Starting phenix.real_space_refine (version: dev) on Thu Dec 22 22:38:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/12_2022/6pyt_20526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/12_2022/6pyt_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_20526/12_2022/6pyt_20526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/12_2022/6pyt_20526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/12_2022/6pyt_20526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pyt_20526/12_2022/6pyt_20526.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 28.72, per 1000 atoms: 0.58 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: 18.75 Conformation dependent library (CDL) restraints added in 7.6 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: 3.02 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: 21.88 Time building geometry restraints manager: 20.46 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 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. 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 16.310 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.410 Process input model: 125.470 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 % 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 *********************** 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 : 5.980 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 outliers start: 48 outliers final: 11 residues processed: 2174 average time/residue: 1.4759 time to fit residues: 4029.0826 Evaluate side-chains 1304 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1293 time to evaluate : 5.829 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 2 residues processed: 10 average time/residue: 0.4123 time to fit residues: 14.9208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 272 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 507 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 378 optimal weight: 0.8980 chunk 588 optimal weight: 0.0030 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 N 350 GLN 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 Q 327 ASN R 11 ASN R 94 GLN B 112 GLN B 136 GLN B 193 ASN 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 ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7983 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 50880 Z= 0.174 Angle : 0.611 8.778 69180 Z= 0.329 Chirality : 0.044 0.276 7836 Planarity : 0.004 0.035 9120 Dihedral : 7.841 89.136 7128 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 6.34 % 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: -3.50 (0.09), residues: 6576 helix: -2.27 (0.10), residues: 1692 sheet: -2.38 (0.12), residues: 1488 loop : -2.28 (0.10), residues: 3396 *********************** 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 1701 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1376 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 325 outliers final: 115 residues processed: 1550 average time/residue: 1.2983 time to fit residues: 2581.3000 Evaluate side-chains 1347 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1232 time to evaluate : 5.215 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 65 residues processed: 52 average time/residue: 0.6012 time to fit residues: 55.6876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 162 optimal weight: 2.9990 chunk 589 optimal weight: 6.9990 chunk 636 optimal weight: 6.9990 chunk 525 optimal weight: 6.9990 chunk 584 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 472 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN M 124 GLN M 377 GLN A 298 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN N 350 GLN O 11 ASN O 347 GLN P 11 ASN ** P 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 327 ASN R 193 ASN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS D 327 ASN E 369 ASN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 5 GLN ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN ** d 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 50880 Z= 0.314 Angle : 0.655 8.311 69180 Z= 0.351 Chirality : 0.047 0.246 7836 Planarity : 0.005 0.049 9120 Dihedral : 7.723 89.225 7128 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 7.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 6576 helix: -0.61 (0.12), residues: 1668 sheet: -2.18 (0.12), residues: 1548 loop : -1.96 (0.10), residues: 3360 *********************** 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 1654 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1276 time to evaluate : 4.851 Fit side-chains revert: symmetry clash outliers start: 378 outliers final: 194 residues processed: 1475 average time/residue: 1.2440 time to fit residues: 2349.9357 Evaluate side-chains 1343 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1149 time to evaluate : 4.434 Switching outliers to nearest non-outliers outliers start: 194 outliers final: 121 residues processed: 77 average time/residue: 0.6584 time to fit residues: 83.7115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 4.9990 chunk 443 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 395 optimal weight: 0.4980 chunk 591 optimal weight: 9.9990 chunk 626 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 560 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 ASN P 298 HIS Q 327 ASN R 11 ASN B 112 GLN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN n 37 GLN o 63 ASN q 37 GLN b 164 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 50880 Z= 0.361 Angle : 0.655 9.501 69180 Z= 0.352 Chirality : 0.047 0.245 7836 Planarity : 0.005 0.050 9120 Dihedral : 7.678 88.773 7128 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer Outliers : 8.51 % 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: -2.17 (0.10), residues: 6576 helix: 0.11 (0.13), residues: 1668 sheet: -2.08 (0.13), residues: 1548 loop : -1.92 (0.10), residues: 3360 *********************** 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 1620 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1184 time to evaluate : 4.293 Fit side-chains outliers start: 436 outliers final: 252 residues processed: 1442 average time/residue: 1.2076 time to fit residues: 2234.5295 Evaluate side-chains 1347 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1095 time to evaluate : 4.270 Switching outliers to nearest non-outliers outliers start: 252 outliers final: 169 residues processed: 91 average time/residue: 0.5219 time to fit residues: 82.5421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 0.9980 chunk 355 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 466 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 534 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 562 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN O 11 ASN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN ** n 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 63 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** 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 9 ASN e 37 GLN ** f 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 164 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 50880 Z= 0.275 Angle : 0.611 10.958 69180 Z= 0.326 Chirality : 0.045 0.245 7836 Planarity : 0.005 0.058 9120 Dihedral : 7.458 89.447 7128 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 8.04 % 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: -1.97 (0.10), residues: 6576 helix: 0.49 (0.13), residues: 1692 sheet: -1.95 (0.13), residues: 1572 loop : -1.94 (0.10), residues: 3312 *********************** 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 1567 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 1155 time to evaluate : 4.905 Fit side-chains revert: symmetry clash outliers start: 412 outliers final: 258 residues processed: 1404 average time/residue: 1.1645 time to fit residues: 2098.5791 Evaluate side-chains 1360 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1102 time to evaluate : 4.227 Switching outliers to nearest non-outliers outliers start: 258 outliers final: 185 residues processed: 81 average time/residue: 0.5794 time to fit residues: 78.2944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 3.9990 chunk 564 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 367 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 626 optimal weight: 6.9990 chunk 520 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** O 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 HIS R 11 ASN R 377 GLN B 112 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 347 GLN E 350 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN n 63 ASN q 37 GLN q 63 ASN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** 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 164 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 50880 Z= 0.369 Angle : 0.660 9.685 69180 Z= 0.352 Chirality : 0.047 0.179 7836 Planarity : 0.005 0.067 9120 Dihedral : 7.477 89.953 7128 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer Outliers : 8.37 % 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: -1.84 (0.10), residues: 6576 helix: 0.63 (0.13), residues: 1692 sheet: -1.78 (0.14), residues: 1452 loop : -1.95 (0.10), residues: 3432 *********************** 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 1536 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 429 poor density : 1107 time to evaluate : 4.429 Fit side-chains revert: symmetry clash outliers start: 429 outliers final: 289 residues processed: 1366 average time/residue: 1.1567 time to fit residues: 2027.5687 Evaluate side-chains 1348 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1059 time to evaluate : 5.026 Switching outliers to nearest non-outliers outliers start: 289 outliers final: 197 residues processed: 99 average time/residue: 0.6097 time to fit residues: 97.4696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 357 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 527 optimal weight: 2.9990 chunk 350 optimal weight: 0.3980 chunk 624 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 380 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN O 11 ASN Q 133 HIS B 112 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 154 ASN a 164 ASN n 78 GLN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** 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 164 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 50880 Z= 0.238 Angle : 0.590 9.976 69180 Z= 0.314 Chirality : 0.045 0.262 7836 Planarity : 0.004 0.049 9120 Dihedral : 7.208 89.790 7128 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 7.81 % 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: -1.68 (0.10), residues: 6576 helix: 0.92 (0.13), residues: 1680 sheet: -1.74 (0.13), residues: 1548 loop : -1.88 (0.10), residues: 3348 *********************** 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 1521 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1121 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 400 outliers final: 264 residues processed: 1369 average time/residue: 1.1265 time to fit residues: 1975.1875 Evaluate side-chains 1332 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1068 time to evaluate : 4.053 Switching outliers to nearest non-outliers outliers start: 264 outliers final: 199 residues processed: 70 average time/residue: 0.5869 time to fit residues: 68.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 0.9980 chunk 249 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 397 optimal weight: 0.9980 chunk 425 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 490 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN O 347 GLN Q 133 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 350 GLN a 164 ASN n 37 GLN q 37 GLN b 5 GLN ** b 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 GLN ** 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 5 GLN e 37 GLN f 164 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 50880 Z= 0.181 Angle : 0.564 11.383 69180 Z= 0.298 Chirality : 0.044 0.246 7836 Planarity : 0.004 0.042 9120 Dihedral : 6.957 88.879 7128 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 6.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 6576 helix: 1.19 (0.13), residues: 1680 sheet: -1.65 (0.13), residues: 1668 loop : -1.82 (0.10), residues: 3228 *********************** 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 1451 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1140 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 311 outliers final: 219 residues processed: 1364 average time/residue: 1.0471 time to fit residues: 1835.3528 Evaluate side-chains 1286 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1067 time to evaluate : 3.678 Switching outliers to nearest non-outliers outliers start: 219 outliers final: 191 residues processed: 34 average time/residue: 0.5336 time to fit residues: 32.8572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0020 chunk 545 optimal weight: 5.9990 chunk 582 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 457 optimal weight: 0.0570 chunk 178 optimal weight: 1.9990 chunk 525 optimal weight: 4.9990 chunk 550 optimal weight: 7.9990 chunk 579 optimal weight: 10.0000 overall best weight: 1.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 ASN P 11 ASN Q 133 HIS ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 112 GLN B 136 GLN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN b 9 ASN ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 78 GLN c 164 ASN d 164 ASN f 78 GLN f 164 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 50880 Z= 0.208 Angle : 0.586 12.646 69180 Z= 0.307 Chirality : 0.044 0.243 7836 Planarity : 0.004 0.043 9120 Dihedral : 6.902 89.021 7128 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 5.62 % 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: -1.40 (0.11), residues: 6576 helix: 1.26 (0.13), residues: 1680 sheet: -1.60 (0.13), residues: 1668 loop : -1.75 (0.10), residues: 3228 *********************** 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 1363 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1075 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 288 outliers final: 231 residues processed: 1288 average time/residue: 1.0019 time to fit residues: 1665.0126 Evaluate side-chains 1273 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1042 time to evaluate : 3.654 Switching outliers to nearest non-outliers outliers start: 231 outliers final: 191 residues processed: 44 average time/residue: 0.5677 time to fit residues: 42.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 4.9990 chunk 615 optimal weight: 3.9990 chunk 375 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 645 optimal weight: 0.5980 chunk 594 optimal weight: 2.9990 chunk 514 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 397 optimal weight: 0.7980 chunk 315 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN Q 133 HIS ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 112 GLN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 350 GLN n 37 GLN ** c 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 ASN ** d 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 ASN e 37 GLN f 164 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 50880 Z= 0.226 Angle : 0.598 12.449 69180 Z= 0.312 Chirality : 0.045 0.241 7836 Planarity : 0.004 0.043 9120 Dihedral : 6.892 89.051 7128 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 4.80 % 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: -1.34 (0.11), residues: 6576 helix: 1.40 (0.13), residues: 1644 sheet: -1.63 (0.13), residues: 1644 loop : -1.69 (0.10), residues: 3288 ********************** 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 1301 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1055 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 246 outliers final: 211 residues processed: 1259 average time/residue: 0.9851 time to fit residues: 1591.7337 Evaluate side-chains 1246 residues out of total 5124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1035 time to evaluate : 3.610 Switching outliers to nearest non-outliers outliers start: 211 outliers final: 191 residues processed: 27 average time/residue: 0.4365 time to fit residues: 24.1077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 8.9990 chunk 547 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 474 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 514 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 528 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 347 GLN N 350 GLN P 11 ASN Q 133 HIS ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 350 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN n 37 GLN ** c 71 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.104301 restraints weight = 63989.149| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.53 r_work: 0.2982 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 50880 Z= 0.308 Angle : 0.642 12.069 69180 Z= 0.337 Chirality : 0.046 0.286 7836 Planarity : 0.005 0.045 9120 Dihedral : 7.044 89.572 7128 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer Outliers : 5.19 % 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: -1.43 (0.11), residues: 6576 helix: 1.16 (0.13), residues: 1668 sheet: -1.69 (0.13), residues: 1656 loop : -1.66 (0.10), residues: 3252 =============================================================================== Job complete usr+sys time: 26752.65 seconds wall clock time: 460 minutes 26.16 seconds (27626.16 seconds total)