Starting phenix.real_space_refine on Mon Mar 25 16:20:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/03_2024/6pyt_20526.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 31500 2.51 5 N 8652 2.21 5 O 9612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49920 Number of models: 1 Model: "" Number of chains: 24 Chain: "m" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "M" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "N" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "O" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "P" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "Q" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "R" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "E" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2897 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain: "a" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "n" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "o" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "p" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "q" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "r" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "b" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "c" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "d" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "e" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain: "f" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 159} Time building chain proxies: 25.38, per 1000 atoms: 0.51 Number of scatterers: 49920 At special positions: 0 Unit cell: (194.667, 192.585, 142.617, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 9612 8.00 N 8652 7.00 C 31500 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 - 3.50 Amino acid : False - 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: 17.92 Conformation dependent library (CDL) restraints added in 9.6 seconds 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12096 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 78 sheets defined 28.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'm' and resid 66 through 71 Processing helix chain 'm' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN m 164 " --> pdb=" O ALA m 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 59 Processing helix chain 'M' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU M 67 " --> pdb=" O SER M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 99 Processing helix chain 'M' and resid 112 through 117 Processing helix chain 'M' and resid 138 through 151 Processing helix chain 'M' and resid 162 through 171 Processing helix chain 'M' and resid 200 through 215 removed outlier: 3.899A pdb=" N ASP M 212 " --> pdb=" O PHE M 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 245 through 252 Processing helix chain 'M' and resid 275 through 279 removed outlier: 3.749A pdb=" N ALA M 279 " --> pdb=" O SER M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET M 291 " --> pdb=" O MET M 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA M 293 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 302 removed outlier: 3.667A pdb=" N ALA M 301 " --> pdb=" O HIS M 298 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL M 302 " --> pdb=" O LYS M 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 298 through 302' Processing helix chain 'M' and resid 309 through 328 removed outlier: 3.568A pdb=" N ASP M 324 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU M 325 " --> pdb=" O PHE M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN M 350 " --> pdb=" O SER M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU M 379 " --> pdb=" O ASP M 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR M 380 " --> pdb=" O GLN M 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 376 through 380' Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.749A pdb=" N ALA A 279 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA A 301 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 302 " --> pdb=" O LYS A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU A 379 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'N' and resid 51 through 59 removed outlier: 3.501A pdb=" N ALA N 58 " --> pdb=" O ASP N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU N 67 " --> pdb=" O SER N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 99 Processing helix chain 'N' and resid 112 through 117 Processing helix chain 'N' and resid 138 through 151 Processing helix chain 'N' and resid 162 through 171 Processing helix chain 'N' and resid 200 through 215 removed outlier: 3.901A pdb=" N ASP N 212 " --> pdb=" O PHE N 208 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 245 through 252 Processing helix chain 'N' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA N 279 " --> pdb=" O SER N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET N 291 " --> pdb=" O MET N 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA N 293 " --> pdb=" O LEU N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 302 removed outlier: 3.667A pdb=" N ALA N 301 " --> pdb=" O HIS N 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL N 302 " --> pdb=" O LYS N 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 298 through 302' Processing helix chain 'N' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP N 324 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU N 325 " --> pdb=" O PHE N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN N 350 " --> pdb=" O SER N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 376 through 380 removed outlier: 3.610A pdb=" N LEU N 379 " --> pdb=" O ASP N 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR N 380 " --> pdb=" O GLN N 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 376 through 380' Processing helix chain 'O' and resid 51 through 59 removed outlier: 3.500A pdb=" N ALA O 58 " --> pdb=" O ASP O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 74 removed outlier: 3.564A pdb=" N LEU O 67 " --> pdb=" O SER O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 99 Processing helix chain 'O' and resid 112 through 117 Processing helix chain 'O' and resid 138 through 151 Processing helix chain 'O' and resid 162 through 171 Processing helix chain 'O' and resid 200 through 215 removed outlier: 3.901A pdb=" N ASP O 212 " --> pdb=" O PHE O 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 245 through 252 Processing helix chain 'O' and resid 275 through 279 removed outlier: 3.749A pdb=" N ALA O 279 " --> pdb=" O SER O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET O 291 " --> pdb=" O MET O 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA O 293 " --> pdb=" O LEU O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 302 removed outlier: 3.665A pdb=" N ALA O 301 " --> pdb=" O HIS O 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL O 302 " --> pdb=" O LYS O 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 298 through 302' Processing helix chain 'O' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP O 324 " --> pdb=" O ALA O 320 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU O 325 " --> pdb=" O PHE O 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN O 350 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU O 379 " --> pdb=" O ASP O 376 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR O 380 " --> pdb=" O GLN O 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 376 through 380' Processing helix chain 'P' and resid 51 through 59 removed outlier: 3.501A pdb=" N ALA P 58 " --> pdb=" O ASP P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU P 67 " --> pdb=" O SER P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 99 Processing helix chain 'P' and resid 112 through 117 Processing helix chain 'P' and resid 138 through 151 Processing helix chain 'P' and resid 162 through 171 Processing helix chain 'P' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP P 212 " --> pdb=" O PHE P 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 252 Processing helix chain 'P' and resid 275 through 279 removed outlier: 3.749A pdb=" N ALA P 279 " --> pdb=" O SER P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 296 removed outlier: 3.818A pdb=" N MET P 291 " --> pdb=" O MET P 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA P 293 " --> pdb=" O LEU P 289 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA P 301 " --> pdb=" O HIS P 298 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL P 302 " --> pdb=" O LYS P 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 298 through 302' Processing helix chain 'P' and resid 309 through 328 removed outlier: 3.568A pdb=" N ASP P 324 " --> pdb=" O ALA P 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU P 325 " --> pdb=" O PHE P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN P 350 " --> pdb=" O SER P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU P 379 " --> pdb=" O ASP P 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR P 380 " --> pdb=" O GLN P 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 376 through 380' Processing helix chain 'Q' and resid 51 through 59 Processing helix chain 'Q' and resid 63 through 74 removed outlier: 3.564A pdb=" N LEU Q 67 " --> pdb=" O SER Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 99 Processing helix chain 'Q' and resid 112 through 117 Processing helix chain 'Q' and resid 138 through 151 Processing helix chain 'Q' and resid 162 through 171 Processing helix chain 'Q' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP Q 212 " --> pdb=" O PHE Q 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 245 through 252 Processing helix chain 'Q' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA Q 279 " --> pdb=" O SER Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET Q 291 " --> pdb=" O MET Q 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA Q 293 " --> pdb=" O LEU Q 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA Q 301 " --> pdb=" O HIS Q 298 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL Q 302 " --> pdb=" O LYS Q 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 298 through 302' Processing helix chain 'Q' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP Q 324 " --> pdb=" O ALA Q 320 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU Q 325 " --> pdb=" O PHE Q 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN Q 350 " --> pdb=" O SER Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU Q 379 " --> pdb=" O ASP Q 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR Q 380 " --> pdb=" O GLN Q 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 376 through 380' Processing helix chain 'R' and resid 51 through 59 removed outlier: 3.500A pdb=" N ALA R 58 " --> pdb=" O ASP R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU R 67 " --> pdb=" O SER R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 99 Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 138 through 151 Processing helix chain 'R' and resid 162 through 171 Processing helix chain 'R' and resid 200 through 215 removed outlier: 3.901A pdb=" N ASP R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 252 Processing helix chain 'R' and resid 275 through 279 removed outlier: 3.749A pdb=" N ALA R 279 " --> pdb=" O SER R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET R 291 " --> pdb=" O MET R 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA R 301 " --> pdb=" O HIS R 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL R 302 " --> pdb=" O LYS R 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 298 through 302' Processing helix chain 'R' and resid 309 through 328 removed outlier: 3.568A pdb=" N ASP R 324 " --> pdb=" O ALA R 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU R 325 " --> pdb=" O PHE R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN R 350 " --> pdb=" O SER R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU R 379 " --> pdb=" O ASP R 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR R 380 " --> pdb=" O GLN R 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 376 through 380' Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.501A pdb=" N ALA B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA B 279 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA B 301 " --> pdb=" O HIS B 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU B 379 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B 380 " --> pdb=" O GLN B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 380' Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.564A pdb=" N LEU C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA C 279 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA C 301 " --> pdb=" O HIS C 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU C 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU C 379 " --> pdb=" O ASP C 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 380 " --> pdb=" O GLN C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 380' Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.501A pdb=" N ALA D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA D 279 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET D 291 " --> pdb=" O MET D 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 removed outlier: 3.667A pdb=" N ALA D 301 " --> pdb=" O HIS D 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 302' Processing helix chain 'D' and resid 309 through 328 removed outlier: 3.568A pdb=" N ASP D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.739A pdb=" N GLN D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU D 379 " --> pdb=" O ASP D 376 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR D 380 " --> pdb=" O GLN D 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 376 through 380' Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.500A pdb=" N ALA E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.564A pdb=" N LEU E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 99 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 252 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA E 279 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET E 291 " --> pdb=" O MET E 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.666A pdb=" N ALA E 301 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL E 302 " --> pdb=" O LYS E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 302' Processing helix chain 'E' and resid 309 through 328 removed outlier: 3.568A pdb=" N ASP E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU E 325 " --> pdb=" O PHE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU E 379 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR E 380 " --> pdb=" O GLN E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 380' Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.500A pdb=" N ALA F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.565A pdb=" N LEU F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'F' and resid 112 through 117 Processing helix chain 'F' and resid 138 through 151 Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'F' and resid 200 through 215 removed outlier: 3.900A pdb=" N ASP F 212 " --> pdb=" O PHE F 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.748A pdb=" N ALA F 279 " --> pdb=" O SER F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.817A pdb=" N MET F 291 " --> pdb=" O MET F 287 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.667A pdb=" N ALA F 301 " --> pdb=" O HIS F 298 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL F 302 " --> pdb=" O LYS F 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 298 through 302' Processing helix chain 'F' and resid 309 through 328 removed outlier: 3.567A pdb=" N ASP F 324 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU F 325 " --> pdb=" O PHE F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 removed outlier: 3.740A pdb=" N GLN F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU F 379 " --> pdb=" O ASP F 376 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR F 380 " --> pdb=" O GLN F 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 376 through 380' Processing helix chain 'a' and resid 66 through 71 Processing helix chain 'a' and resid 159 through 167 removed outlier: 3.516A pdb=" N ASN a 164 " --> pdb=" O ALA a 160 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 71 Processing helix chain 'n' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN n 164 " --> pdb=" O ALA n 160 " (cutoff:3.500A) Processing helix chain 'o' and resid 66 through 71 Processing helix chain 'o' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN o 164 " --> pdb=" O ALA o 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 159 through 167 removed outlier: 3.516A pdb=" N ASN p 164 " --> pdb=" O ALA p 160 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 71 Processing helix chain 'q' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN q 164 " --> pdb=" O ALA q 160 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 71 Processing helix chain 'r' and resid 159 through 167 removed outlier: 3.516A pdb=" N ASN r 164 " --> pdb=" O ALA r 160 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 71 Processing helix chain 'b' and resid 159 through 167 removed outlier: 3.516A pdb=" N ASN b 164 " --> pdb=" O ALA b 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 71 Processing helix chain 'c' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN c 164 " --> pdb=" O ALA c 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 71 Processing helix chain 'd' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 71 Processing helix chain 'e' and resid 159 through 167 removed outlier: 3.517A pdb=" N ASN e 164 " --> pdb=" O ALA e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 71 Processing helix chain 'f' and resid 159 through 167 removed outlier: 3.516A pdb=" N ASN f 164 " --> pdb=" O ALA f 160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'm' and resid 7 through 13 removed outlier: 3.672A pdb=" N ASN m 9 " --> pdb=" O SER m 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL m 136 " --> pdb=" O PRO m 98 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL m 100 " --> pdb=" O LEU m 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU m 134 " --> pdb=" O VAL m 100 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR m 102 " --> pdb=" O TYR m 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR m 132 " --> pdb=" O THR m 102 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG m 104 " --> pdb=" O SER m 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA m 126 " --> pdb=" O LYS m 108 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL m 110 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS m 124 " --> pdb=" O VAL m 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 123 through 136 current: chain 'n' and resid 49 through 53 Processing sheet with id=AA2, first strand: chain 'm' and resid 150 through 152 removed outlier: 5.271A pdb=" N GLU m 140 " --> pdb=" O VAL m 136 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL m 136 " --> pdb=" O GLU m 140 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS m 124 " --> pdb=" O VAL m 110 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL m 110 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA m 126 " --> pdb=" O LYS m 108 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG m 104 " --> pdb=" O SER m 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR m 132 " --> pdb=" O THR m 102 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR m 102 " --> pdb=" O TYR m 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU m 134 " --> pdb=" O VAL m 100 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL m 100 " --> pdb=" O LEU m 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL m 136 " --> pdb=" O PRO m 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 97 through 112 current: chain 'm' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'm' and resid 49 through 53 removed outlier: 5.727A pdb=" N ASP m 50 " --> pdb=" O GLU m 36 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU m 36 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY m 52 " --> pdb=" O LYS m 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS r 108 " --> pdb=" O VAL m 33 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N THR m 35 " --> pdb=" O LEU r 106 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N LEU r 106 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL r 136 " --> pdb=" O PRO r 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL r 100 " --> pdb=" O LEU r 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU r 134 " --> pdb=" O VAL r 100 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR r 102 " --> pdb=" O TYR r 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR r 132 " --> pdb=" O THR r 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG r 104 " --> pdb=" O SER r 130 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA r 126 " --> pdb=" O LYS r 108 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL r 110 " --> pdb=" O LYS r 124 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS r 124 " --> pdb=" O VAL r 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 123 through 136 current: chain 'r' and resid 7 through 13 Processing sheet with id=AA4, first strand: chain 'q' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER r 25 " --> pdb=" O SER r 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS r 124 " --> pdb=" O VAL r 110 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL r 110 " --> pdb=" O LYS r 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA r 126 " --> pdb=" O LYS r 108 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG r 104 " --> pdb=" O SER r 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR r 132 " --> pdb=" O THR r 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR r 102 " --> pdb=" O TYR r 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU r 134 " --> pdb=" O VAL r 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL r 100 " --> pdb=" O LEU r 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL r 136 " --> pdb=" O PRO r 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 97 through 112 current: chain 'r' and resid 150 through 152 Processing sheet with id=AA5, first strand: chain 'm' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER n 25 " --> pdb=" O SER n 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS n 124 " --> pdb=" O VAL n 110 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL n 110 " --> pdb=" O LYS n 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA n 126 " --> pdb=" O LYS n 108 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG n 104 " --> pdb=" O SER n 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR n 132 " --> pdb=" O THR n 102 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR n 102 " --> pdb=" O TYR n 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU n 134 " --> pdb=" O VAL n 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL n 100 " --> pdb=" O LEU n 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL n 136 " --> pdb=" O PRO n 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 97 through 112 current: chain 'n' and resid 150 through 152 Processing sheet with id=AA6, first strand: chain 'n' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN n 9 " --> pdb=" O SER n 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL n 136 " --> pdb=" O PRO n 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL n 100 " --> pdb=" O LEU n 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU n 134 " --> pdb=" O VAL n 100 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR n 102 " --> pdb=" O TYR n 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR n 132 " --> pdb=" O THR n 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG n 104 " --> pdb=" O SER n 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA n 126 " --> pdb=" O LYS n 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL n 110 " --> pdb=" O LYS n 124 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS n 124 " --> pdb=" O VAL n 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 123 through 136 current: chain 'o' and resid 49 through 53 Processing sheet with id=AA7, first strand: chain 'M' and resid 8 through 11 removed outlier: 6.216A pdb=" N THR M 8 " --> pdb=" O PHE N 370 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL N 372 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR M 10 " --> pdb=" O VAL N 372 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL N 374 " --> pdb=" O THR M 10 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 353 " --> pdb=" O ASN N 367 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU N 373 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN M 77 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER M 25 " --> pdb=" O GLN M 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL M 79 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP M 31 " --> pdb=" O VAL M 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE M 33 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU M 128 " --> pdb=" O ILE M 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA M 154 " --> pdb=" O PHE M 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL M 181 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU M 156 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA M 256 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET M 180 " --> pdb=" O ALA M 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'M' and resid 185 through 189 Processing sheet with id=AB2, first strand: chain 'M' and resid 335 through 338 Processing sheet with id=AB3, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.577A pdb=" N VAL A 353 " --> pdb=" O ASN M 367 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU M 373 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 8 through 11 removed outlier: 6.240A pdb=" N THR A 8 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 372 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR A 10 " --> pdb=" O VAL B 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN A 77 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER A 25 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 79 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 31 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 33 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 128 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 154 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 181 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 156 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA A 256 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET A 180 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AB7, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AB8, first strand: chain 'A' and resid 369 through 372 Processing sheet with id=AB9, first strand: chain 'N' and resid 8 through 11 removed outlier: 6.283A pdb=" N THR N 8 " --> pdb=" O PHE O 370 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL O 372 " --> pdb=" O THR N 8 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR N 10 " --> pdb=" O VAL O 372 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL O 374 " --> pdb=" O THR N 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 353 " --> pdb=" O ASN O 367 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU O 373 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN N 77 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER N 25 " --> pdb=" O GLN N 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL N 79 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP N 31 " --> pdb=" O VAL N 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE N 33 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU N 128 " --> pdb=" O ILE N 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA N 154 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL N 181 " --> pdb=" O ALA N 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU N 156 " --> pdb=" O VAL N 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA N 256 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET N 180 " --> pdb=" O ALA N 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'N' and resid 185 through 189 Processing sheet with id=AC4, first strand: chain 'N' and resid 335 through 338 Processing sheet with id=AC5, first strand: chain 'O' and resid 8 through 11 removed outlier: 6.422A pdb=" N THR O 8 " --> pdb=" O PHE P 370 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL P 372 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N THR O 10 " --> pdb=" O VAL P 372 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL P 374 " --> pdb=" O THR O 10 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU P 373 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 46 through 49 removed outlier: 6.036A pdb=" N GLN O 77 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER O 25 " --> pdb=" O GLN O 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 79 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP O 31 " --> pdb=" O VAL O 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE O 33 " --> pdb=" O VAL O 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU O 128 " --> pdb=" O ILE O 155 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA O 154 " --> pdb=" O PHE O 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL O 181 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU O 156 " --> pdb=" O VAL O 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA O 256 " --> pdb=" O LEU O 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET O 180 " --> pdb=" O ALA O 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'O' and resid 185 through 189 Processing sheet with id=AC9, first strand: chain 'O' and resid 335 through 338 Processing sheet with id=AD1, first strand: chain 'P' and resid 8 through 11 removed outlier: 3.518A pdb=" N VAL E 353 " --> pdb=" O ASN Q 367 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Q 373 " --> pdb=" O ILE E 357 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN P 77 " --> pdb=" O ALA P 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER P 25 " --> pdb=" O GLN P 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL P 79 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP P 31 " --> pdb=" O VAL P 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE P 33 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU P 128 " --> pdb=" O ILE P 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA P 154 " --> pdb=" O PHE P 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL P 181 " --> pdb=" O ALA P 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU P 156 " --> pdb=" O VAL P 181 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA P 256 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET P 180 " --> pdb=" O ALA P 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'P' and resid 185 through 189 Processing sheet with id=AD5, first strand: chain 'P' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'Q' and resid 8 through 11 removed outlier: 6.259A pdb=" N THR Q 8 " --> pdb=" O PHE R 370 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL R 372 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR Q 10 " --> pdb=" O VAL R 372 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL R 374 " --> pdb=" O THR Q 10 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 353 " --> pdb=" O ASN R 367 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU R 373 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 46 through 49 removed outlier: 6.036A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER Q 25 " --> pdb=" O GLN Q 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL Q 79 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP Q 31 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE Q 33 " --> pdb=" O VAL Q 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU Q 128 " --> pdb=" O ILE Q 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA Q 154 " --> pdb=" O PHE Q 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL Q 181 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU Q 156 " --> pdb=" O VAL Q 181 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA Q 256 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET Q 180 " --> pdb=" O ALA Q 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 100 through 101 Processing sheet with id=AD9, first strand: chain 'Q' and resid 185 through 189 Processing sheet with id=AE1, first strand: chain 'Q' and resid 335 through 338 Processing sheet with id=AE2, first strand: chain 'R' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN R 77 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER R 25 " --> pdb=" O GLN R 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL R 79 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP R 31 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE R 33 " --> pdb=" O VAL R 85 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU R 128 " --> pdb=" O ILE R 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA R 154 " --> pdb=" O PHE R 179 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL R 181 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU R 156 " --> pdb=" O VAL R 181 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA R 256 " --> pdb=" O LEU R 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET R 180 " --> pdb=" O ALA R 256 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 100 through 101 Processing sheet with id=AE4, first strand: chain 'R' and resid 185 through 189 Processing sheet with id=AE5, first strand: chain 'R' and resid 335 through 338 Processing sheet with id=AE6, first strand: chain 'B' and resid 8 through 11 removed outlier: 6.342A pdb=" N THR B 8 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 372 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR B 10 " --> pdb=" O VAL C 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.036A pdb=" N GLN B 77 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER B 25 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 79 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 31 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 33 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 128 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 154 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B 181 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 156 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA B 256 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET B 180 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AE9, first strand: chain 'B' and resid 185 through 189 Processing sheet with id=AF1, first strand: chain 'C' and resid 8 through 11 removed outlier: 6.336A pdb=" N THR C 8 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL D 372 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR C 10 " --> pdb=" O VAL D 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.036A pdb=" N GLN C 77 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER C 25 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 79 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 31 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 33 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 128 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 154 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL C 181 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 156 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA C 256 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET C 180 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AF4, first strand: chain 'C' and resid 185 through 189 Processing sheet with id=AF5, first strand: chain 'D' and resid 8 through 11 removed outlier: 6.306A pdb=" N THR D 8 " --> pdb=" O PHE E 370 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL E 372 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR D 10 " --> pdb=" O VAL E 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.036A pdb=" N GLN D 77 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER D 25 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 79 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 31 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 33 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU D 128 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 154 " --> pdb=" O PHE D 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL D 181 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 156 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA D 256 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET D 180 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AF8, first strand: chain 'D' and resid 185 through 189 Processing sheet with id=AF9, first strand: chain 'E' and resid 8 through 11 removed outlier: 6.263A pdb=" N THR E 8 " --> pdb=" O PHE F 370 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL F 372 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N THR E 10 " --> pdb=" O VAL F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN E 77 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER E 25 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 79 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 31 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE E 33 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU E 128 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA E 154 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL E 181 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 156 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA E 256 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET E 180 " --> pdb=" O ALA E 256 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AG3, first strand: chain 'E' and resid 185 through 189 Processing sheet with id=AG4, first strand: chain 'F' and resid 46 through 49 removed outlier: 6.037A pdb=" N GLN F 77 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER F 25 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 79 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 31 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE F 33 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU F 128 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA F 154 " --> pdb=" O PHE F 179 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL F 181 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU F 156 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA F 256 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N MET F 180 " --> pdb=" O ALA F 256 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AG6, first strand: chain 'F' and resid 185 through 189 Processing sheet with id=AG7, first strand: chain 'a' and resid 7 through 13 removed outlier: 3.672A pdb=" N ASN a 9 " --> pdb=" O SER a 88 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL a 99 " --> pdb=" O VAL a 136 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL a 136 " --> pdb=" O VAL a 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA a 101 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU a 134 " --> pdb=" O ALA a 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU a 103 " --> pdb=" O TYR a 132 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR a 132 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY a 105 " --> pdb=" O SER a 130 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER a 130 " --> pdb=" O GLY a 105 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU a 107 " --> pdb=" O ALA a 128 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA a 128 " --> pdb=" O LEU a 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 123 through 136 current: chain 'b' and resid 49 through 53 Processing sheet with id=AG8, first strand: chain 'a' and resid 150 through 152 removed outlier: 5.272A pdb=" N GLU a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL a 136 " --> pdb=" O GLU a 140 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA a 128 " --> pdb=" O LEU a 107 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU a 107 " --> pdb=" O ALA a 128 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER a 130 " --> pdb=" O GLY a 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY a 105 " --> pdb=" O SER a 130 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR a 132 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU a 103 " --> pdb=" O TYR a 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU a 134 " --> pdb=" O ALA a 101 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA a 101 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL a 136 " --> pdb=" O VAL a 99 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL a 99 " --> pdb=" O VAL a 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 97 through 112 current: chain 'a' and resid 25 through 27 Processing sheet with id=AG9, first strand: chain 'a' and resid 49 through 53 removed outlier: 5.728A pdb=" N ASP a 50 " --> pdb=" O GLU a 36 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLU a 36 " --> pdb=" O ASP a 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY a 52 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS f 108 " --> pdb=" O VAL a 33 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N THR a 35 " --> pdb=" O LEU f 106 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N LEU f 106 " --> pdb=" O THR a 35 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL f 136 " --> pdb=" O PRO f 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL f 100 " --> pdb=" O LEU f 134 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU f 134 " --> pdb=" O VAL f 100 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR f 102 " --> pdb=" O TYR f 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR f 132 " --> pdb=" O THR f 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG f 104 " --> pdb=" O SER f 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA f 126 " --> pdb=" O LYS f 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL f 110 " --> pdb=" O LYS f 124 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS f 124 " --> pdb=" O VAL f 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 123 through 136 current: chain 'f' and resid 7 through 13 Processing sheet with id=AH1, first strand: chain 'e' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER f 25 " --> pdb=" O SER f 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS f 124 " --> pdb=" O VAL f 110 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL f 110 " --> pdb=" O LYS f 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA f 126 " --> pdb=" O LYS f 108 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG f 104 " --> pdb=" O SER f 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR f 132 " --> pdb=" O THR f 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR f 102 " --> pdb=" O TYR f 132 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU f 134 " --> pdb=" O VAL f 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL f 100 " --> pdb=" O LEU f 134 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL f 136 " --> pdb=" O PRO f 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 97 through 112 current: chain 'f' and resid 150 through 152 Processing sheet with id=AH2, first strand: chain 'a' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER b 25 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA b 128 " --> pdb=" O LEU b 107 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU b 107 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER b 130 " --> pdb=" O GLY b 105 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY b 105 " --> pdb=" O SER b 130 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR b 132 " --> pdb=" O LEU b 103 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU b 103 " --> pdb=" O TYR b 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU b 134 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA b 101 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL b 136 " --> pdb=" O VAL b 99 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL b 99 " --> pdb=" O VAL b 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 97 through 112 current: chain 'b' and resid 150 through 152 Processing sheet with id=AH3, first strand: chain 'b' and resid 7 through 13 removed outlier: 3.672A pdb=" N ASN b 9 " --> pdb=" O SER b 88 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL b 99 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL b 136 " --> pdb=" O VAL b 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA b 101 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU b 134 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU b 103 " --> pdb=" O TYR b 132 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR b 132 " --> pdb=" O LEU b 103 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY b 105 " --> pdb=" O SER b 130 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N SER b 130 " --> pdb=" O GLY b 105 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU b 107 " --> pdb=" O ALA b 128 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA b 128 " --> pdb=" O LEU b 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 123 through 136 current: chain 'c' and resid 49 through 53 Processing sheet with id=AH4, first strand: chain 'n' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER o 25 " --> pdb=" O SER o 61 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS o 124 " --> pdb=" O VAL o 110 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL o 110 " --> pdb=" O LYS o 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA o 126 " --> pdb=" O LYS o 108 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG o 104 " --> pdb=" O SER o 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR o 132 " --> pdb=" O THR o 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR o 102 " --> pdb=" O TYR o 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU o 134 " --> pdb=" O VAL o 100 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL o 100 " --> pdb=" O LEU o 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL o 136 " --> pdb=" O PRO o 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 97 through 112 current: chain 'o' and resid 150 through 152 Processing sheet with id=AH5, first strand: chain 'o' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN o 9 " --> pdb=" O SER o 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL o 136 " --> pdb=" O PRO o 98 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL o 100 " --> pdb=" O LEU o 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU o 134 " --> pdb=" O VAL o 100 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR o 102 " --> pdb=" O TYR o 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR o 132 " --> pdb=" O THR o 102 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG o 104 " --> pdb=" O SER o 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA o 126 " --> pdb=" O LYS o 108 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL o 110 " --> pdb=" O LYS o 124 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS o 124 " --> pdb=" O VAL o 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 123 through 136 current: chain 'p' and resid 49 through 53 Processing sheet with id=AH6, first strand: chain 'o' and resid 114 through 116 removed outlier: 4.189A pdb=" N SER p 25 " --> pdb=" O SER p 61 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA p 128 " --> pdb=" O LEU p 107 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU p 107 " --> pdb=" O ALA p 128 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER p 130 " --> pdb=" O GLY p 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY p 105 " --> pdb=" O SER p 130 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR p 132 " --> pdb=" O LEU p 103 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU p 103 " --> pdb=" O TYR p 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU p 134 " --> pdb=" O ALA p 101 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA p 101 " --> pdb=" O LEU p 134 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL p 136 " --> pdb=" O VAL p 99 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL p 99 " --> pdb=" O VAL p 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 97 through 112 current: chain 'p' and resid 150 through 152 Processing sheet with id=AH7, first strand: chain 'p' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN p 9 " --> pdb=" O SER p 88 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL p 99 " --> pdb=" O VAL p 136 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL p 136 " --> pdb=" O VAL p 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA p 101 " --> pdb=" O LEU p 134 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU p 134 " --> pdb=" O ALA p 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU p 103 " --> pdb=" O TYR p 132 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR p 132 " --> pdb=" O LEU p 103 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY p 105 " --> pdb=" O SER p 130 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER p 130 " --> pdb=" O GLY p 105 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU p 107 " --> pdb=" O ALA p 128 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA p 128 " --> pdb=" O LEU p 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 123 through 136 current: chain 'q' and resid 49 through 53 Processing sheet with id=AH8, first strand: chain 'p' and resid 114 through 116 removed outlier: 4.187A pdb=" N SER q 25 " --> pdb=" O SER q 61 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA q 128 " --> pdb=" O LEU q 107 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU q 107 " --> pdb=" O ALA q 128 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER q 130 " --> pdb=" O GLY q 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY q 105 " --> pdb=" O SER q 130 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR q 132 " --> pdb=" O LEU q 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU q 103 " --> pdb=" O TYR q 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU q 134 " --> pdb=" O ALA q 101 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA q 101 " --> pdb=" O LEU q 134 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL q 136 " --> pdb=" O VAL q 99 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL q 99 " --> pdb=" O VAL q 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'q' and resid 97 through 112 current: chain 'q' and resid 150 through 152 Processing sheet with id=AH9, first strand: chain 'q' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN q 9 " --> pdb=" O SER q 88 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL q 99 " --> pdb=" O VAL q 136 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL q 136 " --> pdb=" O VAL q 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA q 101 " --> pdb=" O LEU q 134 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU q 134 " --> pdb=" O ALA q 101 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU q 103 " --> pdb=" O TYR q 132 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR q 132 " --> pdb=" O LEU q 103 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY q 105 " --> pdb=" O SER q 130 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER q 130 " --> pdb=" O GLY q 105 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU q 107 " --> pdb=" O ALA q 128 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA q 128 " --> pdb=" O LEU q 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'q' and resid 123 through 136 current: chain 'r' and resid 49 through 53 Processing sheet with id=AI1, first strand: chain 'b' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER c 25 " --> pdb=" O SER c 61 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA c 128 " --> pdb=" O LEU c 107 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU c 107 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER c 130 " --> pdb=" O GLY c 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY c 105 " --> pdb=" O SER c 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR c 132 " --> pdb=" O LEU c 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU c 103 " --> pdb=" O TYR c 132 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU c 134 " --> pdb=" O ALA c 101 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA c 101 " --> pdb=" O LEU c 134 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL c 136 " --> pdb=" O VAL c 99 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL c 99 " --> pdb=" O VAL c 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 97 through 112 current: chain 'c' and resid 150 through 152 Processing sheet with id=AI2, first strand: chain 'c' and resid 7 through 13 removed outlier: 3.672A pdb=" N ASN c 9 " --> pdb=" O SER c 88 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL c 99 " --> pdb=" O VAL c 136 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL c 136 " --> pdb=" O VAL c 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA c 101 " --> pdb=" O LEU c 134 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU c 134 " --> pdb=" O ALA c 101 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU c 103 " --> pdb=" O TYR c 132 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR c 132 " --> pdb=" O LEU c 103 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY c 105 " --> pdb=" O SER c 130 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER c 130 " --> pdb=" O GLY c 105 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU c 107 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA c 128 " --> pdb=" O LEU c 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 123 through 136 current: chain 'd' and resid 49 through 53 Processing sheet with id=AI3, first strand: chain 'c' and resid 114 through 116 removed outlier: 4.187A pdb=" N SER d 25 " --> pdb=" O SER d 61 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS d 124 " --> pdb=" O VAL d 110 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL d 110 " --> pdb=" O LYS d 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA d 126 " --> pdb=" O LYS d 108 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG d 104 " --> pdb=" O SER d 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR d 132 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR d 102 " --> pdb=" O TYR d 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU d 134 " --> pdb=" O VAL d 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL d 100 " --> pdb=" O LEU d 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL d 136 " --> pdb=" O PRO d 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 97 through 112 current: chain 'd' and resid 150 through 152 Processing sheet with id=AI4, first strand: chain 'd' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN d 9 " --> pdb=" O SER d 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL d 136 " --> pdb=" O PRO d 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL d 100 " --> pdb=" O LEU d 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU d 134 " --> pdb=" O VAL d 100 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR d 102 " --> pdb=" O TYR d 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR d 132 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG d 104 " --> pdb=" O SER d 130 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA d 126 " --> pdb=" O LYS d 108 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL d 110 " --> pdb=" O LYS d 124 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS d 124 " --> pdb=" O VAL d 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 123 through 136 current: chain 'e' and resid 49 through 53 Processing sheet with id=AI5, first strand: chain 'd' and resid 114 through 116 removed outlier: 4.188A pdb=" N SER e 25 " --> pdb=" O SER e 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS e 124 " --> pdb=" O VAL e 110 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL e 110 " --> pdb=" O LYS e 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA e 126 " --> pdb=" O LYS e 108 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG e 104 " --> pdb=" O SER e 130 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR e 132 " --> pdb=" O THR e 102 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR e 102 " --> pdb=" O TYR e 132 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU e 134 " --> pdb=" O VAL e 100 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL e 100 " --> pdb=" O LEU e 134 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL e 136 " --> pdb=" O PRO e 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 97 through 112 current: chain 'e' and resid 150 through 152 Processing sheet with id=AI6, first strand: chain 'e' and resid 7 through 13 removed outlier: 3.671A pdb=" N ASN e 9 " --> pdb=" O SER e 88 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL e 136 " --> pdb=" O PRO e 98 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL e 100 " --> pdb=" O LEU e 134 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU e 134 " --> pdb=" O VAL e 100 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR e 102 " --> pdb=" O TYR e 132 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR e 132 " --> pdb=" O THR e 102 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG e 104 " --> pdb=" O SER e 130 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA e 126 " --> pdb=" O LYS e 108 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL e 110 " --> pdb=" O LYS e 124 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS e 124 " --> pdb=" O VAL e 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 123 through 136 current: chain 'f' and resid 49 through 53 1732 hydrogen bonds defined for protein. 4764 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: 20.02 Time building geometry restraints manager: 19.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16614 1.34 - 1.46: 9687 1.46 - 1.58: 24303 1.58 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 50880 Sorted by residual: bond pdb=" C ILE Q 27 " pdb=" N GLY Q 28 " ideal model delta sigma weight residual 1.332 1.346 -0.014 5.00e-03 4.00e+04 7.63e+00 bond pdb=" C ILE M 27 " pdb=" N GLY M 28 " ideal model delta sigma weight residual 1.332 1.346 -0.014 5.00e-03 4.00e+04 7.49e+00 bond pdb=" C ILE P 27 " pdb=" N GLY P 28 " ideal model delta sigma weight residual 1.332 1.346 -0.014 5.00e-03 4.00e+04 7.32e+00 bond pdb=" C ILE D 27 " pdb=" N GLY D 28 " ideal model delta sigma weight residual 1.332 1.346 -0.013 5.00e-03 4.00e+04 7.26e+00 bond pdb=" C ILE A 27 " pdb=" N GLY A 28 " ideal model delta sigma weight residual 1.332 1.346 -0.013 5.00e-03 4.00e+04 7.22e+00 ... (remaining 50875 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.06: 960 105.06 - 112.37: 25018 112.37 - 119.69: 17904 119.69 - 127.01: 24789 127.01 - 134.32: 509 Bond angle restraints: 69180 Sorted by residual: angle pdb=" C ASP a 22 " pdb=" N VAL a 23 " pdb=" CA VAL a 23 " ideal model delta sigma weight residual 123.25 117.96 5.29 1.10e+00 8.26e-01 2.31e+01 angle pdb=" C ASP r 22 " pdb=" N VAL r 23 " pdb=" CA VAL r 23 " ideal model delta sigma weight residual 123.25 117.99 5.26 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C ASP c 22 " pdb=" N VAL c 23 " pdb=" CA VAL c 23 " ideal model delta sigma weight residual 123.25 118.00 5.25 1.10e+00 8.26e-01 2.28e+01 angle pdb=" C ASP e 22 " pdb=" N VAL e 23 " pdb=" CA VAL e 23 " ideal model delta sigma weight residual 123.25 118.00 5.25 1.10e+00 8.26e-01 2.28e+01 angle pdb=" C ASP b 22 " pdb=" N VAL b 23 " pdb=" CA VAL b 23 " ideal model delta sigma weight residual 123.25 118.00 5.25 1.10e+00 8.26e-01 2.27e+01 ... (remaining 69175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 28830 17.99 - 35.99: 1242 35.99 - 53.98: 132 53.98 - 71.97: 24 71.97 - 89.97: 24 Dihedral angle restraints: 30252 sinusoidal: 11388 harmonic: 18864 Sorted by residual: dihedral pdb=" CA ILE O 258 " pdb=" C ILE O 258 " pdb=" N ILE O 259 " pdb=" CA ILE O 259 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ILE A 258 " pdb=" C ILE A 258 " pdb=" N ILE A 259 " pdb=" CA ILE A 259 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ILE R 258 " pdb=" C ILE R 258 " pdb=" N ILE R 259 " pdb=" CA ILE R 259 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 30249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5091 0.051 - 0.102: 1906 0.102 - 0.152: 695 0.152 - 0.203: 89 0.203 - 0.254: 55 Chirality restraints: 7836 Sorted by residual: chirality pdb=" CB ILE R 357 " pdb=" CA ILE R 357 " pdb=" CG1 ILE R 357 " pdb=" CG2 ILE R 357 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE O 357 " pdb=" CA ILE O 357 " pdb=" CG1 ILE O 357 " pdb=" CG2 ILE O 357 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE C 357 " pdb=" CA ILE C 357 " pdb=" CG1 ILE C 357 " pdb=" CG2 ILE C 357 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 7833 not shown) Planarity restraints: 9120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 357 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ILE E 357 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE E 357 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG E 358 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 357 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C ILE C 357 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE C 357 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG C 358 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 357 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.15e+00 pdb=" C ILE O 357 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE O 357 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG O 358 " -0.016 2.00e-02 2.50e+03 ... (remaining 9117 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6414 2.75 - 3.29: 47251 3.29 - 3.82: 84151 3.82 - 4.36: 101001 4.36 - 4.90: 175296 Nonbonded interactions: 414113 Sorted by model distance: nonbonded pdb=" OG SER F 222 " pdb=" O TRP F 267 " model vdw 2.212 2.440 nonbonded pdb=" OG SER D 222 " pdb=" O TRP D 267 " model vdw 2.212 2.440 nonbonded pdb=" OG SER N 222 " pdb=" O TRP N 267 " model vdw 2.212 2.440 nonbonded pdb=" OG SER P 222 " pdb=" O TRP P 267 " model vdw 2.212 2.440 nonbonded pdb=" OG SER R 222 " pdb=" O TRP R 267 " model vdw 2.212 2.440 ... (remaining 414108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' 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=0.00 max=1.00 mean=0.95 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: 3.160 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: 0.040 Extract box with map and model: 14.630 Check model and map are aligned: 0.840 Set scattering table: 0.540 Process input model: 125.090 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.009 0.068 50880 Z= 0.572 Angle : 1.008 9.752 69180 Z= 0.550 Chirality : 0.061 0.254 7836 Planarity : 0.007 0.043 9120 Dihedral : 10.879 89.966 18156 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.94 % Allowed : 5.15 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.08), residues: 6576 helix: -4.29 (0.06), residues: 1632 sheet: -2.38 (0.12), residues: 1488 loop : -2.66 (0.09), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP m 115 HIS 0.005 0.002 HIS M 298 PHE 0.045 0.005 PHE q 19 TYR 0.026 0.004 TYR e 142 ARG 0.020 0.003 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2191 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 2143 time to evaluate : 5.594 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: m 9 ASN cc_start: 0.8254 (m-40) cc_final: 0.7824 (m-40) REVERT: m 30 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7938 (tttp) REVERT: m 100 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8746 (t) REVERT: m 102 THR cc_start: 0.9036 (t) cc_final: 0.8722 (p) REVERT: M 14 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6100 (pp) REVERT: M 19 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6745 (pt) REVERT: M 54 ASP cc_start: 0.8379 (m-30) cc_final: 0.8152 (m-30) REVERT: M 85 VAL cc_start: 0.8118 (t) cc_final: 0.7841 (m) REVERT: M 112 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7886 (mp10) REVERT: M 277 LYS cc_start: 0.8446 (tmtp) cc_final: 0.8208 (tptp) REVERT: M 322 MET cc_start: 0.8706 (tpt) cc_final: 0.8397 (tpt) REVERT: M 347 GLN cc_start: 0.8356 (mm110) cc_final: 0.8092 (mm110) REVERT: A 14 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5837 (pp) REVERT: A 17 ARG cc_start: 0.6878 (ptm160) cc_final: 0.5239 (ptp90) REVERT: A 128 LEU cc_start: 0.8622 (mt) cc_final: 0.8372 (mp) REVERT: A 155 ILE cc_start: 0.8669 (mt) cc_final: 0.8248 (mt) REVERT: A 186 GLN cc_start: 0.6846 (tt0) cc_final: 0.6380 (tt0) REVERT: A 259 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6290 (pp) REVERT: N 155 ILE cc_start: 0.8710 (mt) cc_final: 0.8406 (mp) REVERT: N 203 TYR cc_start: 0.8565 (m-80) cc_final: 0.8352 (m-80) REVERT: N 249 LEU cc_start: 0.7848 (tp) cc_final: 0.7606 (tp) REVERT: N 269 ASN cc_start: 0.8271 (p0) cc_final: 0.8024 (p0) REVERT: N 277 LYS cc_start: 0.8265 (tmtp) cc_final: 0.8016 (tptp) REVERT: N 291 MET cc_start: 0.7779 (mmm) cc_final: 0.7243 (mmt) REVERT: N 347 GLN cc_start: 0.8474 (mm110) cc_final: 0.8188 (mm110) REVERT: N 352 LYS cc_start: 0.8270 (mtpt) cc_final: 0.6920 (mmtt) REVERT: O 44 ASN cc_start: 0.7620 (m-40) cc_final: 0.7386 (m-40) REVERT: O 54 ASP cc_start: 0.8519 (m-30) cc_final: 0.8275 (m-30) REVERT: O 157 ASP cc_start: 0.7064 (p0) cc_final: 0.6836 (p0) REVERT: O 171 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7425 (mmtm) REVERT: O 249 LEU cc_start: 0.8070 (tp) cc_final: 0.7808 (tp) REVERT: O 269 ASN cc_start: 0.8525 (p0) cc_final: 0.8241 (p0) REVERT: O 291 MET cc_start: 0.7550 (mmm) cc_final: 0.7164 (mmt) REVERT: O 307 THR cc_start: 0.8547 (p) cc_final: 0.8310 (m) REVERT: O 347 GLN cc_start: 0.8247 (mm110) cc_final: 0.7991 (mm-40) REVERT: O 352 LYS cc_start: 0.8209 (mtpt) cc_final: 0.6868 (mmtt) REVERT: P 14 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.5904 (pp) REVERT: P 45 VAL cc_start: 0.8924 (t) cc_final: 0.8678 (m) REVERT: P 54 ASP cc_start: 0.8539 (m-30) cc_final: 0.8307 (m-30) REVERT: P 249 LEU cc_start: 0.8137 (tp) cc_final: 0.7837 (tp) REVERT: P 269 ASN cc_start: 0.8595 (p0) cc_final: 0.8373 (p0) REVERT: P 287 MET cc_start: 0.7846 (tmt) cc_final: 0.7549 (tmt) REVERT: P 352 LYS cc_start: 0.8343 (mtpt) cc_final: 0.6923 (mmtt) REVERT: Q 128 LEU cc_start: 0.8532 (mt) cc_final: 0.8251 (mp) REVERT: Q 181 VAL cc_start: 0.8438 (t) cc_final: 0.8081 (p) REVERT: Q 249 LEU cc_start: 0.7881 (tp) cc_final: 0.7649 (tp) REVERT: Q 269 ASN cc_start: 0.8332 (p0) cc_final: 0.8087 (p0) REVERT: Q 277 LYS cc_start: 0.8226 (tmtp) cc_final: 0.8003 (tptp) REVERT: Q 291 MET cc_start: 0.7741 (mmm) cc_final: 0.7207 (mmt) REVERT: Q 327 ASN cc_start: 0.8460 (t0) cc_final: 0.8259 (t0) REVERT: Q 352 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7012 (mmtt) REVERT: R 14 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.6075 (pp) REVERT: R 44 ASN cc_start: 0.7670 (m-40) cc_final: 0.7163 (m-40) REVERT: R 77 GLN cc_start: 0.7935 (tt0) cc_final: 0.7728 (tp40) REVERT: R 171 LYS cc_start: 0.7552 (mtmt) cc_final: 0.7349 (mmtm) REVERT: R 176 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8321 (ttpp) REVERT: R 186 GLN cc_start: 0.6960 (tt0) cc_final: 0.6610 (tt0) REVERT: R 203 TYR cc_start: 0.8523 (m-80) cc_final: 0.8264 (m-80) REVERT: R 249 LEU cc_start: 0.7942 (tp) cc_final: 0.7706 (tp) REVERT: R 269 ASN cc_start: 0.8238 (p0) cc_final: 0.7933 (p0) REVERT: R 291 MET cc_start: 0.7609 (mmm) cc_final: 0.7362 (mmp) REVERT: R 347 GLN cc_start: 0.8254 (mm110) cc_final: 0.7957 (mm110) REVERT: R 352 LYS cc_start: 0.7976 (mtpt) cc_final: 0.6683 (mmtt) REVERT: B 17 ARG cc_start: 0.6752 (ptm160) cc_final: 0.5276 (ptp90) REVERT: B 44 ASN cc_start: 0.7744 (m-40) cc_final: 0.7537 (m-40) REVERT: B 54 ASP cc_start: 0.8471 (m-30) cc_final: 0.8262 (m-30) REVERT: B 96 SER cc_start: 0.8535 (t) cc_final: 0.8273 (p) REVERT: B 157 ASP cc_start: 0.7231 (p0) cc_final: 0.6936 (p0) REVERT: B 291 MET cc_start: 0.7643 (mmm) cc_final: 0.7349 (mmm) REVERT: B 347 GLN cc_start: 0.8378 (mm110) cc_final: 0.8080 (mm110) REVERT: C 17 ARG cc_start: 0.6690 (ptm160) cc_final: 0.4986 (ptp90) REVERT: C 54 ASP cc_start: 0.8533 (m-30) cc_final: 0.8296 (m-30) REVERT: C 157 ASP cc_start: 0.7260 (p0) cc_final: 0.7022 (p0) REVERT: C 196 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6661 (ptt-90) REVERT: C 269 ASN cc_start: 0.8440 (p0) cc_final: 0.8117 (p0) REVERT: C 291 MET cc_start: 0.7338 (mmm) cc_final: 0.7044 (mmm) REVERT: D 14 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5717 (pp) REVERT: D 17 ARG cc_start: 0.6917 (ptm160) cc_final: 0.5512 (ptp90) REVERT: D 44 ASN cc_start: 0.7654 (m-40) cc_final: 0.7399 (m-40) REVERT: D 128 LEU cc_start: 0.8648 (mt) cc_final: 0.8415 (mp) REVERT: D 155 ILE cc_start: 0.8731 (mt) cc_final: 0.8316 (mt) REVERT: D 186 GLN cc_start: 0.7009 (tt0) cc_final: 0.6509 (tt0) REVERT: D 203 TYR cc_start: 0.8529 (m-80) cc_final: 0.7715 (m-80) REVERT: D 249 LEU cc_start: 0.7993 (tp) cc_final: 0.7765 (tp) REVERT: D 291 MET cc_start: 0.7302 (mmm) cc_final: 0.6965 (mmm) REVERT: E 17 ARG cc_start: 0.6731 (ptm160) cc_final: 0.5079 (ptp90) REVERT: E 54 ASP cc_start: 0.8401 (m-30) cc_final: 0.8186 (m-30) REVERT: E 96 SER cc_start: 0.8482 (t) cc_final: 0.8254 (p) REVERT: E 171 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7588 (mmtm) REVERT: E 186 GLN cc_start: 0.7100 (tt0) cc_final: 0.6688 (tt0) REVERT: E 347 GLN cc_start: 0.8196 (mm110) cc_final: 0.7973 (mm110) REVERT: F 7 VAL cc_start: 0.8719 (p) cc_final: 0.8516 (t) REVERT: F 17 ARG cc_start: 0.6718 (ptm160) cc_final: 0.4870 (ptp90) REVERT: F 44 ASN cc_start: 0.7697 (m-40) cc_final: 0.7241 (m-40) REVERT: F 54 ASP cc_start: 0.8432 (m-30) cc_final: 0.8210 (m-30) REVERT: F 85 VAL cc_start: 0.8327 (t) cc_final: 0.8089 (m) REVERT: F 109 THR cc_start: 0.7953 (p) cc_final: 0.7736 (m) REVERT: F 155 ILE cc_start: 0.8542 (mt) cc_final: 0.8065 (mt) REVERT: F 186 GLN cc_start: 0.7117 (tt0) cc_final: 0.6627 (tt0) REVERT: F 269 ASN cc_start: 0.8407 (p0) cc_final: 0.8181 (p0) REVERT: F 291 MET cc_start: 0.7365 (mmm) cc_final: 0.7076 (mmm) REVERT: a 2 MET cc_start: 0.8352 (mtt) cc_final: 0.8020 (mtt) REVERT: a 37 GLN cc_start: 0.7806 (mt0) cc_final: 0.7584 (mp10) REVERT: a 43 MET cc_start: 0.8708 (ptt) cc_final: 0.8414 (ptt) REVERT: a 51 MET cc_start: 0.8494 (mmm) cc_final: 0.8201 (mmm) REVERT: n 30 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8108 (tttm) REVERT: n 90 LYS cc_start: 0.8401 (tptm) cc_final: 0.8134 (mtpp) REVERT: n 130 SER cc_start: 0.8731 (t) cc_final: 0.8512 (m) REVERT: o 30 LYS cc_start: 0.8334 (ttpp) cc_final: 0.8019 (tttp) REVERT: o 35 THR cc_start: 0.8836 (p) cc_final: 0.8624 (p) REVERT: o 56 MET cc_start: 0.8348 (mtm) cc_final: 0.7974 (mtm) REVERT: o 93 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8188 (mmtt) REVERT: o 102 THR cc_start: 0.8960 (t) cc_final: 0.8676 (p) REVERT: p 9 ASN cc_start: 0.8231 (m-40) cc_final: 0.7909 (m-40) REVERT: p 30 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7989 (tttp) REVERT: p 100 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8736 (t) REVERT: p 102 THR cc_start: 0.8994 (t) cc_final: 0.8687 (p) REVERT: q 30 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8175 (tttm) REVERT: r 30 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8005 (tttp) REVERT: r 35 THR cc_start: 0.8861 (p) cc_final: 0.8648 (p) REVERT: r 37 GLN cc_start: 0.7795 (mt0) cc_final: 0.7588 (mp-120) REVERT: r 56 MET cc_start: 0.8389 (mtm) cc_final: 0.8094 (mtm) REVERT: r 102 THR cc_start: 0.8962 (t) cc_final: 0.8649 (p) REVERT: b 102 THR cc_start: 0.9136 (t) cc_final: 0.8786 (p) REVERT: b 144 ILE cc_start: 0.8919 (mp) cc_final: 0.8714 (mm) REVERT: c 30 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7912 (tttp) REVERT: c 71 ASN cc_start: 0.8258 (m110) cc_final: 0.7884 (m110) REVERT: c 102 THR cc_start: 0.9049 (t) cc_final: 0.8733 (p) REVERT: d 2 MET cc_start: 0.8227 (mtt) cc_final: 0.7913 (mtt) REVERT: d 37 GLN cc_start: 0.7757 (mt0) cc_final: 0.7533 (mp10) REVERT: d 43 MET cc_start: 0.8703 (ptt) cc_final: 0.8370 (ptt) REVERT: e 56 MET cc_start: 0.8382 (mtm) cc_final: 0.8098 (mtp) REVERT: e 102 THR cc_start: 0.9140 (t) cc_final: 0.8759 (p) REVERT: f 9 ASN cc_start: 0.8354 (m-40) cc_final: 0.8139 (m-40) REVERT: f 30 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7955 (tttp) REVERT: f 102 THR cc_start: 0.9058 (t) cc_final: 0.8699 (p) outliers start: 48 outliers final: 11 residues processed: 2174 average time/residue: 1.6033 time to fit residues: 4316.4466 Evaluate side-chains 1345 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1325 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 100 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain f residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 0.8980 chunk 491 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 507 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 378 optimal weight: 0.9990 chunk 588 optimal weight: 0.0030 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 71 ASN M 124 GLN M 172 ASN M 193 ASN M 298 HIS A 94 GLN A 172 ASN A 193 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN A 377 GLN N 11 ASN N 77 GLN N 172 ASN N 193 ASN O 94 GLN O 193 ASN O 369 ASN P 94 GLN P 112 GLN P 136 GLN P 193 ASN P 298 HIS P 333 ASN Q 77 GLN Q 172 ASN Q 193 ASN R 11 ASN R 94 GLN B 112 GLN B 136 GLN B 193 ASN B 347 GLN B 377 GLN C 94 GLN C 112 GLN C 124 GLN C 193 ASN C 298 HIS C 350 GLN C 369 ASN C 377 GLN D 94 GLN D 193 ASN D 298 HIS D 347 GLN D 369 ASN D 377 GLN E 112 GLN E 172 ASN E 193 ASN E 298 HIS E 347 GLN F 94 GLN F 112 GLN F 124 GLN F 172 ASN F 193 ASN F 298 HIS F 350 GLN F 369 ASN F 377 GLN n 71 ASN o 71 ASN p 71 ASN q 71 ASN r 71 ASN b 37 GLN ** c 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 ASN c 164 ASN d 154 ASN e 37 GLN ** f 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50880 Z= 0.174 Angle : 0.610 8.900 69180 Z= 0.329 Chirality : 0.045 0.255 7836 Planarity : 0.004 0.035 9120 Dihedral : 8.057 89.283 7156 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.84 % Allowed : 16.10 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.09), residues: 6576 helix: -2.22 (0.10), residues: 1680 sheet: -2.40 (0.12), residues: 1488 loop : -2.26 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 188 HIS 0.003 0.001 HIS E 298 PHE 0.014 0.001 PHE o 19 TYR 0.014 0.002 TYR M 264 ARG 0.007 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1404 time to evaluate : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8245 (m-40) cc_final: 0.7907 (m-40) REVERT: m 102 THR cc_start: 0.8889 (t) cc_final: 0.8497 (p) REVERT: m 131 TYR cc_start: 0.8857 (t80) cc_final: 0.8654 (t80) REVERT: m 133 LYS cc_start: 0.8650 (tttm) cc_final: 0.8334 (tttt) REVERT: M 14 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6205 (pp) REVERT: M 85 VAL cc_start: 0.7995 (t) cc_final: 0.7668 (m) REVERT: M 112 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7913 (mp10) REVERT: M 120 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7960 (ttm-80) REVERT: M 249 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7557 (mt) REVERT: M 347 GLN cc_start: 0.8412 (mm110) cc_final: 0.8048 (mm110) REVERT: A 14 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.6047 (pp) REVERT: A 17 ARG cc_start: 0.6729 (ptm160) cc_final: 0.5322 (ptp90) REVERT: A 155 ILE cc_start: 0.8537 (mt) cc_final: 0.8269 (mt) REVERT: A 249 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 332 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7499 (pt) REVERT: A 354 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: N 137 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: N 224 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8500 (mmtp) REVERT: N 269 ASN cc_start: 0.8001 (p0) cc_final: 0.7785 (p0) REVERT: N 277 LYS cc_start: 0.8200 (tmtp) cc_final: 0.7959 (tptp) REVERT: N 283 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7765 (tpp80) REVERT: N 291 MET cc_start: 0.7928 (mmm) cc_final: 0.7421 (mmt) REVERT: N 326 LYS cc_start: 0.8817 (tttm) cc_final: 0.8613 (ttpp) REVERT: N 347 GLN cc_start: 0.8438 (mm110) cc_final: 0.8139 (mm110) REVERT: N 352 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7010 (mmtt) REVERT: O 44 ASN cc_start: 0.7427 (m-40) cc_final: 0.7204 (m-40) REVERT: O 169 TYR cc_start: 0.8599 (t80) cc_final: 0.8263 (t80) REVERT: O 269 ASN cc_start: 0.8255 (p0) cc_final: 0.7930 (p0) REVERT: O 277 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8115 (tptp) REVERT: O 291 MET cc_start: 0.7722 (mmm) cc_final: 0.7298 (mmp) REVERT: O 307 THR cc_start: 0.8611 (p) cc_final: 0.8368 (m) REVERT: O 347 GLN cc_start: 0.8172 (mm110) cc_final: 0.7935 (mm-40) REVERT: O 352 LYS cc_start: 0.8193 (mtpt) cc_final: 0.6853 (mmpt) REVERT: P 14 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6152 (pp) REVERT: P 42 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7602 (mmtp) REVERT: Q 137 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: Q 143 MET cc_start: 0.8298 (mtp) cc_final: 0.8091 (mtt) REVERT: Q 224 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8604 (mmtp) REVERT: Q 269 ASN cc_start: 0.8030 (p0) cc_final: 0.7805 (p0) REVERT: Q 287 MET cc_start: 0.8085 (tmt) cc_final: 0.7611 (tmm) REVERT: Q 291 MET cc_start: 0.7858 (mmm) cc_final: 0.7372 (mmt) REVERT: Q 327 ASN cc_start: 0.8386 (t0) cc_final: 0.8091 (t0) REVERT: Q 352 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7005 (mmtt) REVERT: R 7 VAL cc_start: 0.8673 (p) cc_final: 0.8452 (t) REVERT: R 14 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6296 (pp) REVERT: R 44 ASN cc_start: 0.7206 (m-40) cc_final: 0.6978 (m-40) REVERT: R 137 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: R 269 ASN cc_start: 0.8035 (p0) cc_final: 0.7799 (p0) REVERT: R 277 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7716 (tmmt) REVERT: R 347 GLN cc_start: 0.8198 (mm110) cc_final: 0.7895 (mm110) REVERT: R 352 LYS cc_start: 0.8085 (mtpt) cc_final: 0.6771 (mmtt) REVERT: B 17 ARG cc_start: 0.6688 (ptm160) cc_final: 0.5006 (ttm-80) REVERT: B 96 SER cc_start: 0.8458 (t) cc_final: 0.8182 (p) REVERT: B 120 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.8062 (mtp85) REVERT: B 136 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7327 (mm110) REVERT: B 137 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: B 143 MET cc_start: 0.8156 (mtp) cc_final: 0.7888 (mtt) REVERT: B 180 MET cc_start: 0.8511 (ttm) cc_final: 0.8148 (ttp) REVERT: B 249 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7953 (tm) REVERT: B 347 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8012 (mm110) REVERT: B 354 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: C 7 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8592 (p) REVERT: C 14 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6451 (pp) REVERT: C 17 ARG cc_start: 0.6629 (ptm160) cc_final: 0.4782 (ptp90) REVERT: C 120 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (mtt-85) REVERT: C 249 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7572 (tm) REVERT: C 269 ASN cc_start: 0.8095 (p0) cc_final: 0.7888 (p0) REVERT: D 14 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.5963 (pp) REVERT: D 17 ARG cc_start: 0.6747 (ptm160) cc_final: 0.5303 (ptp90) REVERT: D 44 ASN cc_start: 0.7469 (m-40) cc_final: 0.7248 (m-40) REVERT: D 137 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: D 155 ILE cc_start: 0.8610 (mt) cc_final: 0.8377 (mt) REVERT: D 327 ASN cc_start: 0.8242 (t0) cc_final: 0.8012 (t0) REVERT: D 332 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7427 (pt) REVERT: E 17 ARG cc_start: 0.6596 (ptm160) cc_final: 0.4941 (ttm-80) REVERT: E 96 SER cc_start: 0.8342 (t) cc_final: 0.8129 (p) REVERT: E 120 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.8000 (mtp85) REVERT: E 137 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: E 249 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7808 (tm) REVERT: E 252 ASN cc_start: 0.8437 (m-40) cc_final: 0.7935 (m-40) REVERT: E 347 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8002 (mm110) REVERT: E 354 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: F 14 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6323 (pp) REVERT: F 17 ARG cc_start: 0.6704 (ptm160) cc_final: 0.4907 (ptp90) REVERT: F 42 LYS cc_start: 0.8276 (mmpt) cc_final: 0.7730 (mmtp) REVERT: F 44 ASN cc_start: 0.7321 (m-40) cc_final: 0.7095 (m-40) REVERT: F 85 VAL cc_start: 0.8109 (t) cc_final: 0.7832 (m) REVERT: F 120 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7910 (mtt-85) REVERT: F 155 ILE cc_start: 0.8402 (mt) cc_final: 0.8058 (mt) REVERT: F 249 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7454 (tm) REVERT: F 264 TYR cc_start: 0.5672 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: F 269 ASN cc_start: 0.8168 (p0) cc_final: 0.7965 (p0) REVERT: F 277 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8053 (tttp) REVERT: F 354 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: F 372 VAL cc_start: 0.9323 (p) cc_final: 0.9122 (t) REVERT: a 2 MET cc_start: 0.8299 (mtt) cc_final: 0.7958 (mtt) REVERT: a 43 MET cc_start: 0.8599 (ptt) cc_final: 0.8274 (ptt) REVERT: a 51 MET cc_start: 0.8312 (mmm) cc_final: 0.8034 (mmm) REVERT: a 59 LYS cc_start: 0.8840 (ptpp) cc_final: 0.8277 (mtpt) REVERT: n 30 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8095 (tttm) REVERT: n 59 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8327 (mtmt) REVERT: n 100 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8601 (t) REVERT: n 133 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8661 (tttt) REVERT: o 30 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8009 (tttp) REVERT: o 56 MET cc_start: 0.8247 (mtm) cc_final: 0.7982 (mtm) REVERT: o 63 ASN cc_start: 0.8037 (p0) cc_final: 0.7828 (p0) REVERT: o 100 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8757 (t) REVERT: o 102 THR cc_start: 0.8833 (t) cc_final: 0.8494 (p) REVERT: p 9 ASN cc_start: 0.8229 (m-40) cc_final: 0.7903 (m-40) REVERT: p 59 LYS cc_start: 0.8530 (ptpt) cc_final: 0.8035 (mttt) REVERT: p 100 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8732 (t) REVERT: p 102 THR cc_start: 0.8867 (t) cc_final: 0.8551 (p) REVERT: p 120 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7444 (ttmm) REVERT: p 131 TYR cc_start: 0.8725 (t80) cc_final: 0.8465 (t80) REVERT: p 133 LYS cc_start: 0.8747 (ttpm) cc_final: 0.8484 (ttpt) REVERT: q 30 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8067 (tttm) REVERT: q 59 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8340 (mtmt) REVERT: q 100 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8629 (t) REVERT: q 133 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8480 (ttpt) REVERT: r 30 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8048 (tttp) REVERT: r 56 MET cc_start: 0.8232 (mtm) cc_final: 0.7948 (mtm) REVERT: r 100 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8705 (t) REVERT: b 2 MET cc_start: 0.7969 (mtt) cc_final: 0.7693 (mtm) REVERT: b 59 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8236 (mttt) REVERT: b 100 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8701 (t) REVERT: b 102 THR cc_start: 0.8976 (t) cc_final: 0.8608 (p) REVERT: c 100 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8610 (t) REVERT: c 102 THR cc_start: 0.8921 (t) cc_final: 0.8518 (p) REVERT: c 120 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7437 (ttmt) REVERT: d 2 MET cc_start: 0.8348 (mtt) cc_final: 0.8006 (mtt) REVERT: d 30 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7935 (tttp) REVERT: d 43 MET cc_start: 0.8553 (ptt) cc_final: 0.8148 (ptt) REVERT: d 59 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8444 (mtpt) REVERT: d 100 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8564 (t) REVERT: e 2 MET cc_start: 0.7918 (mtt) cc_final: 0.7642 (mtm) REVERT: e 100 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8741 (t) REVERT: e 102 THR cc_start: 0.9017 (t) cc_final: 0.8622 (p) REVERT: f 30 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7997 (tttp) REVERT: f 59 LYS cc_start: 0.8555 (ptpt) cc_final: 0.8340 (mtpt) REVERT: f 100 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8600 (t) REVERT: f 102 THR cc_start: 0.8996 (t) cc_final: 0.8584 (p) REVERT: f 120 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7447 (ttmt) outliers start: 299 outliers final: 97 residues processed: 1560 average time/residue: 1.4736 time to fit residues: 2907.9724 Evaluate side-chains 1395 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1250 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 288 ASP Chi-restraints excluded: chain O residue 312 LYS Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 276 SER Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain Q residue 353 VAL Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 157 ASP Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 277 LYS Chi-restraints excluded: chain R residue 288 ASP Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 354 TYR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 133 LYS Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 133 LYS Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 59 LYS Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 589 optimal weight: 6.9990 chunk 636 optimal weight: 4.9990 chunk 525 optimal weight: 4.9990 chunk 584 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 472 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN M 347 GLN M 350 GLN M 377 GLN A 298 HIS N 11 ASN N 347 GLN O 11 ASN O 347 GLN ** P 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 327 ASN P 333 ASN ** R 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 ASN R 347 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 369 ASN F 124 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 350 GLN F 377 GLN a 164 ASN n 37 GLN ** n 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 78 GLN o 5 GLN q 37 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 5 GLN ** c 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 164 ASN f 5 GLN ** f 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 50880 Z= 0.339 Angle : 0.663 8.539 69180 Z= 0.356 Chirality : 0.047 0.237 7836 Planarity : 0.005 0.050 9120 Dihedral : 7.891 89.461 7148 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 8.02 % Allowed : 18.25 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6576 helix: -0.86 (0.12), residues: 1764 sheet: -2.19 (0.12), residues: 1548 loop : -2.18 (0.10), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 188 HIS 0.004 0.002 HIS D 5 PHE 0.021 0.003 PHE a 19 TYR 0.024 0.002 TYR Q 354 ARG 0.006 0.001 ARG N 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1687 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 1276 time to evaluate : 5.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8276 (m-40) cc_final: 0.7921 (m-40) REVERT: m 102 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8575 (p) REVERT: m 120 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7551 (ttmm) REVERT: m 127 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8688 (t) REVERT: m 133 LYS cc_start: 0.8674 (tttm) cc_final: 0.8401 (tttt) REVERT: M 14 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6744 (pt) REVERT: M 73 TYR cc_start: 0.8516 (m-80) cc_final: 0.8311 (m-80) REVERT: M 112 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7962 (mp10) REVERT: M 120 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8111 (ttm-80) REVERT: M 137 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: M 249 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7648 (mt) REVERT: M 347 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8239 (mm110) REVERT: A 17 ARG cc_start: 0.6744 (ptm160) cc_final: 0.5365 (ptp90) REVERT: A 137 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: A 155 ILE cc_start: 0.8608 (mt) cc_final: 0.8382 (mt) REVERT: A 312 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7939 (mmtt) REVERT: A 332 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7617 (pt) REVERT: N 17 ARG cc_start: 0.7115 (ptm160) cc_final: 0.6897 (ttp-170) REVERT: N 137 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: N 249 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7822 (mt) REVERT: N 277 LYS cc_start: 0.8242 (tmtp) cc_final: 0.7945 (tptp) REVERT: N 291 MET cc_start: 0.8017 (mmm) cc_final: 0.7676 (mmt) REVERT: N 352 LYS cc_start: 0.8503 (mtpt) cc_final: 0.7092 (mmtt) REVERT: N 380 THR cc_start: 0.7210 (p) cc_final: 0.6979 (m) REVERT: O 44 ASN cc_start: 0.7632 (m-40) cc_final: 0.7426 (m-40) REVERT: O 137 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: O 146 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8548 (tt) REVERT: O 249 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (tp) REVERT: O 269 ASN cc_start: 0.8336 (p0) cc_final: 0.8058 (p0) REVERT: O 347 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8115 (mm-40) REVERT: O 372 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9060 (t) REVERT: P 137 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: P 146 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8283 (tt) REVERT: P 249 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7870 (tm) REVERT: P 282 THR cc_start: 0.8210 (m) cc_final: 0.7750 (p) REVERT: P 287 MET cc_start: 0.7986 (tmt) cc_final: 0.7712 (tmm) REVERT: P 307 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.7979 (m) REVERT: Q 137 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: Q 277 LYS cc_start: 0.8310 (tptp) cc_final: 0.8057 (tptp) REVERT: Q 291 MET cc_start: 0.8060 (mmm) cc_final: 0.7714 (mmt) REVERT: R 7 VAL cc_start: 0.8805 (p) cc_final: 0.8583 (t) REVERT: R 137 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: R 146 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8510 (tt) REVERT: R 224 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8221 (mptp) REVERT: R 269 ASN cc_start: 0.8254 (p0) cc_final: 0.7980 (p0) REVERT: R 347 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8135 (mm-40) REVERT: R 354 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: B 17 ARG cc_start: 0.6910 (ptm160) cc_final: 0.4931 (ttm-80) REVERT: B 137 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: B 180 MET cc_start: 0.8608 (ttm) cc_final: 0.8146 (ttp) REVERT: B 249 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8237 (tp) REVERT: B 347 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8012 (mm110) REVERT: C 14 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6583 (pt) REVERT: C 17 ARG cc_start: 0.6865 (ptm160) cc_final: 0.4886 (ttm-80) REVERT: C 120 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8096 (mtt-85) REVERT: C 249 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7523 (tm) REVERT: C 352 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8119 (mtmp) REVERT: D 17 ARG cc_start: 0.6828 (ptm160) cc_final: 0.5338 (ptp90) REVERT: D 44 ASN cc_start: 0.7683 (m-40) cc_final: 0.7473 (m-40) REVERT: D 137 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: D 155 ILE cc_start: 0.8628 (mt) cc_final: 0.8300 (mt) REVERT: D 246 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7774 (ttm170) REVERT: E 17 ARG cc_start: 0.6762 (ptm160) cc_final: 0.4951 (ttm-80) REVERT: E 137 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: E 249 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8134 (tp) REVERT: E 277 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7911 (tttm) REVERT: E 347 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7983 (mm110) REVERT: F 14 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6382 (pt) REVERT: F 17 ARG cc_start: 0.6743 (ptm160) cc_final: 0.4705 (ptp90) REVERT: F 42 LYS cc_start: 0.8368 (mmpt) cc_final: 0.7832 (mmtp) REVERT: F 44 ASN cc_start: 0.7613 (m-40) cc_final: 0.7363 (m-40) REVERT: F 120 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8063 (mtt-85) REVERT: F 155 ILE cc_start: 0.8380 (mt) cc_final: 0.8038 (mt) REVERT: F 249 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7531 (tm) REVERT: F 264 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5636 (m-80) REVERT: a 37 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: a 43 MET cc_start: 0.8637 (ptt) cc_final: 0.8199 (ptt) REVERT: a 51 MET cc_start: 0.8232 (mmm) cc_final: 0.7991 (mmm) REVERT: a 59 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8276 (mtpt) REVERT: a 127 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8763 (p) REVERT: n 30 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8335 (tttm) REVERT: n 100 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8672 (t) REVERT: n 127 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8754 (p) REVERT: n 133 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8655 (tttt) REVERT: o 37 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: o 56 MET cc_start: 0.8293 (mtm) cc_final: 0.7941 (mtm) REVERT: o 100 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8738 (t) REVERT: o 102 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8604 (p) REVERT: o 127 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8842 (p) REVERT: o 133 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8123 (tttm) REVERT: p 9 ASN cc_start: 0.8276 (m-40) cc_final: 0.7930 (m-40) REVERT: p 102 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8557 (p) REVERT: p 120 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7597 (ttmm) REVERT: p 133 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: q 30 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8328 (tttm) REVERT: q 100 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8668 (t) REVERT: q 133 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8777 (ttpm) REVERT: r 30 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8144 (tttp) REVERT: r 56 MET cc_start: 0.8320 (mtm) cc_final: 0.7940 (mtm) REVERT: r 100 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8698 (t) REVERT: r 102 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8693 (p) REVERT: r 127 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8816 (p) REVERT: r 133 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: b 37 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6876 (mt0) REVERT: b 93 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8309 (mmmt) REVERT: b 100 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8720 (t) REVERT: b 102 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8569 (p) REVERT: c 37 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6424 (mp-120) REVERT: c 59 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8526 (mttm) REVERT: c 100 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8649 (t) REVERT: c 102 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8589 (p) REVERT: c 120 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7697 (ttmt) REVERT: c 133 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8360 (tttm) REVERT: d 37 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: d 43 MET cc_start: 0.8626 (ptt) cc_final: 0.8213 (ptt) REVERT: d 72 PHE cc_start: 0.8819 (m-80) cc_final: 0.8594 (m-80) REVERT: d 100 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8682 (t) REVERT: e 93 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8326 (mmmt) REVERT: e 100 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8754 (t) REVERT: e 102 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8602 (p) REVERT: e 124 LYS cc_start: 0.8659 (mttm) cc_final: 0.8433 (mttp) REVERT: e 127 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8799 (p) REVERT: f 37 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6382 (mp-120) REVERT: f 59 LYS cc_start: 0.8739 (ptpt) cc_final: 0.8403 (mttm) REVERT: f 120 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7685 (ttmt) REVERT: f 133 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8310 (tttm) outliers start: 411 outliers final: 179 residues processed: 1484 average time/residue: 1.4432 time to fit residues: 2724.1800 Evaluate side-chains 1427 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1173 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 137 GLN Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 249 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 312 LYS Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 137 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 271 THR Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 52 LYS Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 288 ASP Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 354 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 133 LYS Chi-restraints excluded: chain o residue 35 THR Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 133 LYS Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 133 LYS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 133 LYS Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 63 ASN Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 122 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 133 LYS Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 133 LYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 35 THR Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 56 MET Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 133 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 2.9990 chunk 443 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 395 optimal weight: 0.9990 chunk 591 optimal weight: 6.9990 chunk 626 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 560 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN N 11 ASN O 11 ASN P 298 HIS R 11 ASN B 112 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN a 164 ASN n 37 GLN ** n 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 37 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 5 GLN c 9 ASN c 164 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 ASN e 37 GLN ** f 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50880 Z= 0.288 Angle : 0.609 8.355 69180 Z= 0.327 Chirality : 0.046 0.253 7836 Planarity : 0.005 0.047 9120 Dihedral : 7.629 88.564 7140 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 8.84 % Allowed : 20.12 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 6576 helix: 0.13 (0.13), residues: 1668 sheet: -2.04 (0.13), residues: 1560 loop : -2.02 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 188 HIS 0.003 0.001 HIS O 5 PHE 0.014 0.002 PHE a 19 TYR 0.017 0.002 TYR d 125 ARG 0.007 0.001 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1651 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 453 poor density : 1198 time to evaluate : 5.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8284 (m-40) cc_final: 0.7918 (m-40) REVERT: m 102 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8494 (p) REVERT: m 120 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: m 127 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8674 (t) REVERT: m 133 LYS cc_start: 0.8670 (tttm) cc_final: 0.8442 (tttp) REVERT: M 65 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8186 (tp) REVERT: M 96 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (p) REVERT: M 120 ARG cc_start: 0.8325 (mtt-85) cc_final: 0.8120 (ttm-80) REVERT: M 146 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8226 (tt) REVERT: M 249 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7590 (mt) REVERT: A 17 ARG cc_start: 0.6703 (ptm160) cc_final: 0.4968 (ttp-110) REVERT: A 137 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: A 155 ILE cc_start: 0.8623 (mt) cc_final: 0.8263 (mt) REVERT: A 332 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7567 (pt) REVERT: A 352 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7693 (mtpm) REVERT: N 17 ARG cc_start: 0.7096 (ptm160) cc_final: 0.6804 (ttp-170) REVERT: N 133 HIS cc_start: 0.8359 (m-70) cc_final: 0.8127 (m90) REVERT: N 137 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: N 249 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7864 (tp) REVERT: N 277 LYS cc_start: 0.8204 (tmtp) cc_final: 0.8004 (tptp) REVERT: N 291 MET cc_start: 0.8001 (mmm) cc_final: 0.7712 (mmp) REVERT: N 380 THR cc_start: 0.7458 (p) cc_final: 0.7168 (m) REVERT: O 42 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7827 (mmtp) REVERT: O 44 ASN cc_start: 0.7544 (m-40) cc_final: 0.7337 (m-40) REVERT: O 137 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: O 269 ASN cc_start: 0.8215 (p0) cc_final: 0.7921 (p0) REVERT: O 277 LYS cc_start: 0.8429 (tptp) cc_final: 0.8219 (tptp) REVERT: O 347 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8129 (mm-40) REVERT: O 352 LYS cc_start: 0.8496 (mtpt) cc_final: 0.7182 (mmpt) REVERT: P 137 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: P 146 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (tt) REVERT: P 287 MET cc_start: 0.8031 (tmt) cc_final: 0.7737 (tmm) REVERT: P 307 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8035 (m) REVERT: Q 137 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: Q 291 MET cc_start: 0.8017 (mmm) cc_final: 0.7722 (mmt) REVERT: R 7 VAL cc_start: 0.8832 (p) cc_final: 0.8552 (t) REVERT: R 42 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7739 (mmtp) REVERT: R 137 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: R 269 ASN cc_start: 0.8229 (p0) cc_final: 0.7945 (p0) REVERT: R 352 LYS cc_start: 0.8366 (mtpt) cc_final: 0.6993 (mmpt) REVERT: B 17 ARG cc_start: 0.6819 (ptm160) cc_final: 0.4911 (ttm-80) REVERT: B 137 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: B 180 MET cc_start: 0.8626 (ttm) cc_final: 0.8245 (ttp) REVERT: B 249 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8225 (tp) REVERT: B 277 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8152 (tptp) REVERT: B 348 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 17 ARG cc_start: 0.6750 (ptm160) cc_final: 0.5011 (ttm-80) REVERT: C 120 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8039 (mtt-85) REVERT: C 146 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8111 (tt) REVERT: C 155 ILE cc_start: 0.8377 (mt) cc_final: 0.8168 (mt) REVERT: C 249 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7441 (tm) REVERT: C 352 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (mtmp) REVERT: D 17 ARG cc_start: 0.6726 (ptm160) cc_final: 0.5037 (ttp-110) REVERT: D 44 ASN cc_start: 0.7626 (m-40) cc_final: 0.7406 (m-40) REVERT: D 133 HIS cc_start: 0.8213 (m-70) cc_final: 0.7919 (m-70) REVERT: D 137 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 155 ILE cc_start: 0.8586 (mt) cc_final: 0.8279 (mt) REVERT: D 246 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: D 283 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7455 (mtt90) REVERT: D 307 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8227 (m) REVERT: E 17 ARG cc_start: 0.6814 (ptm160) cc_final: 0.4890 (ttm-80) REVERT: E 42 LYS cc_start: 0.8356 (mmpt) cc_final: 0.7916 (mmtp) REVERT: E 137 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: E 180 MET cc_start: 0.8591 (ttp) cc_final: 0.8293 (ttp) REVERT: E 249 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (tp) REVERT: E 252 ASN cc_start: 0.8412 (m-40) cc_final: 0.7880 (m-40) REVERT: E 277 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7670 (tmmm) REVERT: F 17 ARG cc_start: 0.6842 (ptm160) cc_final: 0.4926 (ttm-80) REVERT: F 42 LYS cc_start: 0.8323 (mmpt) cc_final: 0.7796 (mmtp) REVERT: F 44 ASN cc_start: 0.7587 (m-40) cc_final: 0.7306 (m-40) REVERT: F 120 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8011 (mtt-85) REVERT: F 155 ILE cc_start: 0.8384 (mt) cc_final: 0.8040 (mt) REVERT: F 249 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7409 (tm) REVERT: F 264 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: F 352 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8083 (mtmp) REVERT: a 37 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: a 43 MET cc_start: 0.8565 (ptt) cc_final: 0.8084 (ptt) REVERT: a 59 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8308 (mtpt) REVERT: a 127 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8737 (p) REVERT: n 30 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8291 (tttm) REVERT: n 100 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8709 (t) REVERT: n 127 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8792 (p) REVERT: n 133 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8656 (tttt) REVERT: o 37 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: o 56 MET cc_start: 0.8312 (mtm) cc_final: 0.7958 (mtm) REVERT: o 100 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8779 (t) REVERT: o 102 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8645 (p) REVERT: o 127 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8828 (p) REVERT: p 9 ASN cc_start: 0.8274 (m-40) cc_final: 0.7927 (m-40) REVERT: p 59 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8513 (mttt) REVERT: p 100 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8833 (t) REVERT: p 102 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8558 (p) REVERT: p 120 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7602 (ttmm) REVERT: p 133 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8496 (ttpt) REVERT: q 30 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8318 (tttm) REVERT: q 100 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8684 (t) REVERT: q 133 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (ttpm) REVERT: r 30 LYS cc_start: 0.8501 (ttpp) cc_final: 0.8233 (tttp) REVERT: r 56 MET cc_start: 0.8327 (mtm) cc_final: 0.7994 (mtm) REVERT: r 100 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8743 (t) REVERT: r 102 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8786 (p) REVERT: r 127 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8810 (p) REVERT: b 37 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.6834 (mt0) REVERT: b 93 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8288 (mmmt) REVERT: b 100 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8745 (t) REVERT: b 102 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8589 (p) REVERT: c 37 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6370 (mp-120) REVERT: c 59 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8354 (mttt) REVERT: c 100 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8675 (t) REVERT: c 102 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8614 (p) REVERT: c 120 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (ttmt) REVERT: d 37 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: d 43 MET cc_start: 0.8557 (ptt) cc_final: 0.8175 (ptt) REVERT: d 72 PHE cc_start: 0.8817 (m-80) cc_final: 0.8571 (m-80) REVERT: d 100 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8666 (t) REVERT: d 127 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8906 (p) REVERT: e 93 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8335 (mmmt) REVERT: e 100 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8772 (t) REVERT: e 102 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8590 (p) REVERT: e 127 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (p) REVERT: e 133 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (tttt) REVERT: f 37 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6344 (mp-120) REVERT: f 59 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8420 (mttm) REVERT: f 102 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8674 (p) REVERT: f 120 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7793 (ttmt) REVERT: f 127 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (p) outliers start: 453 outliers final: 232 residues processed: 1452 average time/residue: 1.4509 time to fit residues: 2669.1580 Evaluate side-chains 1458 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1150 time to evaluate : 6.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 146 LEU Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 290 VAL Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 288 ASP Chi-restraints excluded: chain O residue 312 LYS Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 137 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 288 ASP Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 66 ARG Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 133 LYS Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 35 THR Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 82 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 133 LYS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 63 ASN Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 133 LYS Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 122 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 66 ARG Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 133 LYS Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 466 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 534 optimal weight: 0.0980 chunk 432 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 562 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 350 GLN A 350 GLN N 11 ASN O 11 ASN R 11 ASN R 377 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN a 164 ASN n 37 GLN ** n 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 78 GLN q 37 GLN ** q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 ASN e 37 GLN f 9 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 0.034 50880 Z= 0.177 Angle : 0.545 6.905 69180 Z= 0.293 Chirality : 0.044 0.198 7836 Planarity : 0.004 0.053 9120 Dihedral : 7.296 89.495 7138 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 7.75 % Allowed : 22.37 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.10), residues: 6576 helix: 0.70 (0.13), residues: 1668 sheet: -1.80 (0.13), residues: 1536 loop : -1.93 (0.10), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 188 HIS 0.002 0.001 HIS A 5 PHE 0.008 0.001 PHE F 208 TYR 0.013 0.001 TYR O 354 ARG 0.006 0.000 ARG Q 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 1240 time to evaluate : 5.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8297 (m-40) cc_final: 0.7910 (m-40) REVERT: m 102 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8427 (p) REVERT: m 120 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7529 (ttmm) REVERT: M 120 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.8027 (ttm-80) REVERT: M 249 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7855 (tm) REVERT: M 282 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 17 ARG cc_start: 0.6722 (ptm160) cc_final: 0.5069 (ttp-110) REVERT: A 96 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 137 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: A 249 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7745 (tp) REVERT: A 332 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7385 (pt) REVERT: N 14 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6419 (pp) REVERT: N 133 HIS cc_start: 0.8286 (m-70) cc_final: 0.8067 (m90) REVERT: N 137 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: N 176 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: N 249 LEU cc_start: 0.8384 (tp) cc_final: 0.7816 (tp) REVERT: N 269 ASN cc_start: 0.8123 (p0) cc_final: 0.7899 (p0) REVERT: N 277 LYS cc_start: 0.8182 (tmtp) cc_final: 0.7978 (tptp) REVERT: N 291 MET cc_start: 0.7917 (mmm) cc_final: 0.7604 (mmp) REVERT: O 42 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7771 (mmtp) REVERT: O 44 ASN cc_start: 0.7450 (m-40) cc_final: 0.7211 (m-40) REVERT: O 137 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: O 277 LYS cc_start: 0.8406 (tptp) cc_final: 0.8199 (tptp) REVERT: O 352 LYS cc_start: 0.8557 (mtpt) cc_final: 0.7188 (mmpt) REVERT: O 372 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8997 (t) REVERT: P 17 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6320 (ptm160) REVERT: P 151 ARG cc_start: 0.7695 (mpt-90) cc_final: 0.7298 (mmt90) REVERT: P 224 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8233 (mptm) REVERT: P 249 LEU cc_start: 0.8210 (tp) cc_final: 0.7888 (tm) REVERT: P 282 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7787 (p) REVERT: P 287 MET cc_start: 0.8116 (tmt) cc_final: 0.7815 (tmm) REVERT: P 312 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7652 (tppt) REVERT: Q 133 HIS cc_start: 0.8265 (m-70) cc_final: 0.8039 (m90) REVERT: Q 137 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: Q 269 ASN cc_start: 0.8143 (p0) cc_final: 0.7916 (p0) REVERT: Q 291 MET cc_start: 0.7923 (mmm) cc_final: 0.7672 (mmp) REVERT: R 42 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7730 (mmtp) REVERT: R 65 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8077 (mm) REVERT: R 96 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7848 (p) REVERT: R 137 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: R 352 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7148 (mmpt) REVERT: B 17 ARG cc_start: 0.6801 (ptm160) cc_final: 0.5035 (ttp-110) REVERT: B 96 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 137 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: B 151 ARG cc_start: 0.7242 (mpt-90) cc_final: 0.6959 (mmt90) REVERT: B 180 MET cc_start: 0.8616 (ttm) cc_final: 0.8201 (ttp) REVERT: B 249 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7935 (tm) REVERT: B 348 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8440 (tt) REVERT: C 17 ARG cc_start: 0.6661 (ptm160) cc_final: 0.4900 (ttm-80) REVERT: C 120 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8006 (mtt-85) REVERT: C 146 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8072 (tt) REVERT: C 155 ILE cc_start: 0.8369 (mt) cc_final: 0.8166 (mt) REVERT: C 249 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7435 (tm) REVERT: D 17 ARG cc_start: 0.6742 (ptm160) cc_final: 0.5178 (ttp-110) REVERT: D 44 ASN cc_start: 0.7593 (m-40) cc_final: 0.7346 (m-40) REVERT: D 133 HIS cc_start: 0.8200 (m-70) cc_final: 0.7941 (m-70) REVERT: D 137 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: D 277 LYS cc_start: 0.8107 (tttt) cc_final: 0.7873 (ttpt) REVERT: D 283 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7476 (mtt90) REVERT: D 352 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7750 (mtpm) REVERT: E 4 PHE cc_start: 0.7992 (m-80) cc_final: 0.7782 (m-80) REVERT: E 17 ARG cc_start: 0.6650 (ptm160) cc_final: 0.4972 (ttp-110) REVERT: E 42 LYS cc_start: 0.8388 (mmpt) cc_final: 0.7959 (mmtp) REVERT: E 96 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7987 (p) REVERT: E 120 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.8043 (mtp85) REVERT: E 180 MET cc_start: 0.8540 (ttp) cc_final: 0.8255 (ttp) REVERT: E 249 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8208 (tp) REVERT: E 252 ASN cc_start: 0.8396 (m-40) cc_final: 0.7923 (m-40) REVERT: E 347 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8054 (mm-40) REVERT: F 17 ARG cc_start: 0.6716 (ptm160) cc_final: 0.4841 (ttp-110) REVERT: F 44 ASN cc_start: 0.7554 (m-40) cc_final: 0.7280 (m-40) REVERT: F 120 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7996 (mtt-85) REVERT: F 155 ILE cc_start: 0.8381 (mt) cc_final: 0.8029 (mt) REVERT: F 249 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7405 (tm) REVERT: F 264 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: a 37 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: a 43 MET cc_start: 0.8590 (ptt) cc_final: 0.8040 (ptt) REVERT: a 59 LYS cc_start: 0.8792 (ptpp) cc_final: 0.8259 (mtpt) REVERT: a 72 PHE cc_start: 0.8813 (m-80) cc_final: 0.8584 (m-80) REVERT: a 127 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (p) REVERT: n 30 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8212 (tttm) REVERT: n 63 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7428 (m110) REVERT: n 100 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (t) REVERT: n 133 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8687 (tttt) REVERT: o 37 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: o 56 MET cc_start: 0.8322 (mtm) cc_final: 0.7877 (mtm) REVERT: o 100 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8751 (t) REVERT: o 102 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8636 (p) REVERT: o 127 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8811 (p) REVERT: o 164 ASN cc_start: 0.7914 (t0) cc_final: 0.7647 (t0) REVERT: p 9 ASN cc_start: 0.8273 (m-40) cc_final: 0.7903 (m-40) REVERT: p 59 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8468 (mttt) REVERT: p 100 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8835 (t) REVERT: p 102 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8503 (p) REVERT: p 120 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7584 (ttmm) REVERT: q 30 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8214 (tttm) REVERT: q 100 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8708 (t) REVERT: q 133 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8678 (tttt) REVERT: r 30 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8135 (tttp) REVERT: r 37 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: r 56 MET cc_start: 0.8330 (mtm) cc_final: 0.7888 (mtm) REVERT: r 100 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8736 (t) REVERT: r 102 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8787 (p) REVERT: r 127 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8804 (p) REVERT: r 164 ASN cc_start: 0.7935 (t0) cc_final: 0.7668 (t0) REVERT: b 93 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8307 (mmmt) REVERT: b 100 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8751 (t) REVERT: b 102 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8528 (p) REVERT: c 37 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6325 (mp-120) REVERT: c 59 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (mttt) REVERT: c 100 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8705 (t) REVERT: c 102 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8566 (p) REVERT: d 37 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: d 43 MET cc_start: 0.8586 (ptt) cc_final: 0.8158 (ptt) REVERT: d 100 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8681 (t) REVERT: d 102 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8625 (p) REVERT: e 93 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8316 (mmmt) REVERT: e 100 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8767 (t) REVERT: e 102 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8559 (p) REVERT: e 133 LYS cc_start: 0.8589 (ttpm) cc_final: 0.8324 (tttt) REVERT: f 37 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6331 (mp-120) REVERT: f 59 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8305 (mttt) REVERT: f 100 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8725 (m) REVERT: f 102 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8623 (p) REVERT: f 110 VAL cc_start: 0.8827 (t) cc_final: 0.8464 (m) outliers start: 397 outliers final: 182 residues processed: 1461 average time/residue: 1.4726 time to fit residues: 2725.4970 Evaluate side-chains 1397 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1146 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 143 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 316 GLU Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 66 ARG Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 63 ASN Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 133 LYS Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 82 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 133 LYS Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 37 GLN Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 63 ASN Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 59 LYS Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 66 ARG Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 6.9990 chunk 564 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 626 optimal weight: 3.9990 chunk 520 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 329 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN A 350 GLN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 347 GLN B 350 GLN C 327 ASN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN F 124 GLN F 327 ASN F 350 GLN a 9 ASN a 164 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 164 ASN ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 9 ASN d 164 ASN e 37 GLN e 164 ASN f 78 GLN f 164 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 50880 Z= 0.518 Angle : 0.726 9.550 69180 Z= 0.389 Chirality : 0.051 0.300 7836 Planarity : 0.006 0.064 9120 Dihedral : 7.679 88.576 7138 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 9.17 % Allowed : 21.72 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 6576 helix: 0.46 (0.13), residues: 1692 sheet: -1.88 (0.14), residues: 1464 loop : -1.91 (0.10), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 188 HIS 0.005 0.001 HIS M 298 PHE 0.022 0.003 PHE m 13 TYR 0.022 0.003 TYR d 125 ARG 0.006 0.001 ARG Q 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 470 poor density : 1127 time to evaluate : 5.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8373 (m-40) cc_final: 0.7998 (m-40) REVERT: m 120 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7652 (ttmm) REVERT: m 127 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8667 (t) REVERT: M 17 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6181 (ptm160) REVERT: M 65 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8269 (tp) REVERT: M 96 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8116 (p) REVERT: M 120 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8045 (ttm-80) REVERT: M 282 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 17 ARG cc_start: 0.6792 (ptm160) cc_final: 0.5209 (ttp-110) REVERT: A 96 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 137 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: A 352 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7701 (mtpm) REVERT: N 4 PHE cc_start: 0.8317 (m-80) cc_final: 0.7991 (m-80) REVERT: N 14 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6331 (pp) REVERT: N 133 HIS cc_start: 0.8296 (m-70) cc_final: 0.8093 (m90) REVERT: N 137 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: N 176 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: N 249 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7871 (tp) REVERT: N 277 LYS cc_start: 0.8191 (tmtp) cc_final: 0.7911 (tptp) REVERT: N 291 MET cc_start: 0.8023 (mmm) cc_final: 0.7708 (mmp) REVERT: O 14 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6370 (pp) REVERT: O 42 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7792 (mmtp) REVERT: O 65 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8119 (mm) REVERT: O 137 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: O 146 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8501 (tt) REVERT: O 306 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mp) REVERT: O 352 LYS cc_start: 0.8512 (mtpt) cc_final: 0.7145 (mmpt) REVERT: P 17 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6386 (ptm160) REVERT: P 151 ARG cc_start: 0.7711 (mpt-90) cc_final: 0.7407 (mmt90) REVERT: P 249 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8143 (tp) REVERT: P 282 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7928 (p) REVERT: P 287 MET cc_start: 0.8027 (tmt) cc_final: 0.7782 (tmm) REVERT: Q 4 PHE cc_start: 0.8307 (m-80) cc_final: 0.7974 (m-80) REVERT: Q 14 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6450 (pp) REVERT: Q 133 HIS cc_start: 0.8347 (m-70) cc_final: 0.8132 (m90) REVERT: Q 137 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: Q 249 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8025 (tp) REVERT: Q 291 MET cc_start: 0.8050 (mmm) cc_final: 0.7749 (mmp) REVERT: R 42 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7800 (mmtp) REVERT: R 65 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8224 (mm) REVERT: R 137 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: R 224 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8334 (mptp) REVERT: R 277 LYS cc_start: 0.8513 (tptp) cc_final: 0.8178 (tptp) REVERT: R 352 LYS cc_start: 0.8539 (mtpt) cc_final: 0.7166 (mmpt) REVERT: R 380 THR cc_start: 0.7277 (p) cc_final: 0.7055 (t) REVERT: B 17 ARG cc_start: 0.6864 (ptm160) cc_final: 0.4976 (ttm-80) REVERT: B 96 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 137 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 180 MET cc_start: 0.8659 (ttm) cc_final: 0.8255 (ttp) REVERT: B 249 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 277 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8219 (tptp) REVERT: B 328 GLN cc_start: 0.8438 (pt0) cc_final: 0.8237 (mt0) REVERT: C 17 ARG cc_start: 0.6934 (ptm160) cc_final: 0.4745 (ttm-80) REVERT: C 120 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8149 (mtt-85) REVERT: C 146 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8016 (tt) REVERT: C 155 ILE cc_start: 0.8371 (mt) cc_final: 0.8055 (mt) REVERT: C 249 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7525 (tm) REVERT: C 352 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8150 (mtmp) REVERT: D 17 ARG cc_start: 0.6853 (ptm160) cc_final: 0.5263 (ttp-110) REVERT: D 133 HIS cc_start: 0.8252 (m-70) cc_final: 0.7970 (m-70) REVERT: D 137 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: D 277 LYS cc_start: 0.8189 (tttt) cc_final: 0.7932 (tttp) REVERT: D 283 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7432 (mtt90) REVERT: D 352 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7734 (mtpm) REVERT: E 17 ARG cc_start: 0.6889 (ptm160) cc_final: 0.4946 (ttm-80) REVERT: E 42 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8049 (mmtp) REVERT: E 176 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7933 (ttpp) REVERT: E 180 MET cc_start: 0.8632 (ttp) cc_final: 0.8333 (ttp) REVERT: E 249 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8284 (tp) REVERT: E 252 ASN cc_start: 0.8546 (m-40) cc_final: 0.8080 (m-40) REVERT: F 17 ARG cc_start: 0.6876 (ptm160) cc_final: 0.4907 (ttm-80) REVERT: F 44 ASN cc_start: 0.7712 (m-40) cc_final: 0.7469 (m-40) REVERT: F 120 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8133 (mtt-85) REVERT: F 146 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8038 (tt) REVERT: F 155 ILE cc_start: 0.8343 (mt) cc_final: 0.8014 (mt) REVERT: F 249 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7526 (tm) REVERT: F 264 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: F 372 VAL cc_start: 0.9311 (p) cc_final: 0.9015 (t) REVERT: a 37 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: a 43 MET cc_start: 0.8638 (ptt) cc_final: 0.8267 (ptt) REVERT: a 93 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8008 (mptp) REVERT: n 100 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8746 (t) REVERT: n 127 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8851 (p) REVERT: o 37 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: o 56 MET cc_start: 0.8338 (mtm) cc_final: 0.7959 (mtm) REVERT: o 100 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8763 (t) REVERT: o 102 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8795 (p) REVERT: o 127 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8865 (p) REVERT: o 133 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8076 (tttm) REVERT: p 9 ASN cc_start: 0.8363 (m-40) cc_final: 0.7987 (m-40) REVERT: p 102 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8719 (p) REVERT: p 106 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8682 (tp) REVERT: p 120 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7713 (ttmm) REVERT: p 133 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8207 (tttm) REVERT: q 100 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8747 (t) REVERT: r 30 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8282 (tttp) REVERT: r 37 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: r 56 MET cc_start: 0.8347 (mtm) cc_final: 0.7963 (mtm) REVERT: r 100 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8689 (t) REVERT: r 102 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8776 (p) REVERT: r 127 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8863 (p) REVERT: b 37 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: b 93 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8250 (mmtt) REVERT: b 102 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8638 (p) REVERT: c 37 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6400 (mp-120) REVERT: c 102 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8723 (p) REVERT: c 120 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7930 (ttmt) REVERT: d 2 MET cc_start: 0.8179 (mtt) cc_final: 0.7574 (mtp) REVERT: d 37 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: d 43 MET cc_start: 0.8607 (ptt) cc_final: 0.8252 (ptt) REVERT: d 100 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8689 (t) REVERT: e 93 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8251 (mmtt) REVERT: e 102 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8645 (p) REVERT: e 127 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8799 (p) REVERT: e 133 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8473 (tttt) REVERT: f 37 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.6397 (mp-120) REVERT: f 110 VAL cc_start: 0.8898 (t) cc_final: 0.8412 (p) REVERT: f 120 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7914 (ttmt) REVERT: f 133 LYS cc_start: 0.8872 (tttm) cc_final: 0.8560 (ttpp) outliers start: 470 outliers final: 265 residues processed: 1416 average time/residue: 1.5012 time to fit residues: 2689.0845 Evaluate side-chains 1376 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1037 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 17 ARG Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 187 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 146 LEU Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 306 ILE Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 383 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 ASP Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 383 LEU Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 53 LYS Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 3 ILE Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 66 ARG Chi-restraints excluded: chain a residue 93 LYS Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 162 MET Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 63 ASN Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 35 THR Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 133 LYS Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 106 LEU Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 133 LYS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 37 GLN Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 66 ARG Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 120 LYS Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 133 LYS Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 357 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 527 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 chunk 624 optimal weight: 1.9990 chunk 390 optimal weight: 0.9980 chunk 380 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN O 11 ASN B 94 GLN B 112 GLN B 350 GLN E 94 GLN E 112 GLN a 164 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 164 ASN e 9 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 50880 Z= 0.241 Angle : 0.595 8.965 69180 Z= 0.319 Chirality : 0.045 0.260 7836 Planarity : 0.004 0.046 9120 Dihedral : 7.320 88.766 7138 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 8.06 % Allowed : 23.40 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.10), residues: 6576 helix: 0.87 (0.13), residues: 1668 sheet: -1.78 (0.13), residues: 1548 loop : -1.94 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 188 HIS 0.002 0.001 HIS Q 5 PHE 0.012 0.002 PHE N 238 TYR 0.021 0.002 TYR e 38 ARG 0.006 0.000 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 1115 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8279 (m-40) cc_final: 0.7915 (m-40) REVERT: m 102 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8508 (p) REVERT: m 120 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7567 (ttmm) REVERT: M 65 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8214 (tp) REVERT: M 96 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8084 (p) REVERT: M 120 ARG cc_start: 0.8339 (mtt-85) cc_final: 0.8039 (ttm-80) REVERT: M 249 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7549 (mt) REVERT: M 282 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7957 (p) REVERT: A 17 ARG cc_start: 0.6669 (ptm160) cc_final: 0.5089 (ttp-110) REVERT: A 96 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 133 HIS cc_start: 0.8242 (m-70) cc_final: 0.7924 (m-70) REVERT: A 137 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: A 146 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8307 (tm) REVERT: A 352 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7693 (mtpm) REVERT: A 380 THR cc_start: 0.7417 (p) cc_final: 0.7179 (m) REVERT: N 4 PHE cc_start: 0.8276 (m-80) cc_final: 0.7945 (m-80) REVERT: N 14 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6612 (pp) REVERT: N 133 HIS cc_start: 0.8270 (m-70) cc_final: 0.8070 (m90) REVERT: N 137 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: N 176 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.7963 (ttpp) REVERT: N 249 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7831 (tp) REVERT: N 269 ASN cc_start: 0.8197 (p0) cc_final: 0.7991 (p0) REVERT: N 277 LYS cc_start: 0.8134 (tmtp) cc_final: 0.7854 (tptp) REVERT: N 291 MET cc_start: 0.7992 (mmm) cc_final: 0.7679 (mmp) REVERT: O 14 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6346 (pp) REVERT: O 42 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7765 (mmtp) REVERT: O 65 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8115 (mm) REVERT: O 137 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: O 277 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8274 (tptp) REVERT: P 17 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6294 (ptm160) REVERT: P 19 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7150 (pp) REVERT: P 151 ARG cc_start: 0.7728 (mpt-90) cc_final: 0.7429 (mmt90) REVERT: P 249 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7875 (tm) REVERT: P 282 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7915 (p) REVERT: P 287 MET cc_start: 0.8143 (tmt) cc_final: 0.7838 (tmm) REVERT: Q 4 PHE cc_start: 0.8241 (m-80) cc_final: 0.7885 (m-80) REVERT: Q 14 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6513 (pp) REVERT: Q 137 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: Q 249 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7982 (tp) REVERT: Q 291 MET cc_start: 0.7988 (mmm) cc_final: 0.7679 (mmp) REVERT: Q 383 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7782 (mm) REVERT: R 17 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6808 (ptt180) REVERT: R 42 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7764 (mmtp) REVERT: R 65 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8039 (tp) REVERT: R 96 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7945 (p) REVERT: R 137 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: R 277 LYS cc_start: 0.8455 (tptp) cc_final: 0.8144 (tptp) REVERT: R 352 LYS cc_start: 0.8593 (mtpt) cc_final: 0.7221 (mmpt) REVERT: B 17 ARG cc_start: 0.6637 (ptm160) cc_final: 0.5096 (ttm-80) REVERT: B 96 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 137 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: B 180 MET cc_start: 0.8637 (ttm) cc_final: 0.8236 (ttp) REVERT: B 249 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 277 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8167 (tptp) REVERT: B 328 GLN cc_start: 0.8366 (pt0) cc_final: 0.8140 (mt0) REVERT: C 17 ARG cc_start: 0.6784 (ptm160) cc_final: 0.4845 (ttm-80) REVERT: C 120 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8041 (mtt-85) REVERT: C 146 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 155 ILE cc_start: 0.8364 (mt) cc_final: 0.8077 (mt) REVERT: C 249 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7442 (tm) REVERT: C 352 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (mtmp) REVERT: D 17 ARG cc_start: 0.6665 (ptm160) cc_final: 0.5222 (ttp-110) REVERT: D 133 HIS cc_start: 0.8185 (m-70) cc_final: 0.7946 (m-70) REVERT: D 137 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: D 283 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7436 (mtt90) REVERT: D 312 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7768 (mmmm) REVERT: D 352 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7667 (mtpm) REVERT: E 17 ARG cc_start: 0.6693 (ptm160) cc_final: 0.4835 (ttm-80) REVERT: E 42 LYS cc_start: 0.8385 (mmpt) cc_final: 0.8005 (mmtp) REVERT: E 176 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7958 (ttpp) REVERT: E 180 MET cc_start: 0.8556 (ttp) cc_final: 0.8231 (ttp) REVERT: E 249 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8204 (tp) REVERT: E 252 ASN cc_start: 0.8427 (m-40) cc_final: 0.7917 (m-40) REVERT: E 383 LEU cc_start: 0.8305 (mt) cc_final: 0.8091 (mm) REVERT: F 17 ARG cc_start: 0.6800 (ptm160) cc_final: 0.4793 (ttm-80) REVERT: F 44 ASN cc_start: 0.7622 (m-40) cc_final: 0.7359 (m-40) REVERT: F 120 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8025 (mtt-85) REVERT: F 146 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8117 (tt) REVERT: F 155 ILE cc_start: 0.8364 (mt) cc_final: 0.8009 (mt) REVERT: F 249 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7434 (tm) REVERT: F 264 TYR cc_start: 0.6378 (OUTLIER) cc_final: 0.5730 (m-80) REVERT: a 37 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: a 43 MET cc_start: 0.8599 (ptt) cc_final: 0.8220 (ptt) REVERT: a 72 PHE cc_start: 0.8772 (m-80) cc_final: 0.8565 (m-80) REVERT: n 100 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8713 (t) REVERT: n 133 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8716 (tttt) REVERT: o 37 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: o 56 MET cc_start: 0.8353 (mtm) cc_final: 0.7980 (mtm) REVERT: o 100 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8783 (t) REVERT: o 102 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8734 (p) REVERT: o 127 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8827 (p) REVERT: p 9 ASN cc_start: 0.8269 (m-40) cc_final: 0.7917 (m-40) REVERT: p 59 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8505 (mttt) REVERT: p 100 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8791 (t) REVERT: p 102 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8528 (p) REVERT: p 120 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7641 (ttmm) REVERT: q 100 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8735 (t) REVERT: q 133 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8657 (ttpm) REVERT: r 56 MET cc_start: 0.8372 (mtm) cc_final: 0.7969 (mtm) REVERT: r 100 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8653 (t) REVERT: r 102 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8793 (p) REVERT: r 127 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8820 (p) REVERT: b 37 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: b 93 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8253 (mmtt) REVERT: b 100 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8758 (t) REVERT: b 102 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8640 (p) REVERT: c 2 MET cc_start: 0.8376 (mtm) cc_final: 0.7761 (mtp) REVERT: c 37 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6381 (mp-120) REVERT: c 100 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8675 (t) REVERT: c 102 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8590 (p) REVERT: c 120 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7796 (ttmt) REVERT: d 2 MET cc_start: 0.8263 (mtt) cc_final: 0.7514 (mtp) REVERT: d 37 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: d 43 MET cc_start: 0.8586 (ptt) cc_final: 0.8096 (ptt) REVERT: d 100 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8694 (t) REVERT: d 102 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8707 (p) REVERT: e 93 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8254 (mmtt) REVERT: e 100 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8744 (t) REVERT: e 102 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8666 (p) REVERT: e 133 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8413 (tttt) REVERT: f 37 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6345 (mp-120) REVERT: f 59 LYS cc_start: 0.8603 (ptpt) cc_final: 0.8298 (mttm) REVERT: f 102 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8676 (p) REVERT: f 110 VAL cc_start: 0.8860 (t) cc_final: 0.8503 (m) REVERT: f 120 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7811 (ttmt) outliers start: 413 outliers final: 231 residues processed: 1355 average time/residue: 1.4971 time to fit residues: 2582.0047 Evaluate side-chains 1389 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1082 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 143 MET Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 143 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 227 LYS Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 316 GLU Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain Q residue 383 LEU Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 3 ILE Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 49 ILE Chi-restraints excluded: chain q residue 63 ASN Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 63 ASN Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 122 GLU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 66 ARG Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 133 LYS Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 397 optimal weight: 0.1980 chunk 425 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 490 optimal weight: 0.8980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 63 ASN M 11 ASN N 252 ASN P 11 ASN B 112 GLN B 350 GLN E 94 GLN E 112 GLN a 164 ASN n 63 ASN q 37 GLN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 50880 Z= 0.266 Angle : 0.605 10.026 69180 Z= 0.324 Chirality : 0.046 0.291 7836 Planarity : 0.004 0.047 9120 Dihedral : 7.210 88.851 7138 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 8.10 % Allowed : 23.77 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 6576 helix: 0.90 (0.13), residues: 1692 sheet: -1.76 (0.13), residues: 1680 loop : -1.88 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 188 HIS 0.003 0.001 HIS N 5 PHE 0.013 0.002 PHE m 13 TYR 0.022 0.002 TYR e 38 ARG 0.011 0.001 ARG Q 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1514 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1099 time to evaluate : 5.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8310 (m-40) cc_final: 0.7927 (m-40) REVERT: m 102 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8521 (p) REVERT: m 120 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7584 (ttmm) REVERT: M 17 ARG cc_start: 0.6771 (ttp-170) cc_final: 0.6533 (ptt180) REVERT: M 65 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (tp) REVERT: M 96 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8076 (p) REVERT: M 282 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 17 ARG cc_start: 0.6686 (ptm160) cc_final: 0.5116 (ttp-110) REVERT: A 96 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7953 (p) REVERT: A 133 HIS cc_start: 0.8232 (m-70) cc_final: 0.7906 (m-70) REVERT: A 137 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: A 146 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8294 (tm) REVERT: A 352 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7666 (mtpm) REVERT: A 380 THR cc_start: 0.7284 (p) cc_final: 0.7046 (m) REVERT: N 4 PHE cc_start: 0.8282 (m-80) cc_final: 0.7960 (m-80) REVERT: N 14 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6611 (pp) REVERT: N 133 HIS cc_start: 0.8249 (m-70) cc_final: 0.8048 (m90) REVERT: N 137 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: N 176 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7954 (ttpp) REVERT: N 249 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7832 (tp) REVERT: N 269 ASN cc_start: 0.8229 (p0) cc_final: 0.7995 (p0) REVERT: N 277 LYS cc_start: 0.8126 (tmtp) cc_final: 0.7725 (tptp) REVERT: N 291 MET cc_start: 0.8016 (mmm) cc_final: 0.7688 (mmp) REVERT: O 14 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6326 (pp) REVERT: O 42 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7727 (mmtp) REVERT: O 65 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8104 (mm) REVERT: O 137 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: O 277 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (tptp) REVERT: O 352 LYS cc_start: 0.8519 (mtpt) cc_final: 0.7158 (mmpt) REVERT: O 372 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8999 (t) REVERT: P 17 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6364 (ptm160) REVERT: P 19 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7115 (pp) REVERT: P 151 ARG cc_start: 0.7742 (mpt-90) cc_final: 0.7423 (mmt90) REVERT: P 282 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7908 (p) REVERT: P 287 MET cc_start: 0.8157 (tmt) cc_final: 0.7852 (tmm) REVERT: P 307 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7996 (m) REVERT: Q 4 PHE cc_start: 0.8239 (m-80) cc_final: 0.7886 (m-80) REVERT: Q 14 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6461 (pp) REVERT: Q 137 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: Q 291 MET cc_start: 0.8006 (mmm) cc_final: 0.7687 (mmp) REVERT: R 17 ARG cc_start: 0.7010 (ptm160) cc_final: 0.6783 (ptt180) REVERT: R 42 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7735 (mmtp) REVERT: R 65 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8141 (mm) REVERT: R 137 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: R 277 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8143 (tptp) REVERT: R 352 LYS cc_start: 0.8581 (mtpt) cc_final: 0.7231 (mmpt) REVERT: R 380 THR cc_start: 0.7153 (p) cc_final: 0.6887 (t) REVERT: B 17 ARG cc_start: 0.6667 (ptm160) cc_final: 0.5127 (ttm-80) REVERT: B 96 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 137 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: B 180 MET cc_start: 0.8647 (ttm) cc_final: 0.8255 (ttp) REVERT: B 249 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8218 (tp) REVERT: B 277 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (tptp) REVERT: B 328 GLN cc_start: 0.8341 (pt0) cc_final: 0.8129 (mt0) REVERT: C 17 ARG cc_start: 0.6692 (ptm160) cc_final: 0.4799 (ttm-80) REVERT: C 120 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: C 155 ILE cc_start: 0.8363 (mt) cc_final: 0.8088 (mt) REVERT: C 249 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7453 (tm) REVERT: C 352 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8127 (mtmp) REVERT: C 380 THR cc_start: 0.7685 (p) cc_final: 0.7380 (t) REVERT: D 17 ARG cc_start: 0.6645 (ptm160) cc_final: 0.5189 (ttp-110) REVERT: D 137 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: D 177 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6576 (mmp80) REVERT: D 283 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7388 (mtt90) REVERT: D 352 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7666 (mtpm) REVERT: D 380 THR cc_start: 0.7346 (p) cc_final: 0.7114 (m) REVERT: E 17 ARG cc_start: 0.6578 (ptm160) cc_final: 0.5034 (ttm-80) REVERT: E 42 LYS cc_start: 0.8376 (mmpt) cc_final: 0.8002 (mmtp) REVERT: E 96 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7972 (p) REVERT: E 176 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7941 (ttpp) REVERT: E 180 MET cc_start: 0.8566 (ttp) cc_final: 0.8255 (ttp) REVERT: E 249 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8195 (tp) REVERT: E 252 ASN cc_start: 0.8440 (m-40) cc_final: 0.7938 (m-40) REVERT: E 383 LEU cc_start: 0.8259 (mt) cc_final: 0.8044 (mm) REVERT: F 17 ARG cc_start: 0.6769 (ptm160) cc_final: 0.4794 (ttm-80) REVERT: F 44 ASN cc_start: 0.7611 (m-40) cc_final: 0.7369 (m-40) REVERT: F 120 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8016 (mtt-85) REVERT: F 155 ILE cc_start: 0.8372 (mt) cc_final: 0.8023 (mt) REVERT: F 249 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7455 (tm) REVERT: F 264 TYR cc_start: 0.6423 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: a 37 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7221 (mt0) REVERT: a 43 MET cc_start: 0.8649 (ptt) cc_final: 0.8156 (ptt) REVERT: n 100 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8743 (t) REVERT: n 127 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8824 (p) REVERT: n 133 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8726 (tttt) REVERT: o 37 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: o 56 MET cc_start: 0.8339 (mtm) cc_final: 0.7955 (mtm) REVERT: o 100 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8801 (t) REVERT: o 102 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8714 (p) REVERT: o 127 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8842 (p) REVERT: p 9 ASN cc_start: 0.8297 (m-40) cc_final: 0.7907 (m-40) REVERT: p 59 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8497 (mttt) REVERT: p 100 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8815 (t) REVERT: p 102 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8584 (p) REVERT: p 120 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7654 (ttmm) REVERT: p 133 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8491 (ttpt) REVERT: q 100 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (t) REVERT: q 133 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8708 (tttt) REVERT: r 56 MET cc_start: 0.8373 (mtm) cc_final: 0.8065 (mtm) REVERT: r 100 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8660 (t) REVERT: r 102 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8825 (p) REVERT: r 127 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8828 (p) REVERT: b 37 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: b 93 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8245 (mmtt) REVERT: b 100 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8783 (t) REVERT: b 102 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8616 (p) REVERT: b 124 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8321 (mmtp) REVERT: c 2 MET cc_start: 0.8381 (mtm) cc_final: 0.7732 (mtp) REVERT: c 37 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6339 (mp-120) REVERT: c 100 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8686 (t) REVERT: c 102 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8605 (p) REVERT: c 106 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8331 (tp) REVERT: c 120 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7850 (ttmt) REVERT: d 2 MET cc_start: 0.8259 (mtt) cc_final: 0.7492 (mtp) REVERT: d 37 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: d 43 MET cc_start: 0.8613 (ptt) cc_final: 0.8260 (ptt) REVERT: d 72 PHE cc_start: 0.8811 (m-80) cc_final: 0.8596 (m-80) REVERT: e 93 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8236 (mmtt) REVERT: e 100 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8765 (t) REVERT: e 102 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8590 (p) REVERT: e 133 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8420 (tttt) REVERT: f 2 MET cc_start: 0.8346 (mtm) cc_final: 0.7760 (mtp) REVERT: f 37 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6339 (mp-120) REVERT: f 100 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8774 (m) REVERT: f 102 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8680 (p) REVERT: f 110 VAL cc_start: 0.8864 (t) cc_final: 0.8506 (m) REVERT: f 120 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7821 (ttmt) outliers start: 415 outliers final: 251 residues processed: 1350 average time/residue: 1.4978 time to fit residues: 2564.2868 Evaluate side-chains 1406 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1078 time to evaluate : 5.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 49 ILE Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 143 MET Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 ASP Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 227 LYS Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 143 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 187 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 383 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 227 LYS Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 277 LYS Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 63 ASN Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 82 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 133 LYS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 63 ASN Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 63 ASN Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 56 MET Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 133 LYS Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 9.9990 chunk 598 optimal weight: 1.9990 chunk 545 optimal weight: 10.0000 chunk 582 optimal weight: 3.9990 chunk 350 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 457 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 525 optimal weight: 3.9990 chunk 550 optimal weight: 10.0000 chunk 579 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 63 ASN M 11 ASN P 11 ASN R 11 ASN B 112 GLN E 112 GLN E 350 GLN a 164 ASN n 37 GLN n 63 ASN q 37 GLN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 164 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 50880 Z= 0.387 Angle : 0.671 9.676 69180 Z= 0.357 Chirality : 0.048 0.301 7836 Planarity : 0.005 0.056 9120 Dihedral : 7.323 89.293 7137 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 7.67 % Allowed : 24.28 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 6576 helix: 0.76 (0.13), residues: 1692 sheet: -1.61 (0.13), residues: 1560 loop : -1.94 (0.10), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 188 HIS 0.003 0.001 HIS Q 298 PHE 0.022 0.002 PHE m 13 TYR 0.023 0.002 TYR p 131 ARG 0.008 0.001 ARG R 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1057 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8307 (m-40) cc_final: 0.7919 (m-40) REVERT: m 102 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8645 (p) REVERT: m 120 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7672 (ttmm) REVERT: m 127 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8670 (t) REVERT: M 65 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8202 (tp) REVERT: M 96 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8140 (p) REVERT: M 120 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.8042 (ttm-80) REVERT: M 282 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 17 ARG cc_start: 0.6710 (ptm160) cc_final: 0.5219 (ttp-110) REVERT: A 96 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 133 HIS cc_start: 0.8273 (m-70) cc_final: 0.7965 (m-70) REVERT: A 137 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 352 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7707 (mtpm) REVERT: N 4 PHE cc_start: 0.8332 (m-80) cc_final: 0.8021 (m-80) REVERT: N 14 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6325 (pp) REVERT: N 133 HIS cc_start: 0.8280 (m-70) cc_final: 0.8079 (m90) REVERT: N 137 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: N 176 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8004 (ttpp) REVERT: N 249 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7886 (tp) REVERT: N 291 MET cc_start: 0.7999 (mmm) cc_final: 0.7660 (mmp) REVERT: O 14 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6376 (pp) REVERT: O 42 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7728 (mmtp) REVERT: O 65 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (mm) REVERT: O 137 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: O 277 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8270 (tptp) REVERT: P 17 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6351 (ptm160) REVERT: P 19 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (pp) REVERT: P 151 ARG cc_start: 0.7776 (mpt-90) cc_final: 0.7503 (mmt90) REVERT: P 282 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.7924 (p) REVERT: P 287 MET cc_start: 0.8074 (tmt) cc_final: 0.7750 (tmm) REVERT: P 307 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8014 (m) REVERT: Q 4 PHE cc_start: 0.8281 (m-80) cc_final: 0.7943 (m-80) REVERT: Q 14 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6485 (pp) REVERT: Q 137 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: Q 291 MET cc_start: 0.7994 (mmm) cc_final: 0.7657 (mmp) REVERT: R 17 ARG cc_start: 0.6964 (ptm160) cc_final: 0.6748 (ptt180) REVERT: R 42 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7751 (mmtp) REVERT: R 65 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (mm) REVERT: R 137 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: R 224 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8279 (mptp) REVERT: R 277 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8172 (tptp) REVERT: R 380 THR cc_start: 0.7169 (p) cc_final: 0.6913 (t) REVERT: R 383 LEU cc_start: 0.7861 (mm) cc_final: 0.7655 (mm) REVERT: B 17 ARG cc_start: 0.6728 (ptm160) cc_final: 0.4978 (ttm-80) REVERT: B 96 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 137 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 180 MET cc_start: 0.8661 (ttm) cc_final: 0.8269 (ttp) REVERT: B 249 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 277 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8172 (tptp) REVERT: C 17 ARG cc_start: 0.6684 (ptm160) cc_final: 0.4749 (ttm-80) REVERT: C 120 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8067 (mtt-85) REVERT: C 155 ILE cc_start: 0.8377 (mt) cc_final: 0.8110 (mt) REVERT: C 249 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7506 (tm) REVERT: C 352 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (mtmp) REVERT: C 380 THR cc_start: 0.7673 (p) cc_final: 0.7380 (t) REVERT: D 17 ARG cc_start: 0.6759 (ptm160) cc_final: 0.5209 (ttp-110) REVERT: D 137 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: D 283 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7434 (mtt90) REVERT: D 352 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7662 (mtpm) REVERT: E 17 ARG cc_start: 0.6720 (ptm160) cc_final: 0.4984 (ttm-80) REVERT: E 42 LYS cc_start: 0.8386 (mmpt) cc_final: 0.7995 (mmtp) REVERT: E 96 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (p) REVERT: E 176 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7930 (ttpp) REVERT: E 180 MET cc_start: 0.8574 (ttp) cc_final: 0.8245 (ttp) REVERT: E 249 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8218 (tp) REVERT: E 252 ASN cc_start: 0.8508 (m-40) cc_final: 0.8021 (m-40) REVERT: E 383 LEU cc_start: 0.8241 (mt) cc_final: 0.8021 (mm) REVERT: F 17 ARG cc_start: 0.6789 (ptm160) cc_final: 0.4785 (ttm-80) REVERT: F 44 ASN cc_start: 0.7625 (m-40) cc_final: 0.7386 (m-40) REVERT: F 120 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (mtt-85) REVERT: F 146 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8124 (tt) REVERT: F 155 ILE cc_start: 0.8343 (mt) cc_final: 0.7994 (mt) REVERT: F 249 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7494 (tm) REVERT: F 264 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: a 30 LYS cc_start: 0.8649 (tttm) cc_final: 0.8420 (ttmm) REVERT: a 37 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: n 100 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8770 (t) REVERT: n 127 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8843 (p) REVERT: n 133 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8717 (tttt) REVERT: o 37 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: o 56 MET cc_start: 0.8362 (mtm) cc_final: 0.8056 (mtm) REVERT: o 100 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8810 (t) REVERT: o 102 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8789 (p) REVERT: o 127 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8867 (p) REVERT: p 9 ASN cc_start: 0.8294 (m-40) cc_final: 0.7912 (m-40) REVERT: p 59 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8484 (mttt) REVERT: p 102 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8634 (p) REVERT: p 120 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7738 (ttmm) REVERT: p 133 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8445 (tttt) REVERT: q 100 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8783 (t) REVERT: q 133 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8726 (tttt) REVERT: r 56 MET cc_start: 0.8362 (mtm) cc_final: 0.7938 (mtm) REVERT: r 100 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8655 (t) REVERT: r 102 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8825 (p) REVERT: r 127 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8849 (p) REVERT: b 37 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6587 (mp10) REVERT: b 93 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8250 (mmtt) REVERT: b 100 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8757 (t) REVERT: b 102 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8636 (p) REVERT: b 124 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8339 (mmtp) REVERT: c 37 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6389 (mp-120) REVERT: c 100 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8674 (t) REVERT: c 102 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8642 (p) REVERT: c 106 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8404 (tp) REVERT: c 120 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7925 (ttmt) REVERT: c 133 LYS cc_start: 0.8888 (tttm) cc_final: 0.8497 (tttp) REVERT: d 2 MET cc_start: 0.8244 (mtt) cc_final: 0.7380 (mtp) REVERT: d 37 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: d 43 MET cc_start: 0.8604 (ptt) cc_final: 0.8225 (ptt) REVERT: e 93 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8245 (mmtt) REVERT: e 100 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8783 (t) REVERT: e 102 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8657 (p) REVERT: f 37 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6385 (mp-120) REVERT: f 102 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8669 (p) REVERT: f 120 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7942 (ttmt) REVERT: f 133 LYS cc_start: 0.8846 (tttm) cc_final: 0.8471 (tttp) outliers start: 393 outliers final: 263 residues processed: 1305 average time/residue: 1.5233 time to fit residues: 2532.1694 Evaluate side-chains 1377 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1040 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 48 SER Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 63 ASN Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 157 ASP Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 281 VAL Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 ASP Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 143 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 225 GLU Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 294 ILE Chi-restraints excluded: chain P residue 307 THR Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain P residue 383 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 227 LYS Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain Q residue 332 ILE Chi-restraints excluded: chain Q residue 380 THR Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 277 LYS Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 328 GLN Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 35 THR Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 63 ASN Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 127 VAL Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 48 SER Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 133 LYS Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 63 ASN Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 100 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 3 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 56 MET Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 7.9990 chunk 615 optimal weight: 6.9990 chunk 375 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 645 optimal weight: 0.8980 chunk 594 optimal weight: 4.9990 chunk 514 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 397 optimal weight: 0.9980 chunk 315 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN P 11 ASN P 377 GLN Q 133 HIS R 11 ASN B 112 GLN E 112 GLN E 350 GLN a 164 ASN o 63 ASN r 63 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 164 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 50880 Z= 0.218 Angle : 0.593 10.012 69180 Z= 0.315 Chirality : 0.045 0.275 7836 Planarity : 0.004 0.045 9120 Dihedral : 7.085 88.824 7137 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 6.56 % Allowed : 25.62 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 6576 helix: 0.98 (0.13), residues: 1692 sheet: -1.74 (0.13), residues: 1644 loop : -1.89 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 188 HIS 0.002 0.001 HIS E 298 PHE 0.011 0.002 PHE n 123 TYR 0.024 0.002 TYR e 38 ARG 0.011 0.000 ARG R 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13152 Ramachandran restraints generated. 6576 Oldfield, 0 Emsley, 6576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1097 time to evaluate : 5.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 9 ASN cc_start: 0.8303 (m-40) cc_final: 0.7911 (m-40) REVERT: m 102 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8522 (p) REVERT: m 120 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7642 (ttmm) REVERT: M 96 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8074 (p) REVERT: M 282 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7972 (p) REVERT: M 287 MET cc_start: 0.8154 (tmt) cc_final: 0.7741 (tpp) REVERT: A 17 ARG cc_start: 0.6576 (ptm160) cc_final: 0.5068 (ttp-110) REVERT: A 96 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 133 HIS cc_start: 0.8239 (m-70) cc_final: 0.7931 (m-70) REVERT: A 137 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: N 4 PHE cc_start: 0.8286 (m-80) cc_final: 0.7957 (m-80) REVERT: N 14 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6522 (pp) REVERT: N 137 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: N 176 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7952 (ttpp) REVERT: N 249 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7823 (tp) REVERT: N 269 ASN cc_start: 0.8179 (p0) cc_final: 0.7969 (p0) REVERT: N 291 MET cc_start: 0.8019 (mmm) cc_final: 0.7689 (mmp) REVERT: O 42 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7644 (mmtp) REVERT: O 65 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8083 (mm) REVERT: O 137 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: O 277 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8302 (tptp) REVERT: O 352 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7163 (mmpt) REVERT: O 372 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8980 (t) REVERT: O 380 THR cc_start: 0.7061 (p) cc_final: 0.6737 (t) REVERT: P 17 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6347 (ptm160) REVERT: P 19 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7126 (pp) REVERT: P 151 ARG cc_start: 0.7761 (mpt-90) cc_final: 0.7474 (mmt90) REVERT: P 282 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7922 (p) REVERT: P 287 MET cc_start: 0.8185 (tmt) cc_final: 0.7875 (tmm) REVERT: Q 4 PHE cc_start: 0.8236 (m-80) cc_final: 0.7888 (m-80) REVERT: Q 14 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6478 (pp) REVERT: Q 137 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: Q 291 MET cc_start: 0.8013 (mmm) cc_final: 0.7683 (mmp) REVERT: R 42 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7771 (mmtp) REVERT: R 65 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8096 (mm) REVERT: R 137 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: R 277 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8161 (tptp) REVERT: R 352 LYS cc_start: 0.8608 (mtpt) cc_final: 0.7224 (mmpt) REVERT: B 17 ARG cc_start: 0.6597 (ptm160) cc_final: 0.5042 (ttm-80) REVERT: B 137 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: B 151 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7345 (mpt-90) REVERT: B 180 MET cc_start: 0.8641 (ttm) cc_final: 0.8252 (ttp) REVERT: B 249 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 277 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8212 (tptp) REVERT: C 17 ARG cc_start: 0.6578 (ptm160) cc_final: 0.4755 (ttm-80) REVERT: C 120 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: C 146 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8058 (tt) REVERT: C 155 ILE cc_start: 0.8372 (mt) cc_final: 0.8110 (mt) REVERT: C 249 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7451 (tm) REVERT: C 352 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (mtmp) REVERT: C 380 THR cc_start: 0.7646 (p) cc_final: 0.7343 (t) REVERT: D 17 ARG cc_start: 0.6669 (ptm160) cc_final: 0.5138 (ttp-110) REVERT: D 137 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: D 283 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7345 (mtt90) REVERT: D 352 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7706 (mtpm) REVERT: D 380 THR cc_start: 0.7397 (p) cc_final: 0.7174 (m) REVERT: E 17 ARG cc_start: 0.6628 (ptm160) cc_final: 0.5034 (ttp-110) REVERT: E 42 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7982 (mmtp) REVERT: E 96 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7952 (p) REVERT: E 180 MET cc_start: 0.8549 (ttp) cc_final: 0.8236 (ttp) REVERT: E 249 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8200 (tp) REVERT: E 252 ASN cc_start: 0.8440 (m-40) cc_final: 0.7922 (m-40) REVERT: E 383 LEU cc_start: 0.8128 (mt) cc_final: 0.7927 (mm) REVERT: F 17 ARG cc_start: 0.6637 (ptm160) cc_final: 0.4842 (ttm-80) REVERT: F 44 ASN cc_start: 0.7530 (m-40) cc_final: 0.7292 (m-40) REVERT: F 120 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8010 (mtt-85) REVERT: F 155 ILE cc_start: 0.8334 (mt) cc_final: 0.7998 (mt) REVERT: F 249 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7464 (tm) REVERT: F 264 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: a 37 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: o 30 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8189 (tttm) REVERT: o 56 MET cc_start: 0.8335 (mtm) cc_final: 0.7947 (mtm) REVERT: o 100 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8807 (t) REVERT: o 102 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (p) REVERT: p 9 ASN cc_start: 0.8307 (m-40) cc_final: 0.7921 (m-40) REVERT: p 59 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8388 (mttt) REVERT: p 100 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8811 (t) REVERT: p 102 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8594 (p) REVERT: p 120 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: q 133 LYS cc_start: 0.8913 (ttpp) cc_final: 0.8708 (tttt) REVERT: r 56 MET cc_start: 0.8373 (mtm) cc_final: 0.7967 (mtm) REVERT: r 100 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8615 (t) REVERT: r 102 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8783 (p) REVERT: b 37 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6484 (mp10) REVERT: b 93 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8268 (mmtt) REVERT: b 100 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8777 (t) REVERT: b 102 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8644 (p) REVERT: b 124 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8269 (mmtp) REVERT: c 2 MET cc_start: 0.8379 (mtm) cc_final: 0.7763 (mtp) REVERT: c 37 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6355 (mp-120) REVERT: c 100 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8688 (t) REVERT: c 102 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8584 (p) REVERT: c 106 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8345 (tp) REVERT: c 120 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7868 (ttmt) REVERT: d 2 MET cc_start: 0.8275 (mtt) cc_final: 0.7471 (mtp) REVERT: d 37 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: d 102 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8664 (p) REVERT: e 93 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8248 (mmtt) REVERT: e 100 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8773 (t) REVERT: e 102 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8642 (p) REVERT: e 133 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8413 (tttt) REVERT: f 2 MET cc_start: 0.8297 (mtm) cc_final: 0.7691 (mtp) REVERT: f 37 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6347 (mp-120) REVERT: f 100 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8777 (m) REVERT: f 102 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8689 (p) REVERT: f 120 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7890 (ttmt) outliers start: 336 outliers final: 224 residues processed: 1293 average time/residue: 1.4737 time to fit residues: 2411.6469 Evaluate side-chains 1366 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1077 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 56 MET Chi-restraints excluded: chain m residue 59 LYS Chi-restraints excluded: chain m residue 82 ASN Chi-restraints excluded: chain m residue 88 SER Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 120 LYS Chi-restraints excluded: chain m residue 162 MET Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 245 CYS Chi-restraints excluded: chain M residue 282 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 383 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain N residue 137 GLN Chi-restraints excluded: chain N residue 143 MET Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 ASP Chi-restraints excluded: chain N residue 176 LYS Chi-restraints excluded: chain N residue 245 CYS Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 282 THR Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 302 VAL Chi-restraints excluded: chain N residue 346 SER Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 134 SER Chi-restraints excluded: chain O residue 137 GLN Chi-restraints excluded: chain O residue 143 MET Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 245 CYS Chi-restraints excluded: chain O residue 246 ARG Chi-restraints excluded: chain O residue 277 LYS Chi-restraints excluded: chain O residue 282 THR Chi-restraints excluded: chain O residue 332 ILE Chi-restraints excluded: chain O residue 346 SER Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 14 ILE Chi-restraints excluded: chain P residue 17 ARG Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 134 SER Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 282 THR Chi-restraints excluded: chain P residue 290 VAL Chi-restraints excluded: chain P residue 332 ILE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 157 ASP Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 227 LYS Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 282 THR Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 302 VAL Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 143 MET Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 163 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 246 ARG Chi-restraints excluded: chain R residue 277 LYS Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain R residue 346 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 246 ARG Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 TYR Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 47 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain a residue 127 VAL Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain n residue 51 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain n residue 139 ARG Chi-restraints excluded: chain n residue 162 MET Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 ILE Chi-restraints excluded: chain o residue 63 ASN Chi-restraints excluded: chain o residue 82 ASN Chi-restraints excluded: chain o residue 100 VAL Chi-restraints excluded: chain o residue 102 THR Chi-restraints excluded: chain o residue 162 MET Chi-restraints excluded: chain p residue 3 ILE Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 47 VAL Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 63 ASN Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain p residue 88 SER Chi-restraints excluded: chain p residue 100 VAL Chi-restraints excluded: chain p residue 102 THR Chi-restraints excluded: chain p residue 120 LYS Chi-restraints excluded: chain p residue 127 VAL Chi-restraints excluded: chain p residue 162 MET Chi-restraints excluded: chain q residue 3 ILE Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 63 ASN Chi-restraints excluded: chain q residue 97 VAL Chi-restraints excluded: chain q residue 102 THR Chi-restraints excluded: chain q residue 127 VAL Chi-restraints excluded: chain q residue 139 ARG Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 49 ILE Chi-restraints excluded: chain r residue 63 ASN Chi-restraints excluded: chain r residue 100 VAL Chi-restraints excluded: chain r residue 102 THR Chi-restraints excluded: chain r residue 162 MET Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 82 ASN Chi-restraints excluded: chain b residue 97 VAL Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 162 MET Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 56 MET Chi-restraints excluded: chain c residue 63 ASN Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 106 LEU Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 127 VAL Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 VAL Chi-restraints excluded: chain d residue 49 ILE Chi-restraints excluded: chain d residue 82 ASN Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 162 MET Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 82 ASN Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 100 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 133 LYS Chi-restraints excluded: chain e residue 139 ARG Chi-restraints excluded: chain e residue 162 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 47 VAL Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 82 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 120 LYS Chi-restraints excluded: chain f residue 162 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 0.0370 chunk 547 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 474 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 142 optimal weight: 7.9990 chunk 514 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 528 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN P 11 ASN B 112 GLN E 112 GLN a 164 ASN n 37 GLN o 63 ASN q 37 GLN r 63 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN d 164 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.106600 restraints weight = 63704.954| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.43 r_work: 0.3032 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50880 Z= 0.193 Angle : 0.579 9.749 69180 Z= 0.307 Chirality : 0.044 0.258 7836 Planarity : 0.004 0.044 9120 Dihedral : 6.945 89.179 7135 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.97 % Allowed : 26.42 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.10), residues: 6576 helix: 1.08 (0.13), residues: 1692 sheet: -1.73 (0.13), residues: 1644 loop : -1.83 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 188 HIS 0.002 0.001 HIS F 298 PHE 0.011 0.001 PHE M 33 TYR 0.024 0.002 TYR e 38 ARG 0.008 0.000 ARG Q 126 =============================================================================== Job complete usr+sys time: 33364.16 seconds wall clock time: 581 minutes 11.31 seconds (34871.31 seconds total)