Starting phenix.real_space_refine on Mon Dec 30 02:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3p_18132/12_2024/8q3p_18132.cif" } resolution = 3.5 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= 0.015 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 18 5.21 5 S 306 5.16 5 C 37548 2.51 5 N 10638 2.21 5 O 11376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59922 Number of models: 1 Model: "" Number of chains: 2 Chain: "a" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3301 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "a" 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} Restraints were copied for chains: c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, r Time building chain proxies: 10.71, per 1000 atoms: 0.18 Number of scatterers: 59922 At special positions: 0 Unit cell: (139.776, 140.608, 277.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 36 15.00 Mg 18 11.99 O 11376 8.00 N 10638 7.00 C 37548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.61 Conformation dependent library (CDL) restraints added in 5.8 seconds 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14076 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 72 sheets defined 48.7% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'a' and resid 2 through 9 removed outlier: 3.632A pdb=" N LEU a 6 " --> pdb=" O ASN a 2 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR a 16 " --> pdb=" O SER a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 45 Processing helix chain 'a' and resid 82 through 89 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU a 164 " --> pdb=" O ARG a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU a 218 " --> pdb=" O GLU a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL a 289 " --> pdb=" O THR a 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG a 296 " --> pdb=" O ASN a 292 " (cutoff:3.500A) Proline residue: a 297 - end of helix Processing helix chain 'a' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU a 329 " --> pdb=" O SER a 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL a 330 " --> pdb=" O LYS a 326 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA a 350 " --> pdb=" O SER a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU a 377 " --> pdb=" O THR a 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN a 378 " --> pdb=" O GLN a 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS a 379 " --> pdb=" O GLU a 375 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 406 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE a 412 " --> pdb=" O THR a 408 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU r 6 " --> pdb=" O ASN r 2 " (cutoff:3.500A) Processing helix chain 'r' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR r 16 " --> pdb=" O SER r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 45 Processing helix chain 'r' and resid 82 through 89 Processing helix chain 'r' and resid 123 through 128 Processing helix chain 'r' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU r 164 " --> pdb=" O ARG r 160 " (cutoff:3.500A) Processing helix chain 'r' and resid 183 through 199 Processing helix chain 'r' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU r 218 " --> pdb=" O GLU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS r 239 " --> pdb=" O PRO r 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS r 256 " --> pdb=" O ARG r 252 " (cutoff:3.500A) Processing helix chain 'r' and resid 266 through 278 Processing helix chain 'r' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL r 289 " --> pdb=" O THR r 286 " (cutoff:3.500A) Processing helix chain 'r' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG r 296 " --> pdb=" O ASN r 292 " (cutoff:3.500A) Proline residue: r 297 - end of helix Processing helix chain 'r' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU r 329 " --> pdb=" O SER r 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL r 330 " --> pdb=" O LYS r 326 " (cutoff:3.500A) Processing helix chain 'r' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA r 350 " --> pdb=" O SER r 346 " (cutoff:3.500A) Processing helix chain 'r' and resid 373 through 388 removed outlier: 3.587A pdb=" N LEU r 377 " --> pdb=" O THR r 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN r 378 " --> pdb=" O GLN r 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS r 379 " --> pdb=" O GLU r 375 " (cutoff:3.500A) Processing helix chain 'r' and resid 391 through 406 Processing helix chain 'r' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE r 412 " --> pdb=" O THR r 408 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU q 6 " --> pdb=" O ASN q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 10 through 22 removed outlier: 3.873A pdb=" N THR q 16 " --> pdb=" O SER q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 45 Processing helix chain 'q' and resid 82 through 89 Processing helix chain 'q' and resid 123 through 128 Processing helix chain 'q' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU q 164 " --> pdb=" O ARG q 160 " (cutoff:3.500A) Processing helix chain 'q' and resid 183 through 199 Processing helix chain 'q' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU q 218 " --> pdb=" O GLU q 214 " (cutoff:3.500A) Processing helix chain 'q' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS q 239 " --> pdb=" O PRO q 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS q 256 " --> pdb=" O ARG q 252 " (cutoff:3.500A) Processing helix chain 'q' and resid 266 through 278 Processing helix chain 'q' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL q 289 " --> pdb=" O THR q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG q 296 " --> pdb=" O ASN q 292 " (cutoff:3.500A) Proline residue: q 297 - end of helix Processing helix chain 'q' and resid 325 through 335 removed outlier: 4.163A pdb=" N GLU q 329 " --> pdb=" O SER q 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL q 330 " --> pdb=" O LYS q 326 " (cutoff:3.500A) Processing helix chain 'q' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA q 350 " --> pdb=" O SER q 346 " (cutoff:3.500A) Processing helix chain 'q' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU q 377 " --> pdb=" O THR q 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN q 378 " --> pdb=" O GLN q 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS q 379 " --> pdb=" O GLU q 375 " (cutoff:3.500A) Processing helix chain 'q' and resid 391 through 406 Processing helix chain 'q' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE q 412 " --> pdb=" O THR q 408 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU p 6 " --> pdb=" O ASN p 2 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR p 16 " --> pdb=" O SER p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 30 through 45 Processing helix chain 'p' and resid 82 through 89 Processing helix chain 'p' and resid 123 through 128 Processing helix chain 'p' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU p 164 " --> pdb=" O ARG p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 183 through 199 Processing helix chain 'p' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU p 218 " --> pdb=" O GLU p 214 " (cutoff:3.500A) Processing helix chain 'p' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS p 239 " --> pdb=" O PRO p 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS p 256 " --> pdb=" O ARG p 252 " (cutoff:3.500A) Processing helix chain 'p' and resid 266 through 278 Processing helix chain 'p' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL p 289 " --> pdb=" O THR p 286 " (cutoff:3.500A) Processing helix chain 'p' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG p 296 " --> pdb=" O ASN p 292 " (cutoff:3.500A) Proline residue: p 297 - end of helix Processing helix chain 'p' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU p 329 " --> pdb=" O SER p 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL p 330 " --> pdb=" O LYS p 326 " (cutoff:3.500A) Processing helix chain 'p' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA p 350 " --> pdb=" O SER p 346 " (cutoff:3.500A) Processing helix chain 'p' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU p 377 " --> pdb=" O THR p 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN p 378 " --> pdb=" O GLN p 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS p 379 " --> pdb=" O GLU p 375 " (cutoff:3.500A) Processing helix chain 'p' and resid 391 through 406 Processing helix chain 'p' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE p 412 " --> pdb=" O THR p 408 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU o 6 " --> pdb=" O ASN o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR o 16 " --> pdb=" O SER o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 30 through 45 Processing helix chain 'o' and resid 82 through 89 Processing helix chain 'o' and resid 123 through 128 Processing helix chain 'o' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU o 164 " --> pdb=" O ARG o 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 183 through 199 Processing helix chain 'o' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU o 218 " --> pdb=" O GLU o 214 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS o 239 " --> pdb=" O PRO o 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS o 256 " --> pdb=" O ARG o 252 " (cutoff:3.500A) Processing helix chain 'o' and resid 266 through 278 Processing helix chain 'o' and resid 285 through 289 removed outlier: 4.034A pdb=" N VAL o 289 " --> pdb=" O THR o 286 " (cutoff:3.500A) Processing helix chain 'o' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG o 296 " --> pdb=" O ASN o 292 " (cutoff:3.500A) Proline residue: o 297 - end of helix Processing helix chain 'o' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU o 329 " --> pdb=" O SER o 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL o 330 " --> pdb=" O LYS o 326 " (cutoff:3.500A) Processing helix chain 'o' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA o 350 " --> pdb=" O SER o 346 " (cutoff:3.500A) Processing helix chain 'o' and resid 373 through 388 removed outlier: 3.589A pdb=" N LEU o 377 " --> pdb=" O THR o 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN o 378 " --> pdb=" O GLN o 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS o 379 " --> pdb=" O GLU o 375 " (cutoff:3.500A) Processing helix chain 'o' and resid 391 through 406 Processing helix chain 'o' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE o 412 " --> pdb=" O THR o 408 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 9 removed outlier: 3.632A pdb=" N LEU n 6 " --> pdb=" O ASN n 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR n 16 " --> pdb=" O SER n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 30 through 45 Processing helix chain 'n' and resid 82 through 89 Processing helix chain 'n' and resid 123 through 128 Processing helix chain 'n' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU n 164 " --> pdb=" O ARG n 160 " (cutoff:3.500A) Processing helix chain 'n' and resid 183 through 199 Processing helix chain 'n' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU n 218 " --> pdb=" O GLU n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 235 through 256 removed outlier: 3.553A pdb=" N HIS n 239 " --> pdb=" O PRO n 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS n 256 " --> pdb=" O ARG n 252 " (cutoff:3.500A) Processing helix chain 'n' and resid 266 through 278 Processing helix chain 'n' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL n 289 " --> pdb=" O THR n 286 " (cutoff:3.500A) Processing helix chain 'n' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG n 296 " --> pdb=" O ASN n 292 " (cutoff:3.500A) Proline residue: n 297 - end of helix Processing helix chain 'n' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU n 329 " --> pdb=" O SER n 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL n 330 " --> pdb=" O LYS n 326 " (cutoff:3.500A) Processing helix chain 'n' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA n 350 " --> pdb=" O SER n 346 " (cutoff:3.500A) Processing helix chain 'n' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU n 377 " --> pdb=" O THR n 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN n 378 " --> pdb=" O GLN n 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS n 379 " --> pdb=" O GLU n 375 " (cutoff:3.500A) Processing helix chain 'n' and resid 391 through 406 Processing helix chain 'n' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE n 412 " --> pdb=" O THR n 408 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 9 removed outlier: 3.632A pdb=" N LEU m 6 " --> pdb=" O ASN m 2 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 45 Processing helix chain 'm' and resid 82 through 89 Processing helix chain 'm' and resid 123 through 128 Processing helix chain 'm' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU m 164 " --> pdb=" O ARG m 160 " (cutoff:3.500A) Processing helix chain 'm' and resid 183 through 199 Processing helix chain 'm' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU m 218 " --> pdb=" O GLU m 214 " (cutoff:3.500A) Processing helix chain 'm' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS m 239 " --> pdb=" O PRO m 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS m 256 " --> pdb=" O ARG m 252 " (cutoff:3.500A) Processing helix chain 'm' and resid 266 through 278 Processing helix chain 'm' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL m 289 " --> pdb=" O THR m 286 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG m 296 " --> pdb=" O ASN m 292 " (cutoff:3.500A) Proline residue: m 297 - end of helix Processing helix chain 'm' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU m 329 " --> pdb=" O SER m 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL m 330 " --> pdb=" O LYS m 326 " (cutoff:3.500A) Processing helix chain 'm' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA m 350 " --> pdb=" O SER m 346 " (cutoff:3.500A) Processing helix chain 'm' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU m 377 " --> pdb=" O THR m 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN m 378 " --> pdb=" O GLN m 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS m 379 " --> pdb=" O GLU m 375 " (cutoff:3.500A) Processing helix chain 'm' and resid 391 through 406 Processing helix chain 'm' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE m 412 " --> pdb=" O THR m 408 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 45 Processing helix chain 'l' and resid 82 through 89 Processing helix chain 'l' and resid 123 through 128 Processing helix chain 'l' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU l 164 " --> pdb=" O ARG l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 199 Processing helix chain 'l' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU l 218 " --> pdb=" O GLU l 214 " (cutoff:3.500A) Processing helix chain 'l' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS l 239 " --> pdb=" O PRO l 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS l 256 " --> pdb=" O ARG l 252 " (cutoff:3.500A) Processing helix chain 'l' and resid 266 through 278 Processing helix chain 'l' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL l 289 " --> pdb=" O THR l 286 " (cutoff:3.500A) Processing helix chain 'l' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG l 296 " --> pdb=" O ASN l 292 " (cutoff:3.500A) Proline residue: l 297 - end of helix Processing helix chain 'l' and resid 325 through 335 removed outlier: 4.163A pdb=" N GLU l 329 " --> pdb=" O SER l 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL l 330 " --> pdb=" O LYS l 326 " (cutoff:3.500A) Processing helix chain 'l' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA l 350 " --> pdb=" O SER l 346 " (cutoff:3.500A) Processing helix chain 'l' and resid 373 through 388 removed outlier: 3.589A pdb=" N LEU l 377 " --> pdb=" O THR l 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN l 378 " --> pdb=" O GLN l 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS l 379 " --> pdb=" O GLU l 375 " (cutoff:3.500A) Processing helix chain 'l' and resid 391 through 406 Processing helix chain 'l' and resid 408 through 417 removed outlier: 3.508A pdb=" N PHE l 412 " --> pdb=" O THR l 408 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU k 6 " --> pdb=" O ASN k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 45 Processing helix chain 'k' and resid 82 through 89 Processing helix chain 'k' and resid 123 through 128 Processing helix chain 'k' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU k 164 " --> pdb=" O ARG k 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 183 through 199 Processing helix chain 'k' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU k 218 " --> pdb=" O GLU k 214 " (cutoff:3.500A) Processing helix chain 'k' and resid 235 through 256 removed outlier: 3.553A pdb=" N HIS k 239 " --> pdb=" O PRO k 235 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS k 256 " --> pdb=" O ARG k 252 " (cutoff:3.500A) Processing helix chain 'k' and resid 266 through 278 Processing helix chain 'k' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL k 289 " --> pdb=" O THR k 286 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 303 removed outlier: 4.028A pdb=" N ARG k 296 " --> pdb=" O ASN k 292 " (cutoff:3.500A) Proline residue: k 297 - end of helix Processing helix chain 'k' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU k 329 " --> pdb=" O SER k 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL k 330 " --> pdb=" O LYS k 326 " (cutoff:3.500A) Processing helix chain 'k' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA k 350 " --> pdb=" O SER k 346 " (cutoff:3.500A) Processing helix chain 'k' and resid 373 through 388 removed outlier: 3.589A pdb=" N LEU k 377 " --> pdb=" O THR k 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN k 378 " --> pdb=" O GLN k 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS k 379 " --> pdb=" O GLU k 375 " (cutoff:3.500A) Processing helix chain 'k' and resid 391 through 406 Processing helix chain 'k' and resid 408 through 417 removed outlier: 3.510A pdb=" N PHE k 412 " --> pdb=" O THR k 408 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU j 6 " --> pdb=" O ASN j 2 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR j 16 " --> pdb=" O SER j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 45 Processing helix chain 'j' and resid 82 through 89 Processing helix chain 'j' and resid 123 through 128 Processing helix chain 'j' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU j 164 " --> pdb=" O ARG j 160 " (cutoff:3.500A) Processing helix chain 'j' and resid 183 through 199 Processing helix chain 'j' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU j 218 " --> pdb=" O GLU j 214 " (cutoff:3.500A) Processing helix chain 'j' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS j 239 " --> pdb=" O PRO j 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS j 256 " --> pdb=" O ARG j 252 " (cutoff:3.500A) Processing helix chain 'j' and resid 266 through 278 Processing helix chain 'j' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL j 289 " --> pdb=" O THR j 286 " (cutoff:3.500A) Processing helix chain 'j' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG j 296 " --> pdb=" O ASN j 292 " (cutoff:3.500A) Proline residue: j 297 - end of helix Processing helix chain 'j' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU j 329 " --> pdb=" O SER j 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL j 330 " --> pdb=" O LYS j 326 " (cutoff:3.500A) Processing helix chain 'j' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA j 350 " --> pdb=" O SER j 346 " (cutoff:3.500A) Processing helix chain 'j' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU j 377 " --> pdb=" O THR j 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN j 378 " --> pdb=" O GLN j 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS j 379 " --> pdb=" O GLU j 375 " (cutoff:3.500A) Processing helix chain 'j' and resid 391 through 406 Processing helix chain 'j' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE j 412 " --> pdb=" O THR j 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU b 6 " --> pdb=" O ASN b 2 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR b 16 " --> pdb=" O SER b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 45 Processing helix chain 'b' and resid 82 through 89 Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU b 164 " --> pdb=" O ARG b 160 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU b 218 " --> pdb=" O GLU b 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.553A pdb=" N HIS b 239 " --> pdb=" O PRO b 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 285 through 289 removed outlier: 4.034A pdb=" N VAL b 289 " --> pdb=" O THR b 286 " (cutoff:3.500A) Processing helix chain 'b' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG b 296 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Proline residue: b 297 - end of helix Processing helix chain 'b' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU b 329 " --> pdb=" O SER b 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL b 330 " --> pdb=" O LYS b 326 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA b 350 " --> pdb=" O SER b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 388 removed outlier: 3.589A pdb=" N LEU b 377 " --> pdb=" O THR b 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN b 378 " --> pdb=" O GLN b 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS b 379 " --> pdb=" O GLU b 375 " (cutoff:3.500A) Processing helix chain 'b' and resid 391 through 406 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE b 412 " --> pdb=" O THR b 408 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 9 removed outlier: 3.632A pdb=" N LEU c 6 " --> pdb=" O ASN c 2 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR c 16 " --> pdb=" O SER c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 45 Processing helix chain 'c' and resid 82 through 89 Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU c 164 " --> pdb=" O ARG c 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU c 218 " --> pdb=" O GLU c 214 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.553A pdb=" N HIS c 239 " --> pdb=" O PRO c 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL c 289 " --> pdb=" O THR c 286 " (cutoff:3.500A) Processing helix chain 'c' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG c 296 " --> pdb=" O ASN c 292 " (cutoff:3.500A) Proline residue: c 297 - end of helix Processing helix chain 'c' and resid 325 through 335 removed outlier: 4.163A pdb=" N GLU c 329 " --> pdb=" O SER c 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL c 330 " --> pdb=" O LYS c 326 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA c 350 " --> pdb=" O SER c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 388 removed outlier: 3.587A pdb=" N LEU c 377 " --> pdb=" O THR c 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN c 378 " --> pdb=" O GLN c 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS c 379 " --> pdb=" O GLU c 375 " (cutoff:3.500A) Processing helix chain 'c' and resid 391 through 406 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE c 412 " --> pdb=" O THR c 408 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU d 6 " --> pdb=" O ASN d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 45 Processing helix chain 'd' and resid 82 through 89 Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU d 164 " --> pdb=" O ARG d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU d 218 " --> pdb=" O GLU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL d 289 " --> pdb=" O THR d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 303 removed outlier: 4.028A pdb=" N ARG d 296 " --> pdb=" O ASN d 292 " (cutoff:3.500A) Proline residue: d 297 - end of helix Processing helix chain 'd' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU d 329 " --> pdb=" O SER d 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL d 330 " --> pdb=" O LYS d 326 " (cutoff:3.500A) Processing helix chain 'd' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA d 350 " --> pdb=" O SER d 346 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU d 377 " --> pdb=" O THR d 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN d 378 " --> pdb=" O GLN d 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS d 379 " --> pdb=" O GLU d 375 " (cutoff:3.500A) Processing helix chain 'd' and resid 391 through 406 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.510A pdb=" N PHE d 412 " --> pdb=" O THR d 408 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU e 6 " --> pdb=" O ASN e 2 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 22 removed outlier: 3.872A pdb=" N THR e 16 " --> pdb=" O SER e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 45 Processing helix chain 'e' and resid 82 through 89 Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU e 164 " --> pdb=" O ARG e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU e 218 " --> pdb=" O GLU e 214 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS e 239 " --> pdb=" O PRO e 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL e 289 " --> pdb=" O THR e 286 " (cutoff:3.500A) Processing helix chain 'e' and resid 290 through 303 removed outlier: 4.028A pdb=" N ARG e 296 " --> pdb=" O ASN e 292 " (cutoff:3.500A) Proline residue: e 297 - end of helix Processing helix chain 'e' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU e 329 " --> pdb=" O SER e 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL e 330 " --> pdb=" O LYS e 326 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA e 350 " --> pdb=" O SER e 346 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU e 377 " --> pdb=" O THR e 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN e 378 " --> pdb=" O GLN e 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS e 379 " --> pdb=" O GLU e 375 " (cutoff:3.500A) Processing helix chain 'e' and resid 391 through 406 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE e 412 " --> pdb=" O THR e 408 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU f 6 " --> pdb=" O ASN f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR f 16 " --> pdb=" O SER f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 45 Processing helix chain 'f' and resid 82 through 89 Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU f 164 " --> pdb=" O ARG f 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU f 218 " --> pdb=" O GLU f 214 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS f 239 " --> pdb=" O PRO f 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 285 through 289 removed outlier: 4.034A pdb=" N VAL f 289 " --> pdb=" O THR f 286 " (cutoff:3.500A) Processing helix chain 'f' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG f 296 " --> pdb=" O ASN f 292 " (cutoff:3.500A) Proline residue: f 297 - end of helix Processing helix chain 'f' and resid 325 through 335 removed outlier: 4.163A pdb=" N GLU f 329 " --> pdb=" O SER f 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL f 330 " --> pdb=" O LYS f 326 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA f 350 " --> pdb=" O SER f 346 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU f 377 " --> pdb=" O THR f 373 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLN f 378 " --> pdb=" O GLN f 374 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS f 379 " --> pdb=" O GLU f 375 " (cutoff:3.500A) Processing helix chain 'f' and resid 391 through 406 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.508A pdb=" N PHE f 412 " --> pdb=" O THR f 408 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU g 6 " --> pdb=" O ASN g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 45 Processing helix chain 'g' and resid 82 through 89 Processing helix chain 'g' and resid 123 through 128 Processing helix chain 'g' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU g 164 " --> pdb=" O ARG g 160 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 199 Processing helix chain 'g' and resid 212 through 223 removed outlier: 3.718A pdb=" N GLU g 218 " --> pdb=" O GLU g 214 " (cutoff:3.500A) Processing helix chain 'g' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS g 239 " --> pdb=" O PRO g 235 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS g 256 " --> pdb=" O ARG g 252 " (cutoff:3.500A) Processing helix chain 'g' and resid 266 through 278 Processing helix chain 'g' and resid 285 through 289 removed outlier: 4.035A pdb=" N VAL g 289 " --> pdb=" O THR g 286 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG g 296 " --> pdb=" O ASN g 292 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing helix chain 'g' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU g 329 " --> pdb=" O SER g 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL g 330 " --> pdb=" O LYS g 326 " (cutoff:3.500A) Processing helix chain 'g' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA g 350 " --> pdb=" O SER g 346 " (cutoff:3.500A) Processing helix chain 'g' and resid 373 through 388 removed outlier: 3.589A pdb=" N LEU g 377 " --> pdb=" O THR g 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN g 378 " --> pdb=" O GLN g 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS g 379 " --> pdb=" O GLU g 375 " (cutoff:3.500A) Processing helix chain 'g' and resid 391 through 406 Processing helix chain 'g' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE g 412 " --> pdb=" O THR g 408 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 9 removed outlier: 3.632A pdb=" N LEU h 6 " --> pdb=" O ASN h 2 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 45 Processing helix chain 'h' and resid 82 through 89 Processing helix chain 'h' and resid 123 through 128 Processing helix chain 'h' and resid 157 through 166 removed outlier: 3.625A pdb=" N LEU h 164 " --> pdb=" O ARG h 160 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 Processing helix chain 'h' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU h 218 " --> pdb=" O GLU h 214 " (cutoff:3.500A) Processing helix chain 'h' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS h 239 " --> pdb=" O PRO h 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS h 256 " --> pdb=" O ARG h 252 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 278 Processing helix chain 'h' and resid 285 through 289 removed outlier: 4.034A pdb=" N VAL h 289 " --> pdb=" O THR h 286 " (cutoff:3.500A) Processing helix chain 'h' and resid 290 through 303 removed outlier: 4.028A pdb=" N ARG h 296 " --> pdb=" O ASN h 292 " (cutoff:3.500A) Proline residue: h 297 - end of helix Processing helix chain 'h' and resid 325 through 335 removed outlier: 4.163A pdb=" N GLU h 329 " --> pdb=" O SER h 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL h 330 " --> pdb=" O LYS h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 346 through 352 removed outlier: 3.531A pdb=" N ALA h 350 " --> pdb=" O SER h 346 " (cutoff:3.500A) Processing helix chain 'h' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU h 377 " --> pdb=" O THR h 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN h 378 " --> pdb=" O GLN h 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS h 379 " --> pdb=" O GLU h 375 " (cutoff:3.500A) Processing helix chain 'h' and resid 391 through 406 Processing helix chain 'h' and resid 408 through 417 removed outlier: 3.510A pdb=" N PHE h 412 " --> pdb=" O THR h 408 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 9 removed outlier: 3.633A pdb=" N LEU i 6 " --> pdb=" O ASN i 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 22 removed outlier: 3.871A pdb=" N THR i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 45 Processing helix chain 'i' and resid 82 through 89 Processing helix chain 'i' and resid 123 through 128 Processing helix chain 'i' and resid 157 through 166 removed outlier: 3.624A pdb=" N LEU i 164 " --> pdb=" O ARG i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 183 through 199 Processing helix chain 'i' and resid 212 through 223 removed outlier: 3.719A pdb=" N GLU i 218 " --> pdb=" O GLU i 214 " (cutoff:3.500A) Processing helix chain 'i' and resid 235 through 256 removed outlier: 3.554A pdb=" N HIS i 239 " --> pdb=" O PRO i 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS i 256 " --> pdb=" O ARG i 252 " (cutoff:3.500A) Processing helix chain 'i' and resid 266 through 278 Processing helix chain 'i' and resid 285 through 289 removed outlier: 4.034A pdb=" N VAL i 289 " --> pdb=" O THR i 286 " (cutoff:3.500A) Processing helix chain 'i' and resid 290 through 303 removed outlier: 4.027A pdb=" N ARG i 296 " --> pdb=" O ASN i 292 " (cutoff:3.500A) Proline residue: i 297 - end of helix Processing helix chain 'i' and resid 325 through 335 removed outlier: 4.162A pdb=" N GLU i 329 " --> pdb=" O SER i 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL i 330 " --> pdb=" O LYS i 326 " (cutoff:3.500A) Processing helix chain 'i' and resid 346 through 352 removed outlier: 3.532A pdb=" N ALA i 350 " --> pdb=" O SER i 346 " (cutoff:3.500A) Processing helix chain 'i' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU i 377 " --> pdb=" O THR i 373 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN i 378 " --> pdb=" O GLN i 374 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS i 379 " --> pdb=" O GLU i 375 " (cutoff:3.500A) Processing helix chain 'i' and resid 391 through 406 Processing helix chain 'i' and resid 408 through 417 removed outlier: 3.509A pdb=" N PHE i 412 " --> pdb=" O THR i 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU a 114 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG a 102 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR a 318 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU a 204 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU a 208 " --> pdb=" O SER a 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'r' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE r 79 " --> pdb=" O LEU r 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU r 114 " --> pdb=" O ARG r 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG r 102 " --> pdb=" O LEU r 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL r 116 " --> pdb=" O LYS r 100 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS r 100 " --> pdb=" O VAL r 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE r 49 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'r' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR r 318 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL r 203 " --> pdb=" O ILE r 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU r 263 " --> pdb=" O VAL r 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET r 205 " --> pdb=" O LEU r 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU r 204 " --> pdb=" O GLU r 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL r 228 " --> pdb=" O LEU r 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL r 206 " --> pdb=" O VAL r 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER r 230 " --> pdb=" O VAL r 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU r 208 " --> pdb=" O SER r 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'r' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'r' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE r 168 " --> pdb=" O LEU r 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'q' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE q 79 " --> pdb=" O LEU q 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU q 114 " --> pdb=" O ARG q 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG q 102 " --> pdb=" O LEU q 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL q 116 " --> pdb=" O LYS q 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS q 100 " --> pdb=" O VAL q 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE q 49 " --> pdb=" O ILE q 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'q' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR q 318 " --> pdb=" O LEU q 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL q 203 " --> pdb=" O ILE q 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU q 263 " --> pdb=" O VAL q 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET q 205 " --> pdb=" O LEU q 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU q 204 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL q 228 " --> pdb=" O LEU q 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL q 206 " --> pdb=" O VAL q 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER q 230 " --> pdb=" O VAL q 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU q 208 " --> pdb=" O SER q 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'q' and resid 138 through 139 Processing sheet with id=AB3, first strand: chain 'q' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE q 168 " --> pdb=" O LEU q 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE p 79 " --> pdb=" O LEU p 65 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU p 114 " --> pdb=" O ARG p 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG p 102 " --> pdb=" O LEU p 114 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL p 116 " --> pdb=" O LYS p 100 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS p 100 " --> pdb=" O VAL p 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE p 49 " --> pdb=" O ILE p 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR p 318 " --> pdb=" O LEU p 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL p 203 " --> pdb=" O ILE p 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU p 263 " --> pdb=" O VAL p 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET p 205 " --> pdb=" O LEU p 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU p 204 " --> pdb=" O GLU p 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL p 228 " --> pdb=" O LEU p 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL p 206 " --> pdb=" O VAL p 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER p 230 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU p 208 " --> pdb=" O SER p 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'p' and resid 138 through 139 Processing sheet with id=AB7, first strand: chain 'p' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE p 168 " --> pdb=" O LEU p 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'o' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE o 79 " --> pdb=" O LEU o 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU o 114 " --> pdb=" O ARG o 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG o 102 " --> pdb=" O LEU o 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL o 116 " --> pdb=" O LYS o 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS o 100 " --> pdb=" O VAL o 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE o 49 " --> pdb=" O ILE o 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'o' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR o 318 " --> pdb=" O LEU o 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL o 203 " --> pdb=" O ILE o 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU o 263 " --> pdb=" O VAL o 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET o 205 " --> pdb=" O LEU o 263 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU o 204 " --> pdb=" O GLU o 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL o 228 " --> pdb=" O LEU o 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL o 206 " --> pdb=" O VAL o 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER o 230 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU o 208 " --> pdb=" O SER o 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'o' and resid 138 through 139 Processing sheet with id=AC2, first strand: chain 'o' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE o 168 " --> pdb=" O LEU o 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'n' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE n 79 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU n 114 " --> pdb=" O ARG n 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG n 102 " --> pdb=" O LEU n 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL n 116 " --> pdb=" O LYS n 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS n 100 " --> pdb=" O VAL n 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE n 49 " --> pdb=" O ILE n 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'n' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR n 318 " --> pdb=" O LEU n 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL n 203 " --> pdb=" O ILE n 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU n 263 " --> pdb=" O VAL n 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET n 205 " --> pdb=" O LEU n 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU n 204 " --> pdb=" O GLU n 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL n 228 " --> pdb=" O LEU n 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL n 206 " --> pdb=" O VAL n 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER n 230 " --> pdb=" O VAL n 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU n 208 " --> pdb=" O SER n 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'n' and resid 138 through 139 Processing sheet with id=AC6, first strand: chain 'n' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE n 168 " --> pdb=" O LEU n 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE m 79 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU m 114 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG m 102 " --> pdb=" O LEU m 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL m 116 " --> pdb=" O LYS m 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS m 100 " --> pdb=" O VAL m 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE m 49 " --> pdb=" O ILE m 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR m 318 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL m 203 " --> pdb=" O ILE m 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU m 263 " --> pdb=" O VAL m 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET m 205 " --> pdb=" O LEU m 263 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU m 204 " --> pdb=" O GLU m 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL m 228 " --> pdb=" O LEU m 204 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL m 206 " --> pdb=" O VAL m 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER m 230 " --> pdb=" O VAL m 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU m 208 " --> pdb=" O SER m 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'm' and resid 138 through 139 Processing sheet with id=AD1, first strand: chain 'm' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE m 168 " --> pdb=" O LEU m 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'l' and resid 49 through 57 removed outlier: 3.835A pdb=" N ILE l 79 " --> pdb=" O LEU l 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU l 114 " --> pdb=" O ARG l 102 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG l 102 " --> pdb=" O LEU l 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL l 116 " --> pdb=" O LYS l 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS l 100 " --> pdb=" O VAL l 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE l 49 " --> pdb=" O ILE l 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR l 318 " --> pdb=" O LEU l 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL l 203 " --> pdb=" O ILE l 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU l 263 " --> pdb=" O VAL l 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET l 205 " --> pdb=" O LEU l 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU l 204 " --> pdb=" O GLU l 226 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL l 228 " --> pdb=" O LEU l 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL l 206 " --> pdb=" O VAL l 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER l 230 " --> pdb=" O VAL l 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU l 208 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'l' and resid 138 through 139 Processing sheet with id=AD5, first strand: chain 'l' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE l 168 " --> pdb=" O LEU l 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE k 79 " --> pdb=" O LEU k 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU k 114 " --> pdb=" O ARG k 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG k 102 " --> pdb=" O LEU k 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL k 116 " --> pdb=" O LYS k 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS k 100 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE k 49 " --> pdb=" O ILE k 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR k 318 " --> pdb=" O LEU k 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL k 203 " --> pdb=" O ILE k 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU k 263 " --> pdb=" O VAL k 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET k 205 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU k 204 " --> pdb=" O GLU k 226 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL k 228 " --> pdb=" O LEU k 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL k 206 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER k 230 " --> pdb=" O VAL k 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU k 208 " --> pdb=" O SER k 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'k' and resid 138 through 139 Processing sheet with id=AD9, first strand: chain 'k' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE k 168 " --> pdb=" O LEU k 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'j' and resid 49 through 57 removed outlier: 3.835A pdb=" N ILE j 79 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU j 114 " --> pdb=" O ARG j 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG j 102 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL j 116 " --> pdb=" O LYS j 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS j 100 " --> pdb=" O VAL j 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE j 49 " --> pdb=" O ILE j 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'j' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR j 318 " --> pdb=" O LEU j 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL j 203 " --> pdb=" O ILE j 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU j 263 " --> pdb=" O VAL j 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET j 205 " --> pdb=" O LEU j 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU j 204 " --> pdb=" O GLU j 226 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL j 228 " --> pdb=" O LEU j 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL j 206 " --> pdb=" O VAL j 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER j 230 " --> pdb=" O VAL j 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU j 208 " --> pdb=" O SER j 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 138 through 139 Processing sheet with id=AE4, first strand: chain 'j' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE j 168 " --> pdb=" O LEU j 145 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU b 114 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG b 102 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR b 318 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU b 204 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 138 through 139 Processing sheet with id=AE8, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 49 through 57 removed outlier: 3.835A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU c 114 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG c 102 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR c 318 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU c 204 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 138 through 139 Processing sheet with id=AF3, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 49 through 57 removed outlier: 3.835A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU d 114 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG d 102 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR d 318 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU d 204 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 138 through 139 Processing sheet with id=AF7, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU e 114 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG e 102 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR e 318 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU e 204 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 138 through 139 Processing sheet with id=AG2, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU f 114 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG f 102 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR f 318 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU f 204 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 138 through 139 Processing sheet with id=AG6, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE g 79 " --> pdb=" O LEU g 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU g 114 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG g 102 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL g 116 " --> pdb=" O LYS g 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS g 100 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE g 49 " --> pdb=" O ILE g 101 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR g 318 " --> pdb=" O LEU g 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL g 203 " --> pdb=" O ILE g 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU g 263 " --> pdb=" O VAL g 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET g 205 " --> pdb=" O LEU g 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU g 204 " --> pdb=" O GLU g 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL g 228 " --> pdb=" O LEU g 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL g 206 " --> pdb=" O VAL g 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER g 230 " --> pdb=" O VAL g 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU g 208 " --> pdb=" O SER g 230 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 138 through 139 Processing sheet with id=AH1, first strand: chain 'g' and resid 144 through 145 removed outlier: 4.194A pdb=" N ILE g 168 " --> pdb=" O LEU g 145 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'h' and resid 49 through 57 removed outlier: 3.836A pdb=" N ILE h 79 " --> pdb=" O LEU h 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU h 114 " --> pdb=" O ARG h 102 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG h 102 " --> pdb=" O LEU h 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL h 116 " --> pdb=" O LYS h 100 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS h 100 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE h 49 " --> pdb=" O ILE h 101 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 138 through 139 removed outlier: 3.608A pdb=" N THR h 318 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL h 203 " --> pdb=" O ILE h 261 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU h 263 " --> pdb=" O VAL h 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET h 205 " --> pdb=" O LEU h 263 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU h 204 " --> pdb=" O GLU h 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL h 228 " --> pdb=" O LEU h 204 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL h 206 " --> pdb=" O VAL h 228 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER h 230 " --> pdb=" O VAL h 206 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU h 208 " --> pdb=" O SER h 230 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 138 through 139 Processing sheet with id=AH5, first strand: chain 'h' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE h 168 " --> pdb=" O LEU h 145 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 49 through 57 removed outlier: 3.835A pdb=" N ILE i 79 " --> pdb=" O LEU i 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU i 114 " --> pdb=" O ARG i 102 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG i 102 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL i 116 " --> pdb=" O LYS i 100 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS i 100 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE i 49 " --> pdb=" O ILE i 101 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'i' and resid 138 through 139 removed outlier: 3.607A pdb=" N THR i 318 " --> pdb=" O LEU i 264 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL i 203 " --> pdb=" O ILE i 261 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU i 263 " --> pdb=" O VAL i 203 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N MET i 205 " --> pdb=" O LEU i 263 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU i 204 " --> pdb=" O GLU i 226 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL i 228 " --> pdb=" O LEU i 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL i 206 " --> pdb=" O VAL i 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER i 230 " --> pdb=" O VAL i 206 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU i 208 " --> pdb=" O SER i 230 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'i' and resid 138 through 139 Processing sheet with id=AH9, first strand: chain 'i' and resid 144 through 145 removed outlier: 4.195A pdb=" N ILE i 168 " --> pdb=" O LEU i 145 " (cutoff:3.500A) 2826 hydrogen bonds defined for protein. 8100 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: 30.20 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 20373 1.35 - 1.47: 11971 1.47 - 1.58: 27830 1.58 - 1.70: 54 1.70 - 1.82: 594 Bond restraints: 60822 Sorted by residual: bond pdb=" CB PRO p 103 " pdb=" CG PRO p 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO b 103 " pdb=" CG PRO b 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO n 103 " pdb=" CG PRO n 103 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CB PRO l 103 " pdb=" CG PRO l 103 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.65e+00 bond pdb=" CB PRO k 103 " pdb=" CG PRO k 103 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.64e+00 ... (remaining 60817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 80169 2.47 - 4.95: 1449 4.95 - 7.42: 264 7.42 - 9.90: 90 9.90 - 12.37: 36 Bond angle restraints: 82008 Sorted by residual: angle pdb=" CA TRP n 381 " pdb=" CB TRP n 381 " pdb=" CG TRP n 381 " ideal model delta sigma weight residual 113.60 121.62 -8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CA TRP p 381 " pdb=" CB TRP p 381 " pdb=" CG TRP p 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP k 381 " pdb=" CB TRP k 381 " pdb=" CG TRP k 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP g 381 " pdb=" CB TRP g 381 " pdb=" CG TRP g 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" CA TRP j 381 " pdb=" CB TRP j 381 " pdb=" CG TRP j 381 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 ... (remaining 82003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 32817 21.87 - 43.74: 4245 43.74 - 65.61: 540 65.61 - 87.47: 72 87.47 - 109.34: 18 Dihedral angle restraints: 37692 sinusoidal: 15966 harmonic: 21726 Sorted by residual: dihedral pdb=" O1B ADP k1000 " pdb=" O3A ADP k1000 " pdb=" PB ADP k1000 " pdb=" PA ADP k1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.35 109.34 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O1B ADP r1000 " pdb=" O3A ADP r1000 " pdb=" PB ADP r1000 " pdb=" PA ADP r1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.34 109.34 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 -169.32 109.32 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 37689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 6107 0.033 - 0.066: 2039 0.066 - 0.098: 738 0.098 - 0.131: 389 0.131 - 0.164: 51 Chirality restraints: 9324 Sorted by residual: chirality pdb=" CA ASP b 150 " pdb=" N ASP b 150 " pdb=" C ASP b 150 " pdb=" CB ASP b 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ASP a 150 " pdb=" N ASP a 150 " pdb=" C ASP a 150 " pdb=" CB ASP a 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ASP f 150 " pdb=" N ASP f 150 " pdb=" C ASP f 150 " pdb=" CB ASP f 150 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 9321 not shown) Planarity restraints: 10620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP f 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP f 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP f 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP f 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP f 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP f 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP f 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP i 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP i 381 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP i 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP i 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP i 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP i 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 381 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP i 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 381 " 0.036 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP m 381 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP m 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP m 381 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 381 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP m 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP m 381 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 381 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 381 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP m 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 10617 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1179 2.61 - 3.18: 54006 3.18 - 3.76: 98734 3.76 - 4.33: 128474 4.33 - 4.90: 210980 Nonbonded interactions: 493373 Sorted by model distance: nonbonded pdb=" O2B ADP k1000 " pdb="MG MG k1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP n1000 " pdb="MG MG n1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP r1000 " pdb="MG MG r1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 2.041 2.170 nonbonded pdb=" O2B ADP c1000 " pdb="MG MG c1001 " model vdw 2.041 2.170 ... (remaining 493368 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' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 1.900 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 96.600 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.310 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 60822 Z= 0.245 Angle : 0.829 12.373 82008 Z= 0.400 Chirality : 0.042 0.164 9324 Planarity : 0.006 0.066 10620 Dihedral : 17.667 109.343 23616 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.67 % Allowed : 40.49 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.46 (0.09), residues: 7506 helix: 0.97 (0.09), residues: 3294 sheet: 0.23 (0.14), residues: 1170 loop : -0.29 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.013 TRP i 381 HIS 0.004 0.001 HIS b 239 PHE 0.016 0.001 PHE c 398 TYR 0.006 0.001 TYR m 332 ARG 0.011 0.001 ARG f 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1400 time to evaluate : 5.311 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: a 29 MET cc_start: 0.7373 (ptm) cc_final: 0.7093 (ptp) REVERT: a 205 MET cc_start: 0.8528 (tpp) cc_final: 0.8273 (mmt) REVERT: a 218 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8204 (pt0) REVERT: a 329 GLU cc_start: 0.8220 (mp0) cc_final: 0.7956 (mp0) REVERT: r 85 GLN cc_start: 0.9214 (mp10) cc_final: 0.8705 (mp10) REVERT: r 90 ASN cc_start: 0.7955 (t0) cc_final: 0.7696 (t0) REVERT: r 248 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8686 (mm-30) REVERT: r 299 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8742 (mmt180) REVERT: r 381 TRP cc_start: 0.8590 (t60) cc_final: 0.8286 (t60) REVERT: r 390 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6976 (ptt) REVERT: r 416 MET cc_start: 0.7301 (mmp) cc_final: 0.6786 (ttt) REVERT: q 1 MET cc_start: 0.7301 (mmm) cc_final: 0.6700 (tpt) REVERT: q 72 TYR cc_start: 0.9270 (m-10) cc_final: 0.8821 (m-10) REVERT: q 147 MET cc_start: 0.8590 (mmm) cc_final: 0.8181 (mmm) REVERT: q 162 LEU cc_start: 0.9443 (mm) cc_final: 0.9207 (tt) REVERT: q 204 LEU cc_start: 0.9029 (tp) cc_final: 0.8756 (tp) REVERT: q 241 GLN cc_start: 0.9195 (pt0) cc_final: 0.8779 (pp30) REVERT: q 244 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8445 (mm-30) REVERT: q 249 LYS cc_start: 0.9547 (ttpp) cc_final: 0.9217 (ttpt) REVERT: q 296 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8581 (mmm160) REVERT: q 299 ARG cc_start: 0.9148 (ttp80) cc_final: 0.8562 (ttp80) REVERT: q 411 ASP cc_start: 0.8840 (m-30) cc_final: 0.8568 (m-30) REVERT: p 87 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8674 (ptm160) REVERT: p 189 GLN cc_start: 0.9222 (mt0) cc_final: 0.8961 (mt0) REVERT: p 193 GLN cc_start: 0.9020 (tt0) cc_final: 0.8780 (tt0) REVERT: p 241 GLN cc_start: 0.8807 (pt0) cc_final: 0.8508 (tm-30) REVERT: p 394 ASP cc_start: 0.9017 (p0) cc_final: 0.8631 (p0) REVERT: o 41 GLN cc_start: 0.9065 (tp40) cc_final: 0.8780 (tp40) REVERT: o 193 GLN cc_start: 0.8804 (tt0) cc_final: 0.8544 (tt0) REVERT: o 205 MET cc_start: 0.8535 (tpp) cc_final: 0.8332 (mmt) REVERT: o 326 LYS cc_start: 0.9079 (tmtt) cc_final: 0.8761 (tptp) REVERT: o 329 GLU cc_start: 0.8533 (mp0) cc_final: 0.7886 (mp0) REVERT: o 396 MET cc_start: 0.9596 (tpp) cc_final: 0.8948 (tpp) REVERT: n 100 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9246 (ttmm) REVERT: n 193 GLN cc_start: 0.8748 (tt0) cc_final: 0.8528 (mt0) REVERT: n 326 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8785 (tmtt) REVERT: n 342 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8182 (mm-30) REVERT: n 410 ASP cc_start: 0.9151 (m-30) cc_final: 0.8876 (p0) REVERT: m 12 SER cc_start: 0.9257 (m) cc_final: 0.9006 (m) REVERT: m 100 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8846 (ptmm) REVERT: m 296 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8650 (mmm-85) REVERT: m 326 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8772 (tptt) REVERT: m 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8323 (mp0) REVERT: m 396 MET cc_start: 0.9059 (tpp) cc_final: 0.8749 (tpp) REVERT: m 403 LEU cc_start: 0.9268 (mm) cc_final: 0.8896 (mt) REVERT: l 193 GLN cc_start: 0.8456 (tt0) cc_final: 0.7888 (tm-30) REVERT: l 222 LEU cc_start: 0.9240 (tt) cc_final: 0.8967 (mt) REVERT: l 244 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7827 (mm-30) REVERT: l 326 LYS cc_start: 0.9291 (tmtt) cc_final: 0.9041 (tmtt) REVERT: l 342 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7963 (mm-30) REVERT: l 414 GLU cc_start: 0.8927 (pp20) cc_final: 0.8416 (pp20) REVERT: k 41 GLN cc_start: 0.8660 (tp40) cc_final: 0.8357 (tm-30) REVERT: k 325 SER cc_start: 0.7443 (t) cc_final: 0.6919 (p) REVERT: k 342 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8215 (mp0) REVERT: k 397 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8760 (mt-10) REVERT: j 1 MET cc_start: 0.6247 (mmm) cc_final: 0.6022 (mmm) REVERT: j 30 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6749 (mtp-110) REVERT: j 222 LEU cc_start: 0.9263 (tt) cc_final: 0.8989 (mt) REVERT: j 342 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7867 (pt0) REVERT: j 397 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8749 (mt-10) REVERT: j 415 MET cc_start: 0.9011 (ttp) cc_final: 0.8436 (ttp) REVERT: b 1 MET cc_start: 0.7065 (mmm) cc_final: 0.6821 (tpt) REVERT: b 21 MET cc_start: 0.8316 (ppp) cc_final: 0.7833 (tmm) REVERT: b 29 MET cc_start: 0.7790 (ptm) cc_final: 0.6585 (ptm) REVERT: b 85 GLN cc_start: 0.9464 (mp10) cc_final: 0.9052 (mp10) REVERT: b 215 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7866 (mp0) REVERT: b 244 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8399 (mm-30) REVERT: b 245 MET cc_start: 0.9099 (tpp) cc_final: 0.8819 (tpt) REVERT: b 253 LEU cc_start: 0.9455 (mt) cc_final: 0.9220 (mt) REVERT: b 342 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8291 (mp0) REVERT: c 6 LEU cc_start: 0.9273 (tt) cc_final: 0.8922 (pp) REVERT: c 12 SER cc_start: 0.9560 (m) cc_final: 0.9324 (p) REVERT: c 21 MET cc_start: 0.8421 (ppp) cc_final: 0.8001 (tmm) REVERT: c 30 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7366 (mtp-110) REVERT: c 52 ASP cc_start: 0.8693 (p0) cc_final: 0.8386 (p0) REVERT: c 59 GLN cc_start: 0.8494 (pm20) cc_final: 0.8292 (pm20) REVERT: c 90 ASN cc_start: 0.8390 (t0) cc_final: 0.8154 (t0) REVERT: c 241 GLN cc_start: 0.9084 (pt0) cc_final: 0.8522 (pp30) REVERT: c 292 ASN cc_start: 0.8481 (m-40) cc_final: 0.8193 (p0) REVERT: c 342 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8179 (pm20) REVERT: c 376 GLU cc_start: 0.8396 (tt0) cc_final: 0.8086 (tt0) REVERT: d 52 ASP cc_start: 0.8692 (p0) cc_final: 0.8438 (p0) REVERT: d 322 ASP cc_start: 0.9107 (p0) cc_final: 0.8846 (p0) REVERT: d 342 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7958 (mm-30) REVERT: d 374 GLN cc_start: 0.8904 (tp40) cc_final: 0.8634 (tp-100) REVERT: d 375 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8166 (mp0) REVERT: e 8 ASN cc_start: 0.9160 (m-40) cc_final: 0.8957 (m-40) REVERT: e 52 ASP cc_start: 0.8851 (p0) cc_final: 0.8418 (p0) REVERT: e 95 ASP cc_start: 0.9147 (m-30) cc_final: 0.8892 (m-30) REVERT: e 118 GLU cc_start: 0.8483 (tp30) cc_final: 0.8212 (tp30) REVERT: e 222 LEU cc_start: 0.9410 (tt) cc_final: 0.8909 (tt) REVERT: e 244 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8113 (mm-30) REVERT: e 274 TYR cc_start: 0.8989 (m-80) cc_final: 0.8771 (m-80) REVERT: e 326 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8562 (tptt) REVERT: e 342 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8007 (pt0) REVERT: g 327 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8388 (ttp) REVERT: g 342 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7952 (mt-10) REVERT: g 414 GLU cc_start: 0.8990 (pp20) cc_final: 0.8686 (pp20) REVERT: h 32 GLN cc_start: 0.8993 (mp10) cc_final: 0.8748 (mm-40) REVERT: h 110 TYR cc_start: 0.8606 (m-80) cc_final: 0.8298 (m-80) REVERT: h 378 GLN cc_start: 0.7906 (pm20) cc_final: 0.7420 (pm20) REVERT: h 410 ASP cc_start: 0.9393 (m-30) cc_final: 0.9185 (m-30) REVERT: h 414 GLU cc_start: 0.8787 (pp20) cc_final: 0.8523 (pp20) REVERT: i 8 ASN cc_start: 0.9281 (m-40) cc_final: 0.8963 (m-40) REVERT: i 12 SER cc_start: 0.9246 (m) cc_final: 0.9007 (p) REVERT: i 48 ASP cc_start: 0.8348 (p0) cc_final: 0.7954 (p0) REVERT: i 52 ASP cc_start: 0.8349 (p0) cc_final: 0.8067 (p0) REVERT: i 100 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9132 (ttmm) REVERT: i 342 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8117 (mp0) outliers start: 108 outliers final: 37 residues processed: 1452 average time/residue: 0.6011 time to fit residues: 1421.9386 Evaluate side-chains 999 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 960 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 70 SER Chi-restraints excluded: chain r residue 390 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 70 SER Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain p residue 70 SER Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 260 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 70 SER Chi-restraints excluded: chain n residue 260 VAL Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain j residue 70 SER Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain b residue 260 VAL Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain d residue 70 SER Chi-restraints excluded: chain d residue 260 VAL Chi-restraints excluded: chain e residue 260 VAL Chi-restraints excluded: chain e residue 380 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 380 MET Chi-restraints excluded: chain g residue 70 SER Chi-restraints excluded: chain g residue 260 VAL Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 327 MET Chi-restraints excluded: chain i residue 260 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 0.9980 chunk 559 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 377 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 chunk 578 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 chunk 670 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 ASN r 140 HIS r 344 HIS r 388 HIS q 42 HIS q 388 HIS p 59 GLN l 220 GLN l 374 GLN l 388 HIS k 193 GLN b 8 ASN b 193 GLN c 126 ASN c 172 GLN c 189 GLN c 388 HIS d 8 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 374 GLN i 126 ASN i 374 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 60822 Z= 0.239 Angle : 0.699 9.590 82008 Z= 0.344 Chirality : 0.045 0.169 9324 Planarity : 0.005 0.038 10620 Dihedral : 6.167 84.815 8438 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.51 % Allowed : 28.38 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.62 (0.10), residues: 7506 helix: 1.05 (0.09), residues: 3258 sheet: 0.64 (0.17), residues: 882 loop : -0.19 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP b 381 HIS 0.009 0.001 HIS r 388 PHE 0.019 0.001 PHE q 412 TYR 0.016 0.001 TYR c 110 ARG 0.008 0.001 ARG p 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 357 poor density : 1007 time to evaluate : 5.366 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: a 29 MET cc_start: 0.7701 (ptm) cc_final: 0.7237 (ptp) REVERT: a 215 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: a 329 GLU cc_start: 0.8355 (mp0) cc_final: 0.8033 (mp0) REVERT: r 244 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8444 (mm-30) REVERT: r 248 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8650 (mm-30) REVERT: r 376 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: r 396 MET cc_start: 0.8513 (tpt) cc_final: 0.7899 (tpt) REVERT: r 403 LEU cc_start: 0.8911 (tp) cc_final: 0.8604 (tp) REVERT: r 410 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8458 (p0) REVERT: r 416 MET cc_start: 0.7812 (mmp) cc_final: 0.7130 (ttt) REVERT: q 1 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6816 (tpt) REVERT: q 23 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8525 (mm) REVERT: q 244 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8529 (mm-30) REVERT: q 412 PHE cc_start: 0.8352 (t80) cc_final: 0.7961 (t80) REVERT: p 1 MET cc_start: 0.7180 (tpt) cc_final: 0.6831 (tpt) REVERT: p 33 ASP cc_start: 0.9182 (m-30) cc_final: 0.8927 (m-30) REVERT: p 91 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8826 (pp) REVERT: p 193 GLN cc_start: 0.8947 (tt0) cc_final: 0.8666 (tt0) REVERT: p 219 MET cc_start: 0.9447 (tpp) cc_final: 0.9181 (mmm) REVERT: p 222 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9049 (mp) REVERT: p 241 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: p 325 SER cc_start: 0.8224 (t) cc_final: 0.7797 (p) REVERT: p 342 GLU cc_start: 0.8300 (pm20) cc_final: 0.8011 (pm20) REVERT: p 394 ASP cc_start: 0.8921 (p0) cc_final: 0.8564 (p0) REVERT: p 417 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8964 (mmtm) REVERT: o 205 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: o 244 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8437 (mm-30) REVERT: o 326 LYS cc_start: 0.9096 (tmtt) cc_final: 0.8668 (tptp) REVERT: o 334 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8307 (mm-30) REVERT: o 397 GLU cc_start: 0.8685 (mp0) cc_final: 0.8373 (mp0) REVERT: n 41 GLN cc_start: 0.9037 (tp40) cc_final: 0.8568 (tp40) REVERT: n 44 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8667 (ttpp) REVERT: n 100 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9218 (ttmm) REVERT: n 193 GLN cc_start: 0.8708 (tt0) cc_final: 0.8427 (mt0) REVERT: n 205 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8488 (mtp) REVERT: n 326 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8830 (tmtt) REVERT: n 342 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8258 (mm-30) REVERT: n 411 ASP cc_start: 0.9120 (m-30) cc_final: 0.8852 (m-30) REVERT: m 44 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8717 (ptpp) REVERT: m 125 GLU cc_start: 0.8632 (mp0) cc_final: 0.8358 (pm20) REVERT: m 244 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8264 (mm-30) REVERT: m 296 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8675 (mmm-85) REVERT: m 326 LYS cc_start: 0.9238 (tmtt) cc_final: 0.9009 (tptt) REVERT: m 341 MET cc_start: 0.9089 (tmm) cc_final: 0.8847 (tmm) REVERT: m 342 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8499 (mp0) REVERT: m 354 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.6871 (t) REVERT: m 396 MET cc_start: 0.9139 (tpp) cc_final: 0.8894 (tpp) REVERT: m 397 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8789 (mm-30) REVERT: l 222 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8626 (mt) REVERT: l 244 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7917 (mm-30) REVERT: l 334 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8979 (mm-30) REVERT: l 342 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8050 (mm-30) REVERT: k 12 SER cc_start: 0.9116 (m) cc_final: 0.8752 (p) REVERT: k 13 GLU cc_start: 0.8539 (pm20) cc_final: 0.8265 (pm20) REVERT: k 41 GLN cc_start: 0.8554 (tp40) cc_final: 0.8085 (tm-30) REVERT: k 44 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8656 (ptpp) REVERT: k 56 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: k 60 ASP cc_start: 0.8862 (t0) cc_final: 0.8525 (t0) REVERT: k 78 ASP cc_start: 0.8657 (m-30) cc_final: 0.8418 (m-30) REVERT: k 325 SER cc_start: 0.7758 (t) cc_final: 0.7297 (p) REVERT: k 341 MET cc_start: 0.9033 (tmm) cc_final: 0.8722 (tmm) REVERT: k 342 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8348 (mp0) REVERT: j 1 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5515 (tmm) REVERT: j 23 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8066 (mm) REVERT: j 193 GLN cc_start: 0.8888 (tt0) cc_final: 0.8677 (tt0) REVERT: j 222 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9017 (mt) REVERT: j 342 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8092 (pt0) REVERT: j 397 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8909 (mt-10) REVERT: j 407 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8533 (ttmm) REVERT: b 1 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6752 (tpt) REVERT: b 21 MET cc_start: 0.8333 (ppp) cc_final: 0.7997 (tmm) REVERT: b 193 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8789 (tm-30) REVERT: b 244 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8538 (mm-30) REVERT: b 245 MET cc_start: 0.9124 (tpp) cc_final: 0.8827 (tpt) REVERT: b 253 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9186 (mt) REVERT: b 342 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8351 (mp0) REVERT: b 354 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7784 (t) REVERT: b 396 MET cc_start: 0.9501 (tpp) cc_final: 0.9233 (tpp) REVERT: b 397 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8599 (mt-10) REVERT: c 12 SER cc_start: 0.9554 (m) cc_final: 0.9322 (p) REVERT: c 30 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7606 (mtp-110) REVERT: c 59 GLN cc_start: 0.8603 (pm20) cc_final: 0.8359 (pm20) REVERT: c 85 GLN cc_start: 0.9350 (mp10) cc_final: 0.8661 (mp10) REVERT: c 241 GLN cc_start: 0.9124 (pt0) cc_final: 0.8493 (pp30) REVERT: c 292 ASN cc_start: 0.8499 (m-40) cc_final: 0.8267 (p0) REVERT: c 375 GLU cc_start: 0.8340 (tp30) cc_final: 0.7988 (tp30) REVERT: c 397 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8645 (mt-10) REVERT: d 8 ASN cc_start: 0.9148 (m-40) cc_final: 0.8671 (m110) REVERT: d 21 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7291 (ppp) REVERT: d 84 SER cc_start: 0.9486 (m) cc_final: 0.9253 (t) REVERT: d 85 GLN cc_start: 0.9536 (mt0) cc_final: 0.9140 (mp10) REVERT: d 342 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8136 (mm-30) REVERT: d 354 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7837 (t) REVERT: e 122 ASP cc_start: 0.8631 (t0) cc_final: 0.8393 (t0) REVERT: e 205 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8568 (mmm) REVERT: e 222 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9061 (tt) REVERT: e 342 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8221 (pt0) REVERT: e 354 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7595 (t) REVERT: e 374 GLN cc_start: 0.9474 (tp40) cc_final: 0.9182 (tp-100) REVERT: f 1 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5064 (tmm) REVERT: f 126 ASN cc_start: 0.9331 (m-40) cc_final: 0.9093 (m110) REVERT: g 13 GLU cc_start: 0.8699 (pm20) cc_final: 0.8486 (pm20) REVERT: g 23 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7731 (mm) REVERT: g 30 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6991 (mtp-110) REVERT: g 126 ASN cc_start: 0.9125 (m-40) cc_final: 0.8830 (m-40) REVERT: g 215 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: g 375 GLU cc_start: 0.8460 (tp30) cc_final: 0.7850 (tp30) REVERT: g 397 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8770 (mt-10) REVERT: h 32 GLN cc_start: 0.8959 (mp10) cc_final: 0.8757 (mm-40) REVERT: h 110 TYR cc_start: 0.8634 (m-80) cc_final: 0.8304 (m-80) REVERT: h 205 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8135 (mtp) REVERT: h 308 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8805 (tt0) REVERT: h 374 GLN cc_start: 0.9527 (tp40) cc_final: 0.9128 (tp-100) REVERT: h 411 ASP cc_start: 0.9088 (m-30) cc_final: 0.8805 (m-30) REVERT: i 1 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.5851 (tpt) REVERT: i 12 SER cc_start: 0.9316 (m) cc_final: 0.9113 (p) REVERT: i 44 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8691 (pttm) REVERT: i 91 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8413 (pp) REVERT: i 333 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8619 (mm-30) REVERT: i 342 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8396 (mp0) REVERT: i 375 GLU cc_start: 0.8246 (tp30) cc_final: 0.7691 (tp30) outliers start: 357 outliers final: 163 residues processed: 1254 average time/residue: 0.5687 time to fit residues: 1197.8470 Evaluate side-chains 1083 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 884 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 260 VAL Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain r residue 21 MET Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 354 VAL Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 410 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 318 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 222 LEU Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 205 MET Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 44 LYS Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 205 MET Chi-restraints excluded: chain n residue 215 GLU Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 260 VAL Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 29 MET Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 354 VAL Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 415 MET Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 GLU Chi-restraints excluded: chain k residue 91 LEU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 370 LEU Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 260 VAL Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain b residue 354 VAL Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 44 LYS Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 52 ASP Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 260 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 44 LYS Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 222 LEU Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 327 MET Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 260 VAL Chi-restraints excluded: chain f residue 308 GLU Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 29 MET Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 260 VAL Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 354 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 205 MET Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 308 GLU Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 327 MET Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 44 LYS Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 91 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 126 ASN Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 260 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 557 optimal weight: 0.9990 chunk 456 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 671 optimal weight: 0.0770 chunk 725 optimal weight: 2.9990 chunk 597 optimal weight: 5.9990 chunk 665 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 538 optimal weight: 6.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS ** r 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN p 374 GLN n 189 GLN n 374 GLN ** l 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 193 GLN b 193 GLN c 172 GLN d 32 GLN d 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 374 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 60822 Z= 0.221 Angle : 0.652 14.480 82008 Z= 0.318 Chirality : 0.044 0.168 9324 Planarity : 0.004 0.036 10620 Dihedral : 5.622 72.516 8410 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.45 % Allowed : 26.67 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 7506 helix: 1.09 (0.09), residues: 3258 sheet: 0.02 (0.15), residues: 1170 loop : -0.28 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.008 TRP m 381 HIS 0.007 0.001 HIS a 239 PHE 0.012 0.001 PHE q 412 TYR 0.020 0.001 TYR l 197 ARG 0.010 0.001 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 353 poor density : 974 time to evaluate : 5.261 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: a 29 MET cc_start: 0.7813 (ptm) cc_final: 0.7398 (ptp) REVERT: a 122 ASP cc_start: 0.7575 (t0) cc_final: 0.7287 (t0) REVERT: a 210 ASP cc_start: 0.8116 (m-30) cc_final: 0.7111 (m-30) REVERT: a 215 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: a 244 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8159 (mm-30) REVERT: a 265 ASP cc_start: 0.8449 (p0) cc_final: 0.8187 (p0) REVERT: a 274 TYR cc_start: 0.9088 (m-80) cc_final: 0.8669 (m-80) REVERT: a 374 GLN cc_start: 0.9082 (tp40) cc_final: 0.8850 (tp-100) REVERT: a 397 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8842 (mm-30) REVERT: r 147 MET cc_start: 0.7883 (tpp) cc_final: 0.7609 (tpp) REVERT: r 244 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8508 (mm-30) REVERT: r 248 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8653 (mm-30) REVERT: r 376 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: r 415 MET cc_start: 0.7068 (ptt) cc_final: 0.6724 (ptt) REVERT: r 416 MET cc_start: 0.7938 (mmp) cc_final: 0.7026 (ttt) REVERT: q 1 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6798 (tpt) REVERT: q 23 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (mm) REVERT: q 241 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8785 (pp30) REVERT: q 244 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8463 (mm-30) REVERT: p 1 MET cc_start: 0.7261 (tpt) cc_final: 0.6956 (tpt) REVERT: p 33 ASP cc_start: 0.9163 (m-30) cc_final: 0.8846 (m-30) REVERT: p 91 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8811 (pp) REVERT: p 193 GLN cc_start: 0.8945 (tt0) cc_final: 0.8736 (tt0) REVERT: p 207 LEU cc_start: 0.9136 (tt) cc_final: 0.8749 (tt) REVERT: p 241 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: p 325 SER cc_start: 0.8324 (t) cc_final: 0.7982 (p) REVERT: p 379 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8491 (mtpp) REVERT: p 394 ASP cc_start: 0.8908 (p0) cc_final: 0.8545 (p0) REVERT: o 253 LEU cc_start: 0.9338 (mt) cc_final: 0.9101 (mp) REVERT: o 274 TYR cc_start: 0.9286 (m-80) cc_final: 0.9085 (m-80) REVERT: o 328 ASP cc_start: 0.8891 (m-30) cc_final: 0.8645 (m-30) REVERT: o 334 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8228 (mm-30) REVERT: o 341 MET cc_start: 0.9029 (tmm) cc_final: 0.8823 (ppp) REVERT: o 397 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8487 (mp0) REVERT: n 41 GLN cc_start: 0.9085 (tp40) cc_final: 0.8620 (tp40) REVERT: n 44 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8674 (ttpp) REVERT: n 100 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9170 (ttmm) REVERT: n 126 ASN cc_start: 0.9389 (m-40) cc_final: 0.9135 (m-40) REVERT: n 193 GLN cc_start: 0.8744 (tt0) cc_final: 0.8409 (mt0) REVERT: n 342 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8486 (mt-10) REVERT: n 374 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8372 (tp-100) REVERT: m 44 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8688 (ptpp) REVERT: m 125 GLU cc_start: 0.8693 (mp0) cc_final: 0.8394 (pm20) REVERT: m 244 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8280 (mm-30) REVERT: m 296 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8679 (mmm-85) REVERT: m 326 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8986 (tptt) REVERT: m 329 GLU cc_start: 0.8571 (pm20) cc_final: 0.8319 (pm20) REVERT: m 342 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8483 (mp0) REVERT: m 396 MET cc_start: 0.9061 (tpp) cc_final: 0.8811 (tpp) REVERT: l 23 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7765 (mm) REVERT: l 109 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7560 (mtm-85) REVERT: l 244 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7861 (mm-30) REVERT: l 397 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8971 (mm-30) REVERT: k 12 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8822 (p) REVERT: k 13 GLU cc_start: 0.8573 (pm20) cc_final: 0.8278 (pm20) REVERT: k 41 GLN cc_start: 0.8564 (tp40) cc_final: 0.8129 (tm-30) REVERT: k 44 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8532 (ptpp) REVERT: k 56 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: k 78 ASP cc_start: 0.8663 (m-30) cc_final: 0.8421 (m-30) REVERT: k 341 MET cc_start: 0.9056 (tmm) cc_final: 0.8705 (tmm) REVERT: k 342 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8363 (mp0) REVERT: j 1 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5394 (tmm) REVERT: j 23 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8066 (mm) REVERT: j 222 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9029 (mt) REVERT: j 342 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8085 (pt0) REVERT: j 381 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.8018 (t60) REVERT: j 397 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8870 (mt-10) REVERT: j 407 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8679 (ttmm) REVERT: b 1 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6765 (tpt) REVERT: b 42 HIS cc_start: 0.8767 (t70) cc_final: 0.8267 (t-90) REVERT: b 244 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8534 (mm-30) REVERT: b 253 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9179 (mt) REVERT: b 342 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8323 (mp0) REVERT: b 396 MET cc_start: 0.9502 (tpp) cc_final: 0.9296 (tpp) REVERT: b 397 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8747 (mt-10) REVERT: c 12 SER cc_start: 0.9559 (m) cc_final: 0.9347 (p) REVERT: c 21 MET cc_start: 0.8576 (tmm) cc_final: 0.8147 (ttp) REVERT: c 30 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7923 (mtp-110) REVERT: c 41 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8668 (tm-30) REVERT: c 85 GLN cc_start: 0.9373 (mt0) cc_final: 0.8669 (mp10) REVERT: c 241 GLN cc_start: 0.9147 (pp30) cc_final: 0.8519 (pp30) REVERT: c 269 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8483 (mmp80) REVERT: c 292 ASN cc_start: 0.8550 (m-40) cc_final: 0.8346 (p0) REVERT: c 375 GLU cc_start: 0.8416 (tp30) cc_final: 0.8112 (tp30) REVERT: c 381 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (t60) REVERT: d 21 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7515 (ptp) REVERT: d 29 MET cc_start: 0.8571 (ptp) cc_final: 0.8094 (ptp) REVERT: d 60 ASP cc_start: 0.8996 (t0) cc_final: 0.8592 (t0) REVERT: d 85 GLN cc_start: 0.9556 (mt0) cc_final: 0.9166 (mp10) REVERT: d 342 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8480 (pt0) REVERT: d 381 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.8071 (t60) REVERT: e 122 ASP cc_start: 0.8713 (t0) cc_final: 0.8440 (t0) REVERT: e 222 LEU cc_start: 0.9433 (tt) cc_final: 0.9013 (tt) REVERT: e 241 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (tm-30) REVERT: e 326 LYS cc_start: 0.9304 (tptt) cc_final: 0.9103 (tppt) REVERT: e 329 GLU cc_start: 0.8139 (pm20) cc_final: 0.7820 (pm20) REVERT: e 342 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8267 (pt0) REVERT: e 374 GLN cc_start: 0.9449 (tp40) cc_final: 0.9167 (tp-100) REVERT: e 396 MET cc_start: 0.9318 (tpp) cc_final: 0.9053 (tpp) REVERT: f 1 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5237 (tmm) REVERT: f 123 LYS cc_start: 0.8422 (ptmm) cc_final: 0.8166 (ptmm) REVERT: f 326 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8404 (tmtt) REVERT: f 329 GLU cc_start: 0.8063 (mp0) cc_final: 0.7467 (mp0) REVERT: f 390 MET cc_start: 0.9353 (ptp) cc_final: 0.9013 (ptp) REVERT: g 23 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7706 (mm) REVERT: g 30 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7277 (mtp-110) REVERT: g 126 ASN cc_start: 0.9141 (m-40) cc_final: 0.8833 (m-40) REVERT: g 215 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: g 326 LYS cc_start: 0.9095 (tppt) cc_final: 0.8849 (tppt) REVERT: g 375 GLU cc_start: 0.8488 (tp30) cc_final: 0.7924 (tp30) REVERT: g 397 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8794 (mt-10) REVERT: h 59 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8158 (tp-100) REVERT: h 110 TYR cc_start: 0.8658 (m-80) cc_final: 0.8363 (m-80) REVERT: i 1 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.5793 (tpt) REVERT: i 12 SER cc_start: 0.9348 (m) cc_final: 0.9146 (p) REVERT: i 56 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8599 (pt0) REVERT: i 219 MET cc_start: 0.9107 (tpp) cc_final: 0.8869 (tpp) REVERT: i 333 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8674 (mm-30) REVERT: i 342 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8400 (mp0) REVERT: i 375 GLU cc_start: 0.8473 (tp30) cc_final: 0.8125 (tp30) outliers start: 353 outliers final: 178 residues processed: 1211 average time/residue: 0.5711 time to fit residues: 1154.1988 Evaluate side-chains 1071 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 862 time to evaluate : 5.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 195 ILE Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 318 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 49 ILE Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain p residue 379 LYS Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 286 THR Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 44 LYS Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 264 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 327 MET Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 374 GLN Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 GLU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 193 GLN Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 400 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 202 CYS Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 223 VAL Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 376 GLU Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 202 CYS Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 260 VAL Chi-restraints excluded: chain c residue 269 ARG Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain c residue 415 MET Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 44 LYS Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 264 LEU Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain g residue 21 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 29 MET Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 260 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 126 ASN Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 354 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 0.0050 chunk 504 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 450 optimal weight: 3.9990 chunk 673 optimal weight: 2.9990 chunk 713 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 638 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN a 241 GLN r 344 HIS o 220 GLN o 388 HIS ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 189 GLN b 374 GLN c 172 GLN c 189 GLN d 41 GLN d 374 GLN d 378 GLN e 275 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 193 GLN i 126 ASN i 193 GLN i 374 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 60822 Z= 0.197 Angle : 0.633 11.389 82008 Z= 0.306 Chirality : 0.044 0.178 9324 Planarity : 0.004 0.047 10620 Dihedral : 5.172 55.714 8397 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.74 % Allowed : 26.91 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 7506 helix: 1.15 (0.09), residues: 3258 sheet: -0.13 (0.15), residues: 1134 loop : -0.29 (0.11), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.008 TRP a 381 HIS 0.011 0.001 HIS o 388 PHE 0.010 0.001 PHE c 398 TYR 0.019 0.001 TYR r 197 ARG 0.005 0.001 ARG c 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 954 time to evaluate : 5.248 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: a 29 MET cc_start: 0.7948 (ptm) cc_final: 0.7600 (ptp) REVERT: a 122 ASP cc_start: 0.7697 (t0) cc_final: 0.7318 (t0) REVERT: a 215 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: a 244 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8221 (mm-30) REVERT: a 265 ASP cc_start: 0.8453 (p0) cc_final: 0.8092 (p0) REVERT: a 374 GLN cc_start: 0.9045 (tp40) cc_final: 0.8696 (tp-100) REVERT: a 375 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8233 (mp0) REVERT: r 147 MET cc_start: 0.8033 (tpp) cc_final: 0.7769 (tpp) REVERT: r 244 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8507 (mm-30) REVERT: r 248 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8713 (mm-30) REVERT: r 376 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: r 416 MET cc_start: 0.7918 (mmp) cc_final: 0.6735 (ttt) REVERT: q 1 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6810 (tpt) REVERT: q 23 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8473 (mm) REVERT: q 56 GLU cc_start: 0.8881 (pt0) cc_final: 0.8518 (pt0) REVERT: q 241 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8750 (pp30) REVERT: q 244 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8426 (mm-30) REVERT: q 396 MET cc_start: 0.9096 (tpp) cc_final: 0.8859 (tpp) REVERT: p 1 MET cc_start: 0.7377 (tpt) cc_final: 0.7109 (tpt) REVERT: p 33 ASP cc_start: 0.9142 (m-30) cc_final: 0.8776 (m-30) REVERT: p 91 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8842 (pp) REVERT: p 193 GLN cc_start: 0.9063 (tt0) cc_final: 0.8699 (tt0) REVERT: p 241 GLN cc_start: 0.8684 (pt0) cc_final: 0.8338 (tm-30) REVERT: p 325 SER cc_start: 0.8391 (t) cc_final: 0.8115 (p) REVERT: p 342 GLU cc_start: 0.8327 (mp0) cc_final: 0.8106 (pm20) REVERT: p 394 ASP cc_start: 0.8834 (p0) cc_final: 0.8474 (p0) REVERT: o 253 LEU cc_start: 0.9333 (mt) cc_final: 0.9093 (mp) REVERT: o 396 MET cc_start: 0.9359 (tpp) cc_final: 0.9125 (tpp) REVERT: o 397 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8482 (mp0) REVERT: o 412 PHE cc_start: 0.9477 (t80) cc_final: 0.8759 (t80) REVERT: n 41 GLN cc_start: 0.9107 (tp40) cc_final: 0.8893 (tp40) REVERT: n 100 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9155 (ttmm) REVERT: n 126 ASN cc_start: 0.9388 (m-40) cc_final: 0.9117 (m-40) REVERT: n 193 GLN cc_start: 0.8764 (tt0) cc_final: 0.8449 (mt0) REVERT: n 326 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8804 (tmtt) REVERT: n 342 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8481 (mt-10) REVERT: n 374 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8417 (tp-100) REVERT: m 44 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8700 (ptpp) REVERT: m 123 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8069 (ptmm) REVERT: m 296 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8675 (mmm-85) REVERT: m 326 LYS cc_start: 0.9228 (tmtt) cc_final: 0.8965 (tptt) REVERT: m 329 GLU cc_start: 0.8568 (pm20) cc_final: 0.8290 (pm20) REVERT: m 342 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8451 (mp0) REVERT: l 23 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7730 (mm) REVERT: l 109 ARG cc_start: 0.7856 (ptp-170) cc_final: 0.7583 (mtm-85) REVERT: l 244 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7862 (mm-30) REVERT: l 326 LYS cc_start: 0.9237 (tmtt) cc_final: 0.8956 (tptp) REVERT: l 329 GLU cc_start: 0.8035 (mp0) cc_final: 0.7821 (mp0) REVERT: l 397 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8897 (mm-30) REVERT: k 12 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8826 (p) REVERT: k 13 GLU cc_start: 0.8594 (pm20) cc_final: 0.8304 (pm20) REVERT: k 41 GLN cc_start: 0.8669 (tp40) cc_final: 0.8174 (tm-30) REVERT: k 44 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8534 (ptpp) REVERT: k 56 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8410 (pt0) REVERT: k 78 ASP cc_start: 0.8650 (m-30) cc_final: 0.8408 (m-30) REVERT: k 205 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: k 342 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8366 (mp0) REVERT: j 1 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5452 (tmm) REVERT: j 23 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8088 (mm) REVERT: j 109 ARG cc_start: 0.7720 (ptp-170) cc_final: 0.7363 (mtm110) REVERT: j 222 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9013 (mt) REVERT: j 342 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8090 (pt0) REVERT: j 397 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8855 (mt-10) REVERT: j 407 LYS cc_start: 0.8984 (ptmm) cc_final: 0.8732 (ttmm) REVERT: b 1 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6641 (tpt) REVERT: b 30 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8246 (mtm-85) REVERT: b 42 HIS cc_start: 0.8506 (t70) cc_final: 0.8258 (t-90) REVERT: b 224 LYS cc_start: 0.8425 (pttt) cc_final: 0.8195 (pttp) REVERT: b 244 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8626 (mm-30) REVERT: b 253 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9128 (mt) REVERT: b 342 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8317 (mp0) REVERT: c 29 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8109 (ptm) REVERT: c 30 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8082 (mtp-110) REVERT: c 85 GLN cc_start: 0.9355 (mt0) cc_final: 0.8652 (mp10) REVERT: c 186 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: c 195 ILE cc_start: 0.9476 (mt) cc_final: 0.9224 (mt) REVERT: c 241 GLN cc_start: 0.9151 (pp30) cc_final: 0.8561 (pp30) REVERT: c 375 GLU cc_start: 0.8406 (tp30) cc_final: 0.8034 (tp30) REVERT: d 21 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8082 (ppp) REVERT: d 29 MET cc_start: 0.8568 (ptp) cc_final: 0.8032 (ptp) REVERT: d 41 GLN cc_start: 0.8531 (tt0) cc_final: 0.7919 (tt0) REVERT: d 85 GLN cc_start: 0.9448 (mt0) cc_final: 0.9106 (mp10) REVERT: d 342 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8465 (pt0) REVERT: d 381 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8108 (t60) REVERT: e 122 ASP cc_start: 0.8771 (t0) cc_final: 0.8464 (t0) REVERT: e 197 TYR cc_start: 0.9437 (t80) cc_final: 0.9150 (t80) REVERT: e 222 LEU cc_start: 0.9382 (tt) cc_final: 0.9067 (tt) REVERT: e 241 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8738 (tm-30) REVERT: e 326 LYS cc_start: 0.9336 (tptt) cc_final: 0.9117 (tppt) REVERT: e 329 GLU cc_start: 0.8188 (pm20) cc_final: 0.7749 (pm20) REVERT: e 342 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8242 (pt0) REVERT: e 375 GLU cc_start: 0.8913 (tp30) cc_final: 0.8578 (tp30) REVERT: f 1 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5363 (tmm) REVERT: f 114 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9246 (tp) REVERT: f 123 LYS cc_start: 0.8336 (ptmm) cc_final: 0.8059 (ptmm) REVERT: f 215 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: f 326 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8592 (ttpp) REVERT: f 329 GLU cc_start: 0.8134 (mp0) cc_final: 0.7535 (mp0) REVERT: f 375 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8284 (tp30) REVERT: f 390 MET cc_start: 0.9380 (ptp) cc_final: 0.9062 (ptp) REVERT: g 23 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7800 (mm) REVERT: g 30 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7324 (mtp-110) REVERT: g 44 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8835 (ttpp) REVERT: g 126 ASN cc_start: 0.9147 (m-40) cc_final: 0.8775 (m-40) REVERT: g 205 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: g 211 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7978 (tp30) REVERT: g 215 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: g 326 LYS cc_start: 0.9157 (tppt) cc_final: 0.8918 (tppt) REVERT: g 374 GLN cc_start: 0.9303 (tp-100) cc_final: 0.9048 (tp-100) REVERT: g 375 GLU cc_start: 0.8512 (tp30) cc_final: 0.7955 (tp30) REVERT: g 397 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8819 (mt-10) REVERT: h 59 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8207 (tp-100) REVERT: h 140 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (m170) REVERT: i 1 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5851 (tpt) REVERT: i 12 SER cc_start: 0.9368 (m) cc_final: 0.9167 (p) REVERT: i 56 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: i 333 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8687 (mm-30) REVERT: i 342 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8411 (mp0) REVERT: i 375 GLU cc_start: 0.8491 (tp30) cc_final: 0.8122 (tp30) outliers start: 307 outliers final: 178 residues processed: 1148 average time/residue: 0.5506 time to fit residues: 1068.3848 Evaluate side-chains 1103 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 892 time to evaluate : 5.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 318 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 374 GLN Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 44 LYS Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 56 GLU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 370 LEU Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 202 CYS Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 415 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 52 ASP Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain c residue 415 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 308 GLU Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 379 LYS Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 29 MET Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 205 MET Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 415 MET Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 140 HIS Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 277 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 341 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 2.9990 chunk 404 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 531 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 chunk 608 optimal weight: 7.9990 chunk 493 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 364 optimal weight: 0.5980 chunk 640 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN r 172 GLN r 344 HIS r 388 HIS q 344 HIS p 59 GLN o 189 GLN ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 193 GLN j 275 ASN ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 374 GLN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 374 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 60822 Z= 0.263 Angle : 0.653 11.406 82008 Z= 0.318 Chirality : 0.044 0.190 9324 Planarity : 0.004 0.044 10620 Dihedral : 5.058 44.290 8394 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.25 % Allowed : 27.04 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.44 (0.10), residues: 7506 helix: 1.18 (0.09), residues: 3258 sheet: -0.23 (0.14), residues: 1170 loop : -0.35 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.008 TRP a 381 HIS 0.010 0.001 HIS r 388 PHE 0.013 0.001 PHE c 398 TYR 0.020 0.002 TYR l 197 ARG 0.007 0.001 ARG r 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 340 poor density : 938 time to evaluate : 5.319 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: a 39 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8649 (mm) REVERT: a 122 ASP cc_start: 0.7789 (t0) cc_final: 0.7415 (t0) REVERT: a 215 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: a 244 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8194 (mm-30) REVERT: a 265 ASP cc_start: 0.8447 (p0) cc_final: 0.8182 (p0) REVERT: a 374 GLN cc_start: 0.9170 (tp40) cc_final: 0.8819 (tp-100) REVERT: a 375 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8417 (mp0) REVERT: a 378 GLN cc_start: 0.8249 (mp10) cc_final: 0.8010 (pm20) REVERT: r 244 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8516 (mm-30) REVERT: r 341 MET cc_start: 0.8926 (tmm) cc_final: 0.8643 (ppp) REVERT: r 366 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7876 (tpt170) REVERT: r 416 MET cc_start: 0.7801 (mmp) cc_final: 0.6541 (ttt) REVERT: q 1 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6841 (tpt) REVERT: q 23 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (mm) REVERT: q 56 GLU cc_start: 0.8934 (pt0) cc_final: 0.8516 (pt0) REVERT: q 241 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8745 (pp30) REVERT: q 244 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8509 (mm-30) REVERT: q 390 MET cc_start: 0.8674 (pmm) cc_final: 0.8421 (pmm) REVERT: q 396 MET cc_start: 0.9112 (tpp) cc_final: 0.8799 (tpp) REVERT: p 1 MET cc_start: 0.7393 (tpt) cc_final: 0.7186 (tpt) REVERT: p 33 ASP cc_start: 0.9113 (m-30) cc_final: 0.8737 (m-30) REVERT: p 56 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8579 (pt0) REVERT: p 91 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8894 (pp) REVERT: p 193 GLN cc_start: 0.8973 (tt0) cc_final: 0.8674 (tt0) REVERT: p 325 SER cc_start: 0.8396 (t) cc_final: 0.7968 (p) REVERT: p 394 ASP cc_start: 0.8862 (p0) cc_final: 0.8561 (p0) REVERT: p 397 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8788 (mp0) REVERT: p 405 MET cc_start: 0.8242 (mtp) cc_final: 0.8009 (mtm) REVERT: o 244 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8409 (mm-30) REVERT: o 397 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8588 (mp0) REVERT: o 413 PHE cc_start: 0.9041 (m-10) cc_final: 0.8608 (m-80) REVERT: n 32 GLN cc_start: 0.8859 (mp10) cc_final: 0.8608 (mt0) REVERT: n 41 GLN cc_start: 0.9164 (tp40) cc_final: 0.8609 (tp40) REVERT: n 44 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8723 (ttpp) REVERT: n 100 LYS cc_start: 0.9496 (ttmt) cc_final: 0.9134 (ttmm) REVERT: n 265 ASP cc_start: 0.8534 (p0) cc_final: 0.8272 (t70) REVERT: n 342 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8524 (mt-10) REVERT: n 374 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8511 (tp40) REVERT: m 125 GLU cc_start: 0.8773 (mp0) cc_final: 0.8465 (pm20) REVERT: m 244 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8291 (mm-30) REVERT: m 296 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8696 (mmm-85) REVERT: m 329 GLU cc_start: 0.8531 (pm20) cc_final: 0.8294 (pm20) REVERT: m 342 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8424 (mp0) REVERT: m 374 GLN cc_start: 0.9405 (tp40) cc_final: 0.9026 (tp40) REVERT: m 415 MET cc_start: 0.8943 (ptm) cc_final: 0.8736 (ptm) REVERT: l 109 ARG cc_start: 0.7980 (ptp-170) cc_final: 0.7685 (mtm-85) REVERT: l 244 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7891 (mm-30) REVERT: l 326 LYS cc_start: 0.9278 (tmtt) cc_final: 0.8933 (tptp) REVERT: l 352 LYS cc_start: 0.8063 (tptp) cc_final: 0.7789 (tptp) REVERT: l 397 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8963 (mm-30) REVERT: k 12 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8763 (p) REVERT: k 13 GLU cc_start: 0.8547 (pm20) cc_final: 0.8234 (pm20) REVERT: k 41 GLN cc_start: 0.8687 (tp40) cc_final: 0.8337 (tm-30) REVERT: k 56 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: k 342 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8421 (mp0) REVERT: k 352 LYS cc_start: 0.8416 (tptp) cc_final: 0.8130 (tptp) REVERT: j 1 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.5641 (tmm) REVERT: j 23 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8122 (mm) REVERT: j 205 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: j 222 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8991 (mt) REVERT: j 342 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8126 (pt0) REVERT: j 352 LYS cc_start: 0.8030 (tptp) cc_final: 0.7479 (tptp) REVERT: j 375 GLU cc_start: 0.9045 (tp30) cc_final: 0.8816 (tp30) REVERT: j 379 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8801 (mtmt) REVERT: j 380 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8342 (ptm) REVERT: j 397 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8732 (mt-10) REVERT: j 407 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8822 (ttmm) REVERT: b 1 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6481 (tpt) REVERT: b 30 ARG cc_start: 0.8552 (ttm110) cc_final: 0.8268 (mtm-85) REVERT: b 193 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: b 224 LYS cc_start: 0.8472 (pttt) cc_final: 0.8262 (pttp) REVERT: b 244 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8666 (mm-30) REVERT: b 253 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9112 (mt) REVERT: b 342 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8315 (mp0) REVERT: b 397 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8737 (mt-10) REVERT: c 29 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8239 (ptm) REVERT: c 30 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8216 (mtp-110) REVERT: c 41 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8518 (tm-30) REVERT: c 85 GLN cc_start: 0.9367 (mt0) cc_final: 0.8629 (mp10) REVERT: c 90 ASN cc_start: 0.8176 (t0) cc_final: 0.7630 (t0) REVERT: c 186 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8626 (mtm) REVERT: c 195 ILE cc_start: 0.9476 (mt) cc_final: 0.9227 (mt) REVERT: c 241 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8533 (pp30) REVERT: c 375 GLU cc_start: 0.8431 (tp30) cc_final: 0.8139 (tp30) REVERT: c 381 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (t60) REVERT: c 407 LYS cc_start: 0.8924 (ptmm) cc_final: 0.8552 (tppt) REVERT: d 21 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7735 (ppp) REVERT: d 29 MET cc_start: 0.8619 (ptp) cc_final: 0.8167 (ptp) REVERT: d 56 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: d 85 GLN cc_start: 0.9475 (mt0) cc_final: 0.9068 (mp10) REVERT: d 205 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8382 (mtp) REVERT: d 374 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8807 (tp-100) REVERT: d 378 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: d 381 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.8151 (t60) REVERT: d 415 MET cc_start: 0.8584 (ttp) cc_final: 0.8174 (ttm) REVERT: e 197 TYR cc_start: 0.9439 (t80) cc_final: 0.9127 (t80) REVERT: e 222 LEU cc_start: 0.9395 (tt) cc_final: 0.9125 (tt) REVERT: e 326 LYS cc_start: 0.9364 (tptt) cc_final: 0.9045 (tppt) REVERT: e 329 GLU cc_start: 0.8196 (pm20) cc_final: 0.7823 (pm20) REVERT: e 375 GLU cc_start: 0.8899 (tp30) cc_final: 0.8340 (tp30) REVERT: f 123 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7973 (ptmm) REVERT: f 326 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8694 (ttpp) REVERT: f 329 GLU cc_start: 0.8146 (mp0) cc_final: 0.7496 (mp0) REVERT: f 374 GLN cc_start: 0.9290 (tp-100) cc_final: 0.9015 (tp40) REVERT: f 375 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8501 (mp0) REVERT: g 23 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7834 (mm) REVERT: g 30 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7593 (mtp-110) REVERT: g 215 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: g 244 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7989 (mm-30) REVERT: g 326 LYS cc_start: 0.9145 (tppt) cc_final: 0.8804 (tppt) REVERT: g 329 GLU cc_start: 0.8063 (mp0) cc_final: 0.7760 (mp0) REVERT: g 397 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8848 (mt-10) REVERT: h 12 SER cc_start: 0.9302 (m) cc_final: 0.9044 (t) REVERT: h 59 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8272 (tp40) REVERT: h 215 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: h 374 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.8996 (tp-100) REVERT: i 1 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.5878 (tpt) REVERT: i 56 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: i 197 TYR cc_start: 0.9348 (t80) cc_final: 0.9141 (t80) REVERT: i 329 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8561 (mm-30) REVERT: i 333 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8736 (mm-30) REVERT: i 342 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8395 (mp0) REVERT: i 375 GLU cc_start: 0.8485 (tp30) cc_final: 0.8100 (tp30) REVERT: i 410 ASP cc_start: 0.9258 (m-30) cc_final: 0.8978 (p0) REVERT: i 411 ASP cc_start: 0.8988 (m-30) cc_final: 0.8643 (m-30) outliers start: 340 outliers final: 209 residues processed: 1164 average time/residue: 0.5576 time to fit residues: 1089.2316 Evaluate side-chains 1117 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 873 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 39 LEU Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 21 MET Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 308 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 388 HIS Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 318 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 411 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 327 MET Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 29 MET Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 295 HIS Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain o residue 381 TRP Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 44 LYS Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 264 LEU Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 29 MET Chi-restraints excluded: chain k residue 56 GLU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain k residue 370 LEU Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 202 CYS Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 222 LEU Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 376 GLU Chi-restraints excluded: chain j residue 379 LYS Chi-restraints excluded: chain j residue 380 MET Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 52 ASP Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 186 MET Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 241 GLN Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 379 LYS Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain c residue 387 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 266 SER Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 378 GLN Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 253 LEU Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 215 GLU Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 374 GLN Chi-restraints excluded: chain h residue 376 GLU Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 354 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 3.9990 chunk 642 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 418 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 714 optimal weight: 8.9990 chunk 592 optimal weight: 0.9990 chunk 330 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 374 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN r 344 HIS r 388 HIS n 193 GLN ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 374 GLN j 126 ASN ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 GLN c 172 GLN c 189 GLN ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 220 GLN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 374 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 60822 Z= 0.203 Angle : 0.646 10.952 82008 Z= 0.310 Chirality : 0.044 0.185 9324 Planarity : 0.004 0.044 10620 Dihedral : 4.924 42.860 8394 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.46 % Allowed : 27.96 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.45 (0.10), residues: 7506 helix: 1.24 (0.09), residues: 3258 sheet: -0.29 (0.14), residues: 1170 loop : -0.37 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP a 381 HIS 0.027 0.001 HIS r 388 PHE 0.019 0.001 PHE r 412 TYR 0.021 0.001 TYR l 197 ARG 0.007 0.000 ARG e 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 948 time to evaluate : 5.390 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: a 122 ASP cc_start: 0.7842 (t0) cc_final: 0.7413 (t0) REVERT: a 215 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: a 244 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8190 (mm-30) REVERT: a 265 ASP cc_start: 0.8448 (p0) cc_final: 0.8107 (p0) REVERT: a 374 GLN cc_start: 0.9188 (tp40) cc_final: 0.8784 (tp-100) REVERT: a 375 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8438 (mp0) REVERT: a 378 GLN cc_start: 0.8277 (mp10) cc_final: 0.8058 (pm20) REVERT: r 172 GLN cc_start: 0.8551 (tp40) cc_final: 0.8234 (tp-100) REVERT: r 244 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8545 (mm-30) REVERT: q 1 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6858 (tpt) REVERT: q 23 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8475 (mm) REVERT: q 56 GLU cc_start: 0.8924 (pt0) cc_final: 0.8630 (pt0) REVERT: q 241 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8726 (pp30) REVERT: q 244 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8489 (mm-30) REVERT: q 390 MET cc_start: 0.8670 (pmm) cc_final: 0.8451 (pmm) REVERT: p 33 ASP cc_start: 0.9095 (m-30) cc_final: 0.8787 (m-30) REVERT: p 56 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: p 91 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8880 (pp) REVERT: p 193 GLN cc_start: 0.9009 (tt0) cc_final: 0.8713 (tt0) REVERT: p 325 SER cc_start: 0.8382 (t) cc_final: 0.7949 (p) REVERT: p 394 ASP cc_start: 0.8867 (p0) cc_final: 0.8623 (p0) REVERT: p 397 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8869 (mm-30) REVERT: o 244 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8280 (mm-30) REVERT: o 397 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8417 (mt-10) REVERT: o 405 MET cc_start: 0.9030 (ppp) cc_final: 0.8774 (ppp) REVERT: o 412 PHE cc_start: 0.9304 (t80) cc_final: 0.8869 (t80) REVERT: n 32 GLN cc_start: 0.8871 (mp10) cc_final: 0.8627 (mt0) REVERT: n 41 GLN cc_start: 0.9154 (tp40) cc_final: 0.8559 (tp40) REVERT: n 44 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8745 (ttpp) REVERT: n 100 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9105 (ttmm) REVERT: n 342 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8534 (mt-10) REVERT: n 374 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8554 (tp40) REVERT: m 106 GLU cc_start: 0.8121 (mp0) cc_final: 0.7071 (mp0) REVERT: m 125 GLU cc_start: 0.8773 (mp0) cc_final: 0.8459 (pm20) REVERT: m 244 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8268 (mm-30) REVERT: m 296 ARG cc_start: 0.9103 (tpp80) cc_final: 0.8689 (mmm-85) REVERT: m 342 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8411 (mp0) REVERT: m 374 GLN cc_start: 0.9372 (tp40) cc_final: 0.9054 (tp40) REVERT: m 392 GLU cc_start: 0.8269 (pm20) cc_final: 0.7323 (pt0) REVERT: m 415 MET cc_start: 0.8951 (ptm) cc_final: 0.8660 (ptm) REVERT: l 32 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8486 (mm-40) REVERT: l 109 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7654 (mtm-85) REVERT: l 244 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7884 (mm-30) REVERT: l 326 LYS cc_start: 0.9316 (tmtt) cc_final: 0.8918 (tppp) REVERT: l 352 LYS cc_start: 0.8079 (tptp) cc_final: 0.7738 (tptp) REVERT: l 397 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8933 (mm-30) REVERT: k 12 SER cc_start: 0.9089 (m) cc_final: 0.8733 (p) REVERT: k 13 GLU cc_start: 0.8572 (pm20) cc_final: 0.8251 (pm20) REVERT: k 19 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8803 (mm-30) REVERT: k 41 GLN cc_start: 0.8670 (tp40) cc_final: 0.8172 (tm-30) REVERT: k 44 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8531 (ptpp) REVERT: k 108 GLU cc_start: 0.8496 (pm20) cc_final: 0.8275 (pm20) REVERT: k 352 LYS cc_start: 0.8469 (tptp) cc_final: 0.8169 (tptp) REVERT: k 410 ASP cc_start: 0.9229 (m-30) cc_final: 0.8860 (p0) REVERT: j 1 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5600 (tmm) REVERT: j 23 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8165 (mm) REVERT: j 205 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: j 342 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8135 (pt0) REVERT: j 352 LYS cc_start: 0.7978 (tptp) cc_final: 0.7398 (tptp) REVERT: j 375 GLU cc_start: 0.9003 (tp30) cc_final: 0.8727 (tp30) REVERT: j 380 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8180 (ptm) REVERT: j 397 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8734 (mt-10) REVERT: j 407 LYS cc_start: 0.9071 (ptmm) cc_final: 0.8840 (ttmm) REVERT: b 1 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6447 (tpt) REVERT: b 30 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8298 (mtm-85) REVERT: b 193 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: b 244 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8645 (mm-30) REVERT: b 253 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9104 (mt) REVERT: b 342 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8301 (mp0) REVERT: b 397 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8735 (mt-10) REVERT: c 29 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8180 (ptm) REVERT: c 30 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8194 (mtp-110) REVERT: c 41 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8542 (tm-30) REVERT: c 85 GLN cc_start: 0.9341 (mt0) cc_final: 0.8618 (mp10) REVERT: c 90 ASN cc_start: 0.8117 (t0) cc_final: 0.7558 (t0) REVERT: c 195 ILE cc_start: 0.9467 (mt) cc_final: 0.9230 (mt) REVERT: c 241 GLN cc_start: 0.9149 (pp30) cc_final: 0.8457 (pp30) REVERT: c 374 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8884 (tp-100) REVERT: c 375 GLU cc_start: 0.8381 (tp30) cc_final: 0.8130 (tp30) REVERT: d 21 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8051 (ppp) REVERT: d 49 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9143 (mm) REVERT: d 56 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8599 (pt0) REVERT: d 85 GLN cc_start: 0.9460 (mt0) cc_final: 0.9072 (mp10) REVERT: d 374 GLN cc_start: 0.9106 (tp40) cc_final: 0.8750 (tp-100) REVERT: d 378 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: d 381 TRP cc_start: 0.8592 (OUTLIER) cc_final: 0.8190 (t60) REVERT: d 418 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7774 (ttp80) REVERT: e 56 GLU cc_start: 0.8874 (tt0) cc_final: 0.8070 (tm-30) REVERT: e 122 ASP cc_start: 0.8670 (t0) cc_final: 0.8449 (t0) REVERT: e 197 TYR cc_start: 0.9437 (t80) cc_final: 0.9177 (t80) REVERT: e 222 LEU cc_start: 0.9393 (tt) cc_final: 0.9118 (tt) REVERT: e 326 LYS cc_start: 0.9385 (tptt) cc_final: 0.9140 (tppt) REVERT: e 329 GLU cc_start: 0.8207 (pm20) cc_final: 0.7870 (pm20) REVERT: e 375 GLU cc_start: 0.8849 (tp30) cc_final: 0.7854 (tp30) REVERT: f 123 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7901 (ptmm) REVERT: f 134 GLU cc_start: 0.8968 (mp0) cc_final: 0.8758 (mp0) REVERT: f 140 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7751 (m170) REVERT: f 226 GLU cc_start: 0.8270 (pp20) cc_final: 0.8056 (pp20) REVERT: f 326 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8735 (ttpp) REVERT: f 329 GLU cc_start: 0.8172 (mp0) cc_final: 0.7499 (mp0) REVERT: g 23 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7959 (mm) REVERT: g 30 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7603 (mtp-110) REVERT: g 215 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: g 244 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7985 (mm-30) REVERT: g 374 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.9026 (tp-100) REVERT: g 397 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8883 (mt-10) REVERT: h 59 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8265 (tp-100) REVERT: h 296 ARG cc_start: 0.9117 (mtp85) cc_final: 0.8913 (mmm-85) REVERT: i 1 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.5864 (tpt) REVERT: i 56 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: i 197 TYR cc_start: 0.9392 (t80) cc_final: 0.9080 (t80) REVERT: i 333 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8785 (mm-30) REVERT: i 342 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8398 (mp0) REVERT: i 375 GLU cc_start: 0.8466 (tp30) cc_final: 0.8093 (tp30) REVERT: i 410 ASP cc_start: 0.9219 (m-30) cc_final: 0.8976 (p0) REVERT: i 411 ASP cc_start: 0.8937 (m-30) cc_final: 0.8558 (m-30) outliers start: 289 outliers final: 183 residues processed: 1139 average time/residue: 0.5580 time to fit residues: 1073.8953 Evaluate side-chains 1103 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 893 time to evaluate : 5.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 371 LEU Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 308 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 318 THR Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 327 MET Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 338 THR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 44 LYS Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 376 GLU Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 318 THR Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 ASN Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 194 SER Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 202 CYS Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 380 MET Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 52 ASP Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 379 LYS Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 378 GLN Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 374 GLN Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 379 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 521 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 601 optimal weight: 6.9990 chunk 398 optimal weight: 2.9990 chunk 711 optimal weight: 9.9990 chunk 445 optimal weight: 4.9990 chunk 433 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 20 ASN ** a 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 344 HIS p 135 ASN ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 374 GLN k 220 GLN ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 GLN c 172 GLN ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 60822 Z= 0.276 Angle : 0.675 11.035 82008 Z= 0.327 Chirality : 0.044 0.200 9324 Planarity : 0.004 0.039 10620 Dihedral : 5.018 43.998 8394 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.43 % Allowed : 28.52 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.40 (0.10), residues: 7506 helix: 1.13 (0.09), residues: 3384 sheet: -0.38 (0.14), residues: 1170 loop : -0.36 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.009 TRP a 381 HIS 0.009 0.001 HIS r 295 PHE 0.021 0.001 PHE o 412 TYR 0.022 0.002 TYR l 197 ARG 0.008 0.001 ARG k 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 920 time to evaluate : 5.333 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: a 29 MET cc_start: 0.8138 (ptm) cc_final: 0.7801 (ptp) REVERT: a 122 ASP cc_start: 0.7968 (t0) cc_final: 0.7478 (t0) REVERT: a 215 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: a 244 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8198 (mm-30) REVERT: a 265 ASP cc_start: 0.8469 (p0) cc_final: 0.8148 (p0) REVERT: a 374 GLN cc_start: 0.9268 (tp40) cc_final: 0.8874 (tp-100) REVERT: a 375 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8530 (mp0) REVERT: a 378 GLN cc_start: 0.8271 (mp10) cc_final: 0.8002 (pm20) REVERT: r 172 GLN cc_start: 0.8520 (tp40) cc_final: 0.8319 (tp40) REVERT: r 244 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8552 (mm-30) REVERT: r 366 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7831 (tpt170) REVERT: q 1 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6918 (tpt) REVERT: q 23 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (mm) REVERT: q 56 GLU cc_start: 0.8949 (pt0) cc_final: 0.8618 (pt0) REVERT: q 241 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8747 (pp30) REVERT: q 244 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8495 (mm-30) REVERT: p 33 ASP cc_start: 0.9084 (m-30) cc_final: 0.8800 (m-30) REVERT: p 56 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: p 91 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8898 (pp) REVERT: p 193 GLN cc_start: 0.9010 (tt0) cc_final: 0.8721 (tt0) REVERT: p 241 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: p 325 SER cc_start: 0.8393 (t) cc_final: 0.7900 (p) REVERT: p 394 ASP cc_start: 0.8878 (p0) cc_final: 0.8581 (p0) REVERT: p 397 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8849 (mm-30) REVERT: o 244 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8275 (mm-30) REVERT: o 333 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8635 (tm-30) REVERT: o 341 MET cc_start: 0.9161 (ppp) cc_final: 0.8935 (ppp) REVERT: o 397 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8498 (mp0) REVERT: o 412 PHE cc_start: 0.9224 (t80) cc_final: 0.8808 (t80) REVERT: o 415 MET cc_start: 0.8494 (ppp) cc_final: 0.7713 (ppp) REVERT: n 41 GLN cc_start: 0.9172 (tp40) cc_final: 0.8793 (tp40) REVERT: n 44 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8905 (ttpp) REVERT: n 100 LYS cc_start: 0.9481 (ttmt) cc_final: 0.9110 (ttmm) REVERT: n 342 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8593 (mt-10) REVERT: n 374 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8361 (tp40) REVERT: m 125 GLU cc_start: 0.8794 (mp0) cc_final: 0.8575 (pm20) REVERT: m 244 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8288 (mm-30) REVERT: m 296 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8690 (mmm-85) REVERT: m 342 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8463 (mp0) REVERT: m 374 GLN cc_start: 0.9438 (tp40) cc_final: 0.9135 (tp40) REVERT: m 392 GLU cc_start: 0.8301 (pm20) cc_final: 0.7480 (pt0) REVERT: l 109 ARG cc_start: 0.8039 (ptp-170) cc_final: 0.7697 (mtm-85) REVERT: l 226 GLU cc_start: 0.7986 (pp20) cc_final: 0.7783 (pp20) REVERT: l 244 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7911 (mm-30) REVERT: l 290 ASP cc_start: 0.8681 (m-30) cc_final: 0.8134 (t70) REVERT: l 352 LYS cc_start: 0.8457 (tptp) cc_final: 0.8060 (tptp) REVERT: l 390 MET cc_start: 0.9168 (ptp) cc_final: 0.8899 (ptp) REVERT: l 397 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8834 (mm-30) REVERT: k 12 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8778 (p) REVERT: k 13 GLU cc_start: 0.8568 (pm20) cc_final: 0.8240 (pm20) REVERT: k 41 GLN cc_start: 0.8678 (tp40) cc_final: 0.8158 (tm-30) REVERT: k 44 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8533 (ptpp) REVERT: k 342 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8418 (mp0) REVERT: k 352 LYS cc_start: 0.8869 (tptp) cc_final: 0.8466 (tptp) REVERT: k 410 ASP cc_start: 0.9240 (m-30) cc_final: 0.8869 (p0) REVERT: k 417 LYS cc_start: 0.9446 (mttt) cc_final: 0.9091 (mttp) REVERT: j 1 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.5571 (tmm) REVERT: j 23 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8176 (mm) REVERT: j 205 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8278 (mtp) REVERT: j 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8122 (pt0) REVERT: j 352 LYS cc_start: 0.8286 (tptp) cc_final: 0.7669 (tptp) REVERT: j 375 GLU cc_start: 0.8992 (tp30) cc_final: 0.8604 (tp30) REVERT: j 381 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.8217 (t60) REVERT: j 397 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8736 (mt-10) REVERT: j 407 LYS cc_start: 0.9157 (ptmm) cc_final: 0.8943 (ttmm) REVERT: b 1 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6195 (tpt) REVERT: b 26 LEU cc_start: 0.8387 (mt) cc_final: 0.8178 (mt) REVERT: b 30 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8395 (mtm-85) REVERT: b 244 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8644 (mm-30) REVERT: b 253 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9098 (mt) REVERT: b 342 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8326 (mp0) REVERT: b 352 LYS cc_start: 0.8430 (tptp) cc_final: 0.8153 (tptp) REVERT: b 374 GLN cc_start: 0.9276 (tp40) cc_final: 0.9061 (tp-100) REVERT: c 29 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8213 (ptm) REVERT: c 30 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8287 (mtp-110) REVERT: c 41 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8481 (tm-30) REVERT: c 85 GLN cc_start: 0.9357 (mt0) cc_final: 0.8596 (mp10) REVERT: c 90 ASN cc_start: 0.8152 (t0) cc_final: 0.7604 (t0) REVERT: c 195 ILE cc_start: 0.9488 (mt) cc_final: 0.9234 (mt) REVERT: c 224 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8427 (pttt) REVERT: c 241 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8515 (pp30) REVERT: c 381 TRP cc_start: 0.8709 (t60) cc_final: 0.8492 (t60) REVERT: c 407 LYS cc_start: 0.8929 (ptmm) cc_final: 0.8633 (tppt) REVERT: d 49 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9156 (mm) REVERT: d 85 GLN cc_start: 0.9506 (mt0) cc_final: 0.9073 (mp10) REVERT: d 205 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: d 342 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8239 (mm-30) REVERT: d 374 GLN cc_start: 0.9110 (tp40) cc_final: 0.8793 (tp-100) REVERT: d 381 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.8287 (t60) REVERT: d 397 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8594 (mt-10) REVERT: e 122 ASP cc_start: 0.8740 (t0) cc_final: 0.8464 (t0) REVERT: e 197 TYR cc_start: 0.9428 (t80) cc_final: 0.9122 (t80) REVERT: e 205 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8588 (mtt) REVERT: e 222 LEU cc_start: 0.9408 (tt) cc_final: 0.9130 (tt) REVERT: e 326 LYS cc_start: 0.9366 (tptt) cc_final: 0.9137 (tppt) REVERT: e 329 GLU cc_start: 0.8227 (pm20) cc_final: 0.7849 (pm20) REVERT: e 375 GLU cc_start: 0.8707 (tp30) cc_final: 0.8469 (tp30) REVERT: f 123 LYS cc_start: 0.8178 (ptmm) cc_final: 0.7873 (ptmm) REVERT: f 134 GLU cc_start: 0.8986 (mp0) cc_final: 0.8633 (mp0) REVERT: f 205 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8432 (mtp) REVERT: f 326 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8768 (ttpp) REVERT: f 329 GLU cc_start: 0.8181 (mp0) cc_final: 0.7542 (mp0) REVERT: f 397 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8665 (mm-30) REVERT: g 23 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7909 (mm) REVERT: g 30 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7735 (mtp-110) REVERT: g 215 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: g 244 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8007 (mm-30) REVERT: g 375 GLU cc_start: 0.8862 (tp30) cc_final: 0.8381 (tp30) REVERT: g 397 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8892 (mt-10) REVERT: h 59 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8408 (tp-100) REVERT: h 215 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: i 56 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: i 326 LYS cc_start: 0.9396 (tppt) cc_final: 0.9166 (mmmt) REVERT: i 333 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8843 (mm-30) REVERT: i 342 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8403 (mp0) REVERT: i 375 GLU cc_start: 0.8458 (tp30) cc_final: 0.8108 (tp30) REVERT: i 411 ASP cc_start: 0.8990 (m-30) cc_final: 0.8527 (m-30) outliers start: 287 outliers final: 196 residues processed: 1116 average time/residue: 0.5535 time to fit residues: 1045.1855 Evaluate side-chains 1100 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 876 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 308 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 366 ARG Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 260 VAL Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 338 THR Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 323 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 194 SER Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain o residue 410 ASP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 44 LYS Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 241 GLN Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 323 THR Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain n residue 387 ILE Chi-restraints excluded: chain n residue 394 ASP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 29 MET Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 338 THR Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 387 ILE Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 241 GLN Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 318 THR Chi-restraints excluded: chain l residue 338 THR Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 ASN Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 194 SER Chi-restraints excluded: chain k residue 195 ILE Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 205 MET Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 277 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 253 LEU Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 338 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 218 GLU Chi-restraints excluded: chain c residue 241 GLN Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 338 THR Chi-restraints excluded: chain c residue 379 LYS Chi-restraints excluded: chain c residue 387 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 338 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 140 HIS Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 338 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 383 LEU Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 379 LYS Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 215 GLU Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 376 GLU Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 29 MET Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 264 LEU Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Chi-restraints excluded: chain i residue 379 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 484 optimal weight: 0.0970 chunk 351 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 559 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN ** a 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS r 344 HIS ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 374 GLN b 220 GLN c 172 GLN c 189 GLN ** d 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 193 GLN e 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 374 GLN h 25 ASN ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 60822 Z= 0.177 Angle : 0.660 11.663 82008 Z= 0.316 Chirality : 0.043 0.182 9324 Planarity : 0.004 0.052 10620 Dihedral : 4.837 42.551 8394 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.30 % Allowed : 29.61 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.45 (0.10), residues: 7506 helix: 1.30 (0.09), residues: 3258 sheet: -0.41 (0.14), residues: 1170 loop : -0.41 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP n 381 HIS 0.010 0.001 HIS r 295 PHE 0.016 0.001 PHE o 412 TYR 0.022 0.001 TYR l 197 ARG 0.014 0.001 ARG d 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 957 time to evaluate : 5.221 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: a 29 MET cc_start: 0.8065 (ptm) cc_final: 0.7780 (ptp) REVERT: a 122 ASP cc_start: 0.7952 (t0) cc_final: 0.7492 (t0) REVERT: a 215 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: a 244 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8181 (mm-30) REVERT: a 265 ASP cc_start: 0.8446 (p0) cc_final: 0.8230 (p0) REVERT: a 374 GLN cc_start: 0.9258 (tp40) cc_final: 0.8875 (tp-100) REVERT: a 375 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8456 (mp0) REVERT: r 244 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8543 (mm-30) REVERT: r 416 MET cc_start: 0.7575 (mmm) cc_final: 0.6159 (ttt) REVERT: q 1 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6957 (tpt) REVERT: q 23 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8455 (mm) REVERT: q 56 GLU cc_start: 0.8910 (pt0) cc_final: 0.8629 (pt0) REVERT: q 241 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8713 (pp30) REVERT: q 244 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8487 (mm-30) REVERT: q 375 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8428 (tm-30) REVERT: p 33 ASP cc_start: 0.9094 (m-30) cc_final: 0.8792 (m-30) REVERT: p 56 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8581 (pt0) REVERT: p 91 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (pp) REVERT: p 193 GLN cc_start: 0.9039 (tt0) cc_final: 0.8750 (tt0) REVERT: p 241 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: p 325 SER cc_start: 0.8362 (t) cc_final: 0.7916 (p) REVERT: p 394 ASP cc_start: 0.8865 (p0) cc_final: 0.8566 (p0) REVERT: p 397 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8783 (mm-30) REVERT: o 197 TYR cc_start: 0.9310 (t80) cc_final: 0.9036 (t80) REVERT: o 244 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8248 (mm-30) REVERT: o 326 LYS cc_start: 0.8993 (tppt) cc_final: 0.8785 (tppt) REVERT: o 333 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8603 (tm-30) REVERT: o 341 MET cc_start: 0.9155 (ppp) cc_final: 0.8820 (ppp) REVERT: o 375 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8434 (tm-30) REVERT: o 397 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8523 (mp0) REVERT: o 412 PHE cc_start: 0.9393 (t80) cc_final: 0.8693 (t80) REVERT: o 416 MET cc_start: 0.8963 (mmt) cc_final: 0.8503 (mmt) REVERT: n 41 GLN cc_start: 0.9147 (tp40) cc_final: 0.8745 (tp40) REVERT: n 100 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9100 (ttmm) REVERT: n 244 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8500 (mm-30) REVERT: n 342 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8587 (mt-10) REVERT: n 374 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8242 (tp40) REVERT: m 125 GLU cc_start: 0.8810 (mp0) cc_final: 0.8552 (pm20) REVERT: m 244 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8307 (mm-30) REVERT: m 296 ARG cc_start: 0.9098 (tpp80) cc_final: 0.8686 (mmm-85) REVERT: m 342 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8413 (mp0) REVERT: m 374 GLN cc_start: 0.9410 (tp40) cc_final: 0.9137 (tp40) REVERT: l 109 ARG cc_start: 0.7960 (ptp-170) cc_final: 0.7623 (mtm-85) REVERT: l 244 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7898 (mm-30) REVERT: l 290 ASP cc_start: 0.8625 (m-30) cc_final: 0.8112 (t70) REVERT: l 352 LYS cc_start: 0.8345 (tptp) cc_final: 0.7855 (tptp) REVERT: l 390 MET cc_start: 0.9168 (ptp) cc_final: 0.8867 (ptp) REVERT: l 397 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8833 (mm-30) REVERT: l 414 GLU cc_start: 0.8946 (pp20) cc_final: 0.8641 (pp20) REVERT: k 12 SER cc_start: 0.9092 (m) cc_final: 0.8753 (p) REVERT: k 13 GLU cc_start: 0.8583 (pm20) cc_final: 0.8310 (pm20) REVERT: k 41 GLN cc_start: 0.8631 (tp40) cc_final: 0.8155 (tm-30) REVERT: k 44 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8521 (ptpp) REVERT: k 244 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7998 (mm-30) REVERT: k 333 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8588 (mm-30) REVERT: k 342 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8414 (mp0) REVERT: k 352 LYS cc_start: 0.8721 (tptp) cc_final: 0.8327 (tptp) REVERT: k 410 ASP cc_start: 0.9230 (m-30) cc_final: 0.8938 (p0) REVERT: j 1 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5569 (tmm) REVERT: j 23 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8142 (mm) REVERT: j 342 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8121 (pt0) REVERT: j 375 GLU cc_start: 0.8975 (tp30) cc_final: 0.8568 (tp30) REVERT: j 407 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8821 (ttmm) REVERT: b 1 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6325 (tpt) REVERT: b 30 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8396 (mtm-85) REVERT: b 244 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8629 (mm-30) REVERT: b 253 LEU cc_start: 0.9357 (mt) cc_final: 0.9081 (mt) REVERT: b 307 VAL cc_start: 0.8585 (t) cc_final: 0.8381 (t) REVERT: b 342 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8279 (mp0) REVERT: b 352 LYS cc_start: 0.8325 (tptp) cc_final: 0.8041 (tptp) REVERT: c 29 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (ptm) REVERT: c 30 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8289 (mtp-110) REVERT: c 41 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8514 (tm-30) REVERT: c 85 GLN cc_start: 0.9332 (mt0) cc_final: 0.8607 (mp10) REVERT: c 90 ASN cc_start: 0.8102 (t0) cc_final: 0.7486 (t0) REVERT: c 154 THR cc_start: 0.8918 (m) cc_final: 0.8718 (t) REVERT: c 195 ILE cc_start: 0.9495 (mt) cc_final: 0.9239 (mt) REVERT: c 224 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8335 (pttt) REVERT: c 381 TRP cc_start: 0.8622 (OUTLIER) cc_final: 0.8326 (t60) REVERT: c 407 LYS cc_start: 0.8856 (ptmm) cc_final: 0.8527 (tppt) REVERT: d 49 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9123 (mm) REVERT: d 56 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8715 (pt0) REVERT: d 85 GLN cc_start: 0.9455 (mt0) cc_final: 0.9080 (mp10) REVERT: d 202 CYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8563 (m) REVERT: d 205 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8392 (mtp) REVERT: d 342 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8241 (mm-30) REVERT: d 374 GLN cc_start: 0.9138 (tp40) cc_final: 0.8825 (tp-100) REVERT: d 375 GLU cc_start: 0.9012 (mp0) cc_final: 0.8580 (mp0) REVERT: d 381 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.8304 (t60) REVERT: d 397 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8651 (mt-10) REVERT: e 56 GLU cc_start: 0.8771 (tt0) cc_final: 0.8154 (tm-30) REVERT: e 122 ASP cc_start: 0.8734 (t0) cc_final: 0.8446 (t0) REVERT: e 197 TYR cc_start: 0.9409 (t80) cc_final: 0.9128 (t80) REVERT: e 222 LEU cc_start: 0.9382 (tt) cc_final: 0.9105 (tt) REVERT: e 326 LYS cc_start: 0.9406 (tptt) cc_final: 0.9116 (tppt) REVERT: e 329 GLU cc_start: 0.8227 (pm20) cc_final: 0.7905 (pm20) REVERT: f 123 LYS cc_start: 0.8116 (ptmm) cc_final: 0.7823 (ptmm) REVERT: f 134 GLU cc_start: 0.8993 (mp0) cc_final: 0.8652 (mp0) REVERT: f 326 LYS cc_start: 0.8993 (tmtt) cc_final: 0.8704 (ttpp) REVERT: f 329 GLU cc_start: 0.8194 (mp0) cc_final: 0.7506 (mp0) REVERT: g 23 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7990 (mm) REVERT: g 30 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7692 (mtp-110) REVERT: g 215 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: g 244 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7953 (mm-30) REVERT: g 374 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8882 (tp-100) REVERT: g 375 GLU cc_start: 0.8764 (tp30) cc_final: 0.8002 (tp30) REVERT: g 397 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8856 (mt-10) REVERT: h 59 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8357 (tp-100) REVERT: h 244 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7994 (mm-30) REVERT: i 56 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8680 (pt0) REVERT: i 326 LYS cc_start: 0.9379 (tppt) cc_final: 0.9170 (mmmt) REVERT: i 333 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8827 (mm-30) REVERT: i 342 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8414 (mp0) REVERT: i 375 GLU cc_start: 0.8404 (tp30) cc_final: 0.7983 (tp30) outliers start: 214 outliers final: 143 residues processed: 1092 average time/residue: 0.5475 time to fit residues: 1014.1096 Evaluate side-chains 1058 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 893 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 398 PHE Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 11 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 194 SER Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 ASN Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 207 LEU Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 326 LYS Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 220 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 318 THR Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 218 GLU Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 84 SER Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 205 MET Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 383 LEU Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 374 GLN Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 376 GLU Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 341 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 3.9990 chunk 681 optimal weight: 3.9990 chunk 621 optimal weight: 5.9990 chunk 662 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 520 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 598 optimal weight: 0.6980 chunk 626 optimal weight: 0.5980 chunk 660 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN r 344 HIS q 344 HIS ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 220 GLN ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN d 41 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 GLN d 193 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 60822 Z= 0.218 Angle : 0.682 12.557 82008 Z= 0.326 Chirality : 0.044 0.187 9324 Planarity : 0.004 0.062 10620 Dihedral : 4.863 47.453 8393 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.06 % Allowed : 30.05 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.36 (0.09), residues: 7506 helix: 1.11 (0.09), residues: 3420 sheet: -0.36 (0.15), residues: 1062 loop : -0.43 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.009 TRP n 381 HIS 0.010 0.001 HIS r 295 PHE 0.014 0.001 PHE o 412 TYR 0.021 0.001 TYR l 197 ARG 0.012 0.001 ARG l 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 901 time to evaluate : 5.560 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: a 122 ASP cc_start: 0.7994 (t0) cc_final: 0.7528 (t0) REVERT: a 215 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: a 241 GLN cc_start: 0.9213 (pp30) cc_final: 0.8952 (pp30) REVERT: a 244 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8198 (mm-30) REVERT: a 264 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8878 (tm) REVERT: a 374 GLN cc_start: 0.9258 (tp40) cc_final: 0.8782 (tp-100) REVERT: a 375 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8412 (mp0) REVERT: a 396 MET cc_start: 0.9428 (tpp) cc_final: 0.9144 (tpp) REVERT: a 416 MET cc_start: 0.9029 (mmm) cc_final: 0.8785 (mmp) REVERT: r 244 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8532 (mm-30) REVERT: q 1 MET cc_start: 0.7660 (mmm) cc_final: 0.6957 (tpt) REVERT: q 23 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8242 (mp) REVERT: q 56 GLU cc_start: 0.8940 (pt0) cc_final: 0.8557 (pt0) REVERT: q 241 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8730 (pp30) REVERT: q 244 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8494 (mm-30) REVERT: q 375 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8531 (tm-30) REVERT: p 33 ASP cc_start: 0.9095 (m-30) cc_final: 0.8800 (m-30) REVERT: p 56 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8589 (pt0) REVERT: p 91 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8562 (pp) REVERT: p 193 GLN cc_start: 0.9041 (tt0) cc_final: 0.8749 (tt0) REVERT: p 197 TYR cc_start: 0.9125 (t80) cc_final: 0.8895 (t80) REVERT: p 241 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: p 325 SER cc_start: 0.8364 (t) cc_final: 0.7920 (p) REVERT: p 341 MET cc_start: 0.9025 (ppp) cc_final: 0.8753 (ppp) REVERT: p 394 ASP cc_start: 0.8873 (p0) cc_final: 0.8572 (p0) REVERT: p 397 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8767 (mm-30) REVERT: o 197 TYR cc_start: 0.9306 (t80) cc_final: 0.9022 (t80) REVERT: o 244 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8320 (mm-30) REVERT: o 326 LYS cc_start: 0.9009 (tppt) cc_final: 0.8774 (tppt) REVERT: o 341 MET cc_start: 0.9174 (ppp) cc_final: 0.8830 (ppp) REVERT: o 375 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8468 (tm-30) REVERT: o 397 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8509 (mp0) REVERT: o 415 MET cc_start: 0.8899 (ppp) cc_final: 0.8585 (ppp) REVERT: n 100 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9109 (ttmm) REVERT: n 244 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8521 (mm-30) REVERT: n 342 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8635 (mt-10) REVERT: n 374 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8251 (tp40) REVERT: m 125 GLU cc_start: 0.8799 (mp0) cc_final: 0.8557 (pm20) REVERT: m 244 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8296 (mm-30) REVERT: m 296 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8689 (mmm-85) REVERT: m 342 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8408 (mp0) REVERT: m 374 GLN cc_start: 0.9448 (tp40) cc_final: 0.9167 (tp40) REVERT: m 392 GLU cc_start: 0.8232 (pm20) cc_final: 0.7450 (pt0) REVERT: l 32 GLN cc_start: 0.8983 (mp10) cc_final: 0.8336 (mm-40) REVERT: l 109 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7644 (mtm-85) REVERT: l 244 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7908 (mm-30) REVERT: l 290 ASP cc_start: 0.8593 (m-30) cc_final: 0.8087 (t70) REVERT: l 352 LYS cc_start: 0.8140 (tptp) cc_final: 0.7818 (tptp) REVERT: l 354 VAL cc_start: 0.8453 (t) cc_final: 0.8250 (t) REVERT: l 390 MET cc_start: 0.9184 (ptp) cc_final: 0.8907 (ptp) REVERT: l 397 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8869 (mm-30) REVERT: k 12 SER cc_start: 0.9102 (m) cc_final: 0.8765 (p) REVERT: k 13 GLU cc_start: 0.8566 (pm20) cc_final: 0.8285 (pm20) REVERT: k 41 GLN cc_start: 0.8656 (tp40) cc_final: 0.8198 (tm-30) REVERT: k 44 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8581 (ptpp) REVERT: k 244 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8010 (mm-30) REVERT: k 333 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8670 (mm-30) REVERT: k 342 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8408 (mp0) REVERT: k 352 LYS cc_start: 0.8856 (tptp) cc_final: 0.8497 (tptp) REVERT: k 410 ASP cc_start: 0.9230 (m-30) cc_final: 0.8925 (p0) REVERT: j 1 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.5551 (tmm) REVERT: j 23 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8267 (mm) REVERT: j 342 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8127 (pt0) REVERT: j 407 LYS cc_start: 0.9117 (ptmm) cc_final: 0.8884 (ttmm) REVERT: b 30 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8433 (mtm-85) REVERT: b 244 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8650 (mm-30) REVERT: b 253 LEU cc_start: 0.9361 (mt) cc_final: 0.9080 (mt) REVERT: b 342 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8294 (mp0) REVERT: b 352 LYS cc_start: 0.8414 (tptp) cc_final: 0.8105 (tptp) REVERT: c 29 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8203 (ptm) REVERT: c 30 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8316 (mtp-110) REVERT: c 41 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8518 (tm-30) REVERT: c 85 GLN cc_start: 0.9339 (mt0) cc_final: 0.8615 (mp10) REVERT: c 90 ASN cc_start: 0.8097 (t0) cc_final: 0.7494 (t0) REVERT: c 195 ILE cc_start: 0.9503 (mt) cc_final: 0.9249 (mt) REVERT: c 224 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8382 (pttt) REVERT: c 241 GLN cc_start: 0.9196 (pp30) cc_final: 0.8489 (pp30) REVERT: c 333 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8774 (tm-30) REVERT: c 374 GLN cc_start: 0.9140 (tp-100) cc_final: 0.8609 (tp-100) REVERT: c 378 GLN cc_start: 0.8755 (mt0) cc_final: 0.8465 (mp10) REVERT: c 381 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8326 (t60) REVERT: c 407 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8604 (tppt) REVERT: d 49 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9110 (mm) REVERT: d 56 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: d 202 CYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8641 (m) REVERT: d 205 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8231 (mtp) REVERT: d 226 GLU cc_start: 0.8130 (pp20) cc_final: 0.7917 (pp20) REVERT: d 342 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8191 (mm-30) REVERT: d 374 GLN cc_start: 0.9169 (tp40) cc_final: 0.8868 (tp-100) REVERT: d 375 GLU cc_start: 0.9036 (mp0) cc_final: 0.8598 (mp0) REVERT: d 381 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.8338 (t60) REVERT: d 397 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8826 (mt-10) REVERT: e 122 ASP cc_start: 0.8743 (t0) cc_final: 0.8452 (t0) REVERT: e 197 TYR cc_start: 0.9405 (t80) cc_final: 0.9147 (t80) REVERT: e 326 LYS cc_start: 0.9423 (tptt) cc_final: 0.9166 (tppt) REVERT: e 329 GLU cc_start: 0.8241 (pm20) cc_final: 0.7880 (pm20) REVERT: f 123 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7798 (ptmm) REVERT: f 134 GLU cc_start: 0.8992 (mp0) cc_final: 0.8653 (mp0) REVERT: f 326 LYS cc_start: 0.8984 (tmtt) cc_final: 0.8745 (ttpp) REVERT: f 329 GLU cc_start: 0.8189 (mp0) cc_final: 0.7577 (mp0) REVERT: g 23 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (mm) REVERT: g 30 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7718 (mtp-110) REVERT: g 215 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: g 244 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7980 (mm-30) REVERT: g 329 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8065 (mp0) REVERT: g 374 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8660 (tp-100) REVERT: g 397 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8872 (mt-10) REVERT: h 59 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8480 (tp-100) REVERT: h 244 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8014 (mm-30) REVERT: i 56 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: i 326 LYS cc_start: 0.9382 (tppt) cc_final: 0.9140 (mmmt) REVERT: i 333 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8828 (mm-30) REVERT: i 342 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8393 (mp0) REVERT: i 375 GLU cc_start: 0.8389 (tp30) cc_final: 0.7979 (tp30) outliers start: 198 outliers final: 150 residues processed: 1037 average time/residue: 0.5483 time to fit residues: 966.1557 Evaluate side-chains 1050 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 880 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 308 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 396 MET Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 91 LEU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 205 MET Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 265 ASP Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 123 LYS Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 418 ARG Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 91 LEU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 ASN Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 383 LEU Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 29 MET Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 376 GLU Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 5.9990 chunk 700 optimal weight: 4.9990 chunk 427 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 487 optimal weight: 9.9990 chunk 735 optimal weight: 0.9980 chunk 676 optimal weight: 0.7980 chunk 585 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 452 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN a 220 GLN ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS r 344 HIS q 135 ASN q 344 HIS ** n 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 374 GLN l 378 GLN b 189 GLN ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 60822 Z= 0.226 Angle : 0.689 13.026 82008 Z= 0.330 Chirality : 0.044 0.191 9324 Planarity : 0.004 0.046 10620 Dihedral : 4.894 40.721 8393 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.99 % Allowed : 30.22 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.38 (0.10), residues: 7506 helix: 1.16 (0.09), residues: 3384 sheet: -0.48 (0.14), residues: 1152 loop : -0.38 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.009 TRP n 381 HIS 0.013 0.001 HIS r 295 PHE 0.014 0.001 PHE q 413 TYR 0.022 0.001 TYR b 197 ARG 0.012 0.001 ARG l 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15012 Ramachandran restraints generated. 7506 Oldfield, 0 Emsley, 7506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 887 time to evaluate : 5.383 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: a 29 MET cc_start: 0.7928 (ptm) cc_final: 0.7542 (ppp) REVERT: a 122 ASP cc_start: 0.8042 (t0) cc_final: 0.7563 (t0) REVERT: a 215 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: a 241 GLN cc_start: 0.9213 (pp30) cc_final: 0.8953 (pp30) REVERT: a 244 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8189 (mm-30) REVERT: a 374 GLN cc_start: 0.9221 (tp40) cc_final: 0.8721 (tp-100) REVERT: a 375 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8307 (mp0) REVERT: a 416 MET cc_start: 0.9056 (mmm) cc_final: 0.8818 (mmp) REVERT: r 189 GLN cc_start: 0.9175 (mt0) cc_final: 0.8923 (mp10) REVERT: r 244 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8536 (mm-30) REVERT: q 1 MET cc_start: 0.7574 (mmm) cc_final: 0.6915 (tpt) REVERT: q 23 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8537 (mm) REVERT: q 56 GLU cc_start: 0.8960 (pt0) cc_final: 0.8570 (pt0) REVERT: q 241 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8723 (pp30) REVERT: q 244 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8488 (mm-30) REVERT: q 375 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8536 (tm-30) REVERT: p 33 ASP cc_start: 0.9082 (m-30) cc_final: 0.8791 (m-30) REVERT: p 56 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8581 (pt0) REVERT: p 193 GLN cc_start: 0.9079 (tt0) cc_final: 0.8844 (tt0) REVERT: p 197 TYR cc_start: 0.9134 (t80) cc_final: 0.8905 (t80) REVERT: p 325 SER cc_start: 0.8366 (t) cc_final: 0.7924 (p) REVERT: p 394 ASP cc_start: 0.8868 (p0) cc_final: 0.8553 (p0) REVERT: p 397 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8777 (mm-30) REVERT: o 197 TYR cc_start: 0.9296 (t80) cc_final: 0.9007 (t80) REVERT: o 244 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8356 (mm-30) REVERT: o 333 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8643 (tm-30) REVERT: o 341 MET cc_start: 0.9188 (ppp) cc_final: 0.8825 (ppp) REVERT: o 375 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8515 (tm-30) REVERT: o 397 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8491 (mp0) REVERT: n 100 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9108 (ttmm) REVERT: n 244 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8518 (mm-30) REVERT: n 342 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8633 (mt-10) REVERT: n 374 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8248 (tp40) REVERT: m 244 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8291 (mm-30) REVERT: m 296 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8691 (mmm-85) REVERT: m 342 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8408 (mp0) REVERT: m 374 GLN cc_start: 0.9450 (tp40) cc_final: 0.9177 (tp40) REVERT: m 392 GLU cc_start: 0.8238 (pm20) cc_final: 0.7383 (pt0) REVERT: l 32 GLN cc_start: 0.8972 (mp10) cc_final: 0.8310 (mm-40) REVERT: l 109 ARG cc_start: 0.8011 (ptp-170) cc_final: 0.7653 (mtm-85) REVERT: l 244 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7932 (mm-30) REVERT: l 290 ASP cc_start: 0.8579 (m-30) cc_final: 0.8087 (t70) REVERT: l 352 LYS cc_start: 0.8125 (tptp) cc_final: 0.7818 (tptp) REVERT: l 390 MET cc_start: 0.9204 (ptp) cc_final: 0.8911 (ptp) REVERT: l 397 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8848 (mm-30) REVERT: k 12 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8764 (p) REVERT: k 13 GLU cc_start: 0.8561 (pm20) cc_final: 0.8257 (pm20) REVERT: k 41 GLN cc_start: 0.8647 (tp40) cc_final: 0.8220 (tm-30) REVERT: k 44 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8591 (ptpp) REVERT: k 244 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8009 (mm-30) REVERT: k 333 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8666 (mm-30) REVERT: k 342 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8410 (mp0) REVERT: k 410 ASP cc_start: 0.9210 (m-30) cc_final: 0.8974 (p0) REVERT: j 1 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5601 (tmm) REVERT: j 23 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8246 (mm) REVERT: j 342 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8130 (pt0) REVERT: j 407 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8893 (ttmm) REVERT: b 30 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8449 (mtm-85) REVERT: b 39 LEU cc_start: 0.9264 (mm) cc_final: 0.8984 (mp) REVERT: b 244 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8643 (mm-30) REVERT: b 253 LEU cc_start: 0.9364 (mt) cc_final: 0.9083 (mt) REVERT: b 342 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8301 (mp0) REVERT: b 352 LYS cc_start: 0.8449 (tptp) cc_final: 0.8151 (tptp) REVERT: c 29 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8235 (ptm) REVERT: c 30 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8312 (mtp-110) REVERT: c 41 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8519 (tm-30) REVERT: c 85 GLN cc_start: 0.9340 (mt0) cc_final: 0.8610 (mp10) REVERT: c 90 ASN cc_start: 0.8130 (t0) cc_final: 0.7502 (t0) REVERT: c 195 ILE cc_start: 0.9504 (mt) cc_final: 0.9251 (mt) REVERT: c 224 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8431 (pttt) REVERT: c 241 GLN cc_start: 0.9164 (pp30) cc_final: 0.8520 (pp30) REVERT: c 381 TRP cc_start: 0.8671 (OUTLIER) cc_final: 0.8357 (t60) REVERT: c 407 LYS cc_start: 0.8894 (ptmm) cc_final: 0.8575 (tppt) REVERT: d 49 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9108 (mm) REVERT: d 56 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: d 202 CYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8638 (m) REVERT: d 205 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8378 (mtp) REVERT: d 226 GLU cc_start: 0.8139 (pp20) cc_final: 0.7909 (pp20) REVERT: d 342 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8209 (mm-30) REVERT: d 374 GLN cc_start: 0.9155 (tp40) cc_final: 0.8859 (tp-100) REVERT: d 375 GLU cc_start: 0.9048 (mp0) cc_final: 0.8632 (mp0) REVERT: d 381 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8399 (t60) REVERT: d 397 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8663 (mt-10) REVERT: e 122 ASP cc_start: 0.8751 (t0) cc_final: 0.8468 (t0) REVERT: e 197 TYR cc_start: 0.9405 (t80) cc_final: 0.9143 (t80) REVERT: e 326 LYS cc_start: 0.9423 (tptt) cc_final: 0.9180 (tppt) REVERT: e 329 GLU cc_start: 0.8237 (pm20) cc_final: 0.7872 (pm20) REVERT: f 134 GLU cc_start: 0.9000 (mp0) cc_final: 0.8650 (mp0) REVERT: f 326 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8749 (ttpp) REVERT: f 329 GLU cc_start: 0.8197 (mp0) cc_final: 0.7571 (mp0) REVERT: g 23 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7976 (mm) REVERT: g 30 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7750 (mtp-110) REVERT: g 215 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: g 244 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7977 (mm-30) REVERT: g 329 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8051 (mp0) REVERT: g 374 GLN cc_start: 0.9066 (tp-100) cc_final: 0.8683 (tp-100) REVERT: g 397 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8878 (mt-10) REVERT: h 59 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8502 (tp-100) REVERT: h 374 GLN cc_start: 0.9275 (tp-100) cc_final: 0.8777 (tp40) REVERT: i 56 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8644 (pt0) REVERT: i 326 LYS cc_start: 0.9387 (tppt) cc_final: 0.9177 (mmmt) REVERT: i 333 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8837 (mm-30) REVERT: i 342 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8404 (mp0) REVERT: i 375 GLU cc_start: 0.8407 (tp30) cc_final: 0.7995 (tp30) outliers start: 194 outliers final: 156 residues processed: 1025 average time/residue: 0.5478 time to fit residues: 952.1932 Evaluate side-chains 1039 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 865 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 110 TYR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 202 CYS Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 338 THR Chi-restraints excluded: chain a residue 341 MET Chi-restraints excluded: chain a residue 376 GLU Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 114 LEU Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 308 GLU Chi-restraints excluded: chain r residue 323 THR Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 4 THR Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 202 CYS Chi-restraints excluded: chain q residue 241 GLN Chi-restraints excluded: chain q residue 323 THR Chi-restraints excluded: chain q residue 330 VAL Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 416 MET Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 23 LEU Chi-restraints excluded: chain p residue 55 LEU Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 202 CYS Chi-restraints excluded: chain p residue 260 VAL Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 286 THR Chi-restraints excluded: chain p residue 338 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 274 TYR Chi-restraints excluded: chain o residue 370 LEU Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 23 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 91 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 205 MET Chi-restraints excluded: chain n residue 253 LEU Chi-restraints excluded: chain n residue 265 ASP Chi-restraints excluded: chain n residue 338 THR Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 56 GLU Chi-restraints excluded: chain m residue 59 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 205 MET Chi-restraints excluded: chain m residue 241 GLN Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 380 MET Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 44 LYS Chi-restraints excluded: chain l residue 49 ILE Chi-restraints excluded: chain l residue 56 GLU Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 205 MET Chi-restraints excluded: chain l residue 277 VAL Chi-restraints excluded: chain l residue 341 MET Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 44 LYS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 120 ASN Chi-restraints excluded: chain k residue 162 LEU Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 277 VAL Chi-restraints excluded: chain k residue 327 MET Chi-restraints excluded: chain k residue 338 THR Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 29 MET Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 260 VAL Chi-restraints excluded: chain j residue 318 THR Chi-restraints excluded: chain j residue 338 THR Chi-restraints excluded: chain j residue 366 ARG Chi-restraints excluded: chain j residue 373 THR Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 100 LYS Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain b residue 193 GLN Chi-restraints excluded: chain b residue 218 GLU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 341 MET Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 49 ILE Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain c residue 218 GLU Chi-restraints excluded: chain c residue 323 THR Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 56 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 202 CYS Chi-restraints excluded: chain d residue 205 MET Chi-restraints excluded: chain d residue 246 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 338 THR Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 69 ASP Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 266 SER Chi-restraints excluded: chain e residue 318 THR Chi-restraints excluded: chain e residue 341 MET Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 GLU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 205 MET Chi-restraints excluded: chain f residue 241 GLN Chi-restraints excluded: chain f residue 277 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 341 MET Chi-restraints excluded: chain f residue 366 ARG Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 383 LEU Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 215 GLU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 264 LEU Chi-restraints excluded: chain g residue 338 THR Chi-restraints excluded: chain g residue 341 MET Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain h residue 23 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 56 GLU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 123 LYS Chi-restraints excluded: chain h residue 162 LEU Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 338 THR Chi-restraints excluded: chain h residue 376 GLU Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 338 THR Chi-restraints excluded: chain i residue 341 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 5.9990 chunk 623 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 539 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 586 optimal weight: 4.9990 chunk 245 optimal weight: 0.0370 chunk 602 optimal weight: 0.0980 chunk 74 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 374 GLN ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 295 HIS r 344 HIS q 344 HIS p 172 GLN ** l 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN c 189 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 374 GLN ** h 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.059209 restraints weight = 155261.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061398 restraints weight = 71730.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062803 restraints weight = 43333.138| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 60822 Z= 0.243 Angle : 0.704 12.930 82008 Z= 0.338 Chirality : 0.044 0.190 9324 Planarity : 0.004 0.056 10620 Dihedral : 4.941 41.543 8393 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.01 % Allowed : 30.37 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.38 (0.10), residues: 7506 helix: 1.17 (0.09), residues: 3384 sheet: -0.50 (0.14), residues: 1152 loop : -0.39 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.009 TRP l 381 HIS 0.004 0.001 HIS h 140 PHE 0.016 0.001 PHE r 412 TYR 0.022 0.001 TYR b 197 ARG 0.014 0.001 ARG l 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15216.87 seconds wall clock time: 266 minutes 25.82 seconds (15985.82 seconds total)