Starting phenix.real_space_refine on Mon Dec 30 02:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.map" model { file = "/net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q3q_18133/12_2024/8q3q_18133.cif" } resolution = 3.3 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= 0.014 sd= 0.065 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 288 residue(s): 0.14s 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: 36 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: "r" 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: "q" 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: "p" 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: "o" 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: "n" 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: "m" 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: "l" 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: "k" 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: "j" 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: "i" 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: "h" 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: "g" 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: "f" 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: "e" 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: "d" 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: "c" 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: "b" 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} Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" 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} Time building chain proxies: 24.48, per 1000 atoms: 0.41 Number of scatterers: 59922 At special positions: 0 Unit cell: (138.112, 138.112, 279.552, 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: 11.69 Conformation dependent library (CDL) restraints added in 6.0 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: 342 helices and 54 sheets defined 51.8% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'a' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU a 6 " --> pdb=" O ASN a 2 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR a 16 " --> pdb=" O SER a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 46 Processing helix chain 'a' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE a 86 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 128 removed outlier: 3.534A pdb=" N ARG a 128 " --> pdb=" O PRO a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 136 Processing helix chain 'a' and resid 157 through 166 Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 223 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU a 270 " --> pdb=" O SER a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL a 289 " --> pdb=" O THR a 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'a' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA a 350 " --> pdb=" O SER a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU a 371 " --> pdb=" O LYS a 367 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 391 through 404 Processing helix chain 'a' and resid 408 through 419 Processing helix chain 'r' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU r 6 " --> pdb=" O ASN r 2 " (cutoff:3.500A) Processing helix chain 'r' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR r 16 " --> pdb=" O SER r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 46 Processing helix chain 'r' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE r 86 " --> pdb=" O SER r 82 " (cutoff:3.500A) Processing helix chain 'r' and resid 123 through 128 removed outlier: 3.534A pdb=" N ARG r 128 " --> pdb=" O PRO r 124 " (cutoff:3.500A) Processing helix chain 'r' and resid 132 through 136 Processing helix chain 'r' and resid 157 through 166 Processing helix chain 'r' and resid 183 through 199 Processing helix chain 'r' and resid 212 through 223 Processing helix chain 'r' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS r 239 " --> pdb=" O PRO r 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS r 256 " --> pdb=" O ARG r 252 " (cutoff:3.500A) Processing helix chain 'r' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU r 270 " --> pdb=" O SER r 266 " (cutoff:3.500A) Processing helix chain 'r' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL r 289 " --> pdb=" O THR r 286 " (cutoff:3.500A) Processing helix chain 'r' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'r' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA r 350 " --> pdb=" O SER r 346 " (cutoff:3.500A) Processing helix chain 'r' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU r 371 " --> pdb=" O LYS r 367 " (cutoff:3.500A) Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 391 through 404 Processing helix chain 'r' and resid 408 through 419 Processing helix chain 'q' and resid 2 through 9 removed outlier: 3.777A pdb=" N LEU q 6 " --> pdb=" O ASN q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 10 through 22 removed outlier: 4.303A pdb=" N THR q 16 " --> pdb=" O SER q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 46 Processing helix chain 'q' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE q 86 " --> pdb=" O SER q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG q 128 " --> pdb=" O PRO q 124 " (cutoff:3.500A) Processing helix chain 'q' and resid 132 through 136 Processing helix chain 'q' and resid 157 through 166 Processing helix chain 'q' and resid 183 through 199 Processing helix chain 'q' and resid 212 through 223 Processing helix chain 'q' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS q 239 " --> pdb=" O PRO q 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS q 256 " --> pdb=" O ARG q 252 " (cutoff:3.500A) Processing helix chain 'q' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU q 270 " --> pdb=" O SER q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL q 289 " --> pdb=" O THR q 286 " (cutoff:3.500A) Processing helix chain 'q' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'q' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA q 350 " --> pdb=" O SER q 346 " (cutoff:3.500A) Processing helix chain 'q' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU q 371 " --> pdb=" O LYS q 367 " (cutoff:3.500A) Processing helix chain 'q' and resid 373 through 388 Processing helix chain 'q' and resid 391 through 404 Processing helix chain 'q' and resid 408 through 419 Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU p 6 " --> pdb=" O ASN p 2 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR p 16 " --> pdb=" O SER p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 30 through 46 Processing helix chain 'p' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE p 86 " --> pdb=" O SER p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 123 through 128 removed outlier: 3.534A pdb=" N ARG p 128 " --> pdb=" O PRO p 124 " (cutoff:3.500A) Processing helix chain 'p' and resid 132 through 136 Processing helix chain 'p' and resid 157 through 166 Processing helix chain 'p' and resid 183 through 199 Processing helix chain 'p' and resid 212 through 223 Processing helix chain 'p' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS p 239 " --> pdb=" O PRO p 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS p 256 " --> pdb=" O ARG p 252 " (cutoff:3.500A) Processing helix chain 'p' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU p 270 " --> pdb=" O SER p 266 " (cutoff:3.500A) Processing helix chain 'p' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL p 289 " --> pdb=" O THR p 286 " (cutoff:3.500A) Processing helix chain 'p' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'p' and resid 346 through 353 removed outlier: 3.542A pdb=" N ALA p 350 " --> pdb=" O SER p 346 " (cutoff:3.500A) Processing helix chain 'p' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU p 371 " --> pdb=" O LYS p 367 " (cutoff:3.500A) Processing helix chain 'p' and resid 373 through 388 Processing helix chain 'p' and resid 391 through 404 Processing helix chain 'p' and resid 408 through 419 Processing helix chain 'o' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU o 6 " --> pdb=" O ASN o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR o 16 " --> pdb=" O SER o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 30 through 46 Processing helix chain 'o' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE o 86 " --> pdb=" O SER o 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG o 128 " --> pdb=" O PRO o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 132 through 136 Processing helix chain 'o' and resid 157 through 166 Processing helix chain 'o' and resid 183 through 199 Processing helix chain 'o' and resid 212 through 223 Processing helix chain 'o' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS o 239 " --> pdb=" O PRO o 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS o 256 " --> pdb=" O ARG o 252 " (cutoff:3.500A) Processing helix chain 'o' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU o 270 " --> pdb=" O SER o 266 " (cutoff:3.500A) Processing helix chain 'o' and resid 285 through 289 removed outlier: 4.104A pdb=" N VAL o 289 " --> pdb=" O THR o 286 " (cutoff:3.500A) Processing helix chain 'o' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'o' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA o 350 " --> pdb=" O SER o 346 " (cutoff:3.500A) Processing helix chain 'o' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU o 371 " --> pdb=" O LYS o 367 " (cutoff:3.500A) Processing helix chain 'o' and resid 373 through 388 Processing helix chain 'o' and resid 391 through 404 Processing helix chain 'o' and resid 408 through 419 Processing helix chain 'n' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU n 6 " --> pdb=" O ASN n 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR n 16 " --> pdb=" O SER n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 30 through 46 Processing helix chain 'n' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG n 128 " --> pdb=" O PRO n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 132 through 136 Processing helix chain 'n' and resid 157 through 166 Processing helix chain 'n' and resid 183 through 199 Processing helix chain 'n' and resid 212 through 223 Processing helix chain 'n' and resid 235 through 256 removed outlier: 3.581A pdb=" N HIS n 239 " --> pdb=" O PRO n 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS n 256 " --> pdb=" O ARG n 252 " (cutoff:3.500A) Processing helix chain 'n' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU n 270 " --> pdb=" O SER n 266 " (cutoff:3.500A) Processing helix chain 'n' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL n 289 " --> pdb=" O THR n 286 " (cutoff:3.500A) Processing helix chain 'n' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'n' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA n 350 " --> pdb=" O SER n 346 " (cutoff:3.500A) Processing helix chain 'n' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU n 371 " --> pdb=" O LYS n 367 " (cutoff:3.500A) Processing helix chain 'n' and resid 373 through 388 Processing helix chain 'n' and resid 391 through 404 Processing helix chain 'n' and resid 408 through 419 Processing helix chain 'm' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU m 6 " --> pdb=" O ASN m 2 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 46 Processing helix chain 'm' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE m 86 " --> pdb=" O SER m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 123 through 128 removed outlier: 3.534A pdb=" N ARG m 128 " --> pdb=" O PRO m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 132 through 136 Processing helix chain 'm' and resid 157 through 166 Processing helix chain 'm' and resid 183 through 199 Processing helix chain 'm' and resid 212 through 223 Processing helix chain 'm' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS m 239 " --> pdb=" O PRO m 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS m 256 " --> pdb=" O ARG m 252 " (cutoff:3.500A) Processing helix chain 'm' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU m 270 " --> pdb=" O SER m 266 " (cutoff:3.500A) Processing helix chain 'm' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL m 289 " --> pdb=" O THR m 286 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'm' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA m 350 " --> pdb=" O SER m 346 " (cutoff:3.500A) Processing helix chain 'm' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU m 371 " --> pdb=" O LYS m 367 " (cutoff:3.500A) Processing helix chain 'm' and resid 373 through 388 Processing helix chain 'm' and resid 391 through 404 Processing helix chain 'm' and resid 408 through 419 Processing helix chain 'l' and resid 2 through 9 removed outlier: 3.777A pdb=" N LEU l 6 " --> pdb=" O ASN l 2 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 46 Processing helix chain 'l' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE l 86 " --> pdb=" O SER l 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG l 128 " --> pdb=" O PRO l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 136 Processing helix chain 'l' and resid 157 through 166 Processing helix chain 'l' and resid 183 through 199 Processing helix chain 'l' and resid 212 through 223 Processing helix chain 'l' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS l 239 " --> pdb=" O PRO l 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS l 256 " --> pdb=" O ARG l 252 " (cutoff:3.500A) Processing helix chain 'l' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU l 270 " --> pdb=" O SER l 266 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL l 289 " --> pdb=" O THR l 286 " (cutoff:3.500A) Processing helix chain 'l' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'l' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA l 350 " --> pdb=" O SER l 346 " (cutoff:3.500A) Processing helix chain 'l' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU l 371 " --> pdb=" O LYS l 367 " (cutoff:3.500A) Processing helix chain 'l' and resid 373 through 388 Processing helix chain 'l' and resid 391 through 404 Processing helix chain 'l' and resid 408 through 419 Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU k 6 " --> pdb=" O ASN k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 46 Processing helix chain 'k' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE k 86 " --> pdb=" O SER k 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG k 128 " --> pdb=" O PRO k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 132 through 136 Processing helix chain 'k' and resid 157 through 166 Processing helix chain 'k' and resid 183 through 199 Processing helix chain 'k' and resid 212 through 223 Processing helix chain 'k' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS k 239 " --> pdb=" O PRO k 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS k 256 " --> pdb=" O ARG k 252 " (cutoff:3.500A) Processing helix chain 'k' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU k 270 " --> pdb=" O SER k 266 " (cutoff:3.500A) Processing helix chain 'k' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL k 289 " --> pdb=" O THR k 286 " (cutoff:3.500A) Processing helix chain 'k' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'k' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA k 350 " --> pdb=" O SER k 346 " (cutoff:3.500A) Processing helix chain 'k' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU k 371 " --> pdb=" O LYS k 367 " (cutoff:3.500A) Processing helix chain 'k' and resid 373 through 388 Processing helix chain 'k' and resid 391 through 404 Processing helix chain 'k' and resid 408 through 419 Processing helix chain 'j' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU j 6 " --> pdb=" O ASN j 2 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 22 removed outlier: 4.305A pdb=" N THR j 16 " --> pdb=" O SER j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 46 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE j 86 " --> pdb=" O SER j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG j 128 " --> pdb=" O PRO j 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 136 Processing helix chain 'j' and resid 157 through 166 Processing helix chain 'j' and resid 183 through 199 Processing helix chain 'j' and resid 212 through 223 Processing helix chain 'j' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS j 239 " --> pdb=" O PRO j 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS j 256 " --> pdb=" O ARG j 252 " (cutoff:3.500A) Processing helix chain 'j' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU j 270 " --> pdb=" O SER j 266 " (cutoff:3.500A) Processing helix chain 'j' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL j 289 " --> pdb=" O THR j 286 " (cutoff:3.500A) Processing helix chain 'j' and resid 290 through 303 removed outlier: 3.965A 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 Processing helix chain 'j' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA j 350 " --> pdb=" O SER j 346 " (cutoff:3.500A) Processing helix chain 'j' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU j 371 " --> pdb=" O LYS j 367 " (cutoff:3.500A) Processing helix chain 'j' and resid 373 through 388 Processing helix chain 'j' and resid 391 through 404 Processing helix chain 'j' and resid 408 through 419 Processing helix chain 'i' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU i 6 " --> pdb=" O ASN i 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 46 Processing helix chain 'i' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE i 86 " --> pdb=" O SER i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG i 128 " --> pdb=" O PRO i 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 136 Processing helix chain 'i' and resid 157 through 166 Processing helix chain 'i' and resid 183 through 199 Processing helix chain 'i' and resid 212 through 223 Processing helix chain 'i' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS i 239 " --> pdb=" O PRO i 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS i 256 " --> pdb=" O ARG i 252 " (cutoff:3.500A) Processing helix chain 'i' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU i 270 " --> pdb=" O SER i 266 " (cutoff:3.500A) Processing helix chain 'i' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL i 289 " --> pdb=" O THR i 286 " (cutoff:3.500A) Processing helix chain 'i' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'i' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA i 350 " --> pdb=" O SER i 346 " (cutoff:3.500A) Processing helix chain 'i' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU i 371 " --> pdb=" O LYS i 367 " (cutoff:3.500A) Processing helix chain 'i' and resid 373 through 388 Processing helix chain 'i' and resid 391 through 404 Processing helix chain 'i' and resid 408 through 419 Processing helix chain 'h' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU h 6 " --> pdb=" O ASN h 2 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 46 Processing helix chain 'h' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE h 86 " --> pdb=" O SER h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG h 128 " --> pdb=" O PRO h 124 " (cutoff:3.500A) Processing helix chain 'h' and resid 132 through 136 Processing helix chain 'h' and resid 157 through 166 Processing helix chain 'h' and resid 183 through 199 Processing helix chain 'h' and resid 212 through 223 Processing helix chain 'h' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS h 239 " --> pdb=" O PRO h 235 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS h 256 " --> pdb=" O ARG h 252 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU h 270 " --> pdb=" O SER h 266 " (cutoff:3.500A) Processing helix chain 'h' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL h 289 " --> pdb=" O THR h 286 " (cutoff:3.500A) Processing helix chain 'h' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'h' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA h 350 " --> pdb=" O SER h 346 " (cutoff:3.500A) Processing helix chain 'h' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU h 371 " --> pdb=" O LYS h 367 " (cutoff:3.500A) Processing helix chain 'h' and resid 373 through 388 Processing helix chain 'h' and resid 391 through 404 Processing helix chain 'h' and resid 408 through 419 Processing helix chain 'g' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU g 6 " --> pdb=" O ASN g 2 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 46 Processing helix chain 'g' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG g 128 " --> pdb=" O PRO g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 136 Processing helix chain 'g' and resid 157 through 166 Processing helix chain 'g' and resid 183 through 199 Processing helix chain 'g' and resid 212 through 223 Processing helix chain 'g' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS g 239 " --> pdb=" O PRO g 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS g 256 " --> pdb=" O ARG g 252 " (cutoff:3.500A) Processing helix chain 'g' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU g 270 " --> pdb=" O SER g 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL g 289 " --> pdb=" O THR g 286 " (cutoff:3.500A) Processing helix chain 'g' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'g' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA g 350 " --> pdb=" O SER g 346 " (cutoff:3.500A) Processing helix chain 'g' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU g 371 " --> pdb=" O LYS g 367 " (cutoff:3.500A) Processing helix chain 'g' and resid 373 through 388 Processing helix chain 'g' and resid 391 through 404 Processing helix chain 'g' and resid 408 through 419 Processing helix chain 'f' and resid 2 through 9 removed outlier: 3.777A pdb=" N LEU f 6 " --> pdb=" O ASN f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 22 removed outlier: 4.305A pdb=" N THR f 16 " --> pdb=" O SER f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 46 Processing helix chain 'f' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE f 86 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG f 128 " --> pdb=" O PRO f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 132 through 136 Processing helix chain 'f' and resid 157 through 166 Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 223 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS f 239 " --> pdb=" O PRO f 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU f 270 " --> pdb=" O SER f 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL f 289 " --> pdb=" O THR f 286 " (cutoff:3.500A) Processing helix chain 'f' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'f' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA f 350 " --> pdb=" O SER f 346 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU f 371 " --> pdb=" O LYS f 367 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 391 through 404 Processing helix chain 'f' and resid 408 through 419 Processing helix chain 'e' and resid 2 through 9 removed outlier: 3.777A pdb=" N LEU e 6 " --> pdb=" O ASN e 2 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR e 16 " --> pdb=" O SER e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 46 Processing helix chain 'e' and resid 82 through 89 removed outlier: 3.580A pdb=" N ILE e 86 " --> pdb=" O SER e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG e 128 " --> pdb=" O PRO e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 136 Processing helix chain 'e' and resid 157 through 166 Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 223 Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS e 239 " --> pdb=" O PRO e 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU e 270 " --> pdb=" O SER e 266 " (cutoff:3.500A) Processing helix chain 'e' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL e 289 " --> pdb=" O THR e 286 " (cutoff:3.500A) Processing helix chain 'e' and resid 290 through 303 removed outlier: 3.963A 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 Processing helix chain 'e' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA e 350 " --> pdb=" O SER e 346 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU e 371 " --> pdb=" O LYS e 367 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 391 through 404 Processing helix chain 'e' and resid 408 through 419 Processing helix chain 'd' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU d 6 " --> pdb=" O ASN d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 22 removed outlier: 4.304A pdb=" N THR d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 46 Processing helix chain 'd' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE d 86 " --> pdb=" O SER d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG d 128 " --> pdb=" O PRO d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 136 Processing helix chain 'd' and resid 157 through 166 Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 223 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 removed outlier: 3.704A pdb=" N LEU d 270 " --> pdb=" O SER d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL d 289 " --> pdb=" O THR d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 303 removed outlier: 3.963A 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 Processing helix chain 'd' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA d 350 " --> pdb=" O SER d 346 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU d 371 " --> pdb=" O LYS d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 391 through 404 Processing helix chain 'd' and resid 408 through 419 Processing helix chain 'c' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU c 6 " --> pdb=" O ASN c 2 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 22 removed outlier: 4.305A pdb=" N THR c 16 " --> pdb=" O SER c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 46 Processing helix chain 'c' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE c 86 " --> pdb=" O SER c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG c 128 " --> pdb=" O PRO c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 136 Processing helix chain 'c' and resid 157 through 166 Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 223 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS c 239 " --> pdb=" O PRO c 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU c 270 " --> pdb=" O SER c 266 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL c 289 " --> pdb=" O THR c 286 " (cutoff:3.500A) Processing helix chain 'c' and resid 290 through 303 removed outlier: 3.963A 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 Processing helix chain 'c' and resid 346 through 353 removed outlier: 3.541A pdb=" N ALA c 350 " --> pdb=" O SER c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 372 removed outlier: 4.114A pdb=" N LEU c 371 " --> pdb=" O LYS c 367 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 391 through 404 Processing helix chain 'c' and resid 408 through 419 Processing helix chain 'b' and resid 2 through 9 removed outlier: 3.776A pdb=" N LEU b 6 " --> pdb=" O ASN b 2 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 22 removed outlier: 4.305A pdb=" N THR b 16 " --> pdb=" O SER b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 46 Processing helix chain 'b' and resid 82 through 89 removed outlier: 3.579A pdb=" N ILE b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 removed outlier: 3.535A pdb=" N ARG b 128 " --> pdb=" O PRO b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 136 Processing helix chain 'b' and resid 157 through 166 Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 223 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.580A pdb=" N HIS b 239 " --> pdb=" O PRO b 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 removed outlier: 3.703A pdb=" N LEU b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 289 removed outlier: 4.103A pdb=" N VAL b 289 " --> pdb=" O THR b 286 " (cutoff:3.500A) Processing helix chain 'b' and resid 290 through 303 removed outlier: 3.964A 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 Processing helix chain 'b' and resid 346 through 353 removed outlier: 3.540A pdb=" N ALA b 350 " --> pdb=" O SER b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 372 removed outlier: 4.115A pdb=" N LEU b 371 " --> pdb=" O LYS b 367 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 391 through 404 Processing helix chain 'b' and resid 408 through 419 Processing sheet with id=AA1, first strand: chain 'a' and resid 49 through 57 removed outlier: 3.834A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA a 112 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS a 100 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL a 116 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER a 98 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU a 118 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR a 96 " --> pdb=" O GLU a 118 " (cutoff:3.500A) removed outlier: 4.335A 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: 6.393A pdb=" N VAL a 260 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE a 316 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE a 262 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR a 318 " --> pdb=" O ILE a 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU a 264 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU a 320 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU a 204 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.633A 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 removed outlier: 6.379A pdb=" N ILE a 176 " --> pdb=" O ALA a 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'r' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE r 79 " --> pdb=" O LEU r 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU r 113 " --> pdb=" O TYR r 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA r 112 " --> pdb=" O ARG r 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS r 100 " --> pdb=" O LEU r 114 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL r 116 " --> pdb=" O SER r 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER r 98 " --> pdb=" O VAL r 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU r 118 " --> pdb=" O THR r 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR r 96 " --> pdb=" O GLU r 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE r 49 " --> pdb=" O ILE r 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'r' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL r 260 " --> pdb=" O THR r 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE r 316 " --> pdb=" O VAL r 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE r 262 " --> pdb=" O ILE r 316 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR r 318 " --> pdb=" O ILE r 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU r 264 " --> pdb=" O THR r 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU r 320 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU r 204 " --> pdb=" O GLU r 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL r 228 " --> pdb=" O LEU r 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL r 206 " --> pdb=" O VAL r 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER r 230 " --> pdb=" O VAL r 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU r 208 " --> pdb=" O SER r 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'r' and resid 138 through 139 removed outlier: 6.378A pdb=" N ILE r 176 " --> pdb=" O ALA r 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'q' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE q 79 " --> pdb=" O LEU q 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU q 113 " --> pdb=" O TYR q 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA q 112 " --> pdb=" O ARG q 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS q 100 " --> pdb=" O LEU q 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL q 116 " --> pdb=" O SER q 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER q 98 " --> pdb=" O VAL q 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU q 118 " --> pdb=" O THR q 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR q 96 " --> pdb=" O GLU q 118 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE q 49 " --> pdb=" O ILE q 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'q' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL q 260 " --> pdb=" O THR q 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE q 316 " --> pdb=" O VAL q 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE q 262 " --> pdb=" O ILE q 316 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR q 318 " --> pdb=" O ILE q 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU q 264 " --> pdb=" O THR q 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU q 320 " --> pdb=" O LEU q 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU q 204 " --> pdb=" O GLU q 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL q 228 " --> pdb=" O LEU q 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL q 206 " --> pdb=" O VAL q 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER q 230 " --> pdb=" O VAL q 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU q 208 " --> pdb=" O SER q 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'q' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE q 176 " --> pdb=" O ALA q 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'p' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE p 79 " --> pdb=" O LEU p 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU p 113 " --> pdb=" O TYR p 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA p 112 " --> pdb=" O ARG p 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS p 100 " --> pdb=" O LEU p 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL p 116 " --> pdb=" O SER p 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER p 98 " --> pdb=" O VAL p 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU p 118 " --> pdb=" O THR p 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR p 96 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE p 49 " --> pdb=" O ILE p 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL p 260 " --> pdb=" O THR p 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE p 316 " --> pdb=" O VAL p 260 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE p 262 " --> pdb=" O ILE p 316 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR p 318 " --> pdb=" O ILE p 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU p 264 " --> pdb=" O THR p 318 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N LEU p 320 " --> pdb=" O LEU p 264 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU p 204 " --> pdb=" O GLU p 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL p 228 " --> pdb=" O LEU p 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL p 206 " --> pdb=" O VAL p 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER p 230 " --> pdb=" O VAL p 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU p 208 " --> pdb=" O SER p 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'p' and resid 138 through 139 removed outlier: 6.380A pdb=" N ILE p 176 " --> pdb=" O ALA p 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'o' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE o 79 " --> pdb=" O LEU o 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU o 113 " --> pdb=" O TYR o 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA o 112 " --> pdb=" O ARG o 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS o 100 " --> pdb=" O LEU o 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL o 116 " --> pdb=" O SER o 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER o 98 " --> pdb=" O VAL o 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU o 118 " --> pdb=" O THR o 96 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR o 96 " --> pdb=" O GLU o 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE o 49 " --> pdb=" O ILE o 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL o 260 " --> pdb=" O THR o 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE o 316 " --> pdb=" O VAL o 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE o 262 " --> pdb=" O ILE o 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR o 318 " --> pdb=" O ILE o 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU o 264 " --> pdb=" O THR o 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU o 320 " --> pdb=" O LEU o 264 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU o 204 " --> pdb=" O GLU o 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL o 228 " --> pdb=" O LEU o 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL o 206 " --> pdb=" O VAL o 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER o 230 " --> pdb=" O VAL o 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU o 208 " --> pdb=" O SER o 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 138 through 139 removed outlier: 6.380A pdb=" N ILE o 176 " --> pdb=" O ALA o 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE n 79 " --> pdb=" O LEU n 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU n 113 " --> pdb=" O TYR n 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA n 112 " --> pdb=" O ARG n 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS n 100 " --> pdb=" O LEU n 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL n 116 " --> pdb=" O SER n 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER n 98 " --> pdb=" O VAL n 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU n 118 " --> pdb=" O THR n 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR n 96 " --> pdb=" O GLU n 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE n 49 " --> pdb=" O ILE n 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 138 through 139 removed outlier: 6.392A pdb=" N VAL n 260 " --> pdb=" O THR n 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE n 316 " --> pdb=" O VAL n 260 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE n 262 " --> pdb=" O ILE n 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR n 318 " --> pdb=" O ILE n 262 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU n 264 " --> pdb=" O THR n 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU n 320 " --> pdb=" O LEU n 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU n 204 " --> pdb=" O GLU n 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL n 228 " --> pdb=" O LEU n 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL n 206 " --> pdb=" O VAL n 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER n 230 " --> pdb=" O VAL n 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU n 208 " --> pdb=" O SER n 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'n' and resid 138 through 139 removed outlier: 6.380A pdb=" N ILE n 176 " --> pdb=" O ALA n 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE m 79 " --> pdb=" O LEU m 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU m 113 " --> pdb=" O TYR m 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA m 112 " --> pdb=" O ARG m 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS m 100 " --> pdb=" O LEU m 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL m 116 " --> pdb=" O SER m 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER m 98 " --> pdb=" O VAL m 116 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU m 118 " --> pdb=" O THR m 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR m 96 " --> pdb=" O GLU m 118 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE m 49 " --> pdb=" O ILE m 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL m 260 " --> pdb=" O THR m 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE m 316 " --> pdb=" O VAL m 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE m 262 " --> pdb=" O ILE m 316 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR m 318 " --> pdb=" O ILE m 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU m 264 " --> pdb=" O THR m 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU m 320 " --> pdb=" O LEU m 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU m 204 " --> pdb=" O GLU m 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL m 228 " --> pdb=" O LEU m 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL m 206 " --> pdb=" O VAL m 228 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER m 230 " --> pdb=" O VAL m 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU m 208 " --> pdb=" O SER m 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'm' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE m 176 " --> pdb=" O ALA m 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'l' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE l 79 " --> pdb=" O LEU l 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU l 113 " --> pdb=" O TYR l 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA l 112 " --> pdb=" O ARG l 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS l 100 " --> pdb=" O LEU l 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL l 116 " --> pdb=" O SER l 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER l 98 " --> pdb=" O VAL l 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU l 118 " --> pdb=" O THR l 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR l 96 " --> pdb=" O GLU l 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE l 49 " --> pdb=" O ILE l 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL l 260 " --> pdb=" O THR l 314 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE l 316 " --> pdb=" O VAL l 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE l 262 " --> pdb=" O ILE l 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR l 318 " --> pdb=" O ILE l 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU l 264 " --> pdb=" O THR l 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU l 320 " --> pdb=" O LEU l 264 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU l 204 " --> pdb=" O GLU l 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL l 228 " --> pdb=" O LEU l 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL l 206 " --> pdb=" O VAL l 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER l 230 " --> pdb=" O VAL l 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU l 208 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'l' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE l 176 " --> pdb=" O ALA l 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'k' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE k 79 " --> pdb=" O LEU k 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU k 113 " --> pdb=" O TYR k 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA k 112 " --> pdb=" O ARG k 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS k 100 " --> pdb=" O LEU k 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL k 116 " --> pdb=" O SER k 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER k 98 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU k 118 " --> pdb=" O THR k 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR k 96 " --> pdb=" O GLU k 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE k 49 " --> pdb=" O ILE k 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL k 260 " --> pdb=" O THR k 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE k 316 " --> pdb=" O VAL k 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE k 262 " --> pdb=" O ILE k 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR k 318 " --> pdb=" O ILE k 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU k 264 " --> pdb=" O THR k 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU k 320 " --> pdb=" O LEU k 264 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU k 204 " --> pdb=" O GLU k 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL k 228 " --> pdb=" O LEU k 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL k 206 " --> pdb=" O VAL k 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER k 230 " --> pdb=" O VAL k 206 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU k 208 " --> pdb=" O SER k 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE k 176 " --> pdb=" O ALA k 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'j' and resid 49 through 57 removed outlier: 3.834A pdb=" N ILE j 79 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU j 113 " --> pdb=" O TYR j 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA j 112 " --> pdb=" O ARG j 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS j 100 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL j 116 " --> pdb=" O SER j 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER j 98 " --> pdb=" O VAL j 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU j 118 " --> pdb=" O THR j 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR j 96 " --> pdb=" O GLU j 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE j 49 " --> pdb=" O ILE j 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 138 through 139 removed outlier: 6.394A pdb=" N VAL j 260 " --> pdb=" O THR j 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE j 316 " --> pdb=" O VAL j 260 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE j 262 " --> pdb=" O ILE j 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR j 318 " --> pdb=" O ILE j 262 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU j 264 " --> pdb=" O THR j 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU j 320 " --> pdb=" O LEU j 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU j 204 " --> pdb=" O GLU j 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL j 228 " --> pdb=" O LEU j 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL j 206 " --> pdb=" O VAL j 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER j 230 " --> pdb=" O VAL j 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU j 208 " --> pdb=" O SER j 230 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE j 176 " --> pdb=" O ALA j 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'i' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE i 79 " --> pdb=" O LEU i 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU i 113 " --> pdb=" O TYR i 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA i 112 " --> pdb=" O ARG i 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS i 100 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL i 116 " --> pdb=" O SER i 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER i 98 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU i 118 " --> pdb=" O THR i 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR i 96 " --> pdb=" O GLU i 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE i 49 " --> pdb=" O ILE i 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'i' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL i 260 " --> pdb=" O THR i 314 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE i 316 " --> pdb=" O VAL i 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE i 262 " --> pdb=" O ILE i 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR i 318 " --> pdb=" O ILE i 262 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU i 264 " --> pdb=" O THR i 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU i 320 " --> pdb=" O LEU i 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU i 204 " --> pdb=" O GLU i 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL i 228 " --> pdb=" O LEU i 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL i 206 " --> pdb=" O VAL i 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER i 230 " --> pdb=" O VAL i 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU i 208 " --> pdb=" O SER i 230 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'i' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE i 176 " --> pdb=" O ALA i 319 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE h 79 " --> pdb=" O LEU h 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU h 113 " --> pdb=" O TYR h 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA h 112 " --> pdb=" O ARG h 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS h 100 " --> pdb=" O LEU h 114 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL h 116 " --> pdb=" O SER h 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER h 98 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU h 118 " --> pdb=" O THR h 96 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR h 96 " --> pdb=" O GLU h 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE h 49 " --> pdb=" O ILE h 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'h' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL h 260 " --> pdb=" O THR h 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE h 316 " --> pdb=" O VAL h 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE h 262 " --> pdb=" O ILE h 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR h 318 " --> pdb=" O ILE h 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU h 264 " --> pdb=" O THR h 318 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N LEU h 320 " --> pdb=" O LEU h 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU h 204 " --> pdb=" O GLU h 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL h 228 " --> pdb=" O LEU h 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL h 206 " --> pdb=" O VAL h 228 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER h 230 " --> pdb=" O VAL h 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU h 208 " --> pdb=" O SER h 230 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE h 176 " --> pdb=" O ALA h 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'g' and resid 49 through 57 removed outlier: 3.834A pdb=" N ILE g 79 " --> pdb=" O LEU g 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU g 113 " --> pdb=" O TYR g 80 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA g 112 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS g 100 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL g 116 " --> pdb=" O SER g 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER g 98 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU g 118 " --> pdb=" O THR g 96 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR g 96 " --> pdb=" O GLU g 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE g 49 " --> pdb=" O ILE g 101 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL g 260 " --> pdb=" O THR g 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE g 316 " --> pdb=" O VAL g 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE g 262 " --> pdb=" O ILE g 316 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR g 318 " --> pdb=" O ILE g 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU g 264 " --> pdb=" O THR g 318 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N LEU g 320 " --> pdb=" O LEU g 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU g 204 " --> pdb=" O GLU g 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL g 228 " --> pdb=" O LEU g 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL g 206 " --> pdb=" O VAL g 228 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER g 230 " --> pdb=" O VAL g 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU g 208 " --> pdb=" O SER g 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE g 176 " --> pdb=" O ALA g 319 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA f 112 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS f 100 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL f 116 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER f 98 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU f 118 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR f 96 " --> pdb=" O GLU f 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL f 260 " --> pdb=" O THR f 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE f 316 " --> pdb=" O VAL f 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE f 262 " --> pdb=" O ILE f 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR f 318 " --> pdb=" O ILE f 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU f 264 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU f 320 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU f 204 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'f' and resid 138 through 139 removed outlier: 6.378A pdb=" N ILE f 176 " --> pdb=" O ALA f 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA e 112 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS e 100 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL e 116 " --> pdb=" O SER e 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER e 98 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU e 118 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR e 96 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL e 260 " --> pdb=" O THR e 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE e 316 " --> pdb=" O VAL e 260 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE e 262 " --> pdb=" O ILE e 316 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N THR e 318 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU e 264 " --> pdb=" O THR e 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU e 320 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU e 204 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE e 176 " --> pdb=" O ALA e 319 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA d 112 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS d 100 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL d 116 " --> pdb=" O SER d 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER d 98 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU d 118 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR d 96 " --> pdb=" O GLU d 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL d 260 " --> pdb=" O THR d 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE d 316 " --> pdb=" O VAL d 260 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE d 262 " --> pdb=" O ILE d 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR d 318 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU d 264 " --> pdb=" O THR d 318 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N LEU d 320 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU d 204 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 138 through 139 removed outlier: 6.380A pdb=" N ILE d 176 " --> pdb=" O ALA d 319 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA c 112 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS c 100 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL c 116 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER c 98 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU c 118 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR c 96 " --> pdb=" O GLU c 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL c 260 " --> pdb=" O THR c 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE c 316 " --> pdb=" O VAL c 260 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE c 262 " --> pdb=" O ILE c 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR c 318 " --> pdb=" O ILE c 262 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU c 264 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N LEU c 320 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU c 204 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE c 176 " --> pdb=" O ALA c 319 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 49 through 57 removed outlier: 3.833A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA b 112 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS b 100 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL b 116 " --> pdb=" O SER b 98 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER b 98 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLU b 118 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR b 96 " --> pdb=" O GLU b 118 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 138 through 139 removed outlier: 6.393A pdb=" N VAL b 260 " --> pdb=" O THR b 314 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE b 316 " --> pdb=" O VAL b 260 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE b 262 " --> pdb=" O ILE b 316 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N THR b 318 " --> pdb=" O ILE b 262 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU b 264 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU b 320 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU b 204 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 138 through 139 removed outlier: 6.379A pdb=" N ILE b 176 " --> pdb=" O ALA b 319 " (cutoff:3.500A) 2916 hydrogen bonds defined for protein. 8262 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.90 Time building geometry restraints manager: 13.90 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: 20376 1.35 - 1.47: 12029 1.47 - 1.59: 27769 1.59 - 1.71: 54 1.71 - 1.82: 594 Bond restraints: 60822 Sorted by residual: bond pdb=" CB ARG r 353 " pdb=" CG ARG r 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" CB ARG b 353 " pdb=" CG ARG b 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.87e+00 bond pdb=" CB ARG o 353 " pdb=" CG ARG o 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.85e+00 bond pdb=" CB ARG j 353 " pdb=" CG ARG j 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.85e+00 bond pdb=" CB ARG h 353 " pdb=" CG ARG h 353 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.84e+00 ... (remaining 60817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 79769 2.35 - 4.70: 1843 4.70 - 7.05: 252 7.05 - 9.39: 126 9.39 - 11.74: 18 Bond angle restraints: 82008 Sorted by residual: angle pdb=" CA GLU c 397 " pdb=" CB GLU c 397 " pdb=" CG GLU c 397 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU h 397 " pdb=" CB GLU h 397 " pdb=" CG GLU h 397 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU r 397 " pdb=" CB GLU r 397 " pdb=" CG GLU r 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU p 397 " pdb=" CB GLU p 397 " pdb=" CG GLU p 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA GLU b 397 " pdb=" CB GLU b 397 " pdb=" CG GLU b 397 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 82003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 35977 33.02 - 66.03: 1589 66.03 - 99.05: 119 99.05 - 132.07: 0 132.07 - 165.08: 7 Dihedral angle restraints: 37692 sinusoidal: 15966 harmonic: 21726 Sorted by residual: dihedral pdb=" O1B ADP h1000 " pdb=" O3A ADP h1000 " pdb=" PB ADP h1000 " pdb=" PA ADP h1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.08 -165.08 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP p1000 " pdb=" O3A ADP p1000 " pdb=" PB ADP p1000 " pdb=" PA ADP p1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.08 -165.08 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP o1000 " pdb=" O3A ADP o1000 " pdb=" PB ADP o1000 " pdb=" PA ADP o1000 " ideal model delta sinusoidal sigma weight residual -60.00 105.07 -165.08 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 37689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 5664 0.029 - 0.058: 2249 0.058 - 0.087: 690 0.087 - 0.116: 678 0.116 - 0.145: 43 Chirality restraints: 9324 Sorted by residual: chirality pdb=" CA ASP i 322 " pdb=" N ASP i 322 " pdb=" C ASP i 322 " pdb=" CB ASP i 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ASP g 322 " pdb=" N ASP g 322 " pdb=" C ASP g 322 " pdb=" CB ASP g 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASP l 322 " pdb=" N ASP l 322 " pdb=" C ASP l 322 " pdb=" CB ASP l 322 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 9321 not shown) Planarity restraints: 10620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP k 381 " 0.020 2.00e-02 2.50e+03 1.64e-02 6.71e+00 pdb=" CG TRP k 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP k 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP k 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP k 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP k 381 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP k 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 381 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP k 381 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 381 " 0.020 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP f 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP f 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP f 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP f 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP f 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP f 381 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 381 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP f 381 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP q 381 " 0.020 2.00e-02 2.50e+03 1.63e-02 6.66e+00 pdb=" CG TRP q 381 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP q 381 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP q 381 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP q 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP q 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP q 381 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP q 381 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP q 381 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP q 381 " -0.002 2.00e-02 2.50e+03 ... (remaining 10617 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1315 2.65 - 3.21: 57923 3.21 - 3.78: 97330 3.78 - 4.34: 127942 4.34 - 4.90: 207368 Nonbonded interactions: 491878 Sorted by model distance: nonbonded pdb=" O3B ADP o1000 " pdb="MG MG o1001 " model vdw 2.089 2.170 nonbonded pdb=" O2B ADP f1000 " pdb="MG MG f1001 " model vdw 2.089 2.170 nonbonded pdb=" O2B ADP m1000 " pdb="MG MG m1001 " model vdw 2.089 2.170 nonbonded pdb=" O3B ADP n1000 " pdb="MG MG n1001 " model vdw 2.089 2.170 nonbonded pdb=" O3B ADP h1000 " pdb="MG MG h1001 " model vdw 2.089 2.170 ... (remaining 491873 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.980 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 111.560 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.390 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 0.059 60822 Z= 0.239 Angle : 0.806 11.742 82008 Z= 0.386 Chirality : 0.042 0.145 9324 Planarity : 0.004 0.028 10620 Dihedral : 17.249 165.082 23616 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.07 % Allowed : 39.48 % Favored : 57.45 % 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: 1.28 (0.10), residues: 7506 helix: 1.41 (0.09), residues: 3456 sheet: 1.26 (0.15), residues: 1188 loop : 0.10 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP k 381 HIS 0.003 0.001 HIS h 239 PHE 0.005 0.001 PHE p 355 TYR 0.022 0.003 TYR r 332 ARG 0.008 0.001 ARG f 353 *********************** 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 1611 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1412 time to evaluate : 5.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 MET cc_start: 0.8593 (ttm) cc_final: 0.8373 (ttt) REVERT: a 189 GLN cc_start: 0.8974 (mt0) cc_final: 0.8681 (mt0) REVERT: a 197 TYR cc_start: 0.8892 (t80) cc_final: 0.8467 (t80) REVERT: a 218 GLU cc_start: 0.9304 (tp30) cc_final: 0.8944 (tp30) REVERT: a 222 LEU cc_start: 0.9458 (mp) cc_final: 0.9243 (mm) REVERT: a 265 ASP cc_start: 0.8284 (t0) cc_final: 0.8021 (p0) REVERT: a 341 MET cc_start: 0.9405 (tmt) cc_final: 0.9148 (tmm) REVERT: a 405 MET cc_start: 0.8859 (ttp) cc_final: 0.8639 (ttm) REVERT: r 85 GLN cc_start: 0.8580 (mp10) cc_final: 0.8167 (mp10) REVERT: r 189 GLN cc_start: 0.9134 (mt0) cc_final: 0.8699 (mt0) REVERT: r 233 ASP cc_start: 0.8385 (p0) cc_final: 0.8184 (p0) REVERT: r 248 GLU cc_start: 0.9258 (tp30) cc_final: 0.8843 (mm-30) REVERT: r 328 ASP cc_start: 0.9364 (m-30) cc_final: 0.9123 (m-30) REVERT: r 390 MET cc_start: 0.8863 (pmm) cc_final: 0.8619 (pmm) REVERT: q 29 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (ptm) REVERT: q 33 ASP cc_start: 0.8998 (m-30) cc_final: 0.8695 (m-30) REVERT: q 186 MET cc_start: 0.8987 (ptm) cc_final: 0.8681 (ppp) REVERT: q 201 ASP cc_start: 0.8928 (p0) cc_final: 0.8625 (p0) REVERT: q 241 GLN cc_start: 0.8832 (pp30) cc_final: 0.8437 (pp30) REVERT: q 248 GLU cc_start: 0.9271 (tp30) cc_final: 0.9045 (mm-30) REVERT: q 264 LEU cc_start: 0.9054 (tm) cc_final: 0.8710 (tt) REVERT: q 333 GLU cc_start: 0.9158 (tp30) cc_final: 0.8919 (mm-30) REVERT: q 360 TYR cc_start: 0.8665 (t80) cc_final: 0.8195 (t80) REVERT: q 387 ILE cc_start: 0.9298 (mm) cc_final: 0.8985 (mt) REVERT: p 67 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.9035 (p) REVERT: p 186 MET cc_start: 0.9189 (ptm) cc_final: 0.8820 (ptt) REVERT: p 248 GLU cc_start: 0.9104 (tp30) cc_final: 0.8588 (mp0) REVERT: p 299 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8674 (mtm-85) REVERT: p 327 MET cc_start: 0.8921 (ptp) cc_final: 0.8684 (ptm) REVERT: p 334 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8329 (tm-30) REVERT: p 342 GLU cc_start: 0.8718 (mp0) cc_final: 0.8449 (pm20) REVERT: p 378 GLN cc_start: 0.9123 (mt0) cc_final: 0.8869 (mm-40) REVERT: p 396 MET cc_start: 0.9418 (tpp) cc_final: 0.9204 (tpp) REVERT: p 405 MET cc_start: 0.9106 (ttp) cc_final: 0.8829 (ttm) REVERT: o 33 ASP cc_start: 0.8787 (m-30) cc_final: 0.8560 (m-30) REVERT: o 115 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8850 (ptmm) REVERT: o 143 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8716 (t) REVERT: o 210 ASP cc_start: 0.8236 (m-30) cc_final: 0.7772 (t0) REVERT: o 234 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7143 (mp0) REVERT: o 334 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8566 (tm-30) REVERT: o 348 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8871 (ptpp) REVERT: o 396 MET cc_start: 0.9556 (tpp) cc_final: 0.9218 (tpp) REVERT: o 415 MET cc_start: 0.9258 (ttm) cc_final: 0.8944 (ptm) REVERT: n 19 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8576 (mm-30) REVERT: n 67 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8980 (p) REVERT: n 106 GLU cc_start: 0.7911 (pp20) cc_final: 0.7437 (pp20) REVERT: n 147 MET cc_start: 0.9559 (tpp) cc_final: 0.9128 (mmm) REVERT: n 186 MET cc_start: 0.8698 (ptm) cc_final: 0.8411 (ptp) REVERT: n 292 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8280 (p0) REVERT: n 342 GLU cc_start: 0.8468 (mp0) cc_final: 0.7809 (mp0) REVERT: n 411 ASP cc_start: 0.9283 (m-30) cc_final: 0.8797 (m-30) REVERT: m 21 MET cc_start: 0.8861 (ttm) cc_final: 0.8631 (ttt) REVERT: m 67 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8745 (p) REVERT: m 69 ASP cc_start: 0.8945 (t0) cc_final: 0.8655 (t70) REVERT: m 143 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8627 (p) REVERT: m 193 GLN cc_start: 0.8702 (tt0) cc_final: 0.8306 (tm-30) REVERT: m 362 ARG cc_start: 0.9195 (ttm110) cc_final: 0.8898 (mtp85) REVERT: m 374 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8026 (tm-30) REVERT: m 378 GLN cc_start: 0.9172 (mt0) cc_final: 0.8649 (mt0) REVERT: m 396 MET cc_start: 0.9156 (tpp) cc_final: 0.8849 (tpp) REVERT: m 400 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9155 (mm) REVERT: l 67 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8820 (p) REVERT: l 69 ASP cc_start: 0.8875 (t0) cc_final: 0.8612 (t0) REVERT: l 125 GLU cc_start: 0.8965 (mp0) cc_final: 0.8748 (mp0) REVERT: l 218 GLU cc_start: 0.8720 (tp30) cc_final: 0.8486 (tp30) REVERT: l 222 LEU cc_start: 0.9113 (mp) cc_final: 0.8673 (mm) REVERT: l 334 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: l 342 GLU cc_start: 0.8414 (mp0) cc_final: 0.8205 (mt-10) REVERT: l 400 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9204 (mm) REVERT: k 67 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8540 (p) REVERT: k 69 ASP cc_start: 0.8940 (t0) cc_final: 0.8718 (t0) REVERT: k 218 GLU cc_start: 0.8989 (tp30) cc_final: 0.8502 (tt0) REVERT: k 248 GLU cc_start: 0.8996 (tp30) cc_final: 0.8769 (mm-30) REVERT: k 264 LEU cc_start: 0.8850 (tm) cc_final: 0.8550 (tt) REVERT: k 292 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8150 (p0) REVERT: k 299 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8932 (mtm-85) REVERT: k 348 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8726 (ptmm) REVERT: k 378 GLN cc_start: 0.8985 (mt0) cc_final: 0.8671 (mt0) REVERT: k 406 THR cc_start: 0.7390 (p) cc_final: 0.7172 (p) REVERT: j 1 MET cc_start: 0.7593 (ttp) cc_final: 0.7386 (ttt) REVERT: j 19 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8428 (mm-30) REVERT: j 67 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8400 (p) REVERT: j 218 GLU cc_start: 0.8868 (tp30) cc_final: 0.8562 (tt0) REVERT: j 334 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8219 (tm-30) REVERT: j 341 MET cc_start: 0.8881 (tmt) cc_final: 0.8611 (tmm) REVERT: j 411 ASP cc_start: 0.9072 (m-30) cc_final: 0.8760 (m-30) REVERT: i 19 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8292 (mm-30) REVERT: i 67 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8747 (p) REVERT: i 106 GLU cc_start: 0.7870 (pp20) cc_final: 0.7400 (pp20) REVERT: i 143 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8568 (t) REVERT: i 197 TYR cc_start: 0.9143 (t80) cc_final: 0.8928 (t80) REVERT: i 272 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8526 (mmm-85) REVERT: i 352 LYS cc_start: 0.7649 (tppp) cc_final: 0.7403 (tptp) REVERT: i 374 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7645 (tm-30) REVERT: i 378 GLN cc_start: 0.8990 (mt0) cc_final: 0.8443 (mt0) REVERT: i 416 MET cc_start: 0.8885 (mmm) cc_final: 0.8681 (mmp) REVERT: h 292 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (p0) REVERT: h 299 ARG cc_start: 0.9177 (mmm-85) cc_final: 0.8871 (mtm-85) REVERT: h 308 GLU cc_start: 0.9020 (tt0) cc_final: 0.8746 (tt0) REVERT: h 326 LYS cc_start: 0.8813 (mppt) cc_final: 0.8579 (ttmm) REVERT: h 333 GLU cc_start: 0.8719 (tp30) cc_final: 0.8509 (mm-30) REVERT: h 342 GLU cc_start: 0.8342 (mp0) cc_final: 0.7736 (mp0) REVERT: h 348 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8668 (ptmm) REVERT: h 411 ASP cc_start: 0.8822 (m-30) cc_final: 0.8596 (m-30) REVERT: g 67 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8739 (p) REVERT: g 69 ASP cc_start: 0.8808 (t0) cc_final: 0.8488 (m-30) REVERT: g 218 GLU cc_start: 0.8893 (tp30) cc_final: 0.8602 (tt0) REVERT: g 224 LYS cc_start: 0.9264 (ttmm) cc_final: 0.9047 (tppt) REVERT: g 272 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8772 (ttm-80) REVERT: g 292 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (p0) REVERT: g 328 ASP cc_start: 0.8710 (m-30) cc_final: 0.8317 (m-30) REVERT: g 342 GLU cc_start: 0.8203 (mp0) cc_final: 0.7784 (mm-30) REVERT: g 411 ASP cc_start: 0.9153 (m-30) cc_final: 0.8735 (m-30) REVERT: f 67 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.8871 (t) REVERT: e 67 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8663 (p) REVERT: e 69 ASP cc_start: 0.8952 (t0) cc_final: 0.8643 (t0) REVERT: e 70 SER cc_start: 0.9097 (t) cc_final: 0.8743 (m) REVERT: e 87 ARG cc_start: 0.9288 (mtm110) cc_final: 0.9035 (ttp80) REVERT: e 143 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8593 (t) REVERT: e 197 TYR cc_start: 0.9099 (t80) cc_final: 0.8899 (t80) REVERT: e 292 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8808 (p0) REVERT: e 341 MET cc_start: 0.8633 (tmt) cc_final: 0.8369 (tmm) REVERT: e 405 MET cc_start: 0.8677 (ttp) cc_final: 0.8413 (ttm) REVERT: d 8 ASN cc_start: 0.9402 (t0) cc_final: 0.9086 (t0) REVERT: d 12 SER cc_start: 0.9378 (m) cc_final: 0.9056 (p) REVERT: d 21 MET cc_start: 0.9293 (ttm) cc_final: 0.8978 (ttt) REVERT: d 67 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (t) REVERT: d 189 GLN cc_start: 0.9141 (mt0) cc_final: 0.8609 (mt0) REVERT: d 211 GLU cc_start: 0.8943 (tp30) cc_final: 0.8640 (tp30) REVERT: d 292 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (p0) REVERT: d 327 MET cc_start: 0.8709 (ptp) cc_final: 0.8504 (ptm) REVERT: d 352 LYS cc_start: 0.8060 (tppp) cc_final: 0.7806 (tptp) REVERT: d 362 ARG cc_start: 0.9199 (ttm110) cc_final: 0.8997 (mtp85) REVERT: d 405 MET cc_start: 0.8263 (ttp) cc_final: 0.8028 (ttm) REVERT: d 406 THR cc_start: 0.7624 (p) cc_final: 0.6949 (p) REVERT: c 8 ASN cc_start: 0.9444 (t0) cc_final: 0.9219 (m-40) REVERT: c 12 SER cc_start: 0.9242 (m) cc_final: 0.8967 (p) REVERT: c 19 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8811 (mm-30) REVERT: c 67 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8476 (p) REVERT: c 186 MET cc_start: 0.8667 (ptm) cc_final: 0.8249 (ptt) REVERT: c 197 TYR cc_start: 0.9095 (t80) cc_final: 0.8833 (t80) REVERT: c 248 GLU cc_start: 0.9158 (tp30) cc_final: 0.8877 (mm-30) REVERT: c 272 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8683 (ttm-80) REVERT: c 334 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8514 (tm-30) REVERT: c 397 GLU cc_start: 0.8502 (pp20) cc_final: 0.8267 (pp20) REVERT: c 411 ASP cc_start: 0.8996 (m-30) cc_final: 0.8291 (t70) REVERT: c 414 GLU cc_start: 0.8819 (pp20) cc_final: 0.8572 (pp20) REVERT: b 143 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8270 (p) REVERT: b 181 LYS cc_start: 0.9442 (mtpp) cc_final: 0.9212 (mmmt) REVERT: b 193 GLN cc_start: 0.8654 (tt0) cc_final: 0.8305 (tm-30) REVERT: b 218 GLU cc_start: 0.8978 (tp30) cc_final: 0.8372 (tp30) REVERT: b 219 MET cc_start: 0.9291 (mmm) cc_final: 0.9072 (mmm) REVERT: b 245 MET cc_start: 0.9303 (tpp) cc_final: 0.9052 (mmm) REVERT: b 292 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8411 (p0) REVERT: b 334 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 199 outliers final: 96 residues processed: 1544 average time/residue: 0.6070 time to fit residues: 1520.1415 Evaluate side-chains 1173 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1050 time to evaluate : 5.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 131 ILE Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 292 ASN Chi-restraints excluded: chain q residue 29 MET Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 292 ASN Chi-restraints excluded: chain q residue 381 TRP Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 29 MET Chi-restraints excluded: chain p residue 60 ASP Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 131 ILE Chi-restraints excluded: chain p residue 381 TRP Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 131 ILE Chi-restraints excluded: chain o residue 143 SER Chi-restraints excluded: chain o residue 381 TRP Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 67 SER Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 131 ILE Chi-restraints excluded: chain n residue 292 ASN Chi-restraints excluded: chain n residue 381 TRP Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 143 SER Chi-restraints excluded: chain m residue 292 ASN Chi-restraints excluded: chain m residue 381 TRP Chi-restraints excluded: chain m residue 400 ILE Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 67 SER Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 292 ASN Chi-restraints excluded: chain l residue 381 TRP Chi-restraints excluded: chain l residue 400 ILE Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 131 ILE Chi-restraints excluded: chain k residue 292 ASN Chi-restraints excluded: chain k residue 381 TRP Chi-restraints excluded: chain j residue 67 SER Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 131 ILE Chi-restraints excluded: chain j residue 292 ASN Chi-restraints excluded: chain j residue 381 TRP Chi-restraints excluded: chain j residue 400 ILE Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 143 SER Chi-restraints excluded: chain i residue 292 ASN Chi-restraints excluded: chain i residue 381 TRP Chi-restraints excluded: chain i residue 400 ILE Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 131 ILE Chi-restraints excluded: chain h residue 292 ASN Chi-restraints excluded: chain h residue 381 TRP Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 67 SER Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 292 ASN Chi-restraints excluded: chain g residue 381 TRP Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 67 SER Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain f residue 143 SER Chi-restraints excluded: chain f residue 292 ASN Chi-restraints excluded: chain f residue 381 TRP Chi-restraints excluded: chain f residue 400 ILE Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 143 SER Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 381 TRP Chi-restraints excluded: chain e residue 400 ILE Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 29 MET Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 292 ASN Chi-restraints excluded: chain d residue 381 TRP Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 67 SER Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 292 ASN Chi-restraints excluded: chain c residue 381 TRP Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 131 ILE Chi-restraints excluded: chain b residue 143 SER Chi-restraints excluded: chain b residue 292 ASN Chi-restraints excluded: chain b residue 381 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 3.9990 chunk 559 optimal weight: 5.9990 chunk 310 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 377 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 578 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 430 optimal weight: 1.9990 chunk 670 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 220 GLN ** r 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 388 HIS ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 90 ASN q 172 GLN ** p 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 374 GLN ** o 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 292 ASN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 ASN n 193 GLN n 275 ASN n 295 HIS m 189 GLN ** m 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN l 275 ASN ** k 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 ASN ** j 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 189 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 189 GLN ** g 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 90 ASN e 193 GLN e 374 GLN d 90 ASN d 220 GLN ** d 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 GLN ** c 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** b 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 60822 Z= 0.354 Angle : 0.714 8.176 82008 Z= 0.351 Chirality : 0.045 0.161 9324 Planarity : 0.005 0.050 10620 Dihedral : 7.551 174.654 8589 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.59 % Allowed : 29.51 % Favored : 64.91 % 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: 1.30 (0.10), residues: 7506 helix: 1.53 (0.09), residues: 3492 sheet: 0.99 (0.15), residues: 1224 loop : 0.06 (0.12), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 381 HIS 0.008 0.001 HIS n 295 PHE 0.010 0.001 PHE h 355 TYR 0.025 0.003 TYR k 332 ARG 0.011 0.001 ARG b 353 *********************** 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 1429 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 362 poor density : 1067 time to evaluate : 5.475 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: a 29 MET cc_start: 0.7977 (ptp) cc_final: 0.7531 (ptp) REVERT: a 30 ARG cc_start: 0.7612 (mmm160) cc_final: 0.6807 (mtp85) REVERT: a 56 GLU cc_start: 0.8717 (pt0) cc_final: 0.8482 (pp20) REVERT: a 197 TYR cc_start: 0.9043 (t80) cc_final: 0.8787 (t80) REVERT: a 218 GLU cc_start: 0.9340 (tp30) cc_final: 0.9023 (tp30) REVERT: a 265 ASP cc_start: 0.8598 (t70) cc_final: 0.8148 (p0) REVERT: a 274 TYR cc_start: 0.9054 (m-10) cc_final: 0.8773 (m-80) REVERT: a 328 ASP cc_start: 0.9027 (m-30) cc_final: 0.8808 (m-30) REVERT: a 341 MET cc_start: 0.9507 (tmt) cc_final: 0.9136 (tmm) REVERT: r 21 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8868 (ttt) REVERT: r 132 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8538 (mt) REVERT: r 248 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8906 (mm-30) REVERT: r 292 ASN cc_start: 0.9003 (m110) cc_final: 0.8342 (p0) REVERT: r 328 ASP cc_start: 0.9156 (m-30) cc_final: 0.8666 (m-30) REVERT: r 396 MET cc_start: 0.9228 (tpt) cc_final: 0.8763 (tpp) REVERT: q 33 ASP cc_start: 0.9049 (m-30) cc_final: 0.8701 (m-30) REVERT: q 172 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8934 (tp40) REVERT: q 248 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.9101 (mm-30) REVERT: q 264 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8810 (tt) REVERT: q 333 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8897 (mm-30) REVERT: q 360 TYR cc_start: 0.8893 (t80) cc_final: 0.8439 (t80) REVERT: q 381 TRP cc_start: 0.8462 (m-10) cc_final: 0.8201 (m-10) REVERT: q 412 PHE cc_start: 0.9027 (t80) cc_final: 0.8776 (t80) REVERT: p 56 GLU cc_start: 0.8768 (pt0) cc_final: 0.8421 (pt0) REVERT: p 59 GLN cc_start: 0.8862 (pm20) cc_final: 0.8519 (pm20) REVERT: p 60 ASP cc_start: 0.8854 (m-30) cc_final: 0.7948 (m-30) REVERT: p 186 MET cc_start: 0.9271 (ptm) cc_final: 0.9001 (ptp) REVERT: p 248 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: p 333 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8869 (mm-30) REVERT: p 334 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8401 (tm-30) REVERT: p 342 GLU cc_start: 0.8864 (mp0) cc_final: 0.8588 (pm20) REVERT: p 374 GLN cc_start: 0.8719 (tm130) cc_final: 0.8379 (tm-30) REVERT: p 378 GLN cc_start: 0.9286 (mt0) cc_final: 0.8995 (mm-40) REVERT: o 29 MET cc_start: 0.8503 (ptm) cc_final: 0.8223 (ptp) REVERT: o 33 ASP cc_start: 0.8767 (m-30) cc_final: 0.8544 (m-30) REVERT: o 105 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8212 (tmmt) REVERT: o 115 LYS cc_start: 0.9136 (tmmt) cc_final: 0.8896 (ptmm) REVERT: o 197 TYR cc_start: 0.9534 (t80) cc_final: 0.9319 (t80) REVERT: o 244 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8247 (mm-30) REVERT: o 248 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: o 274 TYR cc_start: 0.9233 (m-80) cc_final: 0.8996 (m-80) REVERT: o 334 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8734 (tm-30) REVERT: n 5 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8855 (pm20) REVERT: n 40 LYS cc_start: 0.9158 (ttpt) cc_final: 0.8821 (ttmm) REVERT: n 59 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8151 (tp40) REVERT: n 197 TYR cc_start: 0.9149 (t80) cc_final: 0.8860 (t80) REVERT: n 326 LYS cc_start: 0.8439 (tptp) cc_final: 0.8145 (tptp) REVERT: n 333 GLU cc_start: 0.9036 (tp30) cc_final: 0.8766 (tp30) REVERT: n 342 GLU cc_start: 0.8641 (mp0) cc_final: 0.8092 (mp0) REVERT: n 397 GLU cc_start: 0.8833 (pp20) cc_final: 0.8627 (pp20) REVERT: n 411 ASP cc_start: 0.9193 (m-30) cc_final: 0.8916 (m-30) REVERT: n 415 MET cc_start: 0.9103 (ttm) cc_final: 0.8842 (tmm) REVERT: m 21 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8336 (ttt) REVERT: m 67 SER cc_start: 0.8906 (m) cc_final: 0.8558 (p) REVERT: m 69 ASP cc_start: 0.9010 (t0) cc_final: 0.8753 (t70) REVERT: m 92 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8050 (pmm-80) REVERT: m 197 TYR cc_start: 0.9289 (t80) cc_final: 0.8794 (t80) REVERT: m 226 GLU cc_start: 0.8348 (tp30) cc_final: 0.7965 (tt0) REVERT: m 265 ASP cc_start: 0.8376 (t70) cc_final: 0.8113 (t0) REVERT: m 299 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8516 (ttp80) REVERT: m 327 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8247 (ttp) REVERT: m 334 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8524 (tm-30) REVERT: m 405 MET cc_start: 0.9254 (ttp) cc_final: 0.8925 (ptp) REVERT: m 411 ASP cc_start: 0.9350 (m-30) cc_final: 0.8657 (m-30) REVERT: l 69 ASP cc_start: 0.9017 (t0) cc_final: 0.8731 (t0) REVERT: l 92 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7696 (pmm-80) REVERT: l 122 ASP cc_start: 0.9044 (t0) cc_final: 0.8651 (t70) REVERT: l 125 GLU cc_start: 0.9064 (mp0) cc_final: 0.8725 (mp0) REVERT: l 218 GLU cc_start: 0.8807 (tp30) cc_final: 0.8557 (tp30) REVERT: l 222 LEU cc_start: 0.9249 (mp) cc_final: 0.8904 (mm) REVERT: l 224 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9292 (mtpp) REVERT: l 334 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8441 (tm-30) REVERT: l 342 GLU cc_start: 0.8640 (mp0) cc_final: 0.8356 (mt-10) REVERT: k 5 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: k 32 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8892 (mp10) REVERT: k 218 GLU cc_start: 0.9015 (tp30) cc_final: 0.8638 (tt0) REVERT: k 264 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8514 (tt) REVERT: k 347 ARG cc_start: 0.8283 (tpt-90) cc_final: 0.8073 (tpt90) REVERT: k 374 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8259 (tm-30) REVERT: j 67 SER cc_start: 0.8915 (m) cc_final: 0.8521 (p) REVERT: j 218 GLU cc_start: 0.8936 (tp30) cc_final: 0.8687 (tt0) REVERT: j 397 GLU cc_start: 0.8917 (pt0) cc_final: 0.8520 (mt-10) REVERT: j 411 ASP cc_start: 0.9149 (m-30) cc_final: 0.8783 (m-30) REVERT: i 13 GLU cc_start: 0.8745 (pm20) cc_final: 0.8507 (pm20) REVERT: i 19 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8461 (mm-30) REVERT: i 67 SER cc_start: 0.9030 (m) cc_final: 0.8679 (p) REVERT: i 92 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7994 (pmm-80) REVERT: i 342 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8492 (mt-10) REVERT: i 352 LYS cc_start: 0.8157 (tppp) cc_final: 0.7748 (tptp) REVERT: i 378 GLN cc_start: 0.9072 (mt0) cc_final: 0.8615 (mt0) REVERT: h 226 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: h 292 ASN cc_start: 0.8893 (m110) cc_final: 0.8607 (p0) REVERT: h 308 GLU cc_start: 0.8985 (tt0) cc_final: 0.8748 (tt0) REVERT: h 326 LYS cc_start: 0.8792 (mppt) cc_final: 0.8464 (tptp) REVERT: h 341 MET cc_start: 0.9001 (tmm) cc_final: 0.8739 (tmm) REVERT: h 397 GLU cc_start: 0.8565 (pp20) cc_final: 0.8253 (pp20) REVERT: g 12 SER cc_start: 0.9378 (m) cc_final: 0.9017 (p) REVERT: g 67 SER cc_start: 0.9073 (m) cc_final: 0.8682 (p) REVERT: g 92 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7985 (pmm-80) REVERT: g 106 GLU cc_start: 0.8189 (pp20) cc_final: 0.7909 (pp20) REVERT: g 145 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (mt) REVERT: g 197 TYR cc_start: 0.9318 (t80) cc_final: 0.9038 (t80) REVERT: g 218 GLU cc_start: 0.8916 (tp30) cc_final: 0.8610 (tt0) REVERT: g 248 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: g 327 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8294 (ttp) REVERT: f 92 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8179 (pmm-80) REVERT: f 375 GLU cc_start: 0.8985 (pm20) cc_final: 0.8777 (pm20) REVERT: e 58 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8965 (mt) REVERT: e 67 SER cc_start: 0.9005 (m) cc_final: 0.8634 (p) REVERT: e 70 SER cc_start: 0.9148 (t) cc_final: 0.8886 (m) REVERT: e 299 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8179 (mtm-85) REVERT: e 341 MET cc_start: 0.8908 (tmt) cc_final: 0.8633 (tmm) REVERT: e 362 ARG cc_start: 0.9281 (ttm110) cc_final: 0.9039 (mtm-85) REVERT: d 5 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: d 12 SER cc_start: 0.9516 (m) cc_final: 0.9254 (p) REVERT: d 264 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8502 (tt) REVERT: d 342 GLU cc_start: 0.8593 (mp0) cc_final: 0.8378 (mp0) REVERT: d 352 LYS cc_start: 0.8335 (tppp) cc_final: 0.8013 (tptp) REVERT: d 362 ARG cc_start: 0.9300 (ttm110) cc_final: 0.9074 (ttm110) REVERT: d 417 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8942 (ptpp) REVERT: c 12 SER cc_start: 0.9363 (m) cc_final: 0.8993 (p) REVERT: c 13 GLU cc_start: 0.8859 (pm20) cc_final: 0.8392 (pm20) REVERT: c 19 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8869 (tp30) REVERT: c 67 SER cc_start: 0.8960 (m) cc_final: 0.8572 (p) REVERT: c 177 VAL cc_start: 0.9378 (t) cc_final: 0.9106 (m) REVERT: c 197 TYR cc_start: 0.9166 (t80) cc_final: 0.8646 (t80) REVERT: c 248 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8978 (mm-30) REVERT: c 272 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8656 (ttm-80) REVERT: c 294 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9126 (tp) REVERT: c 334 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8662 (tm-30) REVERT: c 411 ASP cc_start: 0.9047 (m-30) cc_final: 0.8654 (m-30) REVERT: b 88 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8629 (ttm110) REVERT: b 193 GLN cc_start: 0.8681 (tt0) cc_final: 0.8347 (tm-30) REVERT: b 218 GLU cc_start: 0.9054 (tp30) cc_final: 0.8568 (tp30) REVERT: b 219 MET cc_start: 0.9380 (mmm) cc_final: 0.9056 (mmm) REVERT: b 222 LEU cc_start: 0.9376 (mp) cc_final: 0.8606 (mp) REVERT: b 248 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9165 (mm-30) REVERT: b 264 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8689 (tt) REVERT: b 334 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8563 (tm-30) REVERT: b 342 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8524 (tt0) REVERT: b 352 LYS cc_start: 0.8151 (tppp) cc_final: 0.7620 (tptm) outliers start: 362 outliers final: 167 residues processed: 1344 average time/residue: 0.5966 time to fit residues: 1323.2774 Evaluate side-chains 1169 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 970 time to evaluate : 5.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 21 MET Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 194 SER Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 172 GLN Chi-restraints excluded: chain q residue 194 SER Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 248 GLU Chi-restraints excluded: chain q residue 263 LEU Chi-restraints excluded: chain q residue 264 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 343 LEU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 264 LEU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 29 MET Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain n residue 400 ILE Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 21 MET Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 228 VAL Chi-restraints excluded: chain m residue 242 VAL Chi-restraints excluded: chain m residue 299 ARG Chi-restraints excluded: chain m residue 327 MET Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 162 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 49 ILE Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 92 ARG Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain h residue 383 LEU Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 248 GLU Chi-restraints excluded: chain g residue 327 MET Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 29 MET Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 194 SER Chi-restraints excluded: chain f residue 242 VAL Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 101 ILE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 193 GLN Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 216 VAL Chi-restraints excluded: chain d residue 220 GLN Chi-restraints excluded: chain d residue 228 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 242 VAL Chi-restraints excluded: chain d residue 264 LEU Chi-restraints excluded: chain d residue 341 MET Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 254 VAL Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 327 MET Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 264 LEU Chi-restraints excluded: chain b residue 397 GLU Chi-restraints excluded: chain b residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 557 optimal weight: 1.9990 chunk 456 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 671 optimal weight: 0.5980 chunk 725 optimal weight: 20.0000 chunk 597 optimal weight: 1.9990 chunk 665 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 538 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 374 GLN ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 344 HIS r 378 GLN ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 275 ASN ** n 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 295 HIS m 374 GLN l 378 GLN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 189 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 374 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 189 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 292 ASN ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 292 ASN e 374 GLN d 189 GLN d 275 ASN c 374 GLN b 374 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2729 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= 0.189 Angle : 0.631 7.702 82008 Z= 0.305 Chirality : 0.042 0.150 9324 Planarity : 0.004 0.041 10620 Dihedral : 7.161 179.142 8457 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.92 % Allowed : 27.82 % Favored : 67.25 % 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: 1.41 (0.10), residues: 7506 helix: 1.68 (0.09), residues: 3510 sheet: 1.01 (0.15), residues: 1224 loop : 0.04 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 381 HIS 0.007 0.001 HIS n 295 PHE 0.007 0.001 PHE d 412 TYR 0.021 0.002 TYR r 332 ARG 0.008 0.001 ARG h 362 *********************** 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 1374 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 319 poor density : 1055 time to evaluate : 5.436 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: a 197 TYR cc_start: 0.9055 (t80) cc_final: 0.8795 (t80) REVERT: a 265 ASP cc_start: 0.8496 (t70) cc_final: 0.8206 (p0) REVERT: a 341 MET cc_start: 0.9480 (tmt) cc_final: 0.9106 (tmm) REVERT: r 21 MET cc_start: 0.9088 (ttm) cc_final: 0.8810 (ttt) REVERT: r 85 GLN cc_start: 0.8882 (mp10) cc_final: 0.8428 (mp10) REVERT: r 132 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8526 (mt) REVERT: r 197 TYR cc_start: 0.8033 (t80) cc_final: 0.7791 (t80) REVERT: r 226 GLU cc_start: 0.8903 (tp30) cc_final: 0.8639 (tp30) REVERT: r 248 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8886 (mm-30) REVERT: r 265 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8541 (p0) REVERT: r 292 ASN cc_start: 0.8946 (m110) cc_final: 0.8273 (p0) REVERT: r 328 ASP cc_start: 0.9165 (m-30) cc_final: 0.8786 (m-30) REVERT: r 390 MET cc_start: 0.8485 (pmm) cc_final: 0.8274 (pmm) REVERT: q 33 ASP cc_start: 0.9011 (m-30) cc_final: 0.8625 (m-30) REVERT: q 172 GLN cc_start: 0.9077 (tp40) cc_final: 0.8813 (tp40) REVERT: q 186 MET cc_start: 0.8758 (ptp) cc_final: 0.7994 (ptt) REVERT: q 189 GLN cc_start: 0.9423 (mt0) cc_final: 0.8895 (mt0) REVERT: q 333 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8889 (mm-30) REVERT: q 334 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8661 (tm-30) REVERT: p 56 GLU cc_start: 0.8776 (pt0) cc_final: 0.8412 (pt0) REVERT: p 59 GLN cc_start: 0.8818 (pm20) cc_final: 0.8457 (pm20) REVERT: p 60 ASP cc_start: 0.8843 (m-30) cc_final: 0.7854 (m-30) REVERT: p 186 MET cc_start: 0.9228 (ptm) cc_final: 0.8984 (ptt) REVERT: p 193 GLN cc_start: 0.9127 (tt0) cc_final: 0.8672 (tm-30) REVERT: p 244 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8425 (mm-30) REVERT: p 248 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8719 (mp0) REVERT: p 333 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8886 (mm-30) REVERT: p 334 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8428 (tm-30) REVERT: p 342 GLU cc_start: 0.8896 (mp0) cc_final: 0.8547 (pm20) REVERT: o 30 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7528 (mmm-85) REVERT: o 33 ASP cc_start: 0.8725 (m-30) cc_final: 0.8510 (m-30) REVERT: o 105 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8116 (tmmt) REVERT: o 115 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8852 (ptmm) REVERT: o 128 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8856 (ptp-110) REVERT: o 132 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8590 (tm) REVERT: o 134 GLU cc_start: 0.8832 (mp0) cc_final: 0.8613 (mp0) REVERT: o 218 GLU cc_start: 0.9095 (tp30) cc_final: 0.8823 (tp30) REVERT: o 234 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7722 (mp0) REVERT: o 244 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8077 (mm-30) REVERT: o 248 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: o 264 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8755 (tt) REVERT: o 333 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8851 (mm-30) REVERT: o 334 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8676 (tm-30) REVERT: n 5 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: n 40 LYS cc_start: 0.9142 (ttpt) cc_final: 0.8787 (ttmm) REVERT: n 59 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8232 (tp40) REVERT: n 147 MET cc_start: 0.9560 (tpp) cc_final: 0.8874 (mmm) REVERT: n 197 TYR cc_start: 0.9151 (t80) cc_final: 0.8859 (t80) REVERT: n 326 LYS cc_start: 0.8293 (tptp) cc_final: 0.7947 (tptp) REVERT: n 334 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8376 (tm-30) REVERT: n 342 GLU cc_start: 0.8634 (mp0) cc_final: 0.8088 (mp0) REVERT: n 411 ASP cc_start: 0.9173 (m-30) cc_final: 0.8895 (m-30) REVERT: m 21 MET cc_start: 0.8542 (ttm) cc_final: 0.8286 (ttt) REVERT: m 67 SER cc_start: 0.8961 (m) cc_final: 0.8581 (p) REVERT: m 69 ASP cc_start: 0.9005 (t0) cc_final: 0.8744 (t70) REVERT: m 92 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8027 (pmm-80) REVERT: m 193 GLN cc_start: 0.8795 (tt0) cc_final: 0.8332 (tm-30) REVERT: m 197 TYR cc_start: 0.9311 (t80) cc_final: 0.8892 (t80) REVERT: m 226 GLU cc_start: 0.8412 (tp30) cc_final: 0.8027 (tt0) REVERT: m 334 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8486 (tm-30) REVERT: m 378 GLN cc_start: 0.9349 (mt0) cc_final: 0.9110 (mm-40) REVERT: m 405 MET cc_start: 0.9226 (ttp) cc_final: 0.8945 (ptp) REVERT: m 411 ASP cc_start: 0.9198 (m-30) cc_final: 0.8858 (m-30) REVERT: m 414 GLU cc_start: 0.8650 (pp20) cc_final: 0.8430 (pp20) REVERT: l 69 ASP cc_start: 0.8962 (t0) cc_final: 0.8735 (t0) REVERT: l 92 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7791 (pmm-80) REVERT: l 125 GLU cc_start: 0.9066 (mp0) cc_final: 0.8784 (mp0) REVERT: l 218 GLU cc_start: 0.8787 (tp30) cc_final: 0.8519 (tp30) REVERT: l 222 LEU cc_start: 0.9213 (mp) cc_final: 0.8789 (mm) REVERT: l 224 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9287 (mtpp) REVERT: l 333 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: l 342 GLU cc_start: 0.8634 (mp0) cc_final: 0.8400 (mt-10) REVERT: l 378 GLN cc_start: 0.8846 (mt0) cc_final: 0.8510 (mm-40) REVERT: l 406 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8480 (p) REVERT: k 2 ASN cc_start: 0.8822 (t0) cc_final: 0.8394 (t0) REVERT: k 5 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8662 (pm20) REVERT: k 32 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8903 (mp10) REVERT: k 211 GLU cc_start: 0.8731 (tp30) cc_final: 0.8512 (tp30) REVERT: k 218 GLU cc_start: 0.8954 (tp30) cc_final: 0.8601 (tt0) REVERT: k 264 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8499 (tt) REVERT: k 351 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7874 (mt-10) REVERT: k 374 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8209 (tm-30) REVERT: k 378 GLN cc_start: 0.9275 (mt0) cc_final: 0.9016 (mt0) REVERT: k 394 ASP cc_start: 0.8913 (m-30) cc_final: 0.8580 (m-30) REVERT: j 5 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8841 (pm20) REVERT: j 67 SER cc_start: 0.8880 (m) cc_final: 0.8414 (p) REVERT: j 218 GLU cc_start: 0.8936 (tp30) cc_final: 0.8674 (tt0) REVERT: j 397 GLU cc_start: 0.8877 (pt0) cc_final: 0.8523 (mt-10) REVERT: j 411 ASP cc_start: 0.9118 (m-30) cc_final: 0.8773 (m-30) REVERT: i 13 GLU cc_start: 0.8773 (pm20) cc_final: 0.8490 (pm20) REVERT: i 19 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8420 (mm-30) REVERT: i 67 SER cc_start: 0.8979 (m) cc_final: 0.8544 (p) REVERT: i 106 GLU cc_start: 0.7806 (pp20) cc_final: 0.7550 (pp20) REVERT: i 272 ARG cc_start: 0.9087 (mmm-85) cc_final: 0.8759 (mmt90) REVERT: i 342 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8493 (mt-10) REVERT: i 352 LYS cc_start: 0.8191 (tppp) cc_final: 0.7958 (tptp) REVERT: i 397 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8577 (mt-10) REVERT: h 226 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: h 326 LYS cc_start: 0.8748 (mppt) cc_final: 0.8426 (tptp) REVERT: h 342 GLU cc_start: 0.8551 (mp0) cc_final: 0.8272 (mp0) REVERT: h 375 GLU cc_start: 0.8971 (pm20) cc_final: 0.8766 (pm20) REVERT: h 397 GLU cc_start: 0.8567 (pp20) cc_final: 0.8164 (pp20) REVERT: h 411 ASP cc_start: 0.8937 (m-30) cc_final: 0.8586 (m-30) REVERT: g 12 SER cc_start: 0.9368 (m) cc_final: 0.9015 (p) REVERT: g 67 SER cc_start: 0.9026 (m) cc_final: 0.8543 (p) REVERT: g 72 TYR cc_start: 0.9487 (m-10) cc_final: 0.9273 (m-10) REVERT: g 92 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7922 (pmm-80) REVERT: g 218 GLU cc_start: 0.8884 (tp30) cc_final: 0.8668 (tt0) REVERT: g 415 MET cc_start: 0.9185 (ttm) cc_final: 0.8909 (ttm) REVERT: f 374 GLN cc_start: 0.8730 (tp40) cc_final: 0.8436 (tp40) REVERT: e 58 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8954 (mt) REVERT: e 67 SER cc_start: 0.9001 (m) cc_final: 0.8551 (p) REVERT: e 70 SER cc_start: 0.9080 (t) cc_final: 0.8750 (m) REVERT: e 244 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8300 (mm-30) REVERT: e 299 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8179 (mtm-85) REVERT: e 326 LYS cc_start: 0.8292 (tppt) cc_final: 0.7961 (tppt) REVERT: e 333 GLU cc_start: 0.9019 (tp30) cc_final: 0.8683 (tp30) REVERT: e 341 MET cc_start: 0.8896 (tmt) cc_final: 0.8582 (tmm) REVERT: e 362 ARG cc_start: 0.9280 (ttm110) cc_final: 0.8965 (mtm-85) REVERT: e 406 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (p) REVERT: d 5 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8855 (pm20) REVERT: d 12 SER cc_start: 0.9490 (m) cc_final: 0.9235 (p) REVERT: d 211 GLU cc_start: 0.8800 (tp30) cc_final: 0.8562 (tp30) REVERT: d 264 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8462 (tt) REVERT: d 342 GLU cc_start: 0.8603 (mp0) cc_final: 0.8286 (mp0) REVERT: d 362 ARG cc_start: 0.9285 (ttm110) cc_final: 0.9040 (ttm110) REVERT: d 417 LYS cc_start: 0.9184 (ptmm) cc_final: 0.8883 (ptpp) REVERT: c 12 SER cc_start: 0.9378 (m) cc_final: 0.9032 (p) REVERT: c 13 GLU cc_start: 0.8836 (pm20) cc_final: 0.8401 (pm20) REVERT: c 19 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8862 (tp30) REVERT: c 67 SER cc_start: 0.8949 (m) cc_final: 0.8558 (p) REVERT: c 177 VAL cc_start: 0.9397 (t) cc_final: 0.9103 (m) REVERT: c 197 TYR cc_start: 0.9157 (t80) cc_final: 0.8646 (t80) REVERT: c 244 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7969 (mm-30) REVERT: c 248 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8923 (mm-30) REVERT: c 272 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8649 (ttm-80) REVERT: c 294 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9045 (tp) REVERT: c 352 LYS cc_start: 0.8341 (tptt) cc_final: 0.8096 (tptp) REVERT: c 411 ASP cc_start: 0.8977 (m-30) cc_final: 0.8617 (m-30) REVERT: b 92 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7694 (pmm-80) REVERT: b 193 GLN cc_start: 0.8686 (tt0) cc_final: 0.8437 (tm-30) REVERT: b 218 GLU cc_start: 0.9053 (tp30) cc_final: 0.8794 (tp30) REVERT: b 219 MET cc_start: 0.9357 (mmm) cc_final: 0.9012 (mmm) REVERT: b 244 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8574 (mm-30) REVERT: b 248 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9106 (mm-30) REVERT: b 342 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8448 (tt0) REVERT: b 378 GLN cc_start: 0.9258 (mt0) cc_final: 0.8932 (mt0) outliers start: 319 outliers final: 162 residues processed: 1312 average time/residue: 0.5692 time to fit residues: 1276.5162 Evaluate side-chains 1167 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 977 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 191 ILE Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 89 PHE Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 58 LEU Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 132 LEU Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 52 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 242 VAL Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 89 PHE Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 162 LEU Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 373 THR Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 49 ILE Chi-restraints excluded: chain k residue 89 PHE Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain j residue 5 GLU Chi-restraints excluded: chain j residue 49 ILE Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 354 VAL Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 292 ASN Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 89 PHE Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain f residue 400 ILE Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 29 MET Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 264 LEU Chi-restraints excluded: chain d residue 354 VAL Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain c residue 405 MET Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 397 GLU Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 7.9990 chunk 504 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 320 optimal weight: 0.9990 chunk 450 optimal weight: 0.5980 chunk 673 optimal weight: 0.9980 chunk 713 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 638 optimal weight: 8.9990 chunk 192 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 374 GLN ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 ASN ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 ASN n 25 ASN n 140 HIS n 378 GLN m 275 ASN m 374 GLN k 220 GLN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 189 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 374 GLN h 25 ASN h 189 GLN h 220 GLN ** h 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN g 193 GLN g 275 ASN ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 374 GLN d 189 GLN d 220 GLN ** b 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 60822 Z= 0.164 Angle : 0.623 8.601 82008 Z= 0.299 Chirality : 0.042 0.154 9324 Planarity : 0.004 0.039 10620 Dihedral : 7.036 179.746 8454 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.31 % Allowed : 27.25 % Favored : 68.44 % 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: 1.50 (0.10), residues: 7506 helix: 1.84 (0.09), residues: 3492 sheet: 0.98 (0.15), residues: 1224 loop : 0.00 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 381 HIS 0.007 0.001 HIS n 295 PHE 0.008 0.001 PHE g 300 TYR 0.019 0.002 TYR j 197 ARG 0.010 0.001 ARG h 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 1354 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 1075 time to evaluate : 5.381 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: a 21 MET cc_start: 0.8464 (ttt) cc_final: 0.8190 (ttt) REVERT: a 197 TYR cc_start: 0.9060 (t80) cc_final: 0.8847 (t80) REVERT: a 218 GLU cc_start: 0.9276 (tp30) cc_final: 0.9073 (tp30) REVERT: a 222 LEU cc_start: 0.9621 (tp) cc_final: 0.9316 (tp) REVERT: a 341 MET cc_start: 0.9426 (tmt) cc_final: 0.9110 (tmm) REVERT: r 21 MET cc_start: 0.9034 (ttm) cc_final: 0.8734 (ttt) REVERT: r 60 ASP cc_start: 0.8534 (t0) cc_final: 0.8324 (t0) REVERT: r 85 GLN cc_start: 0.8896 (mp10) cc_final: 0.8463 (mp10) REVERT: r 132 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8517 (mt) REVERT: r 248 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8870 (mm-30) REVERT: r 265 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8603 (p0) REVERT: r 292 ASN cc_start: 0.8916 (m110) cc_final: 0.8308 (p0) REVERT: q 33 ASP cc_start: 0.9000 (m-30) cc_final: 0.8592 (m-30) REVERT: q 186 MET cc_start: 0.8777 (ptp) cc_final: 0.8326 (ptp) REVERT: q 189 GLN cc_start: 0.9070 (mt0) cc_final: 0.8826 (mt0) REVERT: q 333 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8897 (mm-30) REVERT: q 334 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8646 (tm-30) REVERT: q 360 TYR cc_start: 0.8963 (t80) cc_final: 0.8529 (t80) REVERT: q 412 PHE cc_start: 0.9025 (t80) cc_final: 0.8583 (t80) REVERT: q 416 MET cc_start: 0.8719 (mmm) cc_final: 0.8458 (tpt) REVERT: p 59 GLN cc_start: 0.8806 (pm20) cc_final: 0.8505 (pm20) REVERT: p 186 MET cc_start: 0.9212 (ptm) cc_final: 0.8957 (ptt) REVERT: p 244 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8370 (mm-30) REVERT: p 248 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8705 (mp0) REVERT: p 333 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8903 (mm-30) REVERT: p 334 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8458 (tp30) REVERT: p 374 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8301 (tm-30) REVERT: p 378 GLN cc_start: 0.9344 (mt0) cc_final: 0.9050 (mm-40) REVERT: p 415 MET cc_start: 0.9202 (mtp) cc_final: 0.8851 (mtm) REVERT: o 30 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: o 33 ASP cc_start: 0.8750 (m-30) cc_final: 0.8529 (m-30) REVERT: o 105 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8042 (tmmt) REVERT: o 115 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8836 (ptmm) REVERT: o 132 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8524 (tm) REVERT: o 134 GLU cc_start: 0.8819 (mp0) cc_final: 0.8556 (mp0) REVERT: o 177 VAL cc_start: 0.9311 (t) cc_final: 0.9058 (m) REVERT: o 218 GLU cc_start: 0.9132 (tp30) cc_final: 0.8799 (tp30) REVERT: o 234 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7715 (mp0) REVERT: o 244 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7995 (mm-30) REVERT: o 248 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: o 264 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8547 (tt) REVERT: o 326 LYS cc_start: 0.8709 (tppp) cc_final: 0.8481 (tppp) REVERT: o 333 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8786 (mm-30) REVERT: o 334 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8662 (tp30) REVERT: o 342 GLU cc_start: 0.8556 (pt0) cc_final: 0.8021 (pt0) REVERT: n 5 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8932 (pm20) REVERT: n 40 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8781 (ttmm) REVERT: n 147 MET cc_start: 0.9524 (tpp) cc_final: 0.8878 (mmm) REVERT: n 197 TYR cc_start: 0.9176 (t80) cc_final: 0.8911 (t80) REVERT: n 326 LYS cc_start: 0.8280 (tptp) cc_final: 0.7874 (tptp) REVERT: n 334 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8332 (tm-30) REVERT: n 342 GLU cc_start: 0.8655 (mp0) cc_final: 0.8093 (mp0) REVERT: n 411 ASP cc_start: 0.9193 (m-30) cc_final: 0.8936 (m-30) REVERT: m 21 MET cc_start: 0.8524 (ttm) cc_final: 0.8256 (ttt) REVERT: m 67 SER cc_start: 0.8945 (m) cc_final: 0.8509 (p) REVERT: m 69 ASP cc_start: 0.8976 (t0) cc_final: 0.8680 (t70) REVERT: m 92 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8036 (pmm-80) REVERT: m 193 GLN cc_start: 0.8791 (tt0) cc_final: 0.8334 (tm-30) REVERT: m 197 TYR cc_start: 0.9325 (t80) cc_final: 0.8906 (t80) REVERT: m 226 GLU cc_start: 0.8495 (tp30) cc_final: 0.8188 (tt0) REVERT: m 327 MET cc_start: 0.8739 (ptm) cc_final: 0.8469 (ttp) REVERT: m 334 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8411 (tm-30) REVERT: m 378 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9107 (mm-40) REVERT: m 405 MET cc_start: 0.9322 (ttp) cc_final: 0.9074 (ptp) REVERT: m 414 GLU cc_start: 0.8767 (pp20) cc_final: 0.8510 (pp20) REVERT: l 92 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7779 (pmm-80) REVERT: l 122 ASP cc_start: 0.9109 (t0) cc_final: 0.8734 (t70) REVERT: l 125 GLU cc_start: 0.9064 (mp0) cc_final: 0.8817 (mp0) REVERT: l 218 GLU cc_start: 0.8783 (tp30) cc_final: 0.8510 (tp30) REVERT: l 222 LEU cc_start: 0.9228 (mp) cc_final: 0.8833 (mm) REVERT: l 224 LYS cc_start: 0.9493 (ttpt) cc_final: 0.9279 (mtpp) REVERT: l 333 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: l 334 GLU cc_start: 0.8908 (tp30) cc_final: 0.8639 (tm-30) REVERT: l 342 GLU cc_start: 0.8665 (mp0) cc_final: 0.8437 (mt-10) REVERT: l 378 GLN cc_start: 0.8842 (mt0) cc_final: 0.8498 (mm-40) REVERT: l 406 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8472 (p) REVERT: k 2 ASN cc_start: 0.8817 (t0) cc_final: 0.8420 (t0) REVERT: k 5 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: k 218 GLU cc_start: 0.8937 (tp30) cc_final: 0.8596 (tt0) REVERT: k 244 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8309 (mm-30) REVERT: k 264 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8507 (tt) REVERT: k 374 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7920 (tm-30) REVERT: k 378 GLN cc_start: 0.9268 (mt0) cc_final: 0.8869 (mt0) REVERT: k 394 ASP cc_start: 0.8882 (m-30) cc_final: 0.8649 (m-30) REVERT: j 67 SER cc_start: 0.8845 (m) cc_final: 0.8335 (p) REVERT: j 218 GLU cc_start: 0.8915 (tp30) cc_final: 0.8663 (tt0) REVERT: j 397 GLU cc_start: 0.8856 (pt0) cc_final: 0.8555 (mt-10) REVERT: j 411 ASP cc_start: 0.9117 (m-30) cc_final: 0.8762 (m-30) REVERT: i 13 GLU cc_start: 0.8786 (pm20) cc_final: 0.8512 (pm20) REVERT: i 19 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8452 (mm-30) REVERT: i 52 ASP cc_start: 0.8633 (p0) cc_final: 0.8365 (p0) REVERT: i 67 SER cc_start: 0.8932 (m) cc_final: 0.8489 (p) REVERT: i 106 GLU cc_start: 0.7738 (pp20) cc_final: 0.7494 (pp20) REVERT: i 272 ARG cc_start: 0.9098 (mmm-85) cc_final: 0.8759 (mmm-85) REVERT: i 329 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8422 (mm-30) REVERT: i 352 LYS cc_start: 0.8297 (tppp) cc_final: 0.8005 (tptp) REVERT: i 374 GLN cc_start: 0.8526 (tp-100) cc_final: 0.7924 (tp40) REVERT: i 378 GLN cc_start: 0.9073 (mt0) cc_final: 0.8720 (mt0) REVERT: i 397 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8649 (mt-10) REVERT: h 97 ILE cc_start: 0.9014 (mt) cc_final: 0.8806 (mm) REVERT: h 164 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8865 (mm) REVERT: h 226 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: h 326 LYS cc_start: 0.8710 (mppt) cc_final: 0.8254 (tptp) REVERT: h 342 GLU cc_start: 0.8563 (mp0) cc_final: 0.8236 (mp0) REVERT: h 348 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8546 (pttm) REVERT: h 351 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7959 (mm-30) REVERT: h 374 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8435 (tp40) REVERT: h 378 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8948 (mm-40) REVERT: h 397 GLU cc_start: 0.8599 (pp20) cc_final: 0.8230 (pp20) REVERT: g 12 SER cc_start: 0.9358 (m) cc_final: 0.9024 (p) REVERT: g 67 SER cc_start: 0.8976 (m) cc_final: 0.8453 (p) REVERT: g 92 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7887 (pmm-80) REVERT: g 145 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8533 (mt) REVERT: g 218 GLU cc_start: 0.8932 (tp30) cc_final: 0.8692 (tt0) REVERT: g 244 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8454 (mm-30) REVERT: g 351 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8168 (mt-10) REVERT: f 30 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7090 (mtm110) REVERT: f 244 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8359 (mm-30) REVERT: e 58 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8953 (mt) REVERT: e 67 SER cc_start: 0.8985 (m) cc_final: 0.8467 (p) REVERT: e 70 SER cc_start: 0.9012 (t) cc_final: 0.8591 (m) REVERT: e 134 GLU cc_start: 0.8903 (mp0) cc_final: 0.8689 (mp0) REVERT: e 244 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8220 (mm-30) REVERT: e 334 GLU cc_start: 0.8870 (tp30) cc_final: 0.8651 (tm-30) REVERT: e 341 MET cc_start: 0.8930 (tmt) cc_final: 0.8528 (tmm) REVERT: e 351 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8069 (mm-30) REVERT: e 362 ARG cc_start: 0.9268 (ttm110) cc_final: 0.8947 (mtm-85) REVERT: e 406 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8300 (p) REVERT: d 5 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8851 (pm20) REVERT: d 12 SER cc_start: 0.9465 (m) cc_final: 0.9233 (p) REVERT: d 101 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9461 (mp) REVERT: d 244 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8107 (mm-30) REVERT: d 264 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (tt) REVERT: d 342 GLU cc_start: 0.8583 (mp0) cc_final: 0.8279 (mp0) REVERT: d 352 LYS cc_start: 0.8668 (tppt) cc_final: 0.8038 (tptp) REVERT: d 362 ARG cc_start: 0.9263 (ttm110) cc_final: 0.9023 (ttm110) REVERT: d 374 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8105 (tp-100) REVERT: d 417 LYS cc_start: 0.9173 (ptmm) cc_final: 0.8847 (ptpp) REVERT: c 12 SER cc_start: 0.9387 (m) cc_final: 0.9054 (p) REVERT: c 13 GLU cc_start: 0.8840 (pm20) cc_final: 0.8402 (pm20) REVERT: c 19 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8885 (tp30) REVERT: c 67 SER cc_start: 0.8947 (m) cc_final: 0.8518 (p) REVERT: c 244 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8222 (mm-30) REVERT: c 248 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8901 (mm-30) REVERT: c 294 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9029 (tp) REVERT: c 411 ASP cc_start: 0.8995 (m-30) cc_final: 0.8610 (m-30) REVERT: b 92 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7650 (pmm-80) REVERT: b 193 GLN cc_start: 0.8718 (tt0) cc_final: 0.8444 (tm-30) REVERT: b 218 GLU cc_start: 0.9093 (tp30) cc_final: 0.8725 (tp30) REVERT: b 219 MET cc_start: 0.9338 (mmm) cc_final: 0.9133 (mmm) REVERT: b 244 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8554 (mm-30) REVERT: b 248 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9108 (mm-30) REVERT: b 334 GLU cc_start: 0.9042 (tp30) cc_final: 0.8720 (tm-30) REVERT: b 342 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8445 (tt0) REVERT: b 351 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8124 (mt-10) REVERT: b 362 ARG cc_start: 0.9242 (ttm110) cc_final: 0.9024 (ttp-110) REVERT: b 374 GLN cc_start: 0.8694 (tp40) cc_final: 0.8344 (tp40) REVERT: b 378 GLN cc_start: 0.9305 (mt0) cc_final: 0.8913 (mt0) outliers start: 279 outliers final: 163 residues processed: 1291 average time/residue: 0.6105 time to fit residues: 1321.6029 Evaluate side-chains 1195 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1003 time to evaluate : 5.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 29 MET Chi-restraints excluded: chain r residue 80 TYR Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 204 LEU Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 354 VAL Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 380 MET Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 191 ILE Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 132 LEU Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 194 SER Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 373 THR Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 164 LEU Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 265 ASP Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain f residue 400 ILE Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 89 PHE Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 80 TYR Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 101 ILE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 264 LEU Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain c residue 354 VAL Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 132 LEU Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 248 GLU Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 6.9990 chunk 404 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 531 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 608 optimal weight: 4.9990 chunk 493 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 364 optimal weight: 2.9990 chunk 640 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 374 GLN ** r 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 374 GLN l 189 GLN ** k 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 193 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 189 GLN h 193 GLN h 220 GLN g 32 GLN g 189 GLN e 292 ASN e 374 GLN d 189 GLN b 374 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 60822 Z= 0.314 Angle : 0.653 8.783 82008 Z= 0.319 Chirality : 0.043 0.166 9324 Planarity : 0.004 0.056 10620 Dihedral : 7.093 177.117 8443 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.74 % Allowed : 26.96 % Favored : 68.30 % 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: 1.39 (0.10), residues: 7506 helix: 1.75 (0.09), residues: 3492 sheet: 0.57 (0.15), residues: 1332 loop : 0.11 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 381 HIS 0.008 0.001 HIS n 295 PHE 0.010 0.001 PHE q 398 TYR 0.026 0.002 TYR r 332 ARG 0.008 0.001 ARG j 418 *********************** 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 1300 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 993 time to evaluate : 5.440 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: a 193 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8455 (tm-30) REVERT: a 197 TYR cc_start: 0.9044 (t80) cc_final: 0.8735 (t80) REVERT: a 222 LEU cc_start: 0.9608 (tp) cc_final: 0.9347 (tp) REVERT: a 241 GLN cc_start: 0.9091 (pp30) cc_final: 0.8875 (pp30) REVERT: r 21 MET cc_start: 0.9043 (ttm) cc_final: 0.8777 (ttt) REVERT: r 85 GLN cc_start: 0.9006 (mp10) cc_final: 0.8472 (mp10) REVERT: r 132 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8600 (mt) REVERT: r 248 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8868 (mm-30) REVERT: r 265 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8659 (p0) REVERT: r 292 ASN cc_start: 0.8965 (m110) cc_final: 0.8357 (p0) REVERT: q 33 ASP cc_start: 0.9056 (m-30) cc_final: 0.8654 (m-30) REVERT: q 186 MET cc_start: 0.8906 (ptp) cc_final: 0.8656 (ptp) REVERT: q 253 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9408 (mm) REVERT: q 333 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8860 (mm-30) REVERT: q 334 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8607 (tm-30) REVERT: q 390 MET cc_start: 0.8734 (pmm) cc_final: 0.8345 (pmm) REVERT: p 60 ASP cc_start: 0.8897 (m-30) cc_final: 0.8583 (m-30) REVERT: p 186 MET cc_start: 0.9235 (ptm) cc_final: 0.8980 (ptt) REVERT: p 226 GLU cc_start: 0.8798 (tp30) cc_final: 0.8466 (tp30) REVERT: p 244 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8338 (mm-30) REVERT: p 248 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8763 (mp0) REVERT: p 333 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8911 (mm-30) REVERT: p 334 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8435 (tp30) REVERT: p 341 MET cc_start: 0.9367 (ppp) cc_final: 0.9166 (ppp) REVERT: o 105 LYS cc_start: 0.8498 (tmmt) cc_final: 0.7997 (tmmt) REVERT: o 115 LYS cc_start: 0.9132 (tmmt) cc_final: 0.8882 (ptmm) REVERT: o 128 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8832 (ptp-110) REVERT: o 134 GLU cc_start: 0.8861 (mp0) cc_final: 0.8652 (mp0) REVERT: o 218 GLU cc_start: 0.9160 (tp30) cc_final: 0.8838 (tp30) REVERT: o 234 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7648 (mp0) REVERT: o 244 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7890 (mm-30) REVERT: o 248 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: o 253 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9238 (mt) REVERT: o 264 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8504 (tt) REVERT: o 333 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8925 (mm-30) REVERT: o 334 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8629 (tm-30) REVERT: n 5 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: n 147 MET cc_start: 0.9506 (tpp) cc_final: 0.8875 (mmm) REVERT: n 197 TYR cc_start: 0.9184 (t80) cc_final: 0.8917 (t80) REVERT: n 326 LYS cc_start: 0.8367 (tptp) cc_final: 0.8088 (tptp) REVERT: n 334 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8285 (tm-30) REVERT: n 342 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: m 21 MET cc_start: 0.8515 (ttm) cc_final: 0.8167 (ttt) REVERT: m 67 SER cc_start: 0.8819 (m) cc_final: 0.8430 (p) REVERT: m 69 ASP cc_start: 0.9100 (t0) cc_final: 0.8822 (t70) REVERT: m 92 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8159 (pmm-80) REVERT: m 193 GLN cc_start: 0.8786 (tt0) cc_final: 0.8362 (tm-30) REVERT: m 197 TYR cc_start: 0.9308 (t80) cc_final: 0.8900 (t80) REVERT: m 226 GLU cc_start: 0.8386 (tp30) cc_final: 0.7991 (tt0) REVERT: m 327 MET cc_start: 0.8801 (ptm) cc_final: 0.8525 (ttp) REVERT: m 378 GLN cc_start: 0.9404 (mm-40) cc_final: 0.9198 (mm-40) REVERT: m 405 MET cc_start: 0.9394 (ttp) cc_final: 0.9062 (ptp) REVERT: m 414 GLU cc_start: 0.8875 (pp20) cc_final: 0.8654 (pp20) REVERT: l 32 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8554 (mm-40) REVERT: l 92 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7809 (pmm-80) REVERT: l 125 GLU cc_start: 0.9086 (mp0) cc_final: 0.8744 (mp0) REVERT: l 144 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (ttt90) REVERT: l 218 GLU cc_start: 0.8837 (tp30) cc_final: 0.8605 (tp30) REVERT: l 224 LYS cc_start: 0.9518 (ttpt) cc_final: 0.9315 (mtpp) REVERT: l 244 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8621 (mm-30) REVERT: l 333 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: l 334 GLU cc_start: 0.8964 (tp30) cc_final: 0.8755 (tp30) REVERT: l 342 GLU cc_start: 0.8707 (mp0) cc_final: 0.8388 (mt-10) REVERT: l 374 GLN cc_start: 0.8601 (tp40) cc_final: 0.8393 (tp40) REVERT: l 375 GLU cc_start: 0.9141 (mp0) cc_final: 0.8934 (pm20) REVERT: l 378 GLN cc_start: 0.8898 (mt0) cc_final: 0.8537 (mm-40) REVERT: l 406 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8691 (p) REVERT: k 5 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: k 218 GLU cc_start: 0.8894 (tp30) cc_final: 0.8574 (tt0) REVERT: k 244 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8147 (mm-30) REVERT: k 374 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8138 (tm-30) REVERT: j 218 GLU cc_start: 0.8928 (tp30) cc_final: 0.8672 (tt0) REVERT: j 374 GLN cc_start: 0.8519 (tp40) cc_final: 0.7650 (tp40) REVERT: j 378 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8764 (mm-40) REVERT: j 397 GLU cc_start: 0.8881 (pt0) cc_final: 0.8578 (mt-10) REVERT: j 411 ASP cc_start: 0.9171 (m-30) cc_final: 0.8837 (m-30) REVERT: i 13 GLU cc_start: 0.8758 (pm20) cc_final: 0.8500 (pm20) REVERT: i 19 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8468 (mm-30) REVERT: i 67 SER cc_start: 0.8902 (m) cc_final: 0.8500 (p) REVERT: i 197 TYR cc_start: 0.9218 (t80) cc_final: 0.8872 (t80) REVERT: i 272 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8765 (mmt90) REVERT: i 329 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8466 (mm-30) REVERT: i 342 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8527 (mt-10) REVERT: i 352 LYS cc_start: 0.8621 (tppp) cc_final: 0.8349 (tptp) REVERT: i 374 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8159 (tp40) REVERT: i 397 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8663 (mt-10) REVERT: h 226 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: h 292 ASN cc_start: 0.8892 (m110) cc_final: 0.8646 (p0) REVERT: h 326 LYS cc_start: 0.8688 (mppt) cc_final: 0.8351 (tptp) REVERT: h 342 GLU cc_start: 0.8556 (mp0) cc_final: 0.7879 (pm20) REVERT: h 348 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8448 (pttm) REVERT: h 362 ARG cc_start: 0.9338 (mtm-85) cc_final: 0.9100 (ttm110) REVERT: h 393 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (tp) REVERT: h 397 GLU cc_start: 0.8681 (pp20) cc_final: 0.8288 (pp20) REVERT: h 411 ASP cc_start: 0.8965 (m-30) cc_final: 0.8606 (m-30) REVERT: g 12 SER cc_start: 0.9408 (m) cc_final: 0.9105 (p) REVERT: g 92 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7860 (pmm-80) REVERT: g 145 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8734 (mt) REVERT: g 218 GLU cc_start: 0.8952 (tp30) cc_final: 0.8266 (tp30) REVERT: g 244 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8478 (mm-30) REVERT: g 347 ARG cc_start: 0.7965 (tpt-90) cc_final: 0.7566 (tpt-90) REVERT: g 351 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8135 (mm-30) REVERT: f 30 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7299 (mtm110) REVERT: f 226 GLU cc_start: 0.8422 (tt0) cc_final: 0.8025 (tt0) REVERT: e 12 SER cc_start: 0.9586 (m) cc_final: 0.9204 (p) REVERT: e 58 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8999 (mt) REVERT: e 67 SER cc_start: 0.8958 (m) cc_final: 0.8532 (p) REVERT: e 70 SER cc_start: 0.9159 (t) cc_final: 0.8842 (m) REVERT: e 244 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8224 (mm-30) REVERT: e 299 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8149 (mtm-85) REVERT: e 333 GLU cc_start: 0.9065 (tp30) cc_final: 0.8760 (tp30) REVERT: e 341 MET cc_start: 0.8985 (tmt) cc_final: 0.8549 (tmm) REVERT: e 407 LYS cc_start: 0.8971 (tppt) cc_final: 0.8763 (tptt) REVERT: d 5 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8817 (pm20) REVERT: d 12 SER cc_start: 0.9513 (m) cc_final: 0.9297 (p) REVERT: d 132 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8630 (tm) REVERT: d 244 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8146 (mm-30) REVERT: d 333 GLU cc_start: 0.9080 (tp30) cc_final: 0.8541 (mm-30) REVERT: d 352 LYS cc_start: 0.8916 (tppt) cc_final: 0.8291 (tptp) REVERT: d 362 ARG cc_start: 0.9262 (ttm110) cc_final: 0.8955 (ttm110) REVERT: d 374 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8113 (tp-100) REVERT: d 417 LYS cc_start: 0.9219 (ptmm) cc_final: 0.8902 (ptpp) REVERT: c 19 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8901 (tp30) REVERT: c 67 SER cc_start: 0.8937 (m) cc_final: 0.8563 (p) REVERT: c 197 TYR cc_start: 0.9198 (t80) cc_final: 0.8973 (t80) REVERT: c 244 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8136 (mm-30) REVERT: c 248 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8962 (mm-30) REVERT: c 341 MET cc_start: 0.9071 (tmm) cc_final: 0.8789 (tmm) REVERT: c 411 ASP cc_start: 0.9061 (m-30) cc_final: 0.8695 (m-30) REVERT: b 29 MET cc_start: 0.8527 (ttm) cc_final: 0.8322 (ttp) REVERT: b 172 GLN cc_start: 0.8942 (tp40) cc_final: 0.8702 (tp40) REVERT: b 193 GLN cc_start: 0.8727 (tt0) cc_final: 0.8458 (tm-30) REVERT: b 218 GLU cc_start: 0.9118 (tp30) cc_final: 0.8729 (tp30) REVERT: b 244 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8514 (mm-30) REVERT: b 292 ASN cc_start: 0.8914 (m110) cc_final: 0.8634 (p0) REVERT: b 334 GLU cc_start: 0.9052 (tp30) cc_final: 0.8724 (tm-30) REVERT: b 342 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8476 (tt0) REVERT: b 351 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8400 (mt-10) REVERT: b 374 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8518 (tp40) outliers start: 307 outliers final: 188 residues processed: 1235 average time/residue: 0.5741 time to fit residues: 1180.3034 Evaluate side-chains 1160 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 945 time to evaluate : 5.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 4 THR Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 12 SER Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 191 ILE Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 132 LEU Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 204 LEU Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 354 VAL Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 380 MET Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 380 MET Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 89 PHE Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 162 LEU Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 253 LEU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 308 GLU Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 354 VAL Chi-restraints excluded: chain m residue 373 THR Chi-restraints excluded: chain m residue 417 LYS Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 144 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 326 LYS Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain l residue 415 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 354 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 153 SER Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 373 THR Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 52 ASP Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 224 LYS Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 393 ILE Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 265 ASP Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain f residue 415 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 292 ASN Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 6.9990 chunk 642 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 418 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 714 optimal weight: 7.9990 chunk 592 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 374 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 374 GLN ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 25 ASN q 172 GLN q 189 GLN ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 220 GLN ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 374 GLN j 374 GLN ** i 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 292 ASN e 374 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 60822 Z= 0.277 Angle : 0.645 9.025 82008 Z= 0.314 Chirality : 0.043 0.166 9324 Planarity : 0.004 0.039 10620 Dihedral : 6.851 173.786 8436 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.34 % Allowed : 27.10 % Favored : 68.56 % 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: 1.32 (0.10), residues: 7506 helix: 1.78 (0.09), residues: 3492 sheet: 0.42 (0.16), residues: 1170 loop : 0.04 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 381 HIS 0.008 0.001 HIS n 295 PHE 0.017 0.001 PHE r 398 TYR 0.025 0.002 TYR r 332 ARG 0.014 0.001 ARG p 418 *********************** 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 1268 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 987 time to evaluate : 5.430 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: a 21 MET cc_start: 0.8068 (ttt) cc_final: 0.7779 (ttt) REVERT: a 147 MET cc_start: 0.9378 (tpp) cc_final: 0.8840 (mmm) REVERT: a 197 TYR cc_start: 0.9030 (t80) cc_final: 0.8671 (t80) REVERT: a 328 ASP cc_start: 0.8942 (m-30) cc_final: 0.8692 (m-30) REVERT: r 21 MET cc_start: 0.9053 (ttm) cc_final: 0.8739 (ttt) REVERT: r 85 GLN cc_start: 0.8993 (mp10) cc_final: 0.8495 (mp10) REVERT: r 248 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8834 (mm-30) REVERT: r 265 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8734 (p0) REVERT: r 292 ASN cc_start: 0.8985 (m110) cc_final: 0.8394 (p0) REVERT: r 327 MET cc_start: 0.8857 (ppp) cc_final: 0.8507 (ppp) REVERT: q 172 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8629 (tp40) REVERT: q 333 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8851 (mm-30) REVERT: q 334 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8611 (tm-30) REVERT: q 360 TYR cc_start: 0.9256 (t80) cc_final: 0.8994 (t80) REVERT: p 60 ASP cc_start: 0.8912 (m-30) cc_final: 0.8622 (m-30) REVERT: p 186 MET cc_start: 0.9227 (ptm) cc_final: 0.8992 (ptt) REVERT: p 244 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8314 (mm-30) REVERT: p 248 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: p 333 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8950 (mm-30) REVERT: p 334 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8438 (tm-30) REVERT: p 341 MET cc_start: 0.9375 (ppp) cc_final: 0.9149 (ppp) REVERT: p 374 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8232 (tm-30) REVERT: p 378 GLN cc_start: 0.9376 (mt0) cc_final: 0.9073 (mm-40) REVERT: p 415 MET cc_start: 0.9322 (mtm) cc_final: 0.9112 (mtm) REVERT: o 105 LYS cc_start: 0.8469 (tmmt) cc_final: 0.7990 (tmmt) REVERT: o 115 LYS cc_start: 0.9155 (tmmt) cc_final: 0.8904 (ptmm) REVERT: o 128 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8820 (ptp-110) REVERT: o 218 GLU cc_start: 0.9169 (tp30) cc_final: 0.8841 (tp30) REVERT: o 234 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7675 (mp0) REVERT: o 244 GLU cc_start: 0.8665 (mm-30) cc_final: 0.7890 (mm-30) REVERT: o 248 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: o 253 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9214 (mt) REVERT: o 264 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (tt) REVERT: o 333 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8924 (mm-30) REVERT: o 334 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8635 (tm-30) REVERT: n 5 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: n 147 MET cc_start: 0.9480 (tpp) cc_final: 0.8882 (mmm) REVERT: n 197 TYR cc_start: 0.9187 (t80) cc_final: 0.8932 (t80) REVERT: n 226 GLU cc_start: 0.8407 (tt0) cc_final: 0.8153 (tt0) REVERT: n 326 LYS cc_start: 0.8351 (tptp) cc_final: 0.8083 (tptp) REVERT: n 334 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8271 (tm-30) REVERT: n 342 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: n 397 GLU cc_start: 0.8983 (pp20) cc_final: 0.8767 (pp20) REVERT: m 21 MET cc_start: 0.8482 (ttm) cc_final: 0.8105 (ttt) REVERT: m 67 SER cc_start: 0.8850 (m) cc_final: 0.8448 (p) REVERT: m 69 ASP cc_start: 0.9096 (t0) cc_final: 0.8844 (t70) REVERT: m 92 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8121 (pmm-80) REVERT: m 193 GLN cc_start: 0.8784 (tt0) cc_final: 0.8358 (tm-30) REVERT: m 197 TYR cc_start: 0.9304 (t80) cc_final: 0.8951 (t80) REVERT: m 226 GLU cc_start: 0.8428 (tp30) cc_final: 0.8040 (tt0) REVERT: m 244 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8397 (mm-30) REVERT: m 327 MET cc_start: 0.8763 (ptm) cc_final: 0.8500 (ttp) REVERT: m 378 GLN cc_start: 0.9409 (mm-40) cc_final: 0.9177 (mm-40) REVERT: m 414 GLU cc_start: 0.8896 (pp20) cc_final: 0.8659 (pp20) REVERT: l 29 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8125 (ptm) REVERT: l 32 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8537 (mm-40) REVERT: l 92 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7850 (pmm-80) REVERT: l 125 GLU cc_start: 0.9102 (mp0) cc_final: 0.8745 (mp0) REVERT: l 218 GLU cc_start: 0.8856 (tp30) cc_final: 0.8583 (tp30) REVERT: l 224 LYS cc_start: 0.9523 (ttpt) cc_final: 0.9320 (mtpp) REVERT: l 333 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: l 334 GLU cc_start: 0.8934 (tp30) cc_final: 0.8668 (tp30) REVERT: l 342 GLU cc_start: 0.8695 (mp0) cc_final: 0.8390 (mt-10) REVERT: l 374 GLN cc_start: 0.8551 (tp40) cc_final: 0.8325 (tp40) REVERT: l 378 GLN cc_start: 0.8877 (mt0) cc_final: 0.8476 (mm-40) REVERT: l 406 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8719 (p) REVERT: k 5 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: k 218 GLU cc_start: 0.8889 (tp30) cc_final: 0.8572 (tt0) REVERT: k 264 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8499 (tt) REVERT: k 374 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7835 (tm-30) REVERT: k 378 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9098 (mm-40) REVERT: j 218 GLU cc_start: 0.8903 (tp30) cc_final: 0.8655 (tt0) REVERT: j 342 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: j 374 GLN cc_start: 0.8450 (tp-100) cc_final: 0.7528 (tp40) REVERT: j 378 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8676 (mm-40) REVERT: j 410 ASP cc_start: 0.9383 (m-30) cc_final: 0.8955 (t0) REVERT: j 411 ASP cc_start: 0.9191 (m-30) cc_final: 0.8872 (m-30) REVERT: i 13 GLU cc_start: 0.8787 (pm20) cc_final: 0.8527 (pm20) REVERT: i 19 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8434 (mm-30) REVERT: i 67 SER cc_start: 0.8920 (m) cc_final: 0.8493 (p) REVERT: i 197 TYR cc_start: 0.9225 (t80) cc_final: 0.8967 (t80) REVERT: i 272 ARG cc_start: 0.9131 (mmm-85) cc_final: 0.8749 (mmt90) REVERT: i 329 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8437 (mm-30) REVERT: i 342 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8534 (mt-10) REVERT: i 352 LYS cc_start: 0.8682 (tppp) cc_final: 0.8379 (tptp) REVERT: i 374 GLN cc_start: 0.8552 (tp-100) cc_final: 0.7929 (tp40) REVERT: i 378 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8676 (mm-40) REVERT: i 397 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8600 (mt-10) REVERT: h 32 GLN cc_start: 0.9038 (mp10) cc_final: 0.8763 (mp10) REVERT: h 226 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: h 292 ASN cc_start: 0.8875 (m110) cc_final: 0.8630 (p0) REVERT: h 326 LYS cc_start: 0.8674 (mppt) cc_final: 0.8386 (mmmt) REVERT: h 341 MET cc_start: 0.9021 (tmm) cc_final: 0.8649 (tmm) REVERT: h 342 GLU cc_start: 0.8613 (mp0) cc_final: 0.7952 (pm20) REVERT: h 348 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8464 (pttm) REVERT: h 388 HIS cc_start: 0.9419 (t-90) cc_final: 0.8981 (t70) REVERT: h 397 GLU cc_start: 0.8750 (pp20) cc_final: 0.8392 (pp20) REVERT: h 411 ASP cc_start: 0.8993 (m-30) cc_final: 0.8589 (m-30) REVERT: g 12 SER cc_start: 0.9422 (m) cc_final: 0.9128 (p) REVERT: g 92 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7826 (pmm-80) REVERT: g 145 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8729 (mt) REVERT: g 218 GLU cc_start: 0.8953 (tp30) cc_final: 0.8297 (tp30) REVERT: g 244 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8475 (mm-30) REVERT: f 30 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7342 (mtm110) REVERT: f 92 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8106 (pmm-80) REVERT: f 207 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8393 (tt) REVERT: f 211 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8227 (mm-30) REVERT: f 226 GLU cc_start: 0.8424 (tt0) cc_final: 0.8014 (tt0) REVERT: f 244 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8361 (mm-30) REVERT: f 351 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8560 (mm-30) REVERT: e 12 SER cc_start: 0.9595 (m) cc_final: 0.9236 (p) REVERT: e 58 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9002 (mt) REVERT: e 67 SER cc_start: 0.8941 (m) cc_final: 0.8497 (p) REVERT: e 70 SER cc_start: 0.9169 (t) cc_final: 0.8845 (m) REVERT: e 264 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (tt) REVERT: e 299 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8163 (mtm-85) REVERT: e 333 GLU cc_start: 0.9030 (tp30) cc_final: 0.8737 (tp30) REVERT: e 334 GLU cc_start: 0.8845 (tp30) cc_final: 0.8612 (tm-30) REVERT: e 341 MET cc_start: 0.9058 (tmt) cc_final: 0.8704 (tmm) REVERT: e 406 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (p) REVERT: e 407 LYS cc_start: 0.9030 (tppt) cc_final: 0.8777 (tppt) REVERT: d 5 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: d 12 SER cc_start: 0.9508 (m) cc_final: 0.9294 (p) REVERT: d 244 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8100 (mm-30) REVERT: d 333 GLU cc_start: 0.9079 (tp30) cc_final: 0.8534 (mm-30) REVERT: d 352 LYS cc_start: 0.9006 (tppt) cc_final: 0.8495 (tptp) REVERT: d 362 ARG cc_start: 0.9257 (ttm110) cc_final: 0.8945 (ttm110) REVERT: d 417 LYS cc_start: 0.9211 (ptmm) cc_final: 0.8903 (ptpp) REVERT: c 19 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8885 (tp30) REVERT: c 67 SER cc_start: 0.8925 (m) cc_final: 0.8539 (p) REVERT: c 197 TYR cc_start: 0.9178 (t80) cc_final: 0.8952 (t80) REVERT: c 244 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8107 (mm-30) REVERT: c 248 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8916 (mm-30) REVERT: c 341 MET cc_start: 0.9115 (tmm) cc_final: 0.8797 (tmm) REVERT: c 411 ASP cc_start: 0.9069 (m-30) cc_final: 0.8710 (m-30) REVERT: b 92 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7879 (pmm-80) REVERT: b 193 GLN cc_start: 0.8743 (tt0) cc_final: 0.8472 (tm-30) REVERT: b 218 GLU cc_start: 0.9126 (tp30) cc_final: 0.8732 (tp30) REVERT: b 292 ASN cc_start: 0.8916 (m110) cc_final: 0.8656 (p0) REVERT: b 329 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8573 (mm-30) REVERT: b 334 GLU cc_start: 0.9052 (tp30) cc_final: 0.8743 (tm-30) REVERT: b 351 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8447 (mt-10) REVERT: b 374 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8491 (tp40) REVERT: b 378 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8902 (mt0) outliers start: 281 outliers final: 184 residues processed: 1208 average time/residue: 0.5836 time to fit residues: 1174.1982 Evaluate side-chains 1152 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 937 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 89 PHE Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 204 LEU Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 58 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 172 GLN Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 254 VAL Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 380 MET Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 89 PHE Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 253 LEU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 318 THR Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 194 SER Chi-restraints excluded: chain m residue 373 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 89 PHE Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain j residue 342 GLU Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 89 PHE Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 265 ASP Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 373 THR Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 194 SER Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain f residue 415 MET Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 354 VAL Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 327 MET Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 89 PHE Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 132 LEU Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 521 optimal weight: 1.9990 chunk 404 optimal weight: 7.9990 chunk 601 optimal weight: 0.9990 chunk 398 optimal weight: 2.9990 chunk 711 optimal weight: 10.0000 chunk 445 optimal weight: 0.5980 chunk 433 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS a 374 GLN ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 189 GLN ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 378 GLN m 374 GLN l 220 GLN j 189 GLN j 193 GLN i 25 ASN h 220 GLN e 374 GLN d 220 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 60822 Z= 0.202 Angle : 0.641 9.021 82008 Z= 0.309 Chirality : 0.042 0.177 9324 Planarity : 0.004 0.046 10620 Dihedral : 6.629 170.651 8431 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.73 % Allowed : 27.75 % Favored : 68.52 % 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: 1.38 (0.10), residues: 7506 helix: 1.88 (0.09), residues: 3492 sheet: 0.42 (0.16), residues: 1170 loop : 0.01 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 381 HIS 0.010 0.001 HIS a 295 PHE 0.023 0.001 PHE r 398 TYR 0.020 0.002 TYR p 197 ARG 0.012 0.000 ARG e 362 *********************** 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 1260 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1018 time to evaluate : 5.542 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: a 92 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8500 (mmt180) REVERT: a 147 MET cc_start: 0.9381 (tpp) cc_final: 0.8814 (mmm) REVERT: a 197 TYR cc_start: 0.9022 (t80) cc_final: 0.8659 (t80) REVERT: a 264 LEU cc_start: 0.9123 (tm) cc_final: 0.8911 (tt) REVERT: a 362 ARG cc_start: 0.9261 (ttm110) cc_final: 0.8797 (mtm-85) REVERT: r 21 MET cc_start: 0.9055 (ttm) cc_final: 0.8730 (ttt) REVERT: r 85 GLN cc_start: 0.8985 (mt0) cc_final: 0.8494 (mp10) REVERT: r 248 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8816 (mm-30) REVERT: r 265 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8645 (p0) REVERT: r 292 ASN cc_start: 0.8949 (m110) cc_final: 0.8381 (p0) REVERT: r 327 MET cc_start: 0.8839 (ppp) cc_final: 0.8606 (ppp) REVERT: q 33 ASP cc_start: 0.9125 (m-30) cc_final: 0.8751 (m-30) REVERT: q 147 MET cc_start: 0.8884 (tpp) cc_final: 0.8669 (tpp) REVERT: q 172 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8593 (tp40) REVERT: q 186 MET cc_start: 0.8668 (ptt) cc_final: 0.8253 (ppp) REVERT: q 253 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9349 (mm) REVERT: q 333 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8887 (mm-30) REVERT: q 334 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8630 (tm-30) REVERT: q 342 GLU cc_start: 0.8561 (mp0) cc_final: 0.8354 (mp0) REVERT: q 360 TYR cc_start: 0.9251 (t80) cc_final: 0.8985 (t80) REVERT: q 390 MET cc_start: 0.8613 (pmm) cc_final: 0.8408 (pmm) REVERT: p 60 ASP cc_start: 0.8895 (m-30) cc_final: 0.8599 (m-30) REVERT: p 186 MET cc_start: 0.9246 (ptm) cc_final: 0.8984 (ptt) REVERT: p 244 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8263 (mm-30) REVERT: p 248 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: p 333 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8959 (mm-30) REVERT: p 378 GLN cc_start: 0.9379 (mt0) cc_final: 0.9085 (mm-40) REVERT: p 390 MET cc_start: 0.9291 (pmm) cc_final: 0.9048 (pmm) REVERT: o 59 GLN cc_start: 0.8857 (pm20) cc_final: 0.8629 (tp40) REVERT: o 105 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8045 (tmmt) REVERT: o 115 LYS cc_start: 0.9138 (tmmt) cc_final: 0.8893 (ptmm) REVERT: o 128 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8833 (ptp-110) REVERT: o 218 GLU cc_start: 0.9154 (tp30) cc_final: 0.8831 (tp30) REVERT: o 234 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7678 (mp0) REVERT: o 244 GLU cc_start: 0.8645 (mm-30) cc_final: 0.7929 (mm-30) REVERT: o 248 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: o 264 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8294 (tt) REVERT: o 333 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8927 (mm-30) REVERT: o 334 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8646 (tm-30) REVERT: n 5 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8866 (pm20) REVERT: n 147 MET cc_start: 0.9467 (tpp) cc_final: 0.8890 (mmm) REVERT: n 197 TYR cc_start: 0.9169 (t80) cc_final: 0.8899 (t80) REVERT: n 226 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: n 326 LYS cc_start: 0.8297 (tptp) cc_final: 0.8027 (tptp) REVERT: n 334 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8296 (tm-30) REVERT: n 342 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: n 397 GLU cc_start: 0.8980 (pp20) cc_final: 0.8706 (pp20) REVERT: m 21 MET cc_start: 0.8463 (ttm) cc_final: 0.8173 (ttt) REVERT: m 67 SER cc_start: 0.8844 (m) cc_final: 0.8374 (p) REVERT: m 69 ASP cc_start: 0.9071 (t0) cc_final: 0.8802 (t70) REVERT: m 92 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8112 (pmm-80) REVERT: m 193 GLN cc_start: 0.8779 (tt0) cc_final: 0.8351 (tm-30) REVERT: m 197 TYR cc_start: 0.9300 (t80) cc_final: 0.8979 (t80) REVERT: m 226 GLU cc_start: 0.8475 (tp30) cc_final: 0.8076 (tt0) REVERT: m 244 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8435 (mm-30) REVERT: m 327 MET cc_start: 0.8743 (ptm) cc_final: 0.8475 (ttp) REVERT: m 378 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9189 (mm-40) REVERT: m 390 MET cc_start: 0.9492 (ptp) cc_final: 0.9270 (ptm) REVERT: m 414 GLU cc_start: 0.8909 (pp20) cc_final: 0.8685 (pp20) REVERT: l 92 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7847 (pmm-80) REVERT: l 125 GLU cc_start: 0.9103 (mp0) cc_final: 0.8754 (mp0) REVERT: l 218 GLU cc_start: 0.8839 (tp30) cc_final: 0.8535 (tp30) REVERT: l 224 LYS cc_start: 0.9517 (ttpt) cc_final: 0.9308 (mtpp) REVERT: l 244 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8551 (mm-30) REVERT: l 245 MET cc_start: 0.9219 (tpp) cc_final: 0.9010 (mmm) REVERT: l 253 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9150 (mt) REVERT: l 333 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: l 334 GLU cc_start: 0.8929 (tp30) cc_final: 0.8640 (tp30) REVERT: l 342 GLU cc_start: 0.8687 (mp0) cc_final: 0.8443 (mt-10) REVERT: l 374 GLN cc_start: 0.8472 (tp40) cc_final: 0.8089 (tp40) REVERT: l 378 GLN cc_start: 0.8882 (mt0) cc_final: 0.8476 (mm-40) REVERT: l 406 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8643 (p) REVERT: k 5 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8873 (pm20) REVERT: k 218 GLU cc_start: 0.8869 (tp30) cc_final: 0.8566 (tt0) REVERT: k 244 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8230 (mm-30) REVERT: k 264 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8462 (tt) REVERT: k 294 LEU cc_start: 0.9331 (tp) cc_final: 0.9123 (tt) REVERT: k 374 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7765 (tm-30) REVERT: k 378 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9125 (mm-40) REVERT: k 418 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8359 (tmm160) REVERT: j 218 GLU cc_start: 0.8889 (tp30) cc_final: 0.8646 (tt0) REVERT: j 326 LYS cc_start: 0.7752 (tmmt) cc_final: 0.7549 (tmtt) REVERT: j 374 GLN cc_start: 0.8288 (tp-100) cc_final: 0.8019 (tp40) REVERT: j 378 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8976 (mm-40) REVERT: j 410 ASP cc_start: 0.9379 (m-30) cc_final: 0.8958 (t0) REVERT: j 411 ASP cc_start: 0.9170 (m-30) cc_final: 0.8875 (m-30) REVERT: i 13 GLU cc_start: 0.8801 (pm20) cc_final: 0.8524 (pm20) REVERT: i 19 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8440 (mm-30) REVERT: i 23 LEU cc_start: 0.8738 (mt) cc_final: 0.8378 (mt) REVERT: i 67 SER cc_start: 0.8935 (m) cc_final: 0.8497 (p) REVERT: i 197 TYR cc_start: 0.9232 (t80) cc_final: 0.8999 (t80) REVERT: i 272 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8715 (mmm-85) REVERT: i 329 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8420 (mm-30) REVERT: i 342 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8527 (mt-10) REVERT: i 374 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8003 (tp40) REVERT: i 378 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8940 (mm-40) REVERT: i 397 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8805 (mt-10) REVERT: h 32 GLN cc_start: 0.9041 (mp10) cc_final: 0.8760 (mp10) REVERT: h 226 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: h 326 LYS cc_start: 0.8630 (mppt) cc_final: 0.8330 (mmmt) REVERT: h 341 MET cc_start: 0.9007 (tmm) cc_final: 0.8670 (tmm) REVERT: h 348 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8407 (pttm) REVERT: h 374 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8485 (tp40) REVERT: h 397 GLU cc_start: 0.8762 (pp20) cc_final: 0.8410 (pp20) REVERT: h 411 ASP cc_start: 0.8967 (m-30) cc_final: 0.8523 (m-30) REVERT: g 12 SER cc_start: 0.9406 (m) cc_final: 0.9103 (p) REVERT: g 92 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7865 (pmm-80) REVERT: g 145 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8618 (mt) REVERT: g 147 MET cc_start: 0.9467 (mmp) cc_final: 0.9220 (mmp) REVERT: g 218 GLU cc_start: 0.8917 (tp30) cc_final: 0.8679 (tt0) REVERT: g 244 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8454 (mm-30) REVERT: g 327 MET cc_start: 0.8728 (ptm) cc_final: 0.8368 (ttp) REVERT: f 207 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8372 (tt) REVERT: f 211 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8220 (mm-30) REVERT: f 226 GLU cc_start: 0.8452 (tt0) cc_final: 0.8052 (tt0) REVERT: f 244 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8419 (mm-30) REVERT: f 351 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8584 (mm-30) REVERT: e 12 SER cc_start: 0.9583 (m) cc_final: 0.9302 (p) REVERT: e 58 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8989 (mt) REVERT: e 67 SER cc_start: 0.8944 (m) cc_final: 0.8471 (p) REVERT: e 70 SER cc_start: 0.9124 (t) cc_final: 0.8801 (m) REVERT: e 244 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8270 (mm-30) REVERT: e 264 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8660 (tt) REVERT: e 333 GLU cc_start: 0.9012 (tp30) cc_final: 0.8697 (tp30) REVERT: e 334 GLU cc_start: 0.8817 (tp30) cc_final: 0.8610 (tm-30) REVERT: e 341 MET cc_start: 0.9042 (tmt) cc_final: 0.8667 (tmm) REVERT: e 362 ARG cc_start: 0.9285 (ttm110) cc_final: 0.9046 (mtm-85) REVERT: e 406 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8612 (p) REVERT: e 407 LYS cc_start: 0.9064 (tppt) cc_final: 0.8809 (tppt) REVERT: d 5 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: d 12 SER cc_start: 0.9495 (m) cc_final: 0.9289 (p) REVERT: d 244 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7967 (mm-30) REVERT: d 333 GLU cc_start: 0.9065 (tp30) cc_final: 0.8516 (mm-30) REVERT: d 352 LYS cc_start: 0.9006 (tppt) cc_final: 0.8603 (tptp) REVERT: d 417 LYS cc_start: 0.9200 (ptmm) cc_final: 0.8886 (ptpp) REVERT: c 19 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8892 (tp30) REVERT: c 67 SER cc_start: 0.8916 (m) cc_final: 0.8501 (p) REVERT: c 244 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8051 (mm-30) REVERT: c 248 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (mm-30) REVERT: c 341 MET cc_start: 0.9117 (tmm) cc_final: 0.8788 (tmm) REVERT: c 397 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8421 (mt-10) REVERT: c 411 ASP cc_start: 0.9032 (m-30) cc_final: 0.8704 (t0) REVERT: b 29 MET cc_start: 0.8999 (ttp) cc_final: 0.8387 (ttt) REVERT: b 59 GLN cc_start: 0.8740 (pm20) cc_final: 0.8458 (pm20) REVERT: b 92 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7788 (pmm-80) REVERT: b 101 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9106 (mp) REVERT: b 193 GLN cc_start: 0.8742 (tt0) cc_final: 0.8468 (tm-30) REVERT: b 218 GLU cc_start: 0.9109 (tp30) cc_final: 0.8721 (tp30) REVERT: b 292 ASN cc_start: 0.8886 (m110) cc_final: 0.8629 (p0) REVERT: b 329 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8595 (mm-30) REVERT: b 334 GLU cc_start: 0.9046 (tp30) cc_final: 0.8719 (tm-30) REVERT: b 351 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8449 (mt-10) REVERT: b 374 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8393 (tp40) REVERT: b 378 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8867 (mt0) outliers start: 242 outliers final: 165 residues processed: 1203 average time/residue: 0.5735 time to fit residues: 1154.9439 Evaluate side-chains 1163 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 966 time to evaluate : 5.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 274 TYR Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 89 PHE Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 172 GLN Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 354 VAL Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain o residue 400 ILE Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 194 SER Chi-restraints excluded: chain m residue 265 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 253 LEU Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain l residue 415 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 194 SER Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain i residue 417 LYS Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 393 ILE Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 194 SER Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 424 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 452 optimal weight: 0.9990 chunk 484 optimal weight: 1.9990 chunk 351 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 559 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 140 HIS a 295 HIS a 374 GLN ** r 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 GLN ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 193 GLN n 256 HIS m 374 GLN j 193 GLN h 220 GLN e 374 GLN d 189 GLN d 193 GLN d 220 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 60822 Z= 0.228 Angle : 0.654 11.973 82008 Z= 0.316 Chirality : 0.042 0.178 9324 Planarity : 0.004 0.078 10620 Dihedral : 6.475 162.520 8419 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.69 % Allowed : 27.84 % Favored : 68.47 % 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: 1.37 (0.10), residues: 7506 helix: 1.87 (0.09), residues: 3492 sheet: 0.42 (0.16), residues: 1170 loop : -0.00 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 381 HIS 0.012 0.001 HIS a 295 PHE 0.020 0.001 PHE r 398 TYR 0.021 0.002 TYR p 332 ARG 0.013 0.001 ARG q 347 *********************** 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 1223 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 984 time to evaluate : 5.473 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: a 92 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8503 (mmt180) REVERT: a 147 MET cc_start: 0.9389 (tpp) cc_final: 0.8794 (mmm) REVERT: a 197 TYR cc_start: 0.9022 (t80) cc_final: 0.8661 (t80) REVERT: a 264 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8889 (tt) REVERT: a 328 ASP cc_start: 0.8926 (m-30) cc_final: 0.8672 (m-30) REVERT: a 362 ARG cc_start: 0.9254 (ttm110) cc_final: 0.8863 (mtm-85) REVERT: a 410 ASP cc_start: 0.9251 (p0) cc_final: 0.9023 (p0) REVERT: a 411 ASP cc_start: 0.9293 (m-30) cc_final: 0.8907 (m-30) REVERT: r 21 MET cc_start: 0.9056 (ttm) cc_final: 0.8726 (ttt) REVERT: r 186 MET cc_start: 0.8844 (ptp) cc_final: 0.8188 (pmm) REVERT: r 248 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8816 (mm-30) REVERT: r 265 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8588 (p0) REVERT: r 292 ASN cc_start: 0.8942 (m110) cc_final: 0.8380 (p0) REVERT: q 33 ASP cc_start: 0.9110 (m-30) cc_final: 0.8618 (m-30) REVERT: q 186 MET cc_start: 0.8714 (ptt) cc_final: 0.8272 (ppp) REVERT: q 253 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9355 (mm) REVERT: q 333 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8896 (mm-30) REVERT: q 334 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8625 (tm-30) REVERT: q 360 TYR cc_start: 0.9276 (t80) cc_final: 0.9017 (t80) REVERT: q 390 MET cc_start: 0.8606 (pmm) cc_final: 0.8400 (pmm) REVERT: p 60 ASP cc_start: 0.8900 (m-30) cc_final: 0.8596 (m-30) REVERT: p 186 MET cc_start: 0.9204 (ptm) cc_final: 0.8971 (ptt) REVERT: p 244 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8255 (mm-30) REVERT: p 248 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8749 (mp0) REVERT: p 333 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8929 (mm-30) REVERT: p 334 GLU cc_start: 0.8865 (tp30) cc_final: 0.8624 (tm-30) REVERT: p 390 MET cc_start: 0.9296 (pmm) cc_final: 0.9053 (pmm) REVERT: p 415 MET cc_start: 0.9357 (mtm) cc_final: 0.9011 (mtp) REVERT: o 105 LYS cc_start: 0.8522 (tmmt) cc_final: 0.8089 (tmmt) REVERT: o 115 LYS cc_start: 0.9141 (tmmt) cc_final: 0.8892 (ptmm) REVERT: o 128 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8807 (ptp-110) REVERT: o 218 GLU cc_start: 0.9157 (tp30) cc_final: 0.8835 (tp30) REVERT: o 234 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7668 (mp0) REVERT: o 244 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7864 (mm-30) REVERT: o 248 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: o 264 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (tt) REVERT: o 333 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8939 (mm-30) REVERT: o 334 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8641 (tm-30) REVERT: o 374 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8367 (tm-30) REVERT: n 5 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8849 (pm20) REVERT: n 147 MET cc_start: 0.9469 (tpp) cc_final: 0.8890 (mmm) REVERT: n 197 TYR cc_start: 0.9173 (t80) cc_final: 0.8912 (t80) REVERT: n 226 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: n 334 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8285 (tm-30) REVERT: n 342 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: n 383 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9273 (tm) REVERT: n 397 GLU cc_start: 0.8984 (pp20) cc_final: 0.8715 (pp20) REVERT: m 21 MET cc_start: 0.8459 (ttm) cc_final: 0.8177 (ttt) REVERT: m 67 SER cc_start: 0.8801 (m) cc_final: 0.8341 (p) REVERT: m 69 ASP cc_start: 0.9068 (t0) cc_final: 0.8799 (t70) REVERT: m 92 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8132 (pmm-80) REVERT: m 197 TYR cc_start: 0.9310 (t80) cc_final: 0.9022 (t80) REVERT: m 226 GLU cc_start: 0.8484 (tp30) cc_final: 0.8096 (tt0) REVERT: m 244 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8428 (mm-30) REVERT: m 327 MET cc_start: 0.8748 (ptm) cc_final: 0.8451 (ttp) REVERT: m 378 GLN cc_start: 0.9406 (mm-40) cc_final: 0.9190 (mm-40) REVERT: m 390 MET cc_start: 0.9493 (ptp) cc_final: 0.9293 (ptm) REVERT: m 414 GLU cc_start: 0.8927 (pp20) cc_final: 0.8695 (pp20) REVERT: l 92 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7855 (pmm-80) REVERT: l 125 GLU cc_start: 0.9106 (mp0) cc_final: 0.8733 (mp0) REVERT: l 218 GLU cc_start: 0.8843 (tp30) cc_final: 0.8535 (tp30) REVERT: l 224 LYS cc_start: 0.9515 (ttpt) cc_final: 0.9304 (mtpp) REVERT: l 244 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8633 (mm-30) REVERT: l 245 MET cc_start: 0.9214 (tpp) cc_final: 0.8990 (mmm) REVERT: l 253 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9148 (mt) REVERT: l 333 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: l 334 GLU cc_start: 0.8929 (tp30) cc_final: 0.8613 (tp30) REVERT: l 342 GLU cc_start: 0.8696 (mp0) cc_final: 0.8393 (mt-10) REVERT: l 374 GLN cc_start: 0.8503 (tp40) cc_final: 0.8078 (tp40) REVERT: l 378 GLN cc_start: 0.8895 (mt0) cc_final: 0.8474 (mm-40) REVERT: l 406 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8647 (p) REVERT: k 2 ASN cc_start: 0.8878 (t0) cc_final: 0.8487 (t0) REVERT: k 5 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: k 218 GLU cc_start: 0.8856 (tp30) cc_final: 0.8555 (tt0) REVERT: k 244 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8197 (mm-30) REVERT: k 264 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8450 (tt) REVERT: k 374 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7744 (tm-30) REVERT: k 378 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9127 (mm-40) REVERT: j 218 GLU cc_start: 0.8881 (tp30) cc_final: 0.8648 (tt0) REVERT: j 374 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7969 (tp40) REVERT: j 378 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8976 (mm-40) REVERT: j 410 ASP cc_start: 0.9370 (m-30) cc_final: 0.8966 (t0) REVERT: j 411 ASP cc_start: 0.9181 (m-30) cc_final: 0.8904 (m-30) REVERT: i 13 GLU cc_start: 0.8795 (pm20) cc_final: 0.8517 (pm20) REVERT: i 19 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8475 (mm-30) REVERT: i 23 LEU cc_start: 0.8760 (mt) cc_final: 0.8399 (mt) REVERT: i 67 SER cc_start: 0.8918 (m) cc_final: 0.8478 (p) REVERT: i 197 TYR cc_start: 0.9244 (t80) cc_final: 0.9026 (t80) REVERT: i 272 ARG cc_start: 0.9118 (mmm-85) cc_final: 0.8719 (mmm-85) REVERT: i 329 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8415 (mm-30) REVERT: i 342 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8543 (mt-10) REVERT: i 374 GLN cc_start: 0.8428 (tp-100) cc_final: 0.7866 (tp40) REVERT: i 378 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8924 (mm-40) REVERT: i 397 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8807 (mt-10) REVERT: h 32 GLN cc_start: 0.9066 (mp10) cc_final: 0.8788 (mp10) REVERT: h 226 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: h 292 ASN cc_start: 0.8834 (m110) cc_final: 0.8610 (p0) REVERT: h 326 LYS cc_start: 0.8636 (mppt) cc_final: 0.8336 (mmmt) REVERT: h 341 MET cc_start: 0.9025 (tmm) cc_final: 0.8692 (tmm) REVERT: h 348 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8405 (pttm) REVERT: h 411 ASP cc_start: 0.8926 (m-30) cc_final: 0.8530 (m-30) REVERT: g 12 SER cc_start: 0.9404 (m) cc_final: 0.9104 (p) REVERT: g 92 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7839 (pmm-80) REVERT: g 145 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8673 (mt) REVERT: g 218 GLU cc_start: 0.8918 (tp30) cc_final: 0.8687 (tt0) REVERT: g 244 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8444 (mm-30) REVERT: g 327 MET cc_start: 0.8741 (ptm) cc_final: 0.8382 (ttp) REVERT: g 407 LYS cc_start: 0.9286 (tppt) cc_final: 0.8986 (tppt) REVERT: f 207 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8381 (tt) REVERT: f 211 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8218 (mm-30) REVERT: f 226 GLU cc_start: 0.8451 (tt0) cc_final: 0.8067 (tt0) REVERT: f 244 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8373 (mm-30) REVERT: f 342 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: f 351 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8558 (mm-30) REVERT: e 12 SER cc_start: 0.9583 (m) cc_final: 0.9304 (p) REVERT: e 58 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8992 (mt) REVERT: e 67 SER cc_start: 0.8940 (m) cc_final: 0.8464 (p) REVERT: e 70 SER cc_start: 0.9144 (t) cc_final: 0.8804 (m) REVERT: e 244 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8251 (mm-30) REVERT: e 264 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8604 (tt) REVERT: e 333 GLU cc_start: 0.9016 (tp30) cc_final: 0.8678 (tp30) REVERT: e 334 GLU cc_start: 0.8809 (tp30) cc_final: 0.8570 (tm-30) REVERT: e 341 MET cc_start: 0.9050 (tmt) cc_final: 0.8685 (tmm) REVERT: e 362 ARG cc_start: 0.9285 (ttm110) cc_final: 0.9043 (mtm-85) REVERT: e 406 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8591 (p) REVERT: e 407 LYS cc_start: 0.9069 (tppt) cc_final: 0.8815 (tppt) REVERT: d 5 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8769 (pm20) REVERT: d 12 SER cc_start: 0.9496 (m) cc_final: 0.9295 (p) REVERT: d 244 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8034 (mm-30) REVERT: d 333 GLU cc_start: 0.9066 (tp30) cc_final: 0.8593 (mm-30) REVERT: d 342 GLU cc_start: 0.8672 (mp0) cc_final: 0.8131 (mp0) REVERT: d 352 LYS cc_start: 0.9062 (tppt) cc_final: 0.8668 (tptp) REVERT: d 417 LYS cc_start: 0.9202 (ptmm) cc_final: 0.8892 (ptpp) REVERT: c 19 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8878 (tp30) REVERT: c 67 SER cc_start: 0.8911 (m) cc_final: 0.8495 (p) REVERT: c 197 TYR cc_start: 0.9198 (t80) cc_final: 0.8992 (t80) REVERT: c 244 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8104 (mm-30) REVERT: c 248 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8895 (mm-30) REVERT: c 341 MET cc_start: 0.9124 (tmm) cc_final: 0.8778 (tmm) REVERT: c 397 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8403 (mt-10) REVERT: c 411 ASP cc_start: 0.9035 (m-30) cc_final: 0.8708 (t0) REVERT: b 59 GLN cc_start: 0.8725 (pm20) cc_final: 0.8444 (pm20) REVERT: b 92 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7794 (pmm-80) REVERT: b 101 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9100 (mp) REVERT: b 193 GLN cc_start: 0.8746 (tt0) cc_final: 0.8475 (tm-30) REVERT: b 218 GLU cc_start: 0.9101 (tp30) cc_final: 0.8717 (tp30) REVERT: b 292 ASN cc_start: 0.8863 (m110) cc_final: 0.8623 (p0) REVERT: b 329 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8593 (mm-30) REVERT: b 334 GLU cc_start: 0.9039 (tp30) cc_final: 0.8740 (tm-30) REVERT: b 351 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8460 (mt-10) REVERT: b 374 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8391 (tp40) REVERT: b 378 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8899 (mt0) outliers start: 239 outliers final: 172 residues processed: 1161 average time/residue: 0.5635 time to fit residues: 1095.8087 Evaluate side-chains 1158 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 952 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 204 LEU Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 92 ARG Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 193 GLN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 194 SER Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 253 LEU Chi-restraints excluded: chain l residue 333 GLU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain l residue 415 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 390 MET Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 92 ARG Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 393 ILE Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 265 ASP Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 194 SER Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 333 GLU Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 325 SER Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 205 MET Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 0.8980 chunk 681 optimal weight: 4.9990 chunk 621 optimal weight: 8.9990 chunk 662 optimal weight: 10.0000 chunk 398 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 520 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 598 optimal weight: 2.9990 chunk 626 optimal weight: 3.9990 chunk 660 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS a 374 GLN ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 256 HIS n 378 GLN j 193 GLN e 374 GLN d 193 GLN d 220 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 60822 Z= 0.287 Angle : 0.679 11.037 82008 Z= 0.330 Chirality : 0.043 0.168 9324 Planarity : 0.004 0.048 10620 Dihedral : 6.431 154.044 8417 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.75 % Allowed : 27.78 % Favored : 68.47 % 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: 1.31 (0.10), residues: 7506 helix: 1.80 (0.09), residues: 3492 sheet: 0.38 (0.16), residues: 1170 loop : 0.01 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 381 HIS 0.012 0.001 HIS a 295 PHE 0.020 0.001 PHE r 398 TYR 0.022 0.002 TYR j 197 ARG 0.013 0.001 ARG k 418 *********************** 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 1184 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 941 time to evaluate : 5.868 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 32 GLN cc_start: 0.9171 (mp10) cc_final: 0.8849 (pm20) REVERT: a 92 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8480 (mmt180) REVERT: a 197 TYR cc_start: 0.9007 (t80) cc_final: 0.8622 (t80) REVERT: a 264 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8913 (tt) REVERT: a 328 ASP cc_start: 0.8943 (m-30) cc_final: 0.8696 (m-30) REVERT: a 362 ARG cc_start: 0.9244 (ttm110) cc_final: 0.8824 (mtm-85) REVERT: r 21 MET cc_start: 0.9058 (ttm) cc_final: 0.8770 (ttt) REVERT: r 248 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8806 (mm-30) REVERT: r 265 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8624 (p0) REVERT: r 292 ASN cc_start: 0.8974 (m110) cc_final: 0.8430 (p0) REVERT: r 415 MET cc_start: 0.7967 (ppp) cc_final: 0.7745 (ppp) REVERT: q 33 ASP cc_start: 0.9120 (m-30) cc_final: 0.8613 (m-30) REVERT: q 172 GLN cc_start: 0.8957 (tp40) cc_final: 0.8675 (tp40) REVERT: q 186 MET cc_start: 0.8668 (ptt) cc_final: 0.8285 (ppp) REVERT: q 253 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9378 (mm) REVERT: q 333 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8909 (mm-30) REVERT: q 334 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8653 (tm-30) REVERT: q 360 TYR cc_start: 0.9301 (t80) cc_final: 0.9022 (t80) REVERT: q 390 MET cc_start: 0.8619 (pmm) cc_final: 0.8402 (pmm) REVERT: p 60 ASP cc_start: 0.8891 (m-30) cc_final: 0.8580 (m-30) REVERT: p 186 MET cc_start: 0.9222 (ptm) cc_final: 0.8989 (ptt) REVERT: p 193 GLN cc_start: 0.9168 (tt0) cc_final: 0.8674 (tm-30) REVERT: p 244 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8366 (mm-30) REVERT: p 248 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8784 (mp0) REVERT: p 333 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8946 (mm-30) REVERT: p 334 GLU cc_start: 0.8872 (tp30) cc_final: 0.8588 (tm-30) REVERT: p 390 MET cc_start: 0.9266 (pmm) cc_final: 0.9026 (pmm) REVERT: o 105 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8097 (tmmt) REVERT: o 115 LYS cc_start: 0.9140 (tmmt) cc_final: 0.8908 (ptmm) REVERT: o 128 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8955 (ptm160) REVERT: o 218 GLU cc_start: 0.9171 (tp30) cc_final: 0.8862 (tp30) REVERT: o 234 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7687 (mp0) REVERT: o 244 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7920 (mm-30) REVERT: o 248 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: o 264 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8352 (tt) REVERT: o 333 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8939 (mm-30) REVERT: o 334 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8619 (tm-30) REVERT: n 5 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8840 (pm20) REVERT: n 147 MET cc_start: 0.9444 (tpp) cc_final: 0.8874 (mmm) REVERT: n 197 TYR cc_start: 0.9182 (t80) cc_final: 0.8977 (t80) REVERT: n 226 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: n 326 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8502 (tptp) REVERT: n 334 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8274 (tm-30) REVERT: n 342 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: n 383 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9269 (tm) REVERT: n 397 GLU cc_start: 0.9006 (pp20) cc_final: 0.8725 (pp20) REVERT: n 407 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8988 (tppt) REVERT: m 21 MET cc_start: 0.8480 (ttm) cc_final: 0.8096 (ttt) REVERT: m 67 SER cc_start: 0.8790 (m) cc_final: 0.8361 (p) REVERT: m 69 ASP cc_start: 0.9117 (t0) cc_final: 0.8875 (t70) REVERT: m 92 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (pmm-80) REVERT: m 193 GLN cc_start: 0.8784 (tt0) cc_final: 0.8379 (tm-30) REVERT: m 197 TYR cc_start: 0.9311 (t80) cc_final: 0.8993 (t80) REVERT: m 226 GLU cc_start: 0.8439 (tp30) cc_final: 0.8041 (tt0) REVERT: m 244 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8391 (mm-30) REVERT: m 327 MET cc_start: 0.8764 (ptm) cc_final: 0.8469 (ttp) REVERT: m 378 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9183 (mm-40) REVERT: l 29 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8081 (ptm) REVERT: l 92 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7846 (pmm-80) REVERT: l 125 GLU cc_start: 0.9103 (mp0) cc_final: 0.8723 (mp0) REVERT: l 144 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (ttt90) REVERT: l 218 GLU cc_start: 0.8866 (tp30) cc_final: 0.8560 (tp30) REVERT: l 224 LYS cc_start: 0.9523 (ttpt) cc_final: 0.9317 (mtpp) REVERT: l 244 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8581 (mm-30) REVERT: l 245 MET cc_start: 0.9216 (tpp) cc_final: 0.8988 (mmm) REVERT: l 253 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9159 (mt) REVERT: l 334 GLU cc_start: 0.8943 (tp30) cc_final: 0.8590 (tp30) REVERT: l 342 GLU cc_start: 0.8703 (mp0) cc_final: 0.8367 (mt-10) REVERT: l 374 GLN cc_start: 0.8552 (tp40) cc_final: 0.8112 (tp40) REVERT: l 378 GLN cc_start: 0.8899 (mt0) cc_final: 0.8473 (mm-40) REVERT: l 406 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8688 (p) REVERT: k 5 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8871 (pm20) REVERT: k 218 GLU cc_start: 0.8846 (tp30) cc_final: 0.8554 (tt0) REVERT: k 264 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8458 (tt) REVERT: k 374 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7906 (tm-30) REVERT: j 164 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8912 (mm) REVERT: j 218 GLU cc_start: 0.8888 (tp30) cc_final: 0.8659 (tt0) REVERT: j 374 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7978 (tp40) REVERT: j 378 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8961 (mm-40) REVERT: j 410 ASP cc_start: 0.9391 (m-30) cc_final: 0.8995 (t0) REVERT: j 411 ASP cc_start: 0.9211 (m-30) cc_final: 0.8928 (m-30) REVERT: i 13 GLU cc_start: 0.8803 (pm20) cc_final: 0.8548 (pm20) REVERT: i 19 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8515 (mm-30) REVERT: i 23 LEU cc_start: 0.8817 (mt) cc_final: 0.8485 (mt) REVERT: i 67 SER cc_start: 0.8916 (m) cc_final: 0.8498 (p) REVERT: i 197 TYR cc_start: 0.9251 (t80) cc_final: 0.9034 (t80) REVERT: i 272 ARG cc_start: 0.9136 (mmm-85) cc_final: 0.8648 (mmt90) REVERT: i 329 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8432 (mm-30) REVERT: i 374 GLN cc_start: 0.8508 (tp-100) cc_final: 0.7971 (tp40) REVERT: i 378 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8928 (mm-40) REVERT: i 397 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8792 (mt-10) REVERT: h 32 GLN cc_start: 0.9066 (mp10) cc_final: 0.8784 (mp10) REVERT: h 226 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: h 292 ASN cc_start: 0.8885 (m110) cc_final: 0.8649 (p0) REVERT: h 326 LYS cc_start: 0.8654 (mppt) cc_final: 0.8360 (mmmt) REVERT: h 341 MET cc_start: 0.9059 (tmm) cc_final: 0.8474 (tmm) REVERT: h 342 GLU cc_start: 0.8521 (mp0) cc_final: 0.8251 (mm-30) REVERT: h 348 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8338 (pttm) REVERT: h 351 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8340 (mm-30) REVERT: h 397 GLU cc_start: 0.8742 (pp20) cc_final: 0.8443 (pp20) REVERT: h 411 ASP cc_start: 0.8945 (m-30) cc_final: 0.8568 (m-30) REVERT: g 12 SER cc_start: 0.9418 (m) cc_final: 0.9125 (p) REVERT: g 92 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7867 (pmm-80) REVERT: g 145 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8704 (mt) REVERT: g 218 GLU cc_start: 0.8934 (tp30) cc_final: 0.8276 (tp30) REVERT: g 244 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8433 (mm-30) REVERT: g 327 MET cc_start: 0.8758 (ptm) cc_final: 0.8413 (ttp) REVERT: g 407 LYS cc_start: 0.9367 (tppt) cc_final: 0.9066 (tppt) REVERT: f 92 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (pmm-80) REVERT: f 207 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8387 (tt) REVERT: f 211 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8347 (mm-30) REVERT: f 226 GLU cc_start: 0.8414 (tt0) cc_final: 0.8021 (tt0) REVERT: f 244 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8367 (mm-30) REVERT: f 342 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: e 12 SER cc_start: 0.9607 (m) cc_final: 0.9267 (p) REVERT: e 58 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8983 (mt) REVERT: e 67 SER cc_start: 0.8934 (m) cc_final: 0.8475 (p) REVERT: e 70 SER cc_start: 0.9170 (t) cc_final: 0.8841 (m) REVERT: e 244 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8346 (mm-30) REVERT: e 264 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8608 (tt) REVERT: e 299 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: e 333 GLU cc_start: 0.9040 (tp30) cc_final: 0.8731 (tp30) REVERT: e 341 MET cc_start: 0.9051 (tmt) cc_final: 0.8701 (tmm) REVERT: e 406 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8647 (p) REVERT: e 407 LYS cc_start: 0.9090 (tppt) cc_final: 0.8839 (tppt) REVERT: d 5 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8757 (pm20) REVERT: d 92 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (pmm-80) REVERT: d 244 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8078 (mm-30) REVERT: d 333 GLU cc_start: 0.9069 (tp30) cc_final: 0.8604 (mm-30) REVERT: d 342 GLU cc_start: 0.8672 (mp0) cc_final: 0.8155 (mp0) REVERT: d 417 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8901 (ptpp) REVERT: c 19 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8862 (tp30) REVERT: c 67 SER cc_start: 0.8915 (m) cc_final: 0.8530 (p) REVERT: c 197 TYR cc_start: 0.9232 (t80) cc_final: 0.9020 (t80) REVERT: c 244 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8106 (mm-30) REVERT: c 248 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8949 (mm-30) REVERT: c 341 MET cc_start: 0.9135 (tmm) cc_final: 0.8763 (tmm) REVERT: c 397 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8367 (mt-10) REVERT: c 411 ASP cc_start: 0.9068 (m-30) cc_final: 0.8721 (t0) REVERT: b 29 MET cc_start: 0.9038 (ttp) cc_final: 0.8717 (ttp) REVERT: b 59 GLN cc_start: 0.8715 (pm20) cc_final: 0.8448 (pm20) REVERT: b 92 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7904 (pmm-80) REVERT: b 101 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9077 (mp) REVERT: b 193 GLN cc_start: 0.8742 (tt0) cc_final: 0.8479 (tm-30) REVERT: b 218 GLU cc_start: 0.9094 (tp30) cc_final: 0.8714 (tp30) REVERT: b 292 ASN cc_start: 0.8942 (m110) cc_final: 0.8691 (p0) REVERT: b 329 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8597 (mm-30) REVERT: b 334 GLU cc_start: 0.9042 (tp30) cc_final: 0.8728 (tm-30) REVERT: b 351 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8497 (mt-10) REVERT: b 374 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8342 (tp40) outliers start: 243 outliers final: 172 residues processed: 1127 average time/residue: 0.5737 time to fit residues: 1077.9112 Evaluate side-chains 1135 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 925 time to evaluate : 5.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 264 LEU Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 204 LEU Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 265 ASP Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 241 GLN Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 264 LEU Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 89 PHE Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain m residue 265 ASP Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 29 MET Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 144 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 253 LEU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 390 MET Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 164 LEU Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 241 GLN Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 393 ILE Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 265 ASP Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 194 SER Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain e residue 415 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 89 PHE Chi-restraints excluded: chain d residue 92 ARG Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 162 LEU Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 325 SER Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 23 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 205 MET Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 0.8980 chunk 700 optimal weight: 1.9990 chunk 427 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 487 optimal weight: 6.9990 chunk 735 optimal weight: 0.9990 chunk 676 optimal weight: 6.9990 chunk 585 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 452 optimal weight: 0.7980 chunk 358 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 189 GLN a 295 HIS r 140 HIS ** r 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 193 GLN m 374 GLN j 193 GLN h 374 GLN f 374 GLN e 374 GLN d 189 GLN d 193 GLN d 220 GLN b 388 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 60822 Z= 0.211 Angle : 0.677 13.238 82008 Z= 0.327 Chirality : 0.042 0.211 9324 Planarity : 0.004 0.057 10620 Dihedral : 6.236 149.594 8417 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.38 % Allowed : 28.30 % Favored : 68.32 % 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: 1.35 (0.10), residues: 7506 helix: 1.86 (0.09), residues: 3492 sheet: 0.41 (0.16), residues: 1170 loop : -0.02 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 381 HIS 0.008 0.001 HIS b 388 PHE 0.023 0.001 PHE r 398 TYR 0.021 0.002 TYR p 332 ARG 0.014 0.001 ARG e 362 ********************** 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 1185 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 966 time to evaluate : 5.429 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 92 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (mmt180) REVERT: a 197 TYR cc_start: 0.9012 (t80) cc_final: 0.8625 (t80) REVERT: a 362 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8839 (mtm-85) REVERT: r 21 MET cc_start: 0.9049 (ttm) cc_final: 0.8763 (ttt) REVERT: r 186 MET cc_start: 0.8846 (ptp) cc_final: 0.8266 (pmm) REVERT: r 241 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8978 (pp30) REVERT: r 248 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8787 (mm-30) REVERT: r 292 ASN cc_start: 0.8926 (m110) cc_final: 0.8403 (p0) REVERT: r 298 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8509 (tmtt) REVERT: r 327 MET cc_start: 0.8805 (ppp) cc_final: 0.8591 (ppp) REVERT: q 1 MET cc_start: 0.7033 (ttp) cc_final: 0.6284 (tpt) REVERT: q 33 ASP cc_start: 0.9118 (m-30) cc_final: 0.8606 (m-30) REVERT: q 172 GLN cc_start: 0.8898 (tp40) cc_final: 0.8589 (tp40) REVERT: q 186 MET cc_start: 0.8663 (ptt) cc_final: 0.8261 (ppp) REVERT: q 253 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9355 (mm) REVERT: q 333 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8932 (mm-30) REVERT: q 334 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8665 (tm-30) REVERT: q 360 TYR cc_start: 0.9297 (t80) cc_final: 0.9032 (t80) REVERT: q 390 MET cc_start: 0.8602 (pmm) cc_final: 0.8374 (pmm) REVERT: p 60 ASP cc_start: 0.8878 (m-30) cc_final: 0.8592 (m-30) REVERT: p 80 TYR cc_start: 0.9252 (t80) cc_final: 0.8781 (t80) REVERT: p 186 MET cc_start: 0.9206 (ptm) cc_final: 0.8887 (ptt) REVERT: p 189 GLN cc_start: 0.9323 (mt0) cc_final: 0.9003 (mt0) REVERT: p 193 GLN cc_start: 0.9160 (tt0) cc_final: 0.8671 (tm-30) REVERT: p 244 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8247 (mm-30) REVERT: p 248 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: p 333 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8916 (mm-30) REVERT: p 334 GLU cc_start: 0.8869 (tp30) cc_final: 0.8642 (tm-30) REVERT: p 390 MET cc_start: 0.9295 (pmm) cc_final: 0.9053 (pmm) REVERT: p 402 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9102 (mmtt) REVERT: o 105 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8162 (tmmt) REVERT: o 115 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8890 (ptmm) REVERT: o 128 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8820 (ptp-110) REVERT: o 218 GLU cc_start: 0.9174 (tp30) cc_final: 0.8852 (tp30) REVERT: o 234 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7652 (mp0) REVERT: o 244 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7858 (mm-30) REVERT: o 248 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: o 333 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8956 (mm-30) REVERT: o 334 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8633 (tm-30) REVERT: n 5 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8839 (pm20) REVERT: n 147 MET cc_start: 0.9436 (tpp) cc_final: 0.8853 (mmm) REVERT: n 197 TYR cc_start: 0.9167 (t80) cc_final: 0.8946 (t80) REVERT: n 226 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: n 326 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8447 (tptp) REVERT: n 334 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8259 (tm-30) REVERT: n 342 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: n 383 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9276 (tm) REVERT: n 397 GLU cc_start: 0.8976 (pp20) cc_final: 0.8702 (pp20) REVERT: m 21 MET cc_start: 0.8468 (ttm) cc_final: 0.8241 (ttt) REVERT: m 67 SER cc_start: 0.8799 (m) cc_final: 0.8341 (p) REVERT: m 69 ASP cc_start: 0.9081 (t0) cc_final: 0.8832 (t70) REVERT: m 92 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8134 (pmm-80) REVERT: m 193 GLN cc_start: 0.8779 (tt0) cc_final: 0.8387 (tm-30) REVERT: m 197 TYR cc_start: 0.9318 (t80) cc_final: 0.9025 (t80) REVERT: m 226 GLU cc_start: 0.8494 (tp30) cc_final: 0.8102 (tt0) REVERT: m 244 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8332 (mm-30) REVERT: m 327 MET cc_start: 0.8732 (ptm) cc_final: 0.8421 (ttp) REVERT: m 378 GLN cc_start: 0.9401 (mm-40) cc_final: 0.9108 (mm-40) REVERT: m 400 ILE cc_start: 0.9318 (mm) cc_final: 0.9112 (mm) REVERT: l 32 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8539 (mm-40) REVERT: l 92 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7855 (pmm-80) REVERT: l 125 GLU cc_start: 0.9103 (mp0) cc_final: 0.8723 (mp0) REVERT: l 144 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8582 (ttt90) REVERT: l 218 GLU cc_start: 0.8859 (tp30) cc_final: 0.8556 (tp30) REVERT: l 224 LYS cc_start: 0.9514 (ttpt) cc_final: 0.9301 (mtpp) REVERT: l 244 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8596 (mm-30) REVERT: l 245 MET cc_start: 0.9216 (tpp) cc_final: 0.9000 (mmm) REVERT: l 253 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9154 (mt) REVERT: l 334 GLU cc_start: 0.8925 (tp30) cc_final: 0.8599 (tp30) REVERT: l 342 GLU cc_start: 0.8692 (mp0) cc_final: 0.8397 (mt-10) REVERT: l 374 GLN cc_start: 0.8478 (tp40) cc_final: 0.8023 (tp40) REVERT: l 378 GLN cc_start: 0.8858 (mt0) cc_final: 0.8421 (mm-40) REVERT: l 406 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8635 (t) REVERT: k 2 ASN cc_start: 0.8904 (t0) cc_final: 0.8508 (t0) REVERT: k 5 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8796 (pm20) REVERT: k 218 GLU cc_start: 0.8849 (tp30) cc_final: 0.8546 (tt0) REVERT: k 244 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8271 (mm-30) REVERT: k 264 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8452 (tt) REVERT: k 374 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7831 (tm-30) REVERT: j 164 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8936 (mm) REVERT: j 218 GLU cc_start: 0.8875 (tp30) cc_final: 0.8639 (tt0) REVERT: j 374 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7932 (tp40) REVERT: j 378 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8983 (mm-40) REVERT: j 410 ASP cc_start: 0.9381 (m-30) cc_final: 0.8982 (t0) REVERT: j 411 ASP cc_start: 0.9186 (m-30) cc_final: 0.8872 (m-30) REVERT: i 13 GLU cc_start: 0.8814 (pm20) cc_final: 0.8547 (pm20) REVERT: i 19 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8513 (mm-30) REVERT: i 23 LEU cc_start: 0.8764 (mt) cc_final: 0.8400 (mt) REVERT: i 67 SER cc_start: 0.8933 (m) cc_final: 0.8499 (p) REVERT: i 193 GLN cc_start: 0.8895 (tt0) cc_final: 0.8615 (tt0) REVERT: i 197 TYR cc_start: 0.9244 (t80) cc_final: 0.9028 (t80) REVERT: i 272 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8706 (mmm-85) REVERT: i 329 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8453 (mm-30) REVERT: i 342 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8506 (mt-10) REVERT: i 374 GLN cc_start: 0.8403 (tp-100) cc_final: 0.7781 (tp40) REVERT: i 378 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8938 (mm-40) REVERT: i 397 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8801 (mt-10) REVERT: h 32 GLN cc_start: 0.9061 (mp10) cc_final: 0.8778 (mp10) REVERT: h 226 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: h 326 LYS cc_start: 0.8622 (mppt) cc_final: 0.8231 (tptp) REVERT: h 341 MET cc_start: 0.9034 (tmm) cc_final: 0.8702 (tmm) REVERT: h 348 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8342 (pttm) REVERT: h 374 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8418 (tp-100) REVERT: h 397 GLU cc_start: 0.8752 (pp20) cc_final: 0.8438 (pp20) REVERT: h 411 ASP cc_start: 0.8949 (m-30) cc_final: 0.8560 (m-30) REVERT: g 12 SER cc_start: 0.9406 (m) cc_final: 0.9112 (p) REVERT: g 92 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7848 (pmm-80) REVERT: g 145 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8675 (mt) REVERT: g 218 GLU cc_start: 0.8913 (tp30) cc_final: 0.8701 (tt0) REVERT: g 244 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8406 (mm-30) REVERT: g 327 MET cc_start: 0.8718 (ptm) cc_final: 0.8362 (ttp) REVERT: g 407 LYS cc_start: 0.9353 (tppt) cc_final: 0.9063 (tppt) REVERT: f 92 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8167 (pmm-80) REVERT: f 207 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8368 (tt) REVERT: f 211 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8224 (mm-30) REVERT: f 226 GLU cc_start: 0.8435 (tt0) cc_final: 0.8046 (tt0) REVERT: f 244 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8365 (mm-30) REVERT: f 342 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: f 351 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8592 (mm-30) REVERT: e 12 SER cc_start: 0.9594 (m) cc_final: 0.9245 (p) REVERT: e 58 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8992 (mt) REVERT: e 67 SER cc_start: 0.8939 (m) cc_final: 0.8447 (p) REVERT: e 70 SER cc_start: 0.9154 (t) cc_final: 0.8803 (m) REVERT: e 244 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8251 (mm-30) REVERT: e 264 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8615 (tt) REVERT: e 341 MET cc_start: 0.9033 (tmt) cc_final: 0.8666 (tmm) REVERT: e 406 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (p) REVERT: e 407 LYS cc_start: 0.9089 (tppt) cc_final: 0.8838 (tppt) REVERT: d 5 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8742 (pm20) REVERT: d 92 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8394 (pmm-80) REVERT: d 244 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8014 (mm-30) REVERT: d 333 GLU cc_start: 0.9064 (tp30) cc_final: 0.8591 (mm-30) REVERT: d 342 GLU cc_start: 0.8671 (mp0) cc_final: 0.8137 (mp0) REVERT: d 417 LYS cc_start: 0.9199 (ptmm) cc_final: 0.8877 (ptpp) REVERT: c 19 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8854 (tp30) REVERT: c 67 SER cc_start: 0.8914 (m) cc_final: 0.8502 (p) REVERT: c 197 TYR cc_start: 0.9254 (t80) cc_final: 0.8880 (t80) REVERT: c 244 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8105 (mm-30) REVERT: c 248 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: c 341 MET cc_start: 0.9145 (tmm) cc_final: 0.8784 (tmm) REVERT: c 397 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8363 (mt-10) REVERT: c 411 ASP cc_start: 0.9055 (m-30) cc_final: 0.8720 (t0) REVERT: b 29 MET cc_start: 0.9029 (ttp) cc_final: 0.8708 (ttp) REVERT: b 59 GLN cc_start: 0.8692 (pm20) cc_final: 0.8422 (pm20) REVERT: b 92 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7823 (pmm-80) REVERT: b 101 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9076 (mp) REVERT: b 193 GLN cc_start: 0.8745 (tt0) cc_final: 0.8471 (tm-30) REVERT: b 218 GLU cc_start: 0.9112 (tp30) cc_final: 0.8747 (tp30) REVERT: b 292 ASN cc_start: 0.8899 (m110) cc_final: 0.8657 (p0) REVERT: b 326 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8122 (tptp) REVERT: b 329 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8608 (mm-30) REVERT: b 334 GLU cc_start: 0.9031 (tp30) cc_final: 0.8774 (tm-30) REVERT: b 351 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8491 (mt-10) REVERT: b 374 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8448 (tp40) outliers start: 219 outliers final: 165 residues processed: 1134 average time/residue: 0.5732 time to fit residues: 1090.3910 Evaluate side-chains 1143 residues out of total 6480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 943 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 6 LEU Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 55 LEU Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 153 SER Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 295 HIS Chi-restraints excluded: chain a residue 327 MET Chi-restraints excluded: chain a residue 381 TRP Chi-restraints excluded: chain a residue 390 MET Chi-restraints excluded: chain a residue 401 ASN Chi-restraints excluded: chain r residue 58 LEU Chi-restraints excluded: chain r residue 101 ILE Chi-restraints excluded: chain r residue 116 VAL Chi-restraints excluded: chain r residue 153 SER Chi-restraints excluded: chain r residue 202 CYS Chi-restraints excluded: chain r residue 241 GLN Chi-restraints excluded: chain r residue 248 GLU Chi-restraints excluded: chain r residue 295 HIS Chi-restraints excluded: chain r residue 318 THR Chi-restraints excluded: chain r residue 376 GLU Chi-restraints excluded: chain r residue 398 PHE Chi-restraints excluded: chain q residue 6 LEU Chi-restraints excluded: chain q residue 80 TYR Chi-restraints excluded: chain q residue 92 ARG Chi-restraints excluded: chain q residue 116 VAL Chi-restraints excluded: chain q residue 137 THR Chi-restraints excluded: chain q residue 164 LEU Chi-restraints excluded: chain q residue 242 VAL Chi-restraints excluded: chain q residue 253 LEU Chi-restraints excluded: chain q residue 265 ASP Chi-restraints excluded: chain q residue 333 GLU Chi-restraints excluded: chain q residue 354 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 4 THR Chi-restraints excluded: chain p residue 116 VAL Chi-restraints excluded: chain p residue 241 GLN Chi-restraints excluded: chain p residue 242 VAL Chi-restraints excluded: chain p residue 248 GLU Chi-restraints excluded: chain p residue 292 ASN Chi-restraints excluded: chain p residue 333 GLU Chi-restraints excluded: chain p residue 401 ASN Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 116 VAL Chi-restraints excluded: chain o residue 128 ARG Chi-restraints excluded: chain o residue 186 MET Chi-restraints excluded: chain o residue 193 GLN Chi-restraints excluded: chain o residue 226 GLU Chi-restraints excluded: chain o residue 228 VAL Chi-restraints excluded: chain o residue 248 GLU Chi-restraints excluded: chain o residue 327 MET Chi-restraints excluded: chain o residue 390 MET Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 56 GLU Chi-restraints excluded: chain n residue 89 PHE Chi-restraints excluded: chain n residue 116 VAL Chi-restraints excluded: chain n residue 162 LEU Chi-restraints excluded: chain n residue 186 MET Chi-restraints excluded: chain n residue 226 GLU Chi-restraints excluded: chain n residue 318 THR Chi-restraints excluded: chain n residue 342 GLU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain n residue 390 MET Chi-restraints excluded: chain m residue 4 THR Chi-restraints excluded: chain m residue 6 LEU Chi-restraints excluded: chain m residue 92 ARG Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 162 LEU Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain l residue 92 ARG Chi-restraints excluded: chain l residue 116 VAL Chi-restraints excluded: chain l residue 132 LEU Chi-restraints excluded: chain l residue 144 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 194 SER Chi-restraints excluded: chain l residue 222 LEU Chi-restraints excluded: chain l residue 228 VAL Chi-restraints excluded: chain l residue 242 VAL Chi-restraints excluded: chain l residue 253 LEU Chi-restraints excluded: chain l residue 354 VAL Chi-restraints excluded: chain l residue 406 THR Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 134 GLU Chi-restraints excluded: chain k residue 194 SER Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 241 GLN Chi-restraints excluded: chain k residue 264 LEU Chi-restraints excluded: chain k residue 318 THR Chi-restraints excluded: chain k residue 390 MET Chi-restraints excluded: chain k residue 415 MET Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 49 ILE Chi-restraints excluded: chain j residue 55 LEU Chi-restraints excluded: chain j residue 58 LEU Chi-restraints excluded: chain j residue 116 VAL Chi-restraints excluded: chain j residue 164 LEU Chi-restraints excluded: chain j residue 193 GLN Chi-restraints excluded: chain j residue 228 VAL Chi-restraints excluded: chain j residue 241 GLN Chi-restraints excluded: chain j residue 242 VAL Chi-restraints excluded: chain i residue 6 LEU Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 89 PHE Chi-restraints excluded: chain i residue 105 LYS Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 132 LEU Chi-restraints excluded: chain i residue 164 LEU Chi-restraints excluded: chain i residue 186 MET Chi-restraints excluded: chain i residue 228 VAL Chi-restraints excluded: chain i residue 242 VAL Chi-restraints excluded: chain i residue 318 THR Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 49 ILE Chi-restraints excluded: chain h residue 55 LEU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 132 LEU Chi-restraints excluded: chain h residue 153 SER Chi-restraints excluded: chain h residue 186 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 226 GLU Chi-restraints excluded: chain h residue 228 VAL Chi-restraints excluded: chain h residue 241 GLN Chi-restraints excluded: chain h residue 277 VAL Chi-restraints excluded: chain h residue 318 THR Chi-restraints excluded: chain h residue 393 ILE Chi-restraints excluded: chain g residue 4 THR Chi-restraints excluded: chain g residue 6 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 116 VAL Chi-restraints excluded: chain g residue 145 LEU Chi-restraints excluded: chain g residue 241 GLN Chi-restraints excluded: chain g residue 318 THR Chi-restraints excluded: chain g residue 417 LYS Chi-restraints excluded: chain f residue 4 THR Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 327 MET Chi-restraints excluded: chain f residue 342 GLU Chi-restraints excluded: chain f residue 354 VAL Chi-restraints excluded: chain e residue 4 THR Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 23 LEU Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 116 VAL Chi-restraints excluded: chain e residue 228 VAL Chi-restraints excluded: chain e residue 241 GLN Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 406 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 5 GLU Chi-restraints excluded: chain d residue 6 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 92 ARG Chi-restraints excluded: chain d residue 101 ILE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 193 GLN Chi-restraints excluded: chain d residue 241 GLN Chi-restraints excluded: chain d residue 383 LEU Chi-restraints excluded: chain d residue 415 MET Chi-restraints excluded: chain c residue 4 THR Chi-restraints excluded: chain c residue 6 LEU Chi-restraints excluded: chain c residue 29 MET Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 116 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 248 GLU Chi-restraints excluded: chain c residue 325 SER Chi-restraints excluded: chain c residue 383 LEU Chi-restraints excluded: chain b residue 4 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 55 LEU Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain b residue 101 ILE Chi-restraints excluded: chain b residue 116 VAL Chi-restraints excluded: chain b residue 153 SER Chi-restraints excluded: chain b residue 194 SER Chi-restraints excluded: chain b residue 205 MET Chi-restraints excluded: chain b residue 241 GLN Chi-restraints excluded: chain b residue 410 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 8.9990 chunk 623 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 539 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 586 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 602 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 295 HIS a 374 GLN r 140 HIS ** r 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 401 ASN ** p 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 193 GLN ** o 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 59 GLN j 193 GLN h 220 GLN d 193 GLN d 220 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.053402 restraints weight = 152349.092| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.15 r_work: 0.2542 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 60822 Z= 0.298 Angle : 0.694 12.117 82008 Z= 0.337 Chirality : 0.043 0.171 9324 Planarity : 0.004 0.041 10620 Dihedral : 6.245 145.043 8415 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.49 % Allowed : 28.38 % Favored : 68.13 % 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: 1.28 (0.10), residues: 7506 helix: 1.79 (0.09), residues: 3492 sheet: 0.34 (0.16), residues: 1170 loop : -0.02 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 381 HIS 0.022 0.001 HIS a 295 PHE 0.014 0.001 PHE q 398 TYR 0.025 0.002 TYR r 332 ARG 0.015 0.001 ARG p 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17282.16 seconds wall clock time: 300 minutes 57.21 seconds (18057.21 seconds total)