Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:21:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2023/6uov_20833.pdb" } resolution = 3.5 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= 0.001 sd= 0.012 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 Process input model Symmetric amino acids flipped Residue "A ARG 82": "NH1" <-> "NH2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "L TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "N TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "P TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "R TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "T TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "V TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "X TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 82": "NH1" <-> "NH2" Residue "Z TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 82": "NH1" <-> "NH2" Residue "b TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 82": "NH1" <-> "NH2" Residue "d TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "f TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 82": "NH1" <-> "NH2" Residue "h TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 82": "NH1" <-> "NH2" Residue "j TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 82": "NH1" <-> "NH2" Residue "l TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "n TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 82": "NH1" <-> "NH2" Residue "p TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 82": "NH1" <-> "NH2" Residue "r TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 82": "NH1" <-> "NH2" Residue "t TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69851 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "B" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "C" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "D" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "E" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "F" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "G" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "I" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "J" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "K" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "L" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "M" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "N" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "P" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "Q" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "R" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "T" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "U" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "V" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "W" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "X" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "Y" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "Z" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "a" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "b" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "c" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "e" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "f" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "g" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "h" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "i" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "j" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "k" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "l" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "m" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "n" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "o" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "p" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "q" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "r" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "s" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "t" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Time building chain proxies: 29.18, per 1000 atoms: 0.42 Number of scatterers: 69851 At special positions: 0 Unit cell: (247.17, 246.1, 75.97, 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 161 16.00 O 13248 8.00 N 12374 7.00 C 44068 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: 22.76 Conformation dependent library (CDL) restraints added in 8.1 seconds 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16560 Finding SS restraints... Secondary structure from input PDB file: 345 helices and 115 sheets defined 43.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE A 89 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 75 " --> pdb=" O TRP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 75 " --> pdb=" O TRP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 102 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL F 210 " --> pdb=" O TRP F 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN F 229 " --> pdb=" O GLU F 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 308 Processing helix chain 'F' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG F 340 " --> pdb=" O ILE F 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR G 70 " --> pdb=" O THR G 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR G 75 " --> pdb=" O TRP G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 89 removed outlier: 3.532A pdb=" N PHE G 89 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G 102 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP G 166 " --> pdb=" O HIS G 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE G 167 " --> pdb=" O GLN G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL H 210 " --> pdb=" O TRP H 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU H 228 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN H 229 " --> pdb=" O GLU H 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU H 273 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 308 Processing helix chain 'H' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG H 340 " --> pdb=" O ILE H 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN H 341 " --> pdb=" O LEU H 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR I 75 " --> pdb=" O TRP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 102 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 140 Processing helix chain 'I' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP I 166 " --> pdb=" O HIS I 162 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE I 167 " --> pdb=" O GLN I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'J' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU J 205 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL J 210 " --> pdb=" O TRP J 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA J 212 " --> pdb=" O ARG J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU J 228 " --> pdb=" O ASN J 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR J 238 " --> pdb=" O ILE J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 308 Processing helix chain 'J' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG J 340 " --> pdb=" O ILE J 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN J 341 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER J 345 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J 349 " --> pdb=" O SER J 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU K 34 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE K 36 " --> pdb=" O ALA K 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 43 No H-bonds generated for 'chain 'K' and resid 41 through 43' Processing helix chain 'K' and resid 52 through 54 No H-bonds generated for 'chain 'K' and resid 52 through 54' Processing helix chain 'K' and resid 61 through 63 No H-bonds generated for 'chain 'K' and resid 61 through 63' Processing helix chain 'K' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR K 75 " --> pdb=" O TRP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE K 89 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 102 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE K 167 " --> pdb=" O GLN K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 177 Processing helix chain 'L' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU L 205 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 210 " --> pdb=" O TRP L 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA L 212 " --> pdb=" O ARG L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN L 229 " --> pdb=" O GLU L 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU L 273 " --> pdb=" O LYS L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 308 Processing helix chain 'L' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG L 340 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 341 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER L 345 " --> pdb=" O GLN L 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 349 " --> pdb=" O SER L 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU M 34 " --> pdb=" O GLU M 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 36 " --> pdb=" O ALA M 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA M 37 " --> pdb=" O ASN M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 43 No H-bonds generated for 'chain 'M' and resid 41 through 43' Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR M 75 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE M 89 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP M 166 " --> pdb=" O HIS M 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE M 167 " --> pdb=" O GLN M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 177 Processing helix chain 'N' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU N 205 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 210 " --> pdb=" O TRP N 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA N 212 " --> pdb=" O ARG N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU N 228 " --> pdb=" O ASN N 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN N 229 " --> pdb=" O GLU N 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS N 230 " --> pdb=" O ASN N 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR N 238 " --> pdb=" O ILE N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU N 273 " --> pdb=" O LYS N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 308 Processing helix chain 'N' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG N 340 " --> pdb=" O ILE N 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN N 341 " --> pdb=" O LEU N 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER N 345 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR N 349 " --> pdb=" O SER N 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU O 34 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE O 36 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA O 37 " --> pdb=" O ASN O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 52 through 54 No H-bonds generated for 'chain 'O' and resid 52 through 54' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR O 70 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR O 75 " --> pdb=" O TRP O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE O 89 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS O 102 " --> pdb=" O PRO O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP O 166 " --> pdb=" O HIS O 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE O 167 " --> pdb=" O GLN O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 177 Processing helix chain 'P' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU P 205 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL P 210 " --> pdb=" O TRP P 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 212 " --> pdb=" O ARG P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU P 228 " --> pdb=" O ASN P 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN P 229 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS P 230 " --> pdb=" O ASN P 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER P 233 " --> pdb=" O ASN P 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR P 238 " --> pdb=" O ILE P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU P 273 " --> pdb=" O LYS P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 308 Processing helix chain 'P' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG P 340 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN P 341 " --> pdb=" O LEU P 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER P 345 " --> pdb=" O GLN P 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR P 349 " --> pdb=" O SER P 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU Q 34 " --> pdb=" O GLU Q 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE Q 36 " --> pdb=" O ALA Q 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Q 37 " --> pdb=" O ASN Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 52 through 54 No H-bonds generated for 'chain 'Q' and resid 52 through 54' Processing helix chain 'Q' and resid 61 through 63 No H-bonds generated for 'chain 'Q' and resid 61 through 63' Processing helix chain 'Q' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR Q 70 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Q 75 " --> pdb=" O TRP Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE Q 89 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU Q 101 " --> pdb=" O SER Q 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS Q 102 " --> pdb=" O PRO Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 140 Processing helix chain 'Q' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE Q 167 " --> pdb=" O GLN Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU R 205 " --> pdb=" O GLU R 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 210 " --> pdb=" O TRP R 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU R 228 " --> pdb=" O ASN R 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN R 229 " --> pdb=" O GLU R 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER R 233 " --> pdb=" O ASN R 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 308 Processing helix chain 'R' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG R 340 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER R 345 " --> pdb=" O GLN R 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR R 349 " --> pdb=" O SER R 345 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU S 34 " --> pdb=" O GLU S 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 52 through 54 No H-bonds generated for 'chain 'S' and resid 52 through 54' Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS S 73 " --> pdb=" O VAL S 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR S 75 " --> pdb=" O TRP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE S 89 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU S 101 " --> pdb=" O SER S 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS S 102 " --> pdb=" O PRO S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 Processing helix chain 'S' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP S 166 " --> pdb=" O HIS S 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE S 167 " --> pdb=" O GLN S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 177 Processing helix chain 'T' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU T 205 " --> pdb=" O GLU T 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL T 210 " --> pdb=" O TRP T 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 212 " --> pdb=" O ARG T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU T 228 " --> pdb=" O ASN T 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN T 229 " --> pdb=" O GLU T 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS T 230 " --> pdb=" O ASN T 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER T 233 " --> pdb=" O ASN T 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR T 238 " --> pdb=" O ILE T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU T 273 " --> pdb=" O LYS T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 308 Processing helix chain 'T' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG T 340 " --> pdb=" O ILE T 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN T 341 " --> pdb=" O LEU T 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER T 345 " --> pdb=" O GLN T 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR T 349 " --> pdb=" O SER T 345 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE U 36 " --> pdb=" O ALA U 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA U 37 " --> pdb=" O ASN U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 43 No H-bonds generated for 'chain 'U' and resid 41 through 43' Processing helix chain 'U' and resid 52 through 54 No H-bonds generated for 'chain 'U' and resid 52 through 54' Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR U 70 " --> pdb=" O THR U 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 73 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR U 75 " --> pdb=" O TRP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE U 89 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU U 101 " --> pdb=" O SER U 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS U 102 " --> pdb=" O PRO U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 140 Processing helix chain 'U' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP U 166 " --> pdb=" O HIS U 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE U 167 " --> pdb=" O GLN U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU V 205 " --> pdb=" O GLU V 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL V 210 " --> pdb=" O TRP V 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA V 212 " --> pdb=" O ARG V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU V 228 " --> pdb=" O ASN V 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN V 229 " --> pdb=" O GLU V 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS V 230 " --> pdb=" O ASN V 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER V 233 " --> pdb=" O ASN V 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR V 238 " --> pdb=" O ILE V 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 308 Processing helix chain 'V' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG V 340 " --> pdb=" O ILE V 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN V 341 " --> pdb=" O LEU V 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER V 345 " --> pdb=" O GLN V 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR V 349 " --> pdb=" O SER V 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA W 37 " --> pdb=" O ASN W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 43 No H-bonds generated for 'chain 'W' and resid 41 through 43' Processing helix chain 'W' and resid 52 through 54 No H-bonds generated for 'chain 'W' and resid 52 through 54' Processing helix chain 'W' and resid 61 through 63 No H-bonds generated for 'chain 'W' and resid 61 through 63' Processing helix chain 'W' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR W 70 " --> pdb=" O THR W 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS W 73 " --> pdb=" O VAL W 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR W 75 " --> pdb=" O TRP W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE W 89 " --> pdb=" O ALA W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU W 101 " --> pdb=" O SER W 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS W 102 " --> pdb=" O PRO W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 140 Processing helix chain 'W' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP W 166 " --> pdb=" O HIS W 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE W 167 " --> pdb=" O GLN W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 177 Processing helix chain 'X' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU X 205 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 210 " --> pdb=" O TRP X 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA X 212 " --> pdb=" O ARG X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU X 228 " --> pdb=" O ASN X 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN X 229 " --> pdb=" O GLU X 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS X 230 " --> pdb=" O ASN X 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER X 233 " --> pdb=" O ASN X 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR X 238 " --> pdb=" O ILE X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU X 273 " --> pdb=" O LYS X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 295 through 308 Processing helix chain 'X' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN X 341 " --> pdb=" O LEU X 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER X 345 " --> pdb=" O GLN X 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR X 349 " --> pdb=" O SER X 345 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU Y 34 " --> pdb=" O GLU Y 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE Y 36 " --> pdb=" O ALA Y 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 37 " --> pdb=" O ASN Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 43 No H-bonds generated for 'chain 'Y' and resid 41 through 43' Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 61 through 63 No H-bonds generated for 'chain 'Y' and resid 61 through 63' Processing helix chain 'Y' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR Y 70 " --> pdb=" O THR Y 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 73 " --> pdb=" O VAL Y 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Y 75 " --> pdb=" O TRP Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE Y 89 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU Y 101 " --> pdb=" O SER Y 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS Y 102 " --> pdb=" O PRO Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 140 Processing helix chain 'Y' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP Y 166 " --> pdb=" O HIS Y 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE Y 167 " --> pdb=" O GLN Y 163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 177 Processing helix chain 'Z' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU Z 205 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL Z 210 " --> pdb=" O TRP Z 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA Z 212 " --> pdb=" O ARG Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU Z 228 " --> pdb=" O ASN Z 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN Z 229 " --> pdb=" O GLU Z 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS Z 230 " --> pdb=" O ASN Z 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER Z 233 " --> pdb=" O ASN Z 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR Z 238 " --> pdb=" O ILE Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU Z 273 " --> pdb=" O LYS Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 295 through 308 Processing helix chain 'Z' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG Z 340 " --> pdb=" O ILE Z 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN Z 341 " --> pdb=" O LEU Z 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER Z 345 " --> pdb=" O GLN Z 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR Z 349 " --> pdb=" O SER Z 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU a 34 " --> pdb=" O GLU a 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE a 36 " --> pdb=" O ALA a 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA a 37 " --> pdb=" O ASN a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 43 No H-bonds generated for 'chain 'a' and resid 41 through 43' Processing helix chain 'a' and resid 52 through 54 No H-bonds generated for 'chain 'a' and resid 52 through 54' Processing helix chain 'a' and resid 61 through 63 No H-bonds generated for 'chain 'a' and resid 61 through 63' Processing helix chain 'a' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR a 70 " --> pdb=" O THR a 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR a 75 " --> pdb=" O TRP a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE a 89 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU a 101 " --> pdb=" O SER a 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS a 102 " --> pdb=" O PRO a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 140 Processing helix chain 'a' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP a 166 " --> pdb=" O HIS a 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE a 167 " --> pdb=" O GLN a 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU b 205 " --> pdb=" O GLU b 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL b 210 " --> pdb=" O TRP b 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA b 212 " --> pdb=" O ARG b 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU b 228 " --> pdb=" O ASN b 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN b 229 " --> pdb=" O GLU b 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS b 230 " --> pdb=" O ASN b 226 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 233 " --> pdb=" O ASN b 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR b 238 " --> pdb=" O ILE b 234 " (cutoff:3.500A) Processing helix chain 'b' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU b 273 " --> pdb=" O LYS b 269 " (cutoff:3.500A) Processing helix chain 'b' and resid 295 through 308 Processing helix chain 'b' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG b 340 " --> pdb=" O ILE b 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN b 341 " --> pdb=" O LEU b 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER b 345 " --> pdb=" O GLN b 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR b 349 " --> pdb=" O SER b 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE c 36 " --> pdb=" O ALA c 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA c 37 " --> pdb=" O ASN c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 43 No H-bonds generated for 'chain 'c' and resid 41 through 43' Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'c' and resid 61 through 63 No H-bonds generated for 'chain 'c' and resid 61 through 63' Processing helix chain 'c' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR c 70 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS c 73 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR c 75 " --> pdb=" O TRP c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE c 89 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU c 101 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS c 102 " --> pdb=" O PRO c 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 140 Processing helix chain 'c' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE c 167 " --> pdb=" O GLN c 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 177 Processing helix chain 'd' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL d 210 " --> pdb=" O TRP d 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA d 212 " --> pdb=" O ARG d 208 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU d 228 " --> pdb=" O ASN d 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN d 229 " --> pdb=" O GLU d 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS d 230 " --> pdb=" O ASN d 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER d 233 " --> pdb=" O ASN d 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR d 238 " --> pdb=" O ILE d 234 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU d 273 " --> pdb=" O LYS d 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 308 Processing helix chain 'd' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG d 340 " --> pdb=" O ILE d 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN d 341 " --> pdb=" O LEU d 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER d 345 " --> pdb=" O GLN d 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR d 349 " --> pdb=" O SER d 345 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU e 34 " --> pdb=" O GLU e 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE e 36 " --> pdb=" O ALA e 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA e 37 " --> pdb=" O ASN e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 43 No H-bonds generated for 'chain 'e' and resid 41 through 43' Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 61 through 63 No H-bonds generated for 'chain 'e' and resid 61 through 63' Processing helix chain 'e' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR e 70 " --> pdb=" O THR e 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS e 73 " --> pdb=" O VAL e 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR e 75 " --> pdb=" O TRP e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 removed outlier: 3.532A pdb=" N PHE e 89 " --> pdb=" O ALA e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU e 101 " --> pdb=" O SER e 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS e 102 " --> pdb=" O PRO e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 140 Processing helix chain 'e' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE e 167 " --> pdb=" O GLN e 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 177 Processing helix chain 'f' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU f 205 " --> pdb=" O GLU f 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL f 210 " --> pdb=" O TRP f 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA f 212 " --> pdb=" O ARG f 208 " (cutoff:3.500A) Processing helix chain 'f' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU f 228 " --> pdb=" O ASN f 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN f 229 " --> pdb=" O GLU f 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS f 230 " --> pdb=" O ASN f 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER f 233 " --> pdb=" O ASN f 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR f 238 " --> pdb=" O ILE f 234 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU f 273 " --> pdb=" O LYS f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 308 Processing helix chain 'f' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG f 340 " --> pdb=" O ILE f 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN f 341 " --> pdb=" O LEU f 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER f 345 " --> pdb=" O GLN f 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR f 349 " --> pdb=" O SER f 345 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU g 34 " --> pdb=" O GLU g 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE g 36 " --> pdb=" O ALA g 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA g 37 " --> pdb=" O ASN g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 43 No H-bonds generated for 'chain 'g' and resid 41 through 43' Processing helix chain 'g' and resid 52 through 54 No H-bonds generated for 'chain 'g' and resid 52 through 54' Processing helix chain 'g' and resid 61 through 63 No H-bonds generated for 'chain 'g' and resid 61 through 63' Processing helix chain 'g' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR g 70 " --> pdb=" O THR g 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS g 73 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR g 75 " --> pdb=" O TRP g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE g 89 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU g 101 " --> pdb=" O SER g 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS g 102 " --> pdb=" O PRO g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 135 through 140 Processing helix chain 'g' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP g 166 " --> pdb=" O HIS g 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE g 167 " --> pdb=" O GLN g 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 177 Processing helix chain 'h' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU h 205 " --> pdb=" O GLU h 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL h 210 " --> pdb=" O TRP h 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA h 212 " --> pdb=" O ARG h 208 " (cutoff:3.500A) Processing helix chain 'h' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU h 228 " --> pdb=" O ASN h 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN h 229 " --> pdb=" O GLU h 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS h 230 " --> pdb=" O ASN h 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER h 233 " --> pdb=" O ASN h 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR h 238 " --> pdb=" O ILE h 234 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU h 273 " --> pdb=" O LYS h 269 " (cutoff:3.500A) Processing helix chain 'h' and resid 295 through 308 Processing helix chain 'h' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG h 340 " --> pdb=" O ILE h 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN h 341 " --> pdb=" O LEU h 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER h 345 " --> pdb=" O GLN h 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR h 349 " --> pdb=" O SER h 345 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 40 removed outlier: 3.667A pdb=" N GLU i 34 " --> pdb=" O GLU i 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE i 36 " --> pdb=" O ALA i 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 43 No H-bonds generated for 'chain 'i' and resid 41 through 43' Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 61 through 63 No H-bonds generated for 'chain 'i' and resid 61 through 63' Processing helix chain 'i' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR i 70 " --> pdb=" O THR i 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR i 75 " --> pdb=" O TRP i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE i 89 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU i 101 " --> pdb=" O SER i 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS i 102 " --> pdb=" O PRO i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 140 Processing helix chain 'i' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP i 166 " --> pdb=" O HIS i 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE i 167 " --> pdb=" O GLN i 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 172 through 177 Processing helix chain 'j' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU j 205 " --> pdb=" O GLU j 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL j 210 " --> pdb=" O TRP j 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA j 212 " --> pdb=" O ARG j 208 " (cutoff:3.500A) Processing helix chain 'j' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU j 228 " --> pdb=" O ASN j 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN j 229 " --> pdb=" O GLU j 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS j 230 " --> pdb=" O ASN j 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER j 233 " --> pdb=" O ASN j 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR j 238 " --> pdb=" O ILE j 234 " (cutoff:3.500A) Processing helix chain 'j' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU j 273 " --> pdb=" O LYS j 269 " (cutoff:3.500A) Processing helix chain 'j' and resid 295 through 308 Processing helix chain 'j' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG j 340 " --> pdb=" O ILE j 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN j 341 " --> pdb=" O LEU j 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER j 345 " --> pdb=" O GLN j 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR j 349 " --> pdb=" O SER j 345 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU k 34 " --> pdb=" O GLU k 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE k 36 " --> pdb=" O ALA k 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA k 37 " --> pdb=" O ASN k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 43 No H-bonds generated for 'chain 'k' and resid 41 through 43' Processing helix chain 'k' and resid 52 through 54 No H-bonds generated for 'chain 'k' and resid 52 through 54' Processing helix chain 'k' and resid 61 through 63 No H-bonds generated for 'chain 'k' and resid 61 through 63' Processing helix chain 'k' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR k 70 " --> pdb=" O THR k 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR k 75 " --> pdb=" O TRP k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE k 89 " --> pdb=" O ALA k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU k 101 " --> pdb=" O SER k 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS k 102 " --> pdb=" O PRO k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 140 Processing helix chain 'k' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP k 166 " --> pdb=" O HIS k 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE k 167 " --> pdb=" O GLN k 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 172 through 177 Processing helix chain 'l' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU l 205 " --> pdb=" O GLU l 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL l 210 " --> pdb=" O TRP l 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA l 212 " --> pdb=" O ARG l 208 " (cutoff:3.500A) Processing helix chain 'l' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU l 228 " --> pdb=" O ASN l 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN l 229 " --> pdb=" O GLU l 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS l 230 " --> pdb=" O ASN l 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER l 233 " --> pdb=" O ASN l 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR l 238 " --> pdb=" O ILE l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU l 273 " --> pdb=" O LYS l 269 " (cutoff:3.500A) Processing helix chain 'l' and resid 295 through 308 Processing helix chain 'l' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG l 340 " --> pdb=" O ILE l 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN l 341 " --> pdb=" O LEU l 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER l 345 " --> pdb=" O GLN l 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR l 349 " --> pdb=" O SER l 345 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU m 34 " --> pdb=" O GLU m 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE m 36 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA m 37 " --> pdb=" O ASN m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 43 No H-bonds generated for 'chain 'm' and resid 41 through 43' Processing helix chain 'm' and resid 52 through 54 No H-bonds generated for 'chain 'm' and resid 52 through 54' Processing helix chain 'm' and resid 61 through 63 No H-bonds generated for 'chain 'm' and resid 61 through 63' Processing helix chain 'm' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR m 70 " --> pdb=" O THR m 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR m 75 " --> pdb=" O TRP m 71 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE m 89 " --> pdb=" O ALA m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU m 101 " --> pdb=" O SER m 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS m 102 " --> pdb=" O PRO m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 135 through 140 Processing helix chain 'm' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE m 167 " --> pdb=" O GLN m 163 " (cutoff:3.500A) Processing helix chain 'n' and resid 172 through 177 Processing helix chain 'n' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU n 205 " --> pdb=" O GLU n 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL n 210 " --> pdb=" O TRP n 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA n 212 " --> pdb=" O ARG n 208 " (cutoff:3.500A) Processing helix chain 'n' and resid 224 through 240 removed outlier: 3.534A pdb=" N GLU n 228 " --> pdb=" O ASN n 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN n 229 " --> pdb=" O GLU n 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS n 230 " --> pdb=" O ASN n 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER n 233 " --> pdb=" O ASN n 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR n 238 " --> pdb=" O ILE n 234 " (cutoff:3.500A) Processing helix chain 'n' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU n 273 " --> pdb=" O LYS n 269 " (cutoff:3.500A) Processing helix chain 'n' and resid 295 through 308 Processing helix chain 'n' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG n 340 " --> pdb=" O ILE n 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN n 341 " --> pdb=" O LEU n 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER n 345 " --> pdb=" O GLN n 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR n 349 " --> pdb=" O SER n 345 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU o 34 " --> pdb=" O GLU o 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE o 36 " --> pdb=" O ALA o 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA o 37 " --> pdb=" O ASN o 33 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 43 No H-bonds generated for 'chain 'o' and resid 41 through 43' Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 61 through 63 No H-bonds generated for 'chain 'o' and resid 61 through 63' Processing helix chain 'o' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR o 70 " --> pdb=" O THR o 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS o 73 " --> pdb=" O VAL o 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR o 75 " --> pdb=" O TRP o 71 " (cutoff:3.500A) Processing helix chain 'o' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE o 89 " --> pdb=" O ALA o 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU o 101 " --> pdb=" O SER o 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS o 102 " --> pdb=" O PRO o 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 135 through 140 Processing helix chain 'o' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP o 166 " --> pdb=" O HIS o 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE o 167 " --> pdb=" O GLN o 163 " (cutoff:3.500A) Processing helix chain 'p' and resid 172 through 177 Processing helix chain 'p' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU p 205 " --> pdb=" O GLU p 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL p 210 " --> pdb=" O TRP p 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA p 212 " --> pdb=" O ARG p 208 " (cutoff:3.500A) Processing helix chain 'p' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU p 228 " --> pdb=" O ASN p 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN p 229 " --> pdb=" O GLU p 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS p 230 " --> pdb=" O ASN p 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER p 233 " --> pdb=" O ASN p 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR p 238 " --> pdb=" O ILE p 234 " (cutoff:3.500A) Processing helix chain 'p' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU p 273 " --> pdb=" O LYS p 269 " (cutoff:3.500A) Processing helix chain 'p' and resid 295 through 308 Processing helix chain 'p' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN p 341 " --> pdb=" O LEU p 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER p 345 " --> pdb=" O GLN p 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR p 349 " --> pdb=" O SER p 345 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU q 34 " --> pdb=" O GLU q 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE q 36 " --> pdb=" O ALA q 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA q 37 " --> pdb=" O ASN q 33 " (cutoff:3.500A) Processing helix chain 'q' and resid 41 through 43 No H-bonds generated for 'chain 'q' and resid 41 through 43' Processing helix chain 'q' and resid 52 through 54 No H-bonds generated for 'chain 'q' and resid 52 through 54' Processing helix chain 'q' and resid 61 through 63 No H-bonds generated for 'chain 'q' and resid 61 through 63' Processing helix chain 'q' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR q 70 " --> pdb=" O THR q 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS q 73 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR q 75 " --> pdb=" O TRP q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE q 89 " --> pdb=" O ALA q 86 " (cutoff:3.500A) Processing helix chain 'q' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS q 102 " --> pdb=" O PRO q 98 " (cutoff:3.500A) Processing helix chain 'q' and resid 135 through 140 Processing helix chain 'q' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP q 166 " --> pdb=" O HIS q 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE q 167 " --> pdb=" O GLN q 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 172 through 177 Processing helix chain 'r' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU r 205 " --> pdb=" O GLU r 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL r 210 " --> pdb=" O TRP r 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA r 212 " --> pdb=" O ARG r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU r 228 " --> pdb=" O ASN r 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN r 229 " --> pdb=" O GLU r 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS r 230 " --> pdb=" O ASN r 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER r 233 " --> pdb=" O ASN r 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR r 238 " --> pdb=" O ILE r 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU r 273 " --> pdb=" O LYS r 269 " (cutoff:3.500A) Processing helix chain 'r' and resid 295 through 308 Processing helix chain 'r' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG r 340 " --> pdb=" O ILE r 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN r 341 " --> pdb=" O LEU r 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER r 345 " --> pdb=" O GLN r 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR r 349 " --> pdb=" O SER r 345 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU s 34 " --> pdb=" O GLU s 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA s 37 " --> pdb=" O ASN s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 43 No H-bonds generated for 'chain 's' and resid 41 through 43' Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 61 through 63 No H-bonds generated for 'chain 's' and resid 61 through 63' Processing helix chain 's' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR s 70 " --> pdb=" O THR s 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS s 73 " --> pdb=" O VAL s 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR s 75 " --> pdb=" O TRP s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE s 89 " --> pdb=" O ALA s 86 " (cutoff:3.500A) Processing helix chain 's' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU s 101 " --> pdb=" O SER s 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS s 102 " --> pdb=" O PRO s 98 " (cutoff:3.500A) Processing helix chain 's' and resid 135 through 140 Processing helix chain 's' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP s 166 " --> pdb=" O HIS s 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE s 167 " --> pdb=" O GLN s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 172 through 177 Processing helix chain 't' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU t 205 " --> pdb=" O GLU t 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL t 210 " --> pdb=" O TRP t 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA t 212 " --> pdb=" O ARG t 208 " (cutoff:3.500A) Processing helix chain 't' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU t 228 " --> pdb=" O ASN t 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN t 229 " --> pdb=" O GLU t 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS t 230 " --> pdb=" O ASN t 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER t 233 " --> pdb=" O ASN t 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR t 238 " --> pdb=" O ILE t 234 " (cutoff:3.500A) Processing helix chain 't' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU t 273 " --> pdb=" O LYS t 269 " (cutoff:3.500A) Processing helix chain 't' and resid 295 through 308 Processing helix chain 't' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG t 340 " --> pdb=" O ILE t 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN t 341 " --> pdb=" O LEU t 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER t 345 " --> pdb=" O GLN t 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR t 349 " --> pdb=" O SER t 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU A 23 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 60 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS A 25 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 58 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 59 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER A 125 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 152 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 188 removed outlier: 6.712A pdb=" N LEU B 194 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 223 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 196 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR B 245 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER B 261 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 247 " --> pdb=" O TRP B 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE B 258 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET B 294 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 260 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL B 326 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 322 " --> pdb=" O HIS B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU C 23 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL C 60 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS C 25 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 58 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 59 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER C 125 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 152 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU D 194 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE D 223 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 196 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR D 245 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER D 261 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG D 247 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE D 258 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET D 294 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU D 260 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL D 326 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 322 " --> pdb=" O HIS D 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU E 23 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL E 60 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS E 25 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE E 58 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 59 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER E 125 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA E 152 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU F 194 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE F 223 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL F 196 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR F 245 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER F 261 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 247 " --> pdb=" O TRP F 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE F 258 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET F 294 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU F 260 " --> pdb=" O MET F 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL F 326 " --> pdb=" O SER F 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 322 " --> pdb=" O HIS F 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU G 23 " --> pdb=" O VAL G 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL G 60 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS G 25 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE G 58 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR G 59 " --> pdb=" O ASN G 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER G 125 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 152 " --> pdb=" O VAL G 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU H 194 " --> pdb=" O ARG H 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE H 223 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL H 196 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR H 245 " --> pdb=" O SER H 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG H 247 " --> pdb=" O TRP H 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE H 258 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET H 294 " --> pdb=" O PHE H 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU H 260 " --> pdb=" O MET H 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL H 326 " --> pdb=" O SER H 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY H 322 " --> pdb=" O HIS H 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU I 23 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL I 60 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS I 25 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE I 58 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR I 59 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER I 125 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA I 152 " --> pdb=" O VAL I 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU J 194 " --> pdb=" O ARG J 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE J 223 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL J 196 " --> pdb=" O ILE J 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR J 245 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER J 261 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG J 247 " --> pdb=" O TRP J 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE J 258 " --> pdb=" O THR J 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET J 294 " --> pdb=" O PHE J 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU J 260 " --> pdb=" O MET J 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL J 326 " --> pdb=" O SER J 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY J 322 " --> pdb=" O HIS J 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU K 23 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL K 60 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS K 25 " --> pdb=" O ILE K 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE K 58 " --> pdb=" O LYS K 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR K 59 " --> pdb=" O ASN K 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER K 125 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA K 152 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU L 194 " --> pdb=" O ARG L 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE L 223 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL L 196 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR L 245 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER L 261 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG L 247 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE L 258 " --> pdb=" O THR L 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET L 294 " --> pdb=" O PHE L 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU L 260 " --> pdb=" O MET L 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL L 326 " --> pdb=" O SER L 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 322 " --> pdb=" O HIS L 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU M 23 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL M 60 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS M 25 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE M 58 " --> pdb=" O LYS M 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 59 " --> pdb=" O ASN M 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER M 125 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA M 152 " --> pdb=" O VAL M 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU N 194 " --> pdb=" O ARG N 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE N 223 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL N 196 " --> pdb=" O ILE N 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR N 245 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER N 261 " --> pdb=" O TYR N 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG N 247 " --> pdb=" O TRP N 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE N 258 " --> pdb=" O THR N 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET N 294 " --> pdb=" O PHE N 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU N 260 " --> pdb=" O MET N 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL N 326 " --> pdb=" O SER N 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY N 322 " --> pdb=" O HIS N 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU O 23 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL O 60 " --> pdb=" O LEU O 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS O 25 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE O 58 " --> pdb=" O LYS O 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR O 59 " --> pdb=" O ASN O 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER O 125 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA O 152 " --> pdb=" O VAL O 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU P 194 " --> pdb=" O ARG P 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE P 223 " --> pdb=" O LEU P 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL P 196 " --> pdb=" O ILE P 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR P 245 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER P 261 " --> pdb=" O TYR P 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG P 247 " --> pdb=" O TRP P 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE P 258 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET P 294 " --> pdb=" O PHE P 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU P 260 " --> pdb=" O MET P 294 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL P 326 " --> pdb=" O SER P 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY P 322 " --> pdb=" O HIS P 319 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU Q 23 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL Q 60 " --> pdb=" O LEU Q 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS Q 25 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE Q 58 " --> pdb=" O LYS Q 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR Q 59 " --> pdb=" O ASN Q 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER Q 125 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA Q 152 " --> pdb=" O VAL Q 186 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU R 194 " --> pdb=" O ARG R 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE R 223 " --> pdb=" O LEU R 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL R 196 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR R 245 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER R 261 " --> pdb=" O TYR R 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG R 247 " --> pdb=" O TRP R 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE R 258 " --> pdb=" O THR R 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET R 294 " --> pdb=" O PHE R 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU R 260 " --> pdb=" O MET R 294 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL R 326 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY R 322 " --> pdb=" O HIS R 319 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU S 23 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL S 60 " --> pdb=" O LEU S 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS S 25 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE S 58 " --> pdb=" O LYS S 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR S 59 " --> pdb=" O ASN S 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER S 125 " --> pdb=" O VAL S 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA S 152 " --> pdb=" O VAL S 186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU T 194 " --> pdb=" O ARG T 221 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE T 223 " --> pdb=" O LEU T 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL T 196 " --> pdb=" O ILE T 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR T 245 " --> pdb=" O SER T 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER T 261 " --> pdb=" O TYR T 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG T 247 " --> pdb=" O TRP T 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE T 258 " --> pdb=" O THR T 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET T 294 " --> pdb=" O PHE T 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU T 260 " --> pdb=" O MET T 294 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 315 through 319 removed outlier: 3.829A pdb=" N VAL T 326 " --> pdb=" O SER T 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY T 322 " --> pdb=" O HIS T 319 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU U 23 " --> pdb=" O VAL U 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL U 60 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS U 25 " --> pdb=" O ILE U 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE U 58 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 59 " --> pdb=" O ASN U 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 125 through 130 removed outlier: 3.843A pdb=" N SER U 125 " --> pdb=" O VAL U 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA U 152 " --> pdb=" O VAL U 186 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU V 194 " --> pdb=" O ARG V 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE V 223 " --> pdb=" O LEU V 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL V 196 " --> pdb=" O ILE V 223 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR V 245 " --> pdb=" O SER V 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER V 261 " --> pdb=" O TYR V 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG V 247 " --> pdb=" O TRP V 259 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE V 258 " --> pdb=" O THR V 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET V 294 " --> pdb=" O PHE V 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU V 260 " --> pdb=" O MET V 294 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL V 326 " --> pdb=" O SER V 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY V 322 " --> pdb=" O HIS V 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU W 23 " --> pdb=" O VAL W 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL W 60 " --> pdb=" O LEU W 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS W 25 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE W 58 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR W 59 " --> pdb=" O ASN W 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER W 125 " --> pdb=" O VAL W 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA W 152 " --> pdb=" O VAL W 186 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU X 194 " --> pdb=" O ARG X 221 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE X 223 " --> pdb=" O LEU X 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL X 196 " --> pdb=" O ILE X 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR X 245 " --> pdb=" O SER X 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER X 261 " --> pdb=" O TYR X 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG X 247 " --> pdb=" O TRP X 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE X 258 " --> pdb=" O THR X 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET X 294 " --> pdb=" O PHE X 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU X 260 " --> pdb=" O MET X 294 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL X 326 " --> pdb=" O SER X 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY X 322 " --> pdb=" O HIS X 319 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU Y 23 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL Y 60 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS Y 25 " --> pdb=" O ILE Y 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE Y 58 " --> pdb=" O LYS Y 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR Y 59 " --> pdb=" O ASN Y 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER Y 125 " --> pdb=" O VAL Y 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA Y 152 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU Z 194 " --> pdb=" O ARG Z 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE Z 223 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL Z 196 " --> pdb=" O ILE Z 223 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR Z 245 " --> pdb=" O SER Z 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER Z 261 " --> pdb=" O TYR Z 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG Z 247 " --> pdb=" O TRP Z 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE Z 258 " --> pdb=" O THR Z 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET Z 294 " --> pdb=" O PHE Z 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU Z 260 " --> pdb=" O MET Z 294 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL Z 326 " --> pdb=" O SER Z 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY Z 322 " --> pdb=" O HIS Z 319 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU a 23 " --> pdb=" O VAL a 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL a 60 " --> pdb=" O LEU a 23 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS a 25 " --> pdb=" O ILE a 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE a 58 " --> pdb=" O LYS a 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR a 59 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER a 125 " --> pdb=" O VAL a 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA a 152 " --> pdb=" O VAL a 186 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU b 194 " --> pdb=" O ARG b 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE b 223 " --> pdb=" O LEU b 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL b 196 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR b 245 " --> pdb=" O SER b 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER b 261 " --> pdb=" O TYR b 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG b 247 " --> pdb=" O TRP b 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE b 258 " --> pdb=" O THR b 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET b 294 " --> pdb=" O PHE b 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU b 260 " --> pdb=" O MET b 294 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL b 326 " --> pdb=" O SER b 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY b 322 " --> pdb=" O HIS b 319 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'c' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU c 23 " --> pdb=" O VAL c 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL c 60 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS c 25 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE c 58 " --> pdb=" O LYS c 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR c 59 " --> pdb=" O ASN c 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER c 125 " --> pdb=" O VAL c 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA c 152 " --> pdb=" O VAL c 186 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU d 194 " --> pdb=" O ARG d 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE d 223 " --> pdb=" O LEU d 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL d 196 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR d 245 " --> pdb=" O SER d 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER d 261 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG d 247 " --> pdb=" O TRP d 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE d 258 " --> pdb=" O THR d 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET d 294 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU d 260 " --> pdb=" O MET d 294 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL d 326 " --> pdb=" O SER d 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY d 322 " --> pdb=" O HIS d 319 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU e 23 " --> pdb=" O VAL e 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL e 60 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS e 25 " --> pdb=" O ILE e 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE e 58 " --> pdb=" O LYS e 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR e 59 " --> pdb=" O ASN e 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 125 through 130 removed outlier: 3.843A pdb=" N SER e 125 " --> pdb=" O VAL e 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA e 152 " --> pdb=" O VAL e 186 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'f' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU f 194 " --> pdb=" O ARG f 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE f 223 " --> pdb=" O LEU f 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL f 196 " --> pdb=" O ILE f 223 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'f' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR f 245 " --> pdb=" O SER f 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER f 261 " --> pdb=" O TYR f 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG f 247 " --> pdb=" O TRP f 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE f 258 " --> pdb=" O THR f 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET f 294 " --> pdb=" O PHE f 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU f 260 " --> pdb=" O MET f 294 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'f' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL f 326 " --> pdb=" O SER f 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY f 322 " --> pdb=" O HIS f 319 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU g 23 " --> pdb=" O VAL g 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL g 60 " --> pdb=" O LEU g 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS g 25 " --> pdb=" O ILE g 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE g 58 " --> pdb=" O LYS g 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR g 59 " --> pdb=" O ASN g 47 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER g 125 " --> pdb=" O VAL g 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA g 152 " --> pdb=" O VAL g 186 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU h 194 " --> pdb=" O ARG h 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE h 223 " --> pdb=" O LEU h 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL h 196 " --> pdb=" O ILE h 223 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR h 245 " --> pdb=" O SER h 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER h 261 " --> pdb=" O TYR h 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG h 247 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE h 258 " --> pdb=" O THR h 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET h 294 " --> pdb=" O PHE h 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU h 260 " --> pdb=" O MET h 294 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL h 326 " --> pdb=" O SER h 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY h 322 " --> pdb=" O HIS h 319 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'i' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU i 23 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL i 60 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS i 25 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE i 58 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR i 59 " --> pdb=" O ASN i 47 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'i' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER i 125 " --> pdb=" O VAL i 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA i 152 " --> pdb=" O VAL i 186 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'j' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU j 194 " --> pdb=" O ARG j 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE j 223 " --> pdb=" O LEU j 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL j 196 " --> pdb=" O ILE j 223 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'j' and resid 245 through 249 removed outlier: 6.535A pdb=" N TYR j 245 " --> pdb=" O SER j 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER j 261 " --> pdb=" O TYR j 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG j 247 " --> pdb=" O TRP j 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE j 258 " --> pdb=" O THR j 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET j 294 " --> pdb=" O PHE j 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU j 260 " --> pdb=" O MET j 294 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'j' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL j 326 " --> pdb=" O SER j 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY j 322 " --> pdb=" O HIS j 319 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'k' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU k 23 " --> pdb=" O VAL k 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL k 60 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS k 25 " --> pdb=" O ILE k 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE k 58 " --> pdb=" O LYS k 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR k 59 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'k' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER k 125 " --> pdb=" O VAL k 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA k 152 " --> pdb=" O VAL k 186 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'l' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU l 194 " --> pdb=" O ARG l 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE l 223 " --> pdb=" O LEU l 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL l 196 " --> pdb=" O ILE l 223 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'l' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR l 245 " --> pdb=" O SER l 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER l 261 " --> pdb=" O TYR l 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG l 247 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE l 258 " --> pdb=" O THR l 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET l 294 " --> pdb=" O PHE l 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU l 260 " --> pdb=" O MET l 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'l' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL l 326 " --> pdb=" O SER l 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY l 322 " --> pdb=" O HIS l 319 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'm' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU m 23 " --> pdb=" O VAL m 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL m 60 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS m 25 " --> pdb=" O ILE m 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE m 58 " --> pdb=" O LYS m 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR m 59 " --> pdb=" O ASN m 47 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'm' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER m 125 " --> pdb=" O VAL m 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA m 152 " --> pdb=" O VAL m 186 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'n' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU n 194 " --> pdb=" O ARG n 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE n 223 " --> pdb=" O LEU n 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL n 196 " --> pdb=" O ILE n 223 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'n' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR n 245 " --> pdb=" O SER n 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER n 261 " --> pdb=" O TYR n 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG n 247 " --> pdb=" O TRP n 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE n 258 " --> pdb=" O THR n 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET n 294 " --> pdb=" O PHE n 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU n 260 " --> pdb=" O MET n 294 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'n' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL n 326 " --> pdb=" O SER n 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY n 322 " --> pdb=" O HIS n 319 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'o' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU o 23 " --> pdb=" O VAL o 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL o 60 " --> pdb=" O LEU o 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS o 25 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE o 58 " --> pdb=" O LYS o 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR o 59 " --> pdb=" O ASN o 47 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'o' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER o 125 " --> pdb=" O VAL o 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA o 152 " --> pdb=" O VAL o 186 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'p' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU p 194 " --> pdb=" O ARG p 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE p 223 " --> pdb=" O LEU p 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL p 196 " --> pdb=" O ILE p 223 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'p' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR p 245 " --> pdb=" O SER p 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER p 261 " --> pdb=" O TYR p 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG p 247 " --> pdb=" O TRP p 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE p 258 " --> pdb=" O THR p 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET p 294 " --> pdb=" O PHE p 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU p 260 " --> pdb=" O MET p 294 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'p' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL p 326 " --> pdb=" O SER p 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY p 322 " --> pdb=" O HIS p 319 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'q' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU q 23 " --> pdb=" O VAL q 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL q 60 " --> pdb=" O LEU q 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS q 25 " --> pdb=" O ILE q 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE q 58 " --> pdb=" O LYS q 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR q 59 " --> pdb=" O ASN q 47 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'q' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER q 125 " --> pdb=" O VAL q 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA q 152 " --> pdb=" O VAL q 186 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'r' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU r 194 " --> pdb=" O ARG r 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE r 223 " --> pdb=" O LEU r 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL r 196 " --> pdb=" O ILE r 223 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'r' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR r 245 " --> pdb=" O SER r 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER r 261 " --> pdb=" O TYR r 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG r 247 " --> pdb=" O TRP r 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE r 258 " --> pdb=" O THR r 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET r 294 " --> pdb=" O PHE r 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU r 260 " --> pdb=" O MET r 294 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'r' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL r 326 " --> pdb=" O SER r 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY r 322 " --> pdb=" O HIS r 319 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 's' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU s 23 " --> pdb=" O VAL s 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL s 60 " --> pdb=" O LEU s 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS s 25 " --> pdb=" O ILE s 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE s 58 " --> pdb=" O LYS s 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR s 59 " --> pdb=" O ASN s 47 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 's' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER s 125 " --> pdb=" O VAL s 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA s 152 " --> pdb=" O VAL s 186 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 't' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU t 194 " --> pdb=" O ARG t 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE t 223 " --> pdb=" O LEU t 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL t 196 " --> pdb=" O ILE t 223 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 't' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR t 245 " --> pdb=" O SER t 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER t 261 " --> pdb=" O TYR t 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG t 247 " --> pdb=" O TRP t 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE t 258 " --> pdb=" O THR t 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET t 294 " --> pdb=" O PHE t 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU t 260 " --> pdb=" O MET t 294 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 't' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL t 326 " --> pdb=" O SER t 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY t 322 " --> pdb=" O HIS t 319 " (cutoff:3.500A) 2553 hydrogen bonds defined for protein. 7245 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: 31.03 Time building geometry restraints manager: 24.85 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: 23163 1.34 - 1.45: 9418 1.45 - 1.57: 38259 1.57 - 1.68: 69 1.68 - 1.80: 322 Bond restraints: 71231 Sorted by residual: bond pdb=" CB GLU h 360 " pdb=" CG GLU h 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.91e+00 bond pdb=" CB GLU X 360 " pdb=" CG GLU X 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.89e+00 bond pdb=" CB GLU l 360 " pdb=" CG GLU l 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB GLU L 360 " pdb=" CG GLU L 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB GLU B 360 " pdb=" CG GLU B 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 ... (remaining 71226 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.16: 1568 105.16 - 112.39: 34633 112.39 - 119.63: 25308 119.63 - 126.86: 34015 126.86 - 134.09: 915 Bond angle restraints: 96439 Sorted by residual: angle pdb=" CA GLU N 360 " pdb=" CB GLU N 360 " pdb=" CG GLU N 360 " ideal model delta sigma weight residual 114.10 129.32 -15.22 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU H 360 " pdb=" CB GLU H 360 " pdb=" CG GLU H 360 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU p 360 " pdb=" CB GLU p 360 " pdb=" CG GLU p 360 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU f 360 " pdb=" CB GLU f 360 " pdb=" CG GLU f 360 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.78e+01 angle pdb=" CA GLU V 360 " pdb=" CB GLU V 360 " pdb=" CG GLU V 360 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.77e+01 ... (remaining 96434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 37963 11.17 - 22.34: 4056 22.34 - 33.51: 1064 33.51 - 44.68: 410 44.68 - 55.85: 184 Dihedral angle restraints: 43677 sinusoidal: 18055 harmonic: 25622 Sorted by residual: dihedral pdb=" CA ASP n 215 " pdb=" C ASP n 215 " pdb=" N TYR n 216 " pdb=" CA TYR n 216 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASP B 215 " pdb=" C ASP B 215 " pdb=" N TYR B 216 " pdb=" CA TYR B 216 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASP F 215 " pdb=" C ASP F 215 " pdb=" N TYR F 216 " pdb=" CA TYR F 216 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 43674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 8989 0.086 - 0.172: 1350 0.172 - 0.258: 126 0.258 - 0.343: 0 0.343 - 0.429: 23 Chirality restraints: 10488 Sorted by residual: chirality pdb=" CB ILE l 359 " pdb=" CA ILE l 359 " pdb=" CG1 ILE l 359 " pdb=" CG2 ILE l 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE R 359 " pdb=" CA ILE R 359 " pdb=" CG1 ILE R 359 " pdb=" CG2 ILE R 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE D 359 " pdb=" CA ILE D 359 " pdb=" CG1 ILE D 359 " pdb=" CG2 ILE D 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 10485 not shown) Planarity restraints: 12696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 180 " 0.011 2.00e-02 2.50e+03 1.28e-02 3.27e+00 pdb=" CG TYR Q 180 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 180 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 180 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 180 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR Q 180 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR Q 180 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 180 " -0.011 2.00e-02 2.50e+03 1.27e-02 3.25e+00 pdb=" CG TYR G 180 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR G 180 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR G 180 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR G 180 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 180 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 180 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 180 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 180 " 0.011 2.00e-02 2.50e+03 1.27e-02 3.25e+00 pdb=" CG TYR a 180 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR a 180 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR a 180 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR a 180 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR a 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR a 180 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR a 180 " 0.002 2.00e-02 2.50e+03 ... (remaining 12693 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14472 2.77 - 3.30: 63223 3.30 - 3.83: 113799 3.83 - 4.37: 138304 4.37 - 4.90: 235059 Nonbonded interactions: 564857 Sorted by model distance: nonbonded pdb=" OH TYR H 246 " pdb=" OD1 ASP H 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR Z 246 " pdb=" OD1 ASP Z 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR N 246 " pdb=" OD1 ASP N 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR l 246 " pdb=" OD1 ASP l 296 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR d 246 " pdb=" OD1 ASP d 296 " model vdw 2.233 2.440 ... (remaining 564852 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' } 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 161 5.16 5 C 44068 2.51 5 N 12374 2.21 5 O 13248 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.290 Check model and map are aligned: 0.770 Process input model: 146.690 Find NCS groups from input model: 4.230 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Set scattering table: 0.490 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 0.066 71231 Z= 0.604 Angle : 1.131 15.220 96439 Z= 0.600 Chirality : 0.063 0.429 10488 Planarity : 0.006 0.040 12696 Dihedral : 11.361 55.854 27117 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.22 (0.07), residues: 8602 helix: -4.39 (0.04), residues: 3358 sheet: -2.84 (0.11), residues: 2162 loop : -2.35 (0.10), residues: 3082 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2381 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 2128 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 51 residues processed: 2276 average time/residue: 0.7494 time to fit residues: 2769.1846 Evaluate side-chains 1422 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1371 time to evaluate : 6.434 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.5329 time to fit residues: 59.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 718 optimal weight: 5.9990 chunk 645 optimal weight: 0.6980 chunk 357 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 435 optimal weight: 5.9990 chunk 344 optimal weight: 0.9980 chunk 667 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 405 optimal weight: 1.9990 chunk 496 optimal weight: 0.8980 chunk 772 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 224 ASN B 265 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN D 219 ASN D 224 ASN E 29 GLN E 196 GLN F 219 ASN F 224 ASN G 29 GLN G 43 ASN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN G 196 GLN H 242 GLN I 76 GLN I 87 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 ASN J 224 ASN K 29 GLN K 76 GLN K 196 GLN L 224 ASN M 87 GLN ** M 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 ASN O 29 GLN ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN Q 43 ASN Q 76 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN S 76 GLN S 196 GLN T 219 ASN U 43 ASN U 76 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 ASN W 29 GLN W 33 ASN W 43 ASN W 76 GLN ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 GLN Y 43 ASN Z 224 ASN a 43 ASN a 76 GLN b 224 ASN c 29 GLN c 43 ASN c 76 GLN c 115 GLN c 196 GLN d 224 ASN e 29 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN e 196 GLN f 224 ASN g 29 GLN g 43 ASN g 76 GLN g 196 GLN h 224 ASN i 29 GLN i 115 GLN j 219 ASN j 224 ASN k 29 GLN k 33 ASN k 76 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 219 ASN l 224 ASN m 29 GLN m 33 ASN m 43 ASN m 76 GLN m 196 GLN n 224 ASN o 29 GLN o 76 GLN o 196 GLN p 219 ASN p 224 ASN q 29 GLN q 87 GLN q 115 GLN ** q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 ASN s 76 GLN ** s 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 219 ASN t 224 ASN t 265 ASN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 71231 Z= 0.197 Angle : 0.664 11.771 96439 Z= 0.343 Chirality : 0.045 0.177 10488 Planarity : 0.004 0.052 12696 Dihedral : 5.740 23.388 9706 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.88 (0.08), residues: 8602 helix: -3.06 (0.06), residues: 3381 sheet: -2.44 (0.11), residues: 2300 loop : -1.54 (0.10), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1797 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1621 time to evaluate : 6.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 71 residues processed: 1732 average time/residue: 0.7418 time to fit residues: 2123.5843 Evaluate side-chains 1411 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1340 time to evaluate : 6.453 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5222 time to fit residues: 78.9405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 429 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 643 optimal weight: 0.9990 chunk 526 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 774 optimal weight: 0.0980 chunk 836 optimal weight: 9.9990 chunk 689 optimal weight: 2.9990 chunk 767 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 621 optimal weight: 8.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 29 GLN C 76 GLN C 196 GLN D 224 ASN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN F 224 ASN G 29 GLN G 43 ASN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN I 43 ASN I 87 GLN I 111 GLN J 224 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 76 GLN L 219 ASN M 29 GLN M 43 ASN M 196 GLN O 33 ASN O 43 ASN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 43 ASN Q 76 GLN ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 ASN T 224 ASN U 33 ASN U 43 ASN U 76 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN W 29 GLN W 33 ASN W 43 ASN ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 ASN Y 43 ASN Z 224 ASN a 29 GLN a 43 ASN b 224 ASN c 33 ASN c 43 ASN d 224 ASN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 43 ASN g 87 GLN g 196 GLN h 224 ASN i 43 ASN i 111 GLN j 224 ASN k 43 ASN k 76 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN m 29 GLN m 43 ASN m 76 GLN n 224 ASN o 87 GLN p 224 ASN q 43 ASN q 76 GLN q 87 GLN q 196 GLN r 224 ASN s 29 GLN ** s 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 224 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 71231 Z= 0.274 Angle : 0.649 11.888 96439 Z= 0.325 Chirality : 0.046 0.179 10488 Planarity : 0.004 0.040 12696 Dihedral : 5.227 21.748 9706 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.94 (0.08), residues: 8602 helix: -2.14 (0.07), residues: 3381 sheet: -2.19 (0.11), residues: 2300 loop : -0.99 (0.11), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1730 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1497 time to evaluate : 6.561 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: 233 outliers final: 135 residues processed: 1689 average time/residue: 0.7715 time to fit residues: 2173.8899 Evaluate side-chains 1443 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1308 time to evaluate : 6.688 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 0 residues processed: 135 average time/residue: 0.5461 time to fit residues: 147.6414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 764 optimal weight: 4.9990 chunk 582 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 519 optimal weight: 0.9990 chunk 776 optimal weight: 8.9990 chunk 822 optimal weight: 0.9980 chunk 405 optimal weight: 2.9990 chunk 736 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN G 43 ASN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN K 87 GLN L 219 ASN M 43 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN S 29 GLN S 43 ASN T 224 ASN U 29 GLN U 76 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 87 GLN W 196 GLN X 224 ASN a 33 ASN a 43 ASN c 87 GLN f 224 ASN g 29 GLN j 224 ASN k 43 ASN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 43 ASN o 87 GLN q 43 ASN q 196 GLN r 224 ASN s 196 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 71231 Z= 0.262 Angle : 0.639 11.880 96439 Z= 0.315 Chirality : 0.045 0.163 10488 Planarity : 0.004 0.039 12696 Dihedral : 4.976 19.627 9706 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.40 (0.09), residues: 8602 helix: -1.59 (0.08), residues: 3404 sheet: -2.00 (0.11), residues: 2162 loop : -0.85 (0.11), residues: 3036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1575 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1430 time to evaluate : 6.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 66 residues processed: 1541 average time/residue: 0.7446 time to fit residues: 1882.6952 Evaluate side-chains 1370 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1304 time to evaluate : 6.439 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.5199 time to fit residues: 73.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 685 optimal weight: 10.0000 chunk 466 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 612 optimal weight: 9.9990 chunk 339 optimal weight: 2.9990 chunk 701 optimal weight: 5.9990 chunk 568 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 420 optimal weight: 3.9990 chunk 738 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN G 43 ASN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN S 43 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 29 GLN W 87 GLN X 242 GLN Y 87 GLN a 43 ASN d 224 ASN e 87 GLN f 224 ASN ** i 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 224 ASN k 43 ASN k 87 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 43 ASN ** o 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 29 GLN r 224 ASN s 196 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 71231 Z= 0.372 Angle : 0.686 15.900 96439 Z= 0.342 Chirality : 0.047 0.184 10488 Planarity : 0.004 0.044 12696 Dihedral : 5.011 20.814 9706 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.09), residues: 8602 helix: -1.29 (0.08), residues: 3381 sheet: -1.99 (0.11), residues: 2162 loop : -0.78 (0.12), residues: 3059 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1339 time to evaluate : 6.572 Fit side-chains revert: symmetry clash outliers start: 159 outliers final: 107 residues processed: 1455 average time/residue: 0.7534 time to fit residues: 1797.5915 Evaluate side-chains 1346 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1239 time to evaluate : 6.408 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.5259 time to fit residues: 116.0106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 276 optimal weight: 6.9990 chunk 740 optimal weight: 0.0770 chunk 162 optimal weight: 1.9990 chunk 482 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 823 optimal weight: 0.9980 chunk 683 optimal weight: 9.9990 chunk 381 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 272 optimal weight: 0.0370 chunk 432 optimal weight: 4.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 224 ASN G 43 ASN ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN L 219 ASN L 224 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 ASN ** O 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 196 GLN P 224 ASN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 87 GLN Y 87 GLN Z 224 ASN a 43 ASN b 224 ASN d 224 ASN g 87 GLN h 224 ASN i 29 GLN k 76 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN m 43 ASN o 29 GLN o 76 GLN o 87 GLN ** o 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 87 GLN ** q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 71231 Z= 0.177 Angle : 0.600 13.065 96439 Z= 0.294 Chirality : 0.043 0.191 10488 Planarity : 0.003 0.046 12696 Dihedral : 4.683 20.700 9706 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.99 (0.09), residues: 8602 helix: -0.97 (0.08), residues: 3381 sheet: -1.88 (0.11), residues: 2162 loop : -0.92 (0.11), residues: 3059 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1419 time to evaluate : 6.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 39 residues processed: 1471 average time/residue: 0.7447 time to fit residues: 1797.3979 Evaluate side-chains 1352 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1313 time to evaluate : 6.327 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5453 time to fit residues: 48.5112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 793 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 469 optimal weight: 3.9990 chunk 601 optimal weight: 6.9990 chunk 465 optimal weight: 5.9990 chunk 693 optimal weight: 10.0000 chunk 459 optimal weight: 0.2980 chunk 820 optimal weight: 3.9990 chunk 513 optimal weight: 0.8980 chunk 500 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN F 224 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN G 87 GLN I 87 GLN J 224 ASN K 29 GLN L 219 ASN L 224 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 ASN O 29 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 GLN P 224 ASN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 GLN U 87 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN Z 224 ASN ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN a 87 GLN b 224 ASN c 87 GLN g 87 GLN h 224 ASN j 224 ASN k 76 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN m 43 ASN o 76 GLN o 87 GLN p 224 ASN q 43 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 71231 Z= 0.232 Angle : 0.613 12.917 96439 Z= 0.302 Chirality : 0.044 0.268 10488 Planarity : 0.004 0.051 12696 Dihedral : 4.614 20.452 9706 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.79 (0.09), residues: 8602 helix: -0.78 (0.08), residues: 3404 sheet: -1.81 (0.11), residues: 2162 loop : -0.82 (0.12), residues: 3036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1353 time to evaluate : 6.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 46 residues processed: 1404 average time/residue: 0.7540 time to fit residues: 1741.9233 Evaluate side-chains 1330 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1284 time to evaluate : 6.441 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.5148 time to fit residues: 53.9129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 507 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 489 optimal weight: 2.9990 chunk 247 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 158 optimal weight: 0.0980 chunk 521 optimal weight: 3.9990 chunk 558 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 644 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** O 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 196 GLN R 224 ASN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN ** W 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 ASN ** Y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 224 ASN f 224 ASN j 224 ASN k 196 GLN ** m 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 76 GLN ** o 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 43 ASN q 87 GLN ** q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 71231 Z= 0.156 Angle : 0.587 12.584 96439 Z= 0.285 Chirality : 0.043 0.260 10488 Planarity : 0.003 0.055 12696 Dihedral : 4.458 22.860 9706 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.56 (0.09), residues: 8602 helix: -0.51 (0.09), residues: 3381 sheet: -1.67 (0.11), residues: 2162 loop : -0.82 (0.11), residues: 3059 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1436 time to evaluate : 6.401 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: 51 outliers final: 27 residues processed: 1464 average time/residue: 0.7417 time to fit residues: 1791.8326 Evaluate side-chains 1363 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1336 time to evaluate : 6.387 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5283 time to fit residues: 35.9295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 746 optimal weight: 0.9990 chunk 785 optimal weight: 5.9990 chunk 716 optimal weight: 0.8980 chunk 764 optimal weight: 6.9990 chunk 460 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 600 optimal weight: 1.9990 chunk 234 optimal weight: 0.0020 chunk 690 optimal weight: 1.9990 chunk 722 optimal weight: 2.9990 chunk 761 optimal weight: 6.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN G 76 GLN ** G 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN K 29 GLN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN ** O 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 GLN U 87 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN W 87 GLN X 224 ASN Y 29 GLN Y 87 GLN ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 224 ASN e 29 GLN f 224 ASN g 87 GLN j 224 ASN ** o 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 43 ASN q 87 GLN ** q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 71231 Z= 0.188 Angle : 0.607 12.597 96439 Z= 0.294 Chirality : 0.044 0.269 10488 Planarity : 0.004 0.060 12696 Dihedral : 4.402 21.464 9706 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.47 (0.09), residues: 8602 helix: -0.41 (0.09), residues: 3404 sheet: -1.60 (0.11), residues: 2162 loop : -0.83 (0.12), residues: 3036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1355 time to evaluate : 6.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 1388 average time/residue: 0.7631 time to fit residues: 1745.7333 Evaluate side-chains 1316 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1288 time to evaluate : 6.553 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5482 time to fit residues: 38.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 501 optimal weight: 10.0000 chunk 808 optimal weight: 2.9990 chunk 493 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 561 optimal weight: 0.7980 chunk 847 optimal weight: 2.9990 chunk 780 optimal weight: 0.7980 chunk 675 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 521 optimal weight: 6.9990 chunk 413 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN G 76 GLN G 87 GLN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN K 87 GLN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 GLN ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 29 GLN j 224 ASN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 87 GLN l 224 ASN m 87 GLN o 87 GLN ** o 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 43 ASN q 87 GLN ** q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 71231 Z= 0.226 Angle : 0.631 13.675 96439 Z= 0.306 Chirality : 0.044 0.262 10488 Planarity : 0.004 0.062 12696 Dihedral : 4.451 26.984 9706 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.09), residues: 8602 helix: -0.35 (0.09), residues: 3404 sheet: -1.54 (0.11), residues: 2162 loop : -0.81 (0.12), residues: 3036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1309 time to evaluate : 6.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 1324 average time/residue: 0.7678 time to fit residues: 1677.7760 Evaluate side-chains 1284 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1273 time to evaluate : 6.564 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5690 time to fit residues: 20.8253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 536 optimal weight: 3.9990 chunk 719 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 622 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 676 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 694 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN G 87 GLN I 29 GLN I 87 GLN J 224 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN ** O 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN U 29 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 ASN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 224 ASN g 76 GLN j 341 GLN l 224 ASN m 43 ASN ** o 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 ASN q 87 GLN ** q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114418 restraints weight = 106242.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117761 restraints weight = 57322.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119990 restraints weight = 38989.919| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 71231 Z= 0.201 Angle : 0.622 13.878 96439 Z= 0.300 Chirality : 0.044 0.242 10488 Planarity : 0.004 0.063 12696 Dihedral : 4.403 28.120 9706 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.09), residues: 8602 helix: -0.23 (0.09), residues: 3404 sheet: -1.47 (0.11), residues: 2162 loop : -0.82 (0.12), residues: 3036 =============================================================================== Job complete usr+sys time: 24260.40 seconds wall clock time: 421 minutes 12.02 seconds (25272.02 seconds total)