (tt0) cc_final: 0.8181 (tp40) REVERT: A 167 GLN cc_start: 0.8773 (mt0) cc_final: 0.8390 (mp10) REVERT: A 171 TYR cc_start: 0.8389 (m-80) cc_final: 0.8032 (m-80) REVERT: B 178 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8286 (mtm110) REVERT: B 279 ASP cc_start: 0.8412 (m-30) cc_final: 0.8203 (t0) REVERT: C 160 ASN cc_start: 0.8448 (m-40) cc_final: 0.7789 (m110) REVERT: C 363 MET cc_start: 0.8183 (mmm) cc_final: 0.7917 (mmm) REVERT: D 106 ASN cc_start: 0.3884 (p0) cc_final: 0.3468 (p0) REVERT: D 182 TYR cc_start: 0.8314 (t80) cc_final: 0.8110 (t80) REVERT: D 185 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7953 (mm-30) REVERT: E 160 ASN cc_start: 0.8641 (m-40) cc_final: 0.7967 (m-40) REVERT: E 331 ASN cc_start: 0.7887 (m110) cc_final: 0.7622 (p0) REVERT: E 350 PHE cc_start: 0.7765 (m-80) cc_final: 0.7500 (m-80) REVERT: E 366 LYS cc_start: 0.8746 (tppt) cc_final: 0.8535 (tptp) REVERT: h 17 PHE cc_start: 0.6980 (m-80) cc_final: 0.6763 (m-10) REVERT: h 18 ASP cc_start: 0.8185 (p0) cc_final: 0.7789 (p0) REVERT: h 56 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8727 (mm-30) REVERT: h 74 MET cc_start: 0.9043 (mmt) cc_final: 0.8837 (mmm) REVERT: h 148 ARG cc_start: 0.8422 (tpt170) cc_final: 0.8184 (tpm170) REVERT: i 15 ARG cc_start: 0.8415 (ttm170) cc_final: 0.7798 (tpp-160) REVERT: j 60 TYR cc_start: 0.9056 (m-80) cc_final: 0.8811 (m-80) REVERT: k 162 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8360 (mp0) REVERT: l 15 ARG cc_start: 0.8385 (mtm180) cc_final: 0.8133 (mtm180) REVERT: m 18 ASP cc_start: 0.7728 (t70) cc_final: 0.7519 (t0) REVERT: m 162 GLU cc_start: 0.8189 (pm20) cc_final: 0.7901 (mp0) REVERT: n 25 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8670 (mtmm) REVERT: p 149 MET cc_start: 0.8750 (mmm) cc_final: 0.8488 (mmm) REVERT: s 37 ASP cc_start: 0.8585 (m-30) cc_final: 0.8372 (m-30) REVERT: s 58 ASP cc_start: 0.8450 (m-30) cc_final: 0.8221 (m-30) REVERT: s 149 MET cc_start: 0.8810 (mmm) cc_final: 0.8520 (tpp) REVERT: s 181 GLU cc_start: 0.8769 (tt0) cc_final: 0.8231 (tm-30) REVERT: t 10 THR cc_start: 0.7141 (p) cc_final: 0.6898 (t) REVERT: t 56 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8513 (mp0) REVERT: t 84 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8747 (mtpp) REVERT: t 181 GLU cc_start: 0.8725 (tt0) cc_final: 0.8280 (tm-30) REVERT: u 10 THR cc_start: 0.7869 (p) cc_final: 0.7642 (t) REVERT: u 18 ASP cc_start: 0.7883 (m-30) cc_final: 0.7628 (m-30) REVERT: u 84 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8772 (mtpp) REVERT: u 181 GLU cc_start: 0.8780 (tt0) cc_final: 0.8462 (tm-30) REVERT: v 10 THR cc_start: 0.7915 (p) cc_final: 0.7673 (t) REVERT: v 37 ASP cc_start: 0.8793 (m-30) cc_final: 0.8573 (m-30) outliers start: 1 outliers final: 3 residues processed: 745 average time/residue: 2.9790 time to fit residues: 2646.4954 Evaluate side-chains 455 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 452 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain k residue 58 ASP Chi-restraints excluded: chain t residue 74 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 366 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 163 GLN B 72 ASN B 174 GLN E 177 GLN i 46 GLN i 163 GLN j 41 ASN j 46 GLN j 159 GLN k 64 ASN k 159 GLN l 41 ASN l 159 GLN m 34 GLN n 131 GLN p 41 ASN ** q 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN t 129 GLN u 34 GLN u 41 ASN v 41 ASN v 129 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.123567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078619 restraints weight = 183956.758| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.08 r_work: 0.3068 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37359 Z= 0.289 Angle : 0.557 6.764 50447 Z= 0.303 Chirality : 0.042 0.165 5821 Planarity : 0.005 0.089 6529 Dihedral : 5.314 80.706 5226 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.16 % Allowed : 8.46 % Favored : 90.38 % 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: 0.78 (0.12), residues: 4663 helix: 1.66 (0.11), residues: 2340 sheet: -0.38 (0.18), residues: 736 loop : -0.70 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 260 PHE 0.011 0.001 PHE E 304 TYR 0.013 0.001 TYR E 337 ARG 0.015 0.001 ARG q 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 511 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 465 time to evaluate : 5.169 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: B 279 ASP cc_start: 0.8458 (m-30) cc_final: 0.8240 (t0) REVERT: C 160 ASN cc_start: 0.8409 (m-40) cc_final: 0.8035 (m110) REVERT: C 363 MET cc_start: 0.8222 (mmm) cc_final: 0.7977 (mmm) REVERT: C 404 ASP cc_start: 0.8848 (m-30) cc_final: 0.8599 (m-30) REVERT: D 106 ASN cc_start: 0.3935 (p0) cc_final: 0.3578 (p0) REVERT: D 185 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 365 ARG cc_start: 0.8586 (mpp80) cc_final: 0.8202 (mtm-85) REVERT: i 129 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: j 36 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8163 (pp20) REVERT: j 60 TYR cc_start: 0.9220 (m-80) cc_final: 0.8999 (m-80) REVERT: l 136 GLU cc_start: 0.8685 (tt0) cc_final: 0.8427 (tm-30) REVERT: m 162 GLU cc_start: 0.8370 (pm20) cc_final: 0.8065 (mp0) REVERT: n 25 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8829 (mtmm) REVERT: p 149 MET cc_start: 0.8919 (mmm) cc_final: 0.8646 (mmm) REVERT: r 34 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8159 (tp40) REVERT: r 148 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (tpt-90) REVERT: s 37 ASP cc_start: 0.8638 (m-30) cc_final: 0.8410 (m-30) REVERT: s 41 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: s 53 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7749 (mm-30) REVERT: s 149 MET cc_start: 0.8882 (mmm) cc_final: 0.8645 (tpp) REVERT: s 181 GLU cc_start: 0.8739 (tt0) cc_final: 0.8313 (tm-30) REVERT: t 5 MET cc_start: 0.8406 (tpp) cc_final: 0.8201 (tpp) REVERT: t 56 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8569 (mp0) REVERT: t 181 GLU cc_start: 0.8818 (tt0) cc_final: 0.8535 (tm-30) REVERT: u 84 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8745 (mtpp) REVERT: v 10 THR cc_start: 0.7840 (p) cc_final: 0.7600 (t) REVERT: v 36 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7587 (pp20) REVERT: v 37 ASP cc_start: 0.8837 (m-30) cc_final: 0.8570 (m-30) REVERT: v 41 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8048 (m110) outliers start: 46 outliers final: 16 residues processed: 493 average time/residue: 2.7602 time to fit residues: 1646.8295 Evaluate side-chains 433 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 411 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 129 GLN Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 168 THR Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain r residue 148 ARG Chi-restraints excluded: chain s residue 41 ASN Chi-restraints excluded: chain u residue 74 MET Chi-restraints excluded: chain u residue 168 THR Chi-restraints excluded: chain v residue 36 GLU Chi-restraints excluded: chain v residue 41 ASN Chi-restraints excluded: chain v residue 168 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 346 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 384 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 432 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 417 optimal weight: 0.9990 chunk 407 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN D 83 GLN F 342 ASN h 41 ASN ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 159 GLN t 41 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078194 restraints weight = 182989.443| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.07 r_work: 0.3063 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37359 Z= 0.185 Angle : 0.489 6.892 50447 Z= 0.255 Chirality : 0.041 0.176 5821 Planarity : 0.004 0.072 6529 Dihedral : 5.315 81.188 5219 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.98 % Allowed : 9.41 % Favored : 89.60 % 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: 0.87 (0.12), residues: 4663 helix: 1.73 (0.11), residues: 2341 sheet: -0.42 (0.19), residues: 730 loop : -0.61 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 260 PHE 0.017 0.001 PHE F 245 TYR 0.015 0.001 TYR E 337 ARG 0.006 0.000 ARG j 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 424 time to evaluate : 4.644 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: A 171 TYR cc_start: 0.8276 (m-80) cc_final: 0.7801 (m-80) REVERT: B 73 HIS cc_start: 0.8305 (m90) cc_final: 0.7999 (m90) REVERT: C 160 ASN cc_start: 0.8541 (m-40) cc_final: 0.8153 (m110) REVERT: C 363 MET cc_start: 0.8223 (mmm) cc_final: 0.7974 (mmm) REVERT: D 185 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7882 (mm-30) REVERT: E 365 ARG cc_start: 0.8640 (mpp80) cc_final: 0.8285 (mtm-85) REVERT: h 36 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: i 15 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7680 (ttp-110) REVERT: j 36 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: j 60 TYR cc_start: 0.9145 (m-80) cc_final: 0.8930 (m-80) REVERT: l 136 GLU cc_start: 0.8703 (tt0) cc_final: 0.8435 (tm-30) REVERT: m 162 GLU cc_start: 0.8370 (pm20) cc_final: 0.8035 (mp0) REVERT: n 25 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8605 (mtmm) REVERT: p 36 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: p 149 MET cc_start: 0.8933 (mmm) cc_final: 0.8559 (mmm) REVERT: r 34 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8115 (tp40) REVERT: r 148 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8178 (tpt-90) REVERT: s 25 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8901 (ttpp) REVERT: s 37 ASP cc_start: 0.8601 (m-30) cc_final: 0.8384 (m-30) REVERT: s 149 MET cc_start: 0.8939 (mmm) cc_final: 0.8655 (tpp) REVERT: s 181 GLU cc_start: 0.8765 (tt0) cc_final: 0.8290 (tm-30) REVERT: t 5 MET cc_start: 0.8398 (tpp) cc_final: 0.8185 (tpp) REVERT: t 15 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.7344 (tpt170) REVERT: t 25 LYS cc_start: 0.9285 (mtpp) cc_final: 0.9049 (ttmm) REVERT: t 56 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8601 (mp0) REVERT: t 181 GLU cc_start: 0.8825 (tt0) cc_final: 0.8569 (tm-30) REVERT: u 41 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8143 (m110) REVERT: u 84 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8621 (mtpp) REVERT: v 10 THR cc_start: 0.7867 (p) cc_final: 0.7614 (t) REVERT: v 37 ASP cc_start: 0.8742 (m-30) cc_final: 0.8517 (m-30) outliers start: 39 outliers final: 10 residues processed: 449 average time/residue: 2.6787 time to fit residues: 1463.7735 Evaluate side-chains 404 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 389 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 41 ASN Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain r residue 148 ARG Chi-restraints excluded: chain s residue 120 MET Chi-restraints excluded: chain s residue 153 MET Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 360 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 443 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN i 41 ASN s 9 GLN t 41 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.121044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075393 restraints weight = 183795.595| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.05 r_work: 0.2984 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37359 Z= 0.290 Angle : 0.512 10.040 50447 Z= 0.268 Chirality : 0.041 0.153 5821 Planarity : 0.004 0.087 6529 Dihedral : 5.568 85.080 5219 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.93 % Allowed : 9.62 % Favored : 89.45 % 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: 0.85 (0.12), residues: 4663 helix: 1.74 (0.11), residues: 2350 sheet: -0.22 (0.19), residues: 647 loop : -0.78 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS t 122 PHE 0.018 0.001 PHE F 245 TYR 0.015 0.001 TYR F 96 ARG 0.007 0.000 ARG j 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 435 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 398 time to evaluate : 4.991 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: B 73 HIS cc_start: 0.8329 (m90) cc_final: 0.7984 (m90) REVERT: C 160 ASN cc_start: 0.8524 (m-40) cc_final: 0.8085 (m110) REVERT: C 390 MET cc_start: 0.8165 (mtt) cc_final: 0.7900 (mtt) REVERT: D 185 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 300 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8401 (mp) REVERT: i 15 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7721 (ttp-110) REVERT: j 36 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: l 136 GLU cc_start: 0.8733 (tt0) cc_final: 0.8511 (tm-30) REVERT: m 162 GLU cc_start: 0.8510 (pm20) cc_final: 0.8144 (mp0) REVERT: n 25 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8765 (mtmm) REVERT: p 36 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: p 149 MET cc_start: 0.8979 (mmm) cc_final: 0.8568 (mmm) REVERT: r 34 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8241 (tp40) REVERT: r 74 MET cc_start: 0.8667 (mmp) cc_final: 0.8250 (mmp) REVERT: s 149 MET cc_start: 0.8907 (mmm) cc_final: 0.8684 (tpp) REVERT: s 181 GLU cc_start: 0.8826 (tt0) cc_final: 0.8417 (tm-30) REVERT: t 15 ARG cc_start: 0.7653 (tpp-160) cc_final: 0.7381 (tpt170) REVERT: t 25 LYS cc_start: 0.9312 (mtpp) cc_final: 0.9096 (ttmm) REVERT: u 37 ASP cc_start: 0.8557 (m-30) cc_final: 0.8293 (m-30) REVERT: u 41 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8149 (m110) REVERT: v 10 THR cc_start: 0.7870 (p) cc_final: 0.7628 (t) REVERT: v 74 MET cc_start: 0.8921 (mmp) cc_final: 0.8691 (mmp) outliers start: 37 outliers final: 13 residues processed: 419 average time/residue: 2.6953 time to fit residues: 1374.2568 Evaluate side-chains 394 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 377 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 168 THR Chi-restraints excluded: chain s residue 153 MET Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 460 optimal weight: 4.9990 chunk 342 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 458 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 232 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 304 optimal weight: 0.6980 chunk 356 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 342 ASN q 123 GLN s 41 ASN t 41 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.120108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.074127 restraints weight = 183300.414| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.04 r_work: 0.2949 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37359 Z= 0.284 Angle : 0.506 7.151 50447 Z= 0.263 Chirality : 0.041 0.146 5821 Planarity : 0.004 0.074 6529 Dihedral : 5.693 77.526 5219 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.93 % Allowed : 10.22 % Favored : 88.84 % 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: 0.87 (0.12), residues: 4663 helix: 1.76 (0.11), residues: 2351 sheet: -0.24 (0.19), residues: 630 loop : -0.76 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS p 122 PHE 0.015 0.001 PHE v 17 TYR 0.018 0.001 TYR F 96 ARG 0.007 0.000 ARG k 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 380 time to evaluate : 4.478 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: C 160 ASN cc_start: 0.8585 (m-40) cc_final: 0.8091 (m110) REVERT: D 185 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7948 (mm-30) REVERT: i 15 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7650 (ttp-110) REVERT: j 15 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: j 36 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8208 (pp20) REVERT: l 136 GLU cc_start: 0.8742 (tt0) cc_final: 0.8491 (tm-30) REVERT: m 162 GLU cc_start: 0.8545 (pm20) cc_final: 0.8154 (mp0) REVERT: n 25 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8818 (ttmm) REVERT: p 36 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: p 149 MET cc_start: 0.9034 (mmm) cc_final: 0.8710 (mmm) REVERT: q 98 MET cc_start: 0.8513 (tpp) cc_final: 0.8306 (tpp) REVERT: r 34 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8269 (tp40) REVERT: r 74 MET cc_start: 0.8497 (mmp) cc_final: 0.8268 (mmp) REVERT: s 37 ASP cc_start: 0.8678 (m-30) cc_final: 0.8451 (m-30) REVERT: s 149 MET cc_start: 0.8965 (mmm) cc_final: 0.8733 (tpp) REVERT: s 181 GLU cc_start: 0.8878 (tt0) cc_final: 0.8482 (tm-30) REVERT: t 25 LYS cc_start: 0.9318 (mtpp) cc_final: 0.9090 (ttmm) REVERT: u 37 ASP cc_start: 0.8558 (m-30) cc_final: 0.8249 (m-30) REVERT: u 41 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8141 (m110) REVERT: u 84 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8551 (mtpp) outliers start: 37 outliers final: 18 residues processed: 401 average time/residue: 2.6350 time to fit residues: 1287.9708 Evaluate side-chains 390 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 368 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 15 ARG Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 168 THR Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain s residue 153 MET Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 122 optimal weight: 3.9990 chunk 347 optimal weight: 0.9980 chunk 340 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 445 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 41 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074197 restraints weight = 183757.496| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.04 r_work: 0.2992 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37359 Z= 0.251 Angle : 0.494 7.172 50447 Z= 0.257 Chirality : 0.041 0.146 5821 Planarity : 0.004 0.104 6529 Dihedral : 5.684 74.339 5219 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.88 % Allowed : 10.73 % Favored : 88.39 % 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: 0.93 (0.12), residues: 4663 helix: 1.73 (0.11), residues: 2380 sheet: -0.18 (0.19), residues: 646 loop : -0.67 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS B 73 PHE 0.014 0.001 PHE v 17 TYR 0.018 0.001 TYR F 96 ARG 0.011 0.000 ARG j 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 412 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 377 time to evaluate : 4.521 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: C 160 ASN cc_start: 0.8485 (m-40) cc_final: 0.8049 (m110) REVERT: D 185 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 216 GLU cc_start: 0.6445 (tp30) cc_final: 0.5967 (mt-10) REVERT: i 15 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7653 (ttp-110) REVERT: j 15 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7842 (ttm110) REVERT: j 36 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: l 136 GLU cc_start: 0.8755 (tt0) cc_final: 0.8490 (tm-30) REVERT: m 162 GLU cc_start: 0.8534 (pm20) cc_final: 0.8140 (mp0) REVERT: p 15 ARG cc_start: 0.7948 (tpt90) cc_final: 0.7589 (tpt90) REVERT: p 36 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: p 149 MET cc_start: 0.9036 (mmm) cc_final: 0.8687 (mmm) REVERT: s 5 MET cc_start: 0.8330 (mmm) cc_final: 0.8103 (mmt) REVERT: s 149 MET cc_start: 0.8969 (mmm) cc_final: 0.8740 (tpp) REVERT: s 181 GLU cc_start: 0.8873 (tt0) cc_final: 0.8486 (tm-30) REVERT: t 25 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9100 (ttmm) REVERT: u 37 ASP cc_start: 0.8578 (m-30) cc_final: 0.8236 (m-30) REVERT: u 41 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8120 (m110) outliers start: 35 outliers final: 18 residues processed: 398 average time/residue: 2.6633 time to fit residues: 1292.7259 Evaluate side-chains 386 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 365 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain h residue 187 SER Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain s residue 153 MET Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Chi-restraints excluded: chain v residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 124 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 407 optimal weight: 0.9980 chunk 359 optimal weight: 6.9990 chunk 463 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN i 41 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074064 restraints weight = 183169.251| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.03 r_work: 0.2973 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37359 Z= 0.237 Angle : 0.489 7.925 50447 Z= 0.254 Chirality : 0.040 0.145 5821 Planarity : 0.004 0.102 6529 Dihedral : 5.664 72.862 5219 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.88 % Allowed : 11.16 % Favored : 87.96 % 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: 0.99 (0.12), residues: 4663 helix: 1.79 (0.11), residues: 2383 sheet: -0.18 (0.19), residues: 646 loop : -0.65 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 73 PHE 0.016 0.001 PHE v 17 TYR 0.014 0.001 TYR F 96 ARG 0.011 0.000 ARG j 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 4.459 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: B 316 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: C 160 ASN cc_start: 0.8488 (m-40) cc_final: 0.8014 (m110) REVERT: D 185 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8121 (mm-30) REVERT: D 406 GLN cc_start: 0.9108 (mt0) cc_final: 0.8854 (mm-40) REVERT: E 216 GLU cc_start: 0.6676 (tp30) cc_final: 0.6118 (mt-10) REVERT: h 15 ARG cc_start: 0.8277 (ttp-170) cc_final: 0.8064 (ttp-170) REVERT: j 15 ARG cc_start: 0.8317 (ttp-170) cc_final: 0.7825 (ttm110) REVERT: j 36 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8307 (pp20) REVERT: k 135 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8398 (tt) REVERT: l 7 ILE cc_start: 0.9327 (pt) cc_final: 0.9084 (mm) REVERT: l 136 GLU cc_start: 0.8754 (tt0) cc_final: 0.8484 (tm-30) REVERT: m 162 GLU cc_start: 0.8587 (pm20) cc_final: 0.8178 (mp0) REVERT: n 14 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: p 15 ARG cc_start: 0.7989 (tpt90) cc_final: 0.7389 (tpt90) REVERT: p 36 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7680 (pp20) REVERT: p 149 MET cc_start: 0.9023 (mmm) cc_final: 0.8660 (mmm) REVERT: q 92 MET cc_start: 0.8603 (ptm) cc_final: 0.8209 (ptp) REVERT: s 5 MET cc_start: 0.8330 (mmm) cc_final: 0.8082 (mmt) REVERT: s 149 MET cc_start: 0.8951 (mmm) cc_final: 0.8720 (tpp) REVERT: s 181 GLU cc_start: 0.8874 (tt0) cc_final: 0.8491 (tm-30) REVERT: t 25 LYS cc_start: 0.9326 (mtpp) cc_final: 0.9088 (ttmm) REVERT: t 34 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8109 (mm110) REVERT: u 37 ASP cc_start: 0.8558 (m-30) cc_final: 0.8216 (m-30) REVERT: u 41 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8136 (m110) REVERT: u 84 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8443 (mtpp) outliers start: 35 outliers final: 15 residues processed: 391 average time/residue: 2.7628 time to fit residues: 1331.0349 Evaluate side-chains 379 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 358 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 36 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain s residue 153 MET Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 295 optimal weight: 2.9990 chunk 465 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 309 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 370 optimal weight: 4.9990 chunk 466 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 420 optimal weight: 8.9990 chunk 403 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN t 41 ASN u 41 ASN u 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072350 restraints weight = 184425.053| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.03 r_work: 0.2937 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 37359 Z= 0.354 Angle : 0.530 8.180 50447 Z= 0.277 Chirality : 0.042 0.146 5821 Planarity : 0.004 0.095 6529 Dihedral : 5.844 73.305 5219 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.86 % Allowed : 11.53 % Favored : 87.61 % 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: 0.87 (0.12), residues: 4663 helix: 1.68 (0.11), residues: 2383 sheet: -0.22 (0.19), residues: 643 loop : -0.68 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS s 122 PHE 0.014 0.001 PHE h 17 TYR 0.016 0.001 TYR l 60 ARG 0.013 0.001 ARG j 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 391 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 4.435 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: C 160 ASN cc_start: 0.8492 (m-40) cc_final: 0.7997 (m110) REVERT: D 185 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8154 (mm-30) REVERT: D 406 GLN cc_start: 0.9114 (mt0) cc_final: 0.8854 (mm-40) REVERT: j 15 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.7769 (ttm110) REVERT: j 36 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (pp20) REVERT: l 7 ILE cc_start: 0.9336 (pt) cc_final: 0.9099 (mm) REVERT: l 36 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8173 (pp20) REVERT: l 136 GLU cc_start: 0.8789 (tt0) cc_final: 0.8525 (tm-30) REVERT: m 162 GLU cc_start: 0.8630 (pm20) cc_final: 0.8201 (mp0) REVERT: n 14 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: p 34 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8386 (tp40) REVERT: p 36 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: p 149 MET cc_start: 0.9010 (mmm) cc_final: 0.8803 (mmm) REVERT: q 120 MET cc_start: 0.8995 (tmm) cc_final: 0.8702 (tmm) REVERT: s 149 MET cc_start: 0.8949 (mmm) cc_final: 0.8707 (tpp) REVERT: s 181 GLU cc_start: 0.8892 (tt0) cc_final: 0.8616 (tm-30) REVERT: t 25 LYS cc_start: 0.9321 (mtpp) cc_final: 0.9099 (ttmm) outliers start: 34 outliers final: 17 residues processed: 378 average time/residue: 2.7487 time to fit residues: 1264.1845 Evaluate side-chains 369 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 348 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain j residue 36 GLU Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 36 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 168 THR Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain u residue 41 ASN Chi-restraints excluded: chain u residue 168 THR Chi-restraints excluded: chain v residue 90 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 200 optimal weight: 20.0000 chunk 324 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN t 41 ASN u 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074293 restraints weight = 183797.422| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.04 r_work: 0.2982 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 37359 Z= 0.162 Angle : 0.485 8.968 50447 Z= 0.250 Chirality : 0.040 0.143 5821 Planarity : 0.004 0.085 6529 Dihedral : 5.697 72.727 5219 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.63 % Allowed : 11.96 % Favored : 87.41 % 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: 1.03 (0.12), residues: 4663 helix: 1.81 (0.11), residues: 2387 sheet: -0.16 (0.19), residues: 643 loop : -0.59 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 73 PHE 0.020 0.001 PHE t 101 TYR 0.012 0.001 TYR E 413 ARG 0.016 0.000 ARG k 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 358 time to evaluate : 4.480 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: C 160 ASN cc_start: 0.8493 (m-40) cc_final: 0.7994 (m110) REVERT: D 185 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8042 (mm-30) REVERT: D 406 GLN cc_start: 0.9117 (mt0) cc_final: 0.8858 (mm-40) REVERT: j 15 ARG cc_start: 0.8274 (ttp-170) cc_final: 0.7721 (ttm110) REVERT: l 7 ILE cc_start: 0.9322 (pt) cc_final: 0.9095 (mm) REVERT: l 136 GLU cc_start: 0.8747 (tt0) cc_final: 0.8475 (tm-30) REVERT: m 162 GLU cc_start: 0.8618 (pm20) cc_final: 0.8186 (mp0) REVERT: n 14 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: p 34 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8355 (tp40) REVERT: p 149 MET cc_start: 0.8994 (mmm) cc_final: 0.8628 (mmm) REVERT: s 5 MET cc_start: 0.8295 (mmm) cc_final: 0.8071 (mmt) REVERT: s 149 MET cc_start: 0.8918 (mmm) cc_final: 0.8672 (tpp) REVERT: s 181 GLU cc_start: 0.8886 (tt0) cc_final: 0.8617 (tm-30) REVERT: t 25 LYS cc_start: 0.9326 (mtpp) cc_final: 0.9085 (ttmm) outliers start: 25 outliers final: 13 residues processed: 378 average time/residue: 2.6309 time to fit residues: 1215.8996 Evaluate side-chains 362 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 348 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain i residue 186 ASP Chi-restraints excluded: chain k residue 92 MET Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain r residue 81 GLN Chi-restraints excluded: chain u residue 168 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 213 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 428 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 393 optimal weight: 0.8980 chunk 402 optimal weight: 6.9990 chunk 316 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN u 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074789 restraints weight = 182887.520| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.03 r_work: 0.2986 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 37359 Z= 0.163 Angle : 0.477 9.962 50447 Z= 0.245 Chirality : 0.040 0.140 5821 Planarity : 0.004 0.093 6529 Dihedral : 5.591 75.360 5219 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.38 % Allowed : 12.27 % Favored : 87.35 % 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: 1.09 (0.12), residues: 4663 helix: 1.85 (0.11), residues: 2401 sheet: -0.10 (0.20), residues: 643 loop : -0.60 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS s 122 PHE 0.014 0.001 PHE l 17 TYR 0.012 0.001 TYR F 77 ARG 0.018 0.000 ARG k 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9326 Ramachandran restraints generated. 4663 Oldfield, 0 Emsley, 4663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue ILE 215 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 357 time to evaluate : 4.513 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: C 160 ASN cc_start: 0.8489 (m-40) cc_final: 0.7986 (m110) REVERT: D 185 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8107 (mm-30) REVERT: D 406 GLN cc_start: 0.9109 (mt0) cc_final: 0.8861 (mm-40) REVERT: j 15 ARG cc_start: 0.8247 (ttp-170) cc_final: 0.7674 (ttm110) REVERT: l 7 ILE cc_start: 0.9325 (pt) cc_final: 0.9093 (mm) REVERT: l 136 GLU cc_start: 0.8740 (tt0) cc_final: 0.8454 (tm-30) REVERT: m 162 GLU cc_start: 0.8609 (pm20) cc_final: 0.8190 (mp0) REVERT: n 14 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: p 34 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8350 (tp40) REVERT: p 149 MET cc_start: 0.8992 (mmm) cc_final: 0.8676 (mmm) REVERT: s 5 MET cc_start: 0.8324 (mmm) cc_final: 0.8101 (mmt) REVERT: s 149 MET cc_start: 0.8930 (mmm) cc_final: 0.8689 (tpp) REVERT: s 181 GLU cc_start: 0.8884 (tt0) cc_final: 0.8624 (tm-30) REVERT: t 25 LYS cc_start: 0.9350 (mtpp) cc_final: 0.9107 (ttmm) outliers start: 15 outliers final: 8 residues processed: 367 average time/residue: 2.6282 time to fit residues: 1179.9366 Evaluate side-chains 358 residues out of total 3963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 349 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain k residue 113 CYS Chi-restraints excluded: chain l residue 153 MET Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain r residue 81 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 371 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 67 optimal weight: 0.0070 chunk 184 optimal weight: 10.0000 chunk 391 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 438 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN F 342 ASN t 41 ASN u 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075689 restraints weight = 183679.652| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.04 r_work: 0.3007 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37359 Z= 0.141 Angle : 0.471 9.634 50447 Z= 0.240 Chirality : 0.040 0.140 5821 Planarity : 0.003 0.078 6529 Dihedral : 5.484 77.468 5219 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.30 % Allowed : 12.34 % Favored : 87.35 % 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: 1.22 (0.12), residues: 4663 helix: 1.94 (0.11), residues: 2401 sheet: -0.13 (0.20), residues: 617 loop : -0.46 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS s 122 PHE 0.013 0.001 PHE l 17 TYR 0.023 0.001 TYR F 77 ARG 0.012 0.000 ARG k 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51743.83 seconds wall clock time: 880 minutes 41.98 seconds (52841.98 seconds total)