Starting phenix.real_space_refine on Tue Dec 12 14:01:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gy6_0088/12_2023/6gy6_0088.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 45513 2.51 5 N 12272 2.21 5 O 14482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 294": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 147": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H ARG 294": "NH1" <-> "NH2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 107": "NH1" <-> "NH2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K ARG 147": "NH1" <-> "NH2" Residue "K ARG 253": "NH1" <-> "NH2" Residue "K ARG 294": "NH1" <-> "NH2" Residue "L ARG 34": "NH1" <-> "NH2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 147": "NH1" <-> "NH2" Residue "L ARG 253": "NH1" <-> "NH2" Residue "L ARG 294": "NH1" <-> "NH2" Residue "N ARG 34": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 147": "NH1" <-> "NH2" Residue "N ARG 253": "NH1" <-> "NH2" Residue "N ARG 294": "NH1" <-> "NH2" Residue "O ARG 34": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 147": "NH1" <-> "NH2" Residue "O ARG 253": "NH1" <-> "NH2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "U ARG 34": "NH1" <-> "NH2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U ARG 107": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 147": "NH1" <-> "NH2" Residue "U ARG 253": "NH1" <-> "NH2" Residue "U ARG 294": "NH1" <-> "NH2" Residue "V ARG 34": "NH1" <-> "NH2" Residue "V ARG 100": "NH1" <-> "NH2" Residue "V ARG 107": "NH1" <-> "NH2" Residue "V ARG 128": "NH1" <-> "NH2" Residue "V ARG 147": "NH1" <-> "NH2" Residue "V ARG 253": "NH1" <-> "NH2" Residue "V ARG 294": "NH1" <-> "NH2" Residue "W ARG 34": "NH1" <-> "NH2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "W ARG 128": "NH1" <-> "NH2" Residue "W ARG 147": "NH1" <-> "NH2" Residue "W ARG 253": "NH1" <-> "NH2" Residue "W ARG 294": "NH1" <-> "NH2" Residue "X ARG 34": "NH1" <-> "NH2" Residue "X ARG 100": "NH1" <-> "NH2" Residue "X ARG 107": "NH1" <-> "NH2" Residue "X ARG 128": "NH1" <-> "NH2" Residue "X ARG 147": "NH1" <-> "NH2" Residue "X ARG 253": "NH1" <-> "NH2" Residue "X ARG 294": "NH1" <-> "NH2" Residue "Y ARG 34": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Y ARG 128": "NH1" <-> "NH2" Residue "Y ARG 147": "NH1" <-> "NH2" Residue "Y ARG 253": "NH1" <-> "NH2" Residue "Y ARG 294": "NH1" <-> "NH2" Residue "Z ARG 34": "NH1" <-> "NH2" Residue "Z ARG 100": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 128": "NH1" <-> "NH2" Residue "Z ARG 147": "NH1" <-> "NH2" Residue "Z ARG 253": "NH1" <-> "NH2" Residue "Z ARG 294": "NH1" <-> "NH2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "F TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 356": "NH1" <-> "NH2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 356": "NH1" <-> "NH2" Residue "M TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 356": "NH1" <-> "NH2" Residue "P TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 356": "NH1" <-> "NH2" Residue "Q TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 356": "NH1" <-> "NH2" Residue "R TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 356": "NH1" <-> "NH2" Residue "S TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 356": "NH1" <-> "NH2" Residue "T TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 356": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 72462 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "G" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "H" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "K" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "L" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "N" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "O" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "U" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "V" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "W" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "X" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "Y" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "Z" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2699 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "C" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "D" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "E" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "F" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "I" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "J" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "M" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "P" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "Q" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "R" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "S" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Chain: "T" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2875 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 5, 'TRANS': 359} Time building chain proxies: 27.23, per 1000 atoms: 0.38 Number of scatterers: 72462 At special positions: 0 Unit cell: (265.29, 264.18, 180.93, 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 195 16.00 O 14482 8.00 N 12272 7.00 C 45513 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: 22.88 Conformation dependent library (CDL) restraints added in 9.3 seconds 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17472 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 26 sheets defined 87.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU A 156 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL A 269 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 270 " --> pdb=" O GLY A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 404 Proline residue: A 381 - end of helix removed outlier: 4.092A pdb=" N ASP A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 66 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 192 removed outlier: 3.704A pdb=" N THR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 4.114A pdb=" N ALA B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS B 219 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 220' Processing helix chain 'B' and resid 221 through 222 No H-bonds generated for 'chain 'B' and resid 221 through 222' Processing helix chain 'B' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 306 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 33 " --> pdb=" O TRP G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 66 Processing helix chain 'G' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE G 122 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 4.114A pdb=" N ALA G 178 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET G 198 " --> pdb=" O ASN G 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 214 Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.634A pdb=" N LYS G 219 " --> pdb=" O GLN G 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU G 220 " --> pdb=" O PRO G 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 220' Processing helix chain 'G' and resid 221 through 222 No H-bonds generated for 'chain 'G' and resid 221 through 222' Processing helix chain 'G' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 240 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 292 " --> pdb=" O MET G 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS G 303 " --> pdb=" O THR G 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE G 304 " --> pdb=" O GLU G 300 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN G 306 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL G 307 " --> pdb=" O LYS G 303 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN G 345 " --> pdb=" O ASN G 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN H 23 " --> pdb=" O LYS H 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN H 33 " --> pdb=" O TRP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 66 Processing helix chain 'H' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA H 91 " --> pdb=" O ASP H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE H 122 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG H 128 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) Proline residue: H 168 - end of helix removed outlier: 4.114A pdb=" N ALA H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET H 198 " --> pdb=" O ASN H 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 214 Processing helix chain 'H' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS H 219 " --> pdb=" O GLN H 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU H 220 " --> pdb=" O PRO H 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 216 through 220' Processing helix chain 'H' and resid 221 through 222 No H-bonds generated for 'chain 'H' and resid 221 through 222' Processing helix chain 'H' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG H 275 " --> pdb=" O LYS H 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP H 291 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR H 292 " --> pdb=" O MET H 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU H 300 " --> pdb=" O THR H 296 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS H 303 " --> pdb=" O THR H 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 304 " --> pdb=" O GLU H 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN H 306 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE H 311 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN H 335 " --> pdb=" O LEU H 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 345 " --> pdb=" O ASN H 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR H 346 " --> pdb=" O LEU H 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN K 33 " --> pdb=" O TRP K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 66 Processing helix chain 'K' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU K 74 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE K 122 " --> pdb=" O ILE K 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG K 128 " --> pdb=" O SER K 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS K 131 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS K 135 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) Proline residue: K 168 - end of helix removed outlier: 4.114A pdb=" N ALA K 178 " --> pdb=" O ASN K 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE K 203 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 214 Processing helix chain 'K' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS K 219 " --> pdb=" O GLN K 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU K 220 " --> pdb=" O PRO K 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 216 through 220' Processing helix chain 'K' and resid 221 through 222 No H-bonds generated for 'chain 'K' and resid 221 through 222' Processing helix chain 'K' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE K 232 " --> pdb=" O GLN K 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU K 237 " --> pdb=" O ALA K 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG K 275 " --> pdb=" O LYS K 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR K 292 " --> pdb=" O MET K 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 300 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS K 303 " --> pdb=" O THR K 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE K 304 " --> pdb=" O GLU K 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN K 306 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL K 307 " --> pdb=" O LYS K 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE K 311 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN K 345 " --> pdb=" O ASN K 341 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR K 346 " --> pdb=" O LEU K 342 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN L 23 " --> pdb=" O LYS L 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN L 33 " --> pdb=" O TRP L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 66 Processing helix chain 'L' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS L 131 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS L 135 " --> pdb=" O LYS L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 192 removed outlier: 3.704A pdb=" N THR L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) Proline residue: L 168 - end of helix removed outlier: 4.115A pdb=" N ALA L 178 " --> pdb=" O ASN L 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET L 198 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE L 203 " --> pdb=" O PHE L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 214 Processing helix chain 'L' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS L 219 " --> pdb=" O GLN L 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 220 " --> pdb=" O PRO L 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 216 through 220' Processing helix chain 'L' and resid 221 through 222 No H-bonds generated for 'chain 'L' and resid 221 through 222' Processing helix chain 'L' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU L 231 " --> pdb=" O LYS L 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU L 237 " --> pdb=" O ALA L 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 260 " --> pdb=" O LEU L 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 275 " --> pdb=" O LYS L 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP L 291 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 292 " --> pdb=" O MET L 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 300 " --> pdb=" O THR L 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 303 " --> pdb=" O THR L 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 304 " --> pdb=" O GLU L 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN L 306 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL L 307 " --> pdb=" O LYS L 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE L 311 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN L 335 " --> pdb=" O LEU L 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN L 345 " --> pdb=" O ASN L 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR L 346 " --> pdb=" O LEU L 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN N 33 " --> pdb=" O TRP N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 66 Processing helix chain 'N' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS N 72 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU N 74 " --> pdb=" O VAL N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE N 122 " --> pdb=" O ILE N 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG N 128 " --> pdb=" O SER N 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS N 131 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS N 135 " --> pdb=" O LYS N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR N 155 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N 164 " --> pdb=" O THR N 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) Proline residue: N 168 - end of helix removed outlier: 4.114A pdb=" N ALA N 178 " --> pdb=" O ASN N 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE N 183 " --> pdb=" O ASP N 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL N 189 " --> pdb=" O GLU N 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE N 190 " --> pdb=" O SER N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET N 198 " --> pdb=" O ASN N 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 203 " --> pdb=" O PHE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 207 through 214 Processing helix chain 'N' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS N 219 " --> pdb=" O GLN N 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU N 220 " --> pdb=" O PRO N 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 216 through 220' Processing helix chain 'N' and resid 221 through 222 No H-bonds generated for 'chain 'N' and resid 221 through 222' Processing helix chain 'N' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU N 231 " --> pdb=" O LYS N 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE N 232 " --> pdb=" O GLN N 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU N 237 " --> pdb=" O ALA N 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL N 240 " --> pdb=" O ILE N 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE N 260 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG N 275 " --> pdb=" O LYS N 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP N 291 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR N 292 " --> pdb=" O MET N 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU N 300 " --> pdb=" O THR N 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS N 303 " --> pdb=" O THR N 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE N 304 " --> pdb=" O GLU N 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN N 306 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL N 307 " --> pdb=" O LYS N 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE N 311 " --> pdb=" O VAL N 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN N 335 " --> pdb=" O LEU N 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN N 345 " --> pdb=" O ASN N 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR N 346 " --> pdb=" O LEU N 342 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN O 23 " --> pdb=" O LYS O 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA O 24 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN O 33 " --> pdb=" O TRP O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 66 Processing helix chain 'O' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU O 74 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA O 91 " --> pdb=" O ASP O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE O 122 " --> pdb=" O ILE O 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG O 128 " --> pdb=" O SER O 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS O 131 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS O 135 " --> pdb=" O LYS O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR O 155 " --> pdb=" O LEU O 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER O 164 " --> pdb=" O THR O 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP O 165 " --> pdb=" O GLU O 161 " (cutoff:3.500A) Proline residue: O 168 - end of helix removed outlier: 4.115A pdb=" N ALA O 178 " --> pdb=" O ASN O 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE O 183 " --> pdb=" O ASP O 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL O 189 " --> pdb=" O GLU O 185 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET O 198 " --> pdb=" O ASN O 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE O 203 " --> pdb=" O PHE O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 214 Processing helix chain 'O' and resid 216 through 220 removed outlier: 3.636A pdb=" N LYS O 219 " --> pdb=" O GLN O 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU O 220 " --> pdb=" O PRO O 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 216 through 220' Processing helix chain 'O' and resid 221 through 222 No H-bonds generated for 'chain 'O' and resid 221 through 222' Processing helix chain 'O' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 240 " --> pdb=" O ILE O 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE O 260 " --> pdb=" O LEU O 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR O 292 " --> pdb=" O MET O 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU O 300 " --> pdb=" O THR O 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS O 303 " --> pdb=" O THR O 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE O 304 " --> pdb=" O GLU O 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN O 306 " --> pdb=" O VAL O 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL O 307 " --> pdb=" O LYS O 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN O 335 " --> pdb=" O LEU O 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN O 345 " --> pdb=" O ASN O 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR O 346 " --> pdb=" O LEU O 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN U 23 " --> pdb=" O LYS U 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA U 24 " --> pdb=" O ALA U 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN U 33 " --> pdb=" O TRP U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 66 Processing helix chain 'U' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU U 74 " --> pdb=" O VAL U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR U 82 " --> pdb=" O ALA U 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA U 91 " --> pdb=" O ASP U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE U 122 " --> pdb=" O ILE U 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG U 128 " --> pdb=" O SER U 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS U 135 " --> pdb=" O LYS U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR U 155 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER U 164 " --> pdb=" O THR U 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP U 165 " --> pdb=" O GLU U 161 " (cutoff:3.500A) Proline residue: U 168 - end of helix removed outlier: 4.115A pdb=" N ALA U 178 " --> pdb=" O ASN U 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE U 183 " --> pdb=" O ASP U 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL U 189 " --> pdb=" O GLU U 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE U 190 " --> pdb=" O SER U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 194 through 203 removed outlier: 3.614A pdb=" N MET U 198 " --> pdb=" O ASN U 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE U 203 " --> pdb=" O PHE U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 214 Processing helix chain 'U' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS U 219 " --> pdb=" O GLN U 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU U 220 " --> pdb=" O PRO U 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 216 through 220' Processing helix chain 'U' and resid 221 through 222 No H-bonds generated for 'chain 'U' and resid 221 through 222' Processing helix chain 'U' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU U 231 " --> pdb=" O LYS U 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE U 232 " --> pdb=" O GLN U 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU U 237 " --> pdb=" O ALA U 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL U 240 " --> pdb=" O ILE U 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE U 260 " --> pdb=" O LEU U 256 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG U 275 " --> pdb=" O LYS U 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR U 292 " --> pdb=" O MET U 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU U 300 " --> pdb=" O THR U 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS U 303 " --> pdb=" O THR U 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE U 304 " --> pdb=" O GLU U 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN U 306 " --> pdb=" O VAL U 302 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL U 307 " --> pdb=" O LYS U 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE U 311 " --> pdb=" O VAL U 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP U 321 " --> pdb=" O LYS U 317 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 348 removed outlier: 3.581A pdb=" N GLN U 335 " --> pdb=" O LEU U 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 345 " --> pdb=" O ASN U 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN V 23 " --> pdb=" O LYS V 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA V 24 " --> pdb=" O ALA V 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN V 33 " --> pdb=" O TRP V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 66 Processing helix chain 'V' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS V 72 " --> pdb=" O ALA V 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU V 74 " --> pdb=" O VAL V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR V 82 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA V 91 " --> pdb=" O ASP V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE V 122 " --> pdb=" O ILE V 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG V 128 " --> pdb=" O SER V 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS V 131 " --> pdb=" O GLY V 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS V 135 " --> pdb=" O LYS V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR V 155 " --> pdb=" O LEU V 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER V 164 " --> pdb=" O THR V 160 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP V 165 " --> pdb=" O GLU V 161 " (cutoff:3.500A) Proline residue: V 168 - end of helix removed outlier: 4.114A pdb=" N ALA V 178 " --> pdb=" O ASN V 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE V 183 " --> pdb=" O ASP V 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL V 189 " --> pdb=" O GLU V 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE V 190 " --> pdb=" O SER V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET V 198 " --> pdb=" O ASN V 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE V 203 " --> pdb=" O PHE V 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 207 through 214 Processing helix chain 'V' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS V 219 " --> pdb=" O GLN V 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU V 220 " --> pdb=" O PRO V 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 216 through 220' Processing helix chain 'V' and resid 221 through 222 No H-bonds generated for 'chain 'V' and resid 221 through 222' Processing helix chain 'V' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU V 231 " --> pdb=" O LYS V 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE V 232 " --> pdb=" O GLN V 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU V 237 " --> pdb=" O ALA V 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL V 240 " --> pdb=" O ILE V 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE V 260 " --> pdb=" O LEU V 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG V 275 " --> pdb=" O LYS V 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP V 291 " --> pdb=" O VAL V 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR V 292 " --> pdb=" O MET V 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU V 300 " --> pdb=" O THR V 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS V 303 " --> pdb=" O THR V 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE V 304 " --> pdb=" O GLU V 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN V 306 " --> pdb=" O VAL V 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL V 307 " --> pdb=" O LYS V 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE V 311 " --> pdb=" O VAL V 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP V 321 " --> pdb=" O LYS V 317 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN V 335 " --> pdb=" O LEU V 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN V 345 " --> pdb=" O ASN V 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR V 346 " --> pdb=" O LEU V 342 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA W 24 " --> pdb=" O ALA W 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN W 33 " --> pdb=" O TRP W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 66 Processing helix chain 'W' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU W 74 " --> pdb=" O VAL W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR W 82 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA W 91 " --> pdb=" O ASP W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE W 122 " --> pdb=" O ILE W 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG W 128 " --> pdb=" O SER W 124 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS W 131 " --> pdb=" O GLY W 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS W 135 " --> pdb=" O LYS W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR W 155 " --> pdb=" O LEU W 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER W 164 " --> pdb=" O THR W 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP W 165 " --> pdb=" O GLU W 161 " (cutoff:3.500A) Proline residue: W 168 - end of helix removed outlier: 4.115A pdb=" N ALA W 178 " --> pdb=" O ASN W 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE W 183 " --> pdb=" O ASP W 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL W 189 " --> pdb=" O GLU W 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE W 190 " --> pdb=" O SER W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 194 through 203 removed outlier: 3.616A pdb=" N MET W 198 " --> pdb=" O ASN W 194 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE W 203 " --> pdb=" O PHE W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 214 Processing helix chain 'W' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS W 219 " --> pdb=" O GLN W 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU W 220 " --> pdb=" O PRO W 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 216 through 220' Processing helix chain 'W' and resid 221 through 222 No H-bonds generated for 'chain 'W' and resid 221 through 222' Processing helix chain 'W' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU W 231 " --> pdb=" O LYS W 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE W 232 " --> pdb=" O GLN W 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU W 237 " --> pdb=" O ALA W 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL W 240 " --> pdb=" O ILE W 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE W 260 " --> pdb=" O LEU W 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG W 275 " --> pdb=" O LYS W 271 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR W 292 " --> pdb=" O MET W 288 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU W 300 " --> pdb=" O THR W 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS W 303 " --> pdb=" O THR W 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE W 304 " --> pdb=" O GLU W 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN W 306 " --> pdb=" O VAL W 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL W 307 " --> pdb=" O LYS W 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE W 311 " --> pdb=" O VAL W 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP W 321 " --> pdb=" O LYS W 317 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN W 335 " --> pdb=" O LEU W 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN W 345 " --> pdb=" O ASN W 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR W 346 " --> pdb=" O LEU W 342 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN X 23 " --> pdb=" O LYS X 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN X 33 " --> pdb=" O TRP X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 66 Processing helix chain 'X' and resid 67 through 76 removed outlier: 3.717A pdb=" N LYS X 72 " --> pdb=" O ALA X 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU X 74 " --> pdb=" O VAL X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR X 82 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA X 91 " --> pdb=" O ASP X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE X 122 " --> pdb=" O ILE X 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG X 128 " --> pdb=" O SER X 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS X 135 " --> pdb=" O LYS X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 148 through 192 removed outlier: 3.706A pdb=" N THR X 155 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER X 164 " --> pdb=" O THR X 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP X 165 " --> pdb=" O GLU X 161 " (cutoff:3.500A) Proline residue: X 168 - end of helix removed outlier: 4.114A pdb=" N ALA X 178 " --> pdb=" O ASN X 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE X 183 " --> pdb=" O ASP X 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL X 189 " --> pdb=" O GLU X 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE X 190 " --> pdb=" O SER X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET X 198 " --> pdb=" O ASN X 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE X 203 " --> pdb=" O PHE X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 214 Processing helix chain 'X' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS X 219 " --> pdb=" O GLN X 216 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU X 220 " --> pdb=" O PRO X 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 216 through 220' Processing helix chain 'X' and resid 221 through 222 No H-bonds generated for 'chain 'X' and resid 221 through 222' Processing helix chain 'X' and resid 223 through 322 removed outlier: 4.174A pdb=" N GLU X 231 " --> pdb=" O LYS X 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE X 232 " --> pdb=" O GLN X 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU X 237 " --> pdb=" O ALA X 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL X 240 " --> pdb=" O ILE X 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE X 260 " --> pdb=" O LEU X 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG X 275 " --> pdb=" O LYS X 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP X 291 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR X 292 " --> pdb=" O MET X 288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU X 300 " --> pdb=" O THR X 296 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS X 303 " --> pdb=" O THR X 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE X 304 " --> pdb=" O GLU X 300 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN X 306 " --> pdb=" O VAL X 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL X 307 " --> pdb=" O LYS X 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE X 311 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP X 321 " --> pdb=" O LYS X 317 " (cutoff:3.500A) Processing helix chain 'X' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN X 335 " --> pdb=" O LEU X 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN X 345 " --> pdb=" O ASN X 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR X 346 " --> pdb=" O LEU X 342 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 35 removed outlier: 3.612A pdb=" N GLN Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Y 24 " --> pdb=" O ALA Y 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN Y 33 " --> pdb=" O TRP Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 66 Processing helix chain 'Y' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS Y 72 " --> pdb=" O ALA Y 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Y 74 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 91 removed outlier: 3.514A pdb=" N THR Y 82 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA Y 91 " --> pdb=" O ASP Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 138 removed outlier: 3.541A pdb=" N ILE Y 122 " --> pdb=" O ILE Y 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG Y 128 " --> pdb=" O SER Y 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Y 131 " --> pdb=" O GLY Y 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS Y 135 " --> pdb=" O LYS Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR Y 155 " --> pdb=" O LEU Y 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER Y 164 " --> pdb=" O THR Y 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP Y 165 " --> pdb=" O GLU Y 161 " (cutoff:3.500A) Proline residue: Y 168 - end of helix removed outlier: 4.114A pdb=" N ALA Y 178 " --> pdb=" O ASN Y 174 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Y 183 " --> pdb=" O ASP Y 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Y 189 " --> pdb=" O GLU Y 185 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE Y 190 " --> pdb=" O SER Y 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET Y 198 " --> pdb=" O ASN Y 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Y 203 " --> pdb=" O PHE Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 214 Processing helix chain 'Y' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS Y 219 " --> pdb=" O GLN Y 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Y 220 " --> pdb=" O PRO Y 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 216 through 220' Processing helix chain 'Y' and resid 221 through 222 No H-bonds generated for 'chain 'Y' and resid 221 through 222' Processing helix chain 'Y' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU Y 231 " --> pdb=" O LYS Y 227 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE Y 232 " --> pdb=" O GLN Y 228 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU Y 237 " --> pdb=" O ALA Y 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 240 " --> pdb=" O ILE Y 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Y 260 " --> pdb=" O LEU Y 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Y 275 " --> pdb=" O LYS Y 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP Y 291 " --> pdb=" O VAL Y 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR Y 292 " --> pdb=" O MET Y 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU Y 300 " --> pdb=" O THR Y 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Y 303 " --> pdb=" O THR Y 299 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE Y 304 " --> pdb=" O GLU Y 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN Y 306 " --> pdb=" O VAL Y 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL Y 307 " --> pdb=" O LYS Y 303 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE Y 311 " --> pdb=" O VAL Y 307 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP Y 321 " --> pdb=" O LYS Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN Y 335 " --> pdb=" O LEU Y 331 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN Y 345 " --> pdb=" O ASN Y 341 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR Y 346 " --> pdb=" O LEU Y 342 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 35 removed outlier: 3.611A pdb=" N GLN Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA Z 24 " --> pdb=" O ALA Z 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN Z 33 " --> pdb=" O TRP Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 66 Processing helix chain 'Z' and resid 67 through 76 removed outlier: 3.718A pdb=" N LYS Z 72 " --> pdb=" O ALA Z 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU Z 74 " --> pdb=" O VAL Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 91 removed outlier: 3.515A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA Z 91 " --> pdb=" O ASP Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 138 removed outlier: 3.540A pdb=" N ILE Z 122 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG Z 128 " --> pdb=" O SER Z 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Z 131 " --> pdb=" O GLY Z 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS Z 135 " --> pdb=" O LYS Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 192 removed outlier: 3.705A pdb=" N THR Z 155 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER Z 164 " --> pdb=" O THR Z 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP Z 165 " --> pdb=" O GLU Z 161 " (cutoff:3.500A) Proline residue: Z 168 - end of helix removed outlier: 4.115A pdb=" N ALA Z 178 " --> pdb=" O ASN Z 174 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE Z 183 " --> pdb=" O ASP Z 179 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Z 189 " --> pdb=" O GLU Z 185 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE Z 190 " --> pdb=" O SER Z 186 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 203 removed outlier: 3.615A pdb=" N MET Z 198 " --> pdb=" O ASN Z 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Z 203 " --> pdb=" O PHE Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 214 Processing helix chain 'Z' and resid 216 through 220 removed outlier: 3.635A pdb=" N LYS Z 219 " --> pdb=" O GLN Z 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Z 220 " --> pdb=" O PRO Z 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 216 through 220' Processing helix chain 'Z' and resid 221 through 222 No H-bonds generated for 'chain 'Z' and resid 221 through 222' Processing helix chain 'Z' and resid 223 through 322 removed outlier: 4.175A pdb=" N GLU Z 231 " --> pdb=" O LYS Z 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE Z 232 " --> pdb=" O GLN Z 228 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU Z 237 " --> pdb=" O ALA Z 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 240 " --> pdb=" O ILE Z 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE Z 260 " --> pdb=" O LEU Z 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Z 275 " --> pdb=" O LYS Z 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP Z 291 " --> pdb=" O VAL Z 287 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR Z 292 " --> pdb=" O MET Z 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU Z 300 " --> pdb=" O THR Z 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Z 303 " --> pdb=" O THR Z 299 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE Z 304 " --> pdb=" O GLU Z 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN Z 306 " --> pdb=" O VAL Z 302 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL Z 307 " --> pdb=" O LYS Z 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE Z 311 " --> pdb=" O VAL Z 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 326 through 348 removed outlier: 3.582A pdb=" N GLN Z 335 " --> pdb=" O LEU Z 331 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Z 345 " --> pdb=" O ASN Z 341 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR Z 346 " --> pdb=" O LEU Z 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.593A pdb=" N GLU C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 73 Processing helix chain 'C' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU C 156 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'C' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 4.023A pdb=" N VAL C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 270 " --> pdb=" O GLY C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'C' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA C 276 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 404 Proline residue: C 381 - end of helix removed outlier: 4.093A pdb=" N ASP C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 123 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS D 143 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU D 156 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS D 255 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 270 " --> pdb=" O GLY D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 270' Processing helix chain 'D' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 322 " --> pdb=" O GLN D 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS D 358 " --> pdb=" O THR D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 404 Proline residue: D 381 - end of helix removed outlier: 4.093A pdb=" N ASP D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 395 " --> pdb=" O GLN D 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU E 60 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS E 143 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR E 150 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU E 156 " --> pdb=" O GLN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 186 " --> pdb=" O LYS E 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 202 " --> pdb=" O PHE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 229 Processing helix chain 'E' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL E 269 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY E 270 " --> pdb=" O GLY E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 270' Processing helix chain 'E' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA E 276 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 404 Proline residue: E 381 - end of helix removed outlier: 4.093A pdb=" N ASP E 384 " --> pdb=" O GLU E 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 395 " --> pdb=" O GLN E 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E 398 " --> pdb=" O GLN E 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 404 " --> pdb=" O LEU E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP F 101 " --> pdb=" O HIS F 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR F 150 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU F 156 " --> pdb=" O GLN F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 203 removed outlier: 4.281A pdb=" N GLU F 175 " --> pdb=" O GLY F 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 186 " --> pdb=" O LYS F 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU F 202 " --> pdb=" O PHE F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 248 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY F 262 " --> pdb=" O ASN F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL F 269 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY F 270 " --> pdb=" O GLY F 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 266 through 270' Processing helix chain 'F' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA F 276 " --> pdb=" O ILE F 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS F 285 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 322 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 404 Proline residue: F 381 - end of helix removed outlier: 4.092A pdb=" N ASP F 384 " --> pdb=" O GLU F 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR F 395 " --> pdb=" O GLN F 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 398 " --> pdb=" O GLN F 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA F 399 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 404 " --> pdb=" O LEU F 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU I 60 " --> pdb=" O LYS I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 73 Processing helix chain 'I' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP I 101 " --> pdb=" O HIS I 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR I 123 " --> pdb=" O GLY I 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL I 142 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS I 143 " --> pdb=" O ILE I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR I 150 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU I 156 " --> pdb=" O GLN I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU I 175 " --> pdb=" O GLY I 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU I 186 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU I 202 " --> pdb=" O PHE I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 229 Processing helix chain 'I' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE I 236 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 248 " --> pdb=" O ASP I 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS I 255 " --> pdb=" O ASP I 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY I 262 " --> pdb=" O ASN I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL I 269 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY I 270 " --> pdb=" O GLY I 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 266 through 270' Processing helix chain 'I' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA I 276 " --> pdb=" O ILE I 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 277 " --> pdb=" O ILE I 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 297 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU I 322 " --> pdb=" O GLN I 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 358 " --> pdb=" O THR I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 404 Proline residue: I 381 - end of helix removed outlier: 4.092A pdb=" N ASP I 384 " --> pdb=" O GLU I 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR I 395 " --> pdb=" O GLN I 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU I 398 " --> pdb=" O GLN I 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA I 399 " --> pdb=" O THR I 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I 404 " --> pdb=" O LEU I 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU J 60 " --> pdb=" O LYS J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 73 Processing helix chain 'J' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER J 100 " --> pdb=" O ASP J 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP J 101 " --> pdb=" O HIS J 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR J 123 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 134 " --> pdb=" O ILE J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL J 142 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS J 143 " --> pdb=" O ILE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR J 150 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU J 156 " --> pdb=" O GLN J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU J 202 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 229 Processing helix chain 'J' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS J 237 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS J 248 " --> pdb=" O ASP J 244 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY J 262 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY J 270 " --> pdb=" O GLY J 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 266 through 270' Processing helix chain 'J' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA J 276 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP J 284 " --> pdb=" O GLY J 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 297 " --> pdb=" O LYS J 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU J 322 " --> pdb=" O GLN J 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS J 358 " --> pdb=" O THR J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 404 Proline residue: J 381 - end of helix removed outlier: 4.092A pdb=" N ASP J 384 " --> pdb=" O GLU J 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR J 395 " --> pdb=" O GLN J 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 398 " --> pdb=" O GLN J 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA J 399 " --> pdb=" O THR J 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J 402 " --> pdb=" O GLU J 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 404 " --> pdb=" O LEU J 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 73 Processing helix chain 'M' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER M 100 " --> pdb=" O ASP M 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP M 101 " --> pdb=" O HIS M 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR M 123 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP M 134 " --> pdb=" O ILE M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 144 removed outlier: 3.827A pdb=" N VAL M 142 " --> pdb=" O ILE M 138 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS M 143 " --> pdb=" O ILE M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR M 150 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU M 156 " --> pdb=" O GLN M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU M 186 " --> pdb=" O LYS M 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 202 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 229 Processing helix chain 'M' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS M 237 " --> pdb=" O SER M 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M 248 " --> pdb=" O ASP M 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS M 255 " --> pdb=" O ASP M 251 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY M 262 " --> pdb=" O ASN M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL M 269 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY M 270 " --> pdb=" O GLY M 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 266 through 270' Processing helix chain 'M' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA M 276 " --> pdb=" O ILE M 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE M 277 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP M 284 " --> pdb=" O GLY M 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 285 " --> pdb=" O ILE M 281 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE M 297 " --> pdb=" O LYS M 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP M 298 " --> pdb=" O ASN M 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU M 322 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS M 358 " --> pdb=" O THR M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 404 Proline residue: M 381 - end of helix removed outlier: 4.093A pdb=" N ASP M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR M 395 " --> pdb=" O GLN M 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU M 398 " --> pdb=" O GLN M 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA M 399 " --> pdb=" O THR M 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M 402 " --> pdb=" O GLU M 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 404 " --> pdb=" O LEU M 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU P 60 " --> pdb=" O LYS P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 73 Processing helix chain 'P' and resid 83 through 134 removed outlier: 3.518A pdb=" N SER P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP P 101 " --> pdb=" O HIS P 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR P 123 " --> pdb=" O GLY P 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP P 134 " --> pdb=" O ILE P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL P 142 " --> pdb=" O ILE P 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS P 143 " --> pdb=" O ILE P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 150 removed outlier: 3.750A pdb=" N THR P 150 " --> pdb=" O GLY P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU P 156 " --> pdb=" O GLN P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU P 175 " --> pdb=" O GLY P 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU P 186 " --> pdb=" O LYS P 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU P 202 " --> pdb=" O PHE P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 229 Processing helix chain 'P' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE P 236 " --> pdb=" O LEU P 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS P 237 " --> pdb=" O SER P 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 248 " --> pdb=" O ASP P 244 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS P 255 " --> pdb=" O ASP P 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY P 262 " --> pdb=" O ASN P 258 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL P 269 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY P 270 " --> pdb=" O GLY P 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 266 through 270' Processing helix chain 'P' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE P 277 " --> pdb=" O ILE P 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP P 284 " --> pdb=" O GLY P 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 285 " --> pdb=" O ILE P 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 322 " --> pdb=" O GLN P 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 358 " --> pdb=" O THR P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 404 Proline residue: P 381 - end of helix removed outlier: 4.092A pdb=" N ASP P 384 " --> pdb=" O GLU P 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR P 395 " --> pdb=" O GLN P 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU P 398 " --> pdb=" O GLN P 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA P 399 " --> pdb=" O THR P 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P 402 " --> pdb=" O GLU P 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS P 404 " --> pdb=" O LEU P 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 73 Processing helix chain 'Q' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP Q 101 " --> pdb=" O HIS Q 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR Q 123 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP Q 134 " --> pdb=" O ILE Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL Q 142 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS Q 143 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR Q 150 " --> pdb=" O GLY Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 157 removed outlier: 3.629A pdb=" N GLU Q 156 " --> pdb=" O GLN Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU Q 186 " --> pdb=" O LYS Q 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU Q 202 " --> pdb=" O PHE Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 229 Processing helix chain 'Q' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE Q 236 " --> pdb=" O LEU Q 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS Q 237 " --> pdb=" O SER Q 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS Q 248 " --> pdb=" O ASP Q 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS Q 255 " --> pdb=" O ASP Q 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY Q 262 " --> pdb=" O ASN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL Q 269 " --> pdb=" O SER Q 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Q 270 " --> pdb=" O GLY Q 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 266 through 270' Processing helix chain 'Q' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE Q 277 " --> pdb=" O ILE Q 273 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP Q 284 " --> pdb=" O GLY Q 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS Q 285 " --> pdb=" O ILE Q 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE Q 297 " --> pdb=" O LYS Q 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Q 322 " --> pdb=" O GLN Q 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS Q 358 " --> pdb=" O THR Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 404 Proline residue: Q 381 - end of helix removed outlier: 4.093A pdb=" N ASP Q 384 " --> pdb=" O GLU Q 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU Q 398 " --> pdb=" O GLN Q 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA Q 399 " --> pdb=" O THR Q 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU Q 402 " --> pdb=" O GLU Q 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 404 " --> pdb=" O LEU Q 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.591A pdb=" N GLU R 60 " --> pdb=" O LYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 73 Processing helix chain 'R' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER R 100 " --> pdb=" O ASP R 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP R 101 " --> pdb=" O HIS R 97 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR R 123 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP R 134 " --> pdb=" O ILE R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS R 143 " --> pdb=" O ILE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR R 150 " --> pdb=" O GLY R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU R 156 " --> pdb=" O GLN R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU R 175 " --> pdb=" O GLY R 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 229 Processing helix chain 'R' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE R 236 " --> pdb=" O LEU R 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS R 237 " --> pdb=" O SER R 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS R 248 " --> pdb=" O ASP R 244 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS R 255 " --> pdb=" O ASP R 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY R 262 " --> pdb=" O ASN R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL R 269 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY R 270 " --> pdb=" O GLY R 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 266 through 270' Processing helix chain 'R' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE R 277 " --> pdb=" O ILE R 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS R 285 " --> pdb=" O ILE R 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE R 297 " --> pdb=" O LYS R 293 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU R 322 " --> pdb=" O GLN R 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS R 358 " --> pdb=" O THR R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 404 Proline residue: R 381 - end of helix removed outlier: 4.092A pdb=" N ASP R 384 " --> pdb=" O GLU R 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR R 395 " --> pdb=" O GLN R 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU R 398 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA R 399 " --> pdb=" O THR R 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 404 " --> pdb=" O LEU R 400 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU S 60 " --> pdb=" O LYS S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 73 Processing helix chain 'S' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER S 100 " --> pdb=" O ASP S 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP S 101 " --> pdb=" O HIS S 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER S 102 " --> pdb=" O ALA S 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY S 103 " --> pdb=" O LEU S 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR S 123 " --> pdb=" O GLY S 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP S 134 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL S 142 " --> pdb=" O ILE S 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS S 143 " --> pdb=" O ILE S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.752A pdb=" N THR S 150 " --> pdb=" O GLY S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU S 156 " --> pdb=" O GLN S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 203 removed outlier: 4.279A pdb=" N GLU S 175 " --> pdb=" O GLY S 171 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU S 202 " --> pdb=" O PHE S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 229 Processing helix chain 'S' and resid 231 through 265 removed outlier: 3.706A pdb=" N ILE S 236 " --> pdb=" O LEU S 232 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS S 237 " --> pdb=" O SER S 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 248 " --> pdb=" O ASP S 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS S 255 " --> pdb=" O ASP S 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY S 262 " --> pdb=" O ASN S 258 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL S 269 " --> pdb=" O SER S 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY S 270 " --> pdb=" O GLY S 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 266 through 270' Processing helix chain 'S' and resid 271 through 360 removed outlier: 4.057A pdb=" N ALA S 276 " --> pdb=" O ILE S 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE S 277 " --> pdb=" O ILE S 273 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP S 284 " --> pdb=" O GLY S 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS S 285 " --> pdb=" O ILE S 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE S 297 " --> pdb=" O LYS S 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU S 322 " --> pdb=" O GLN S 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS S 358 " --> pdb=" O THR S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 404 Proline residue: S 381 - end of helix removed outlier: 4.093A pdb=" N ASP S 384 " --> pdb=" O GLU S 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR S 395 " --> pdb=" O GLN S 391 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU S 398 " --> pdb=" O GLN S 394 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA S 399 " --> pdb=" O THR S 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU S 402 " --> pdb=" O GLU S 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 404 " --> pdb=" O LEU S 400 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 60 removed outlier: 3.592A pdb=" N GLU T 60 " --> pdb=" O LYS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'T' and resid 83 through 134 removed outlier: 3.517A pdb=" N SER T 100 " --> pdb=" O ASP T 96 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP T 101 " --> pdb=" O HIS T 97 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR T 123 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP T 134 " --> pdb=" O ILE T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 144 removed outlier: 3.826A pdb=" N VAL T 142 " --> pdb=" O ILE T 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS T 143 " --> pdb=" O ILE T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 146 through 150 removed outlier: 3.751A pdb=" N THR T 150 " --> pdb=" O GLY T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 157 removed outlier: 3.628A pdb=" N GLU T 156 " --> pdb=" O GLN T 153 " (cutoff:3.500A) Processing helix chain 'T' and resid 169 through 203 removed outlier: 4.280A pdb=" N GLU T 175 " --> pdb=" O GLY T 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU T 202 " --> pdb=" O PHE T 198 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 229 Processing helix chain 'T' and resid 231 through 265 removed outlier: 3.705A pdb=" N ILE T 236 " --> pdb=" O LEU T 232 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS T 237 " --> pdb=" O SER T 233 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS T 248 " --> pdb=" O ASP T 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS T 255 " --> pdb=" O ASP T 251 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY T 262 " --> pdb=" O ASN T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 270 removed outlier: 4.022A pdb=" N VAL T 269 " --> pdb=" O SER T 266 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY T 270 " --> pdb=" O GLY T 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 266 through 270' Processing helix chain 'T' and resid 271 through 360 removed outlier: 4.058A pdb=" N ALA T 276 " --> pdb=" O ILE T 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE T 277 " --> pdb=" O ILE T 273 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP T 284 " --> pdb=" O GLY T 280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS T 285 " --> pdb=" O ILE T 281 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE T 297 " --> pdb=" O LYS T 293 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU T 322 " --> pdb=" O GLN T 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T 358 " --> pdb=" O THR T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 367 through 404 Proline residue: T 381 - end of helix removed outlier: 4.092A pdb=" N ASP T 384 " --> pdb=" O GLU T 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR T 395 " --> pdb=" O GLN T 391 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU T 398 " --> pdb=" O GLN T 394 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA T 399 " --> pdb=" O THR T 395 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU T 402 " --> pdb=" O GLU T 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS T 404 " --> pdb=" O LEU T 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206 Processing sheet with id=AA3, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA4, first strand: chain 'C' and resid 205 through 206 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'D' and resid 205 through 206 Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'E' and resid 205 through 206 Processing sheet with id=AA9, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 205 through 206 Processing sheet with id=AB2, first strand: chain 'I' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'I' and resid 205 through 206 Processing sheet with id=AB4, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'J' and resid 205 through 206 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AB7, first strand: chain 'M' and resid 205 through 206 Processing sheet with id=AB8, first strand: chain 'P' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'P' and resid 205 through 206 Processing sheet with id=AC1, first strand: chain 'Q' and resid 159 through 160 Processing sheet with id=AC2, first strand: chain 'Q' and resid 205 through 206 Processing sheet with id=AC3, first strand: chain 'R' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'R' and resid 205 through 206 Processing sheet with id=AC5, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'S' and resid 205 through 206 Processing sheet with id=AC7, first strand: chain 'T' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'T' and resid 205 through 206 5837 hydrogen bonds defined for protein. 17355 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: 24.93 Time building geometry restraints manager: 25.10 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: 24200 1.34 - 1.46: 9919 1.46 - 1.57: 38733 1.57 - 1.69: 0 1.69 - 1.81: 390 Bond restraints: 73242 Sorted by residual: bond pdb=" CB GLU U 300 " pdb=" CG GLU U 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB GLU O 300 " pdb=" CG GLU O 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB GLU Y 300 " pdb=" CG GLU Y 300 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB GLU H 300 " pdb=" CG GLU H 300 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" CB GLU K 300 " pdb=" CG GLU K 300 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 73237 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.35: 650 105.35 - 112.53: 39672 112.53 - 119.71: 25138 119.71 - 126.88: 32624 126.88 - 134.06: 482 Bond angle restraints: 98566 Sorted by residual: angle pdb=" C SER W 205 " pdb=" N ALA W 206 " pdb=" CA ALA W 206 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C SER G 205 " pdb=" N ALA G 206 " pdb=" CA ALA G 206 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER V 205 " pdb=" N ALA V 206 " pdb=" CA ALA V 206 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER K 205 " pdb=" N ALA K 206 " pdb=" CA ALA K 206 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C SER L 205 " pdb=" N ALA L 206 " pdb=" CA ALA L 206 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 ... (remaining 98561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 43118 14.94 - 29.89: 1810 29.89 - 44.83: 728 44.83 - 59.78: 52 59.78 - 74.72: 39 Dihedral angle restraints: 45747 sinusoidal: 19019 harmonic: 26728 Sorted by residual: dihedral pdb=" CA LYS Q 367 " pdb=" C LYS Q 367 " pdb=" N LEU Q 368 " pdb=" CA LEU Q 368 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS J 367 " pdb=" C LYS J 367 " pdb=" N LEU J 368 " pdb=" CA LEU J 368 " ideal model delta harmonic sigma weight residual -180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS E 367 " pdb=" C LYS E 367 " pdb=" N LEU E 368 " pdb=" CA LEU E 368 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 45744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7233 0.043 - 0.086: 3573 0.086 - 0.129: 572 0.129 - 0.172: 141 0.172 - 0.215: 25 Chirality restraints: 11544 Sorted by residual: chirality pdb=" CB ILE J 139 " pdb=" CA ILE J 139 " pdb=" CG1 ILE J 139 " pdb=" CG2 ILE J 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE Q 139 " pdb=" CA ILE Q 139 " pdb=" CG1 ILE Q 139 " pdb=" CG2 ILE Q 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE D 139 " pdb=" CA ILE D 139 " pdb=" CG1 ILE D 139 " pdb=" CG2 ILE D 139 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 11541 not shown) Planarity restraints: 12701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP L 92 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO L 93 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 93 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 92 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO G 93 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 93 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 93 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP O 92 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO O 93 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO O 93 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO O 93 " 0.034 5.00e-02 4.00e+02 ... (remaining 12698 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14970 2.77 - 3.30: 73755 3.30 - 3.83: 119723 3.83 - 4.37: 147124 4.37 - 4.90: 235675 Nonbonded interactions: 591247 Sorted by model distance: nonbonded pdb=" OH TYR V 246 " pdb=" OD1 ASP P 256 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR U 246 " pdb=" OD1 ASP M 256 " model vdw 2.239 2.440 nonbonded pdb=" OH TYR K 246 " pdb=" OD1 ASP E 256 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR O 246 " pdb=" OD1 ASP J 256 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR X 246 " pdb=" OD1 ASP R 256 " model vdw 2.243 2.440 ... (remaining 591242 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 11.360 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 140.240 Find NCS groups from input model: 4.200 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.006 0.063 73242 Z= 0.364 Angle : 0.879 9.799 98566 Z= 0.451 Chirality : 0.049 0.215 11544 Planarity : 0.005 0.060 12701 Dihedral : 10.549 74.723 28275 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.08 % Allowed : 4.68 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.06), residues: 9087 helix: -2.76 (0.04), residues: 7462 sheet: None (None), residues: 0 loop : -2.27 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 101 HIS 0.011 0.003 HIS R 340 PHE 0.033 0.003 PHE Y 202 TYR 0.019 0.003 TYR I 260 ARG 0.012 0.001 ARG H 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1798 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1710 time to evaluate : 6.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 88 outliers final: 7 residues processed: 1774 average time/residue: 0.7204 time to fit residues: 2158.1343 Evaluate side-chains 632 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 625 time to evaluate : 6.474 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6449 time to fit residues: 16.8319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 757 optimal weight: 4.9990 chunk 679 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 458 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 703 optimal weight: 0.3980 chunk 272 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 chunk 814 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 318 GLN A 377 GLN B 120 ASN B 192 GLN G 26 ASN G 120 ASN H 26 ASN H 120 ASN K 26 ASN K 120 ASN L 26 ASN L 120 ASN N 26 ASN N 120 ASN N 192 GLN O 26 ASN O 120 ASN U 26 ASN U 120 ASN V 120 ASN W 26 ASN W 120 ASN X 26 ASN X 120 ASN X 192 GLN Y 26 ASN Y 120 ASN Y 340 ASN Z 26 ASN Z 120 ASN C 95 HIS C 318 GLN C 377 GLN D 95 HIS D 318 GLN D 377 GLN E 95 HIS E 318 GLN E 377 GLN F 95 HIS F 318 GLN F 377 GLN I 95 HIS I 318 GLN I 377 GLN J 95 HIS J 318 GLN J 377 GLN M 95 HIS M 318 GLN M 377 GLN P 95 HIS P 318 GLN P 377 GLN Q 95 HIS Q 318 GLN Q 377 GLN R 95 HIS R 318 GLN R 377 GLN S 95 HIS S 318 GLN S 377 GLN T 95 HIS T 318 GLN T 377 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 73242 Z= 0.222 Angle : 0.631 8.768 98566 Z= 0.346 Chirality : 0.039 0.157 11544 Planarity : 0.004 0.035 12701 Dihedral : 5.042 24.301 9529 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.58 % Allowed : 9.56 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.08), residues: 9087 helix: 0.10 (0.06), residues: 7514 sheet: None (None), residues: 0 loop : -1.63 (0.14), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 101 HIS 0.004 0.001 HIS P 95 PHE 0.023 0.001 PHE T 375 TYR 0.028 0.002 TYR F 257 ARG 0.006 0.001 ARG I 383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 889 time to evaluate : 6.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 52 residues processed: 1072 average time/residue: 0.6293 time to fit residues: 1193.0160 Evaluate side-chains 610 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 558 time to evaluate : 6.597 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5104 time to fit residues: 59.6910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 452 optimal weight: 8.9990 chunk 252 optimal weight: 0.7980 chunk 677 optimal weight: 9.9990 chunk 554 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 816 optimal weight: 0.8980 chunk 881 optimal weight: 0.9990 chunk 726 optimal weight: 0.9990 chunk 809 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 654 optimal weight: 5.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 134 ASN N 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 73242 Z= 0.168 Angle : 0.565 10.022 98566 Z= 0.296 Chirality : 0.037 0.194 11544 Planarity : 0.003 0.033 12701 Dihedral : 4.676 24.365 9529 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.67 % Allowed : 11.70 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 9087 helix: 1.12 (0.06), residues: 7358 sheet: None (None), residues: 0 loop : -1.25 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 275 HIS 0.002 0.001 HIS F 97 PHE 0.020 0.001 PHE M 375 TYR 0.016 0.001 TYR H 346 ARG 0.006 0.000 ARG Q 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 743 time to evaluate : 6.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 52 residues processed: 865 average time/residue: 0.6386 time to fit residues: 974.8598 Evaluate side-chains 603 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 551 time to evaluate : 6.519 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5222 time to fit residues: 61.1658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 806 optimal weight: 9.9990 chunk 613 optimal weight: 10.0000 chunk 423 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 389 optimal weight: 5.9990 chunk 547 optimal weight: 9.9990 chunk 818 optimal weight: 2.9990 chunk 867 optimal weight: 0.9990 chunk 427 optimal weight: 2.9990 chunk 776 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 316 HIS H 316 HIS K 316 HIS N 316 HIS O 316 HIS W 316 HIS X 316 HIS J 258 ASN P 258 ASN S 258 ASN T 258 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 73242 Z= 0.205 Angle : 0.573 8.929 98566 Z= 0.299 Chirality : 0.038 0.164 11544 Planarity : 0.003 0.035 12701 Dihedral : 4.531 21.123 9529 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 12.96 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 9087 helix: 1.56 (0.06), residues: 7423 sheet: None (None), residues: 0 loop : -1.10 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 275 HIS 0.003 0.001 HIS F 95 PHE 0.011 0.001 PHE O 202 TYR 0.018 0.002 TYR X 346 ARG 0.007 0.000 ARG U 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 636 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 43 residues processed: 713 average time/residue: 0.6319 time to fit residues: 796.8617 Evaluate side-chains 565 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 522 time to evaluate : 6.635 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5275 time to fit residues: 51.7235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 722 optimal weight: 0.8980 chunk 492 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 645 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 chunk 739 optimal weight: 0.0770 chunk 599 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 442 optimal weight: 3.9990 chunk 778 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 340 ASN K 340 ASN U 316 HIS ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 340 ASN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 316 HIS C 258 ASN D 258 ASN I 258 ASN ** T 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 73242 Z= 0.151 Angle : 0.531 9.420 98566 Z= 0.276 Chirality : 0.037 0.164 11544 Planarity : 0.003 0.034 12701 Dihedral : 4.387 21.428 9529 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.97 % Allowed : 13.11 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.09), residues: 9087 helix: 1.89 (0.06), residues: 7462 sheet: None (None), residues: 0 loop : -0.91 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 101 HIS 0.002 0.001 HIS I 95 PHE 0.011 0.001 PHE F 324 TYR 0.019 0.001 TYR I 257 ARG 0.015 0.001 ARG X 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 689 time to evaluate : 6.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 79 outliers final: 12 residues processed: 757 average time/residue: 0.6615 time to fit residues: 875.0155 Evaluate side-chains 552 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 540 time to evaluate : 6.518 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5546 time to fit residues: 21.0789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 291 optimal weight: 2.9990 chunk 780 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 509 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 867 optimal weight: 0.9990 chunk 720 optimal weight: 2.9990 chunk 401 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS B 224 GLN G 340 ASN U 117 HIS ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 340 ASN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 ASN R 258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 73242 Z= 0.168 Angle : 0.549 10.071 98566 Z= 0.284 Chirality : 0.038 0.218 11544 Planarity : 0.003 0.034 12701 Dihedral : 4.316 20.098 9529 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.98 % Allowed : 14.08 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.09), residues: 9087 helix: 2.02 (0.06), residues: 7410 sheet: None (None), residues: 0 loop : -0.77 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 345 HIS 0.003 0.001 HIS I 95 PHE 0.011 0.001 PHE F 324 TYR 0.020 0.001 TYR P 257 ARG 0.007 0.000 ARG Y 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 586 time to evaluate : 6.539 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 outliers start: 80 outliers final: 31 residues processed: 654 average time/residue: 0.6481 time to fit residues: 747.2612 Evaluate side-chains 514 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 483 time to evaluate : 6.495 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5288 time to fit residues: 39.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 836 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 494 optimal weight: 0.6980 chunk 633 optimal weight: 2.9990 chunk 491 optimal weight: 4.9990 chunk 730 optimal weight: 0.8980 chunk 484 optimal weight: 6.9990 chunk 864 optimal weight: 6.9990 chunk 541 optimal weight: 0.2980 chunk 527 optimal weight: 3.9990 chunk 399 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN K 117 HIS N 117 HIS ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 GLN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 73242 Z= 0.166 Angle : 0.555 12.623 98566 Z= 0.287 Chirality : 0.038 0.252 11544 Planarity : 0.003 0.032 12701 Dihedral : 4.293 25.814 9529 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.63 % Allowed : 14.44 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.09), residues: 9087 helix: 2.12 (0.06), residues: 7423 sheet: None (None), residues: 0 loop : -0.73 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 101 HIS 0.002 0.001 HIS R 95 PHE 0.014 0.001 PHE K 125 TYR 0.021 0.001 TYR T 257 ARG 0.006 0.000 ARG Y 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 579 time to evaluate : 6.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 15 residues processed: 618 average time/residue: 0.6706 time to fit residues: 728.3318 Evaluate side-chains 510 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 495 time to evaluate : 6.709 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5916 time to fit residues: 25.4929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 534 optimal weight: 0.9980 chunk 345 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 549 optimal weight: 20.0000 chunk 589 optimal weight: 8.9990 chunk 427 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 679 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN H 117 HIS ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 GLN X 117 HIS X 224 GLN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 73242 Z= 0.164 Angle : 0.559 11.569 98566 Z= 0.287 Chirality : 0.038 0.285 11544 Planarity : 0.003 0.033 12701 Dihedral : 4.256 23.438 9529 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.41 % Allowed : 15.19 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.09), residues: 9087 helix: 2.17 (0.06), residues: 7462 sheet: None (None), residues: 0 loop : -0.92 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 345 HIS 0.002 0.001 HIS Q 95 PHE 0.016 0.001 PHE V 125 TYR 0.020 0.001 TYR I 260 ARG 0.007 0.000 ARG Y 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 551 time to evaluate : 6.625 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 outliers start: 33 outliers final: 9 residues processed: 579 average time/residue: 0.6607 time to fit residues: 677.6894 Evaluate side-chains 491 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 482 time to evaluate : 6.499 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5232 time to fit residues: 18.0606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 786 optimal weight: 0.8980 chunk 828 optimal weight: 0.4980 chunk 755 optimal weight: 0.9990 chunk 805 optimal weight: 8.9990 chunk 484 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 632 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 728 optimal weight: 7.9990 chunk 761 optimal weight: 10.0000 chunk 802 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 GLN X 224 GLN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 316 HIS C 340 HIS ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 73242 Z= 0.189 Angle : 0.577 12.181 98566 Z= 0.298 Chirality : 0.038 0.216 11544 Planarity : 0.003 0.032 12701 Dihedral : 4.270 26.198 9529 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.49 % Allowed : 15.21 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.09), residues: 9087 helix: 2.17 (0.06), residues: 7462 sheet: None (None), residues: 0 loop : -0.91 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP U 308 HIS 0.004 0.001 HIS N 316 PHE 0.023 0.001 PHE V 125 TYR 0.023 0.001 TYR R 260 ARG 0.008 0.001 ARG Z 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 493 time to evaluate : 6.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 522 average time/residue: 0.6587 time to fit residues: 607.9677 Evaluate side-chains 465 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 452 time to evaluate : 6.622 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5608 time to fit residues: 22.7772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 529 optimal weight: 0.7980 chunk 851 optimal weight: 1.9990 chunk 519 optimal weight: 0.7980 chunk 404 optimal weight: 6.9990 chunk 592 optimal weight: 5.9990 chunk 893 optimal weight: 8.9990 chunk 822 optimal weight: 0.7980 chunk 711 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 549 optimal weight: 20.0000 chunk 436 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 224 GLN L 117 HIS ** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 GLN W 134 ASN X 224 GLN ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73242 Z= 0.163 Angle : 0.571 12.706 98566 Z= 0.294 Chirality : 0.038 0.227 11544 Planarity : 0.003 0.035 12701 Dihedral : 4.257 24.183 9529 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.23 % Allowed : 15.37 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.09), residues: 9087 helix: 2.17 (0.06), residues: 7488 sheet: None (None), residues: 0 loop : -0.83 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G 308 HIS 0.003 0.001 HIS U 316 PHE 0.027 0.001 PHE R 91 TYR 0.022 0.001 TYR R 260 ARG 0.009 0.000 ARG K 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18174 Ramachandran restraints generated. 9087 Oldfield, 0 Emsley, 9087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 532 time to evaluate : 6.595 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: 19 outliers final: 10 residues processed: 549 average time/residue: 0.6897 time to fit residues: 664.4387 Evaluate side-chains 476 residues out of total 8125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 466 time to evaluate : 6.581 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5545 time to fit residues: 19.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 897 random chunks: chunk 565 optimal weight: 5.9990 chunk 758 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 656 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 712 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 731 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN H 306 GLN L 316 HIS ** O 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 GLN ** W 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051767 restraints weight = 389811.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052950 restraints weight = 244495.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053763 restraints weight = 175247.591| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 73242 Z= 0.223 Angle : 0.618 15.049 98566 Z= 0.321 Chirality : 0.040 0.252 11544 Planarity : 0.003 0.052 12701 Dihedral : 4.315 24.305 9529 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.23 % Allowed : 15.72 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.09), residues: 9087 helix: 2.11 (0.06), residues: 7488 sheet: None (None), residues: 0 loop : -0.84 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP V 308 HIS 0.003 0.001 HIS E 95 PHE 0.020 0.001 PHE V 125 TYR 0.025 0.002 TYR R 260 ARG 0.011 0.001 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14901.25 seconds wall clock time: 265 minutes 19.28 seconds (15919.28 seconds total)