Starting phenix.real_space_refine on Mon Nov 20 23:31:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc1_6461/11_2023/3jc1_6461.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc1_6461/11_2023/3jc1_6461.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/3jc1_6461/11_2023/3jc1_6461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc1_6461/11_2023/3jc1_6461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc1_6461/11_2023/3jc1_6461.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jc1_6461/11_2023/3jc1_6461.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 ------------------------------------------------------------------------------- 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= 0.015 sd= 3.645 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 680 5.16 5 C 57766 2.51 5 N 16184 2.21 5 O 17476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Am PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "As PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Au PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aw PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ay PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bm PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bs PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bu PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "By PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ca PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ce PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cg PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ci PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ck PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cm PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Co PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 92106 Number of models: 1 Model: "" Number of chains: 68 Chain: "Aa" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ab" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ac" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ad" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ae" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Af" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ag" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ah" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ai" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Aj" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ak" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Al" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Am" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "An" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ao" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ap" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Aq" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ar" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "As" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "At" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Au" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Av" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Aw" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ax" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ay" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Az" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ba" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bb" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bc" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bd" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Be" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bf" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bg" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bh" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bi" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bj" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bk" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bl" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bm" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bn" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bo" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bp" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bq" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Br" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bs" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bt" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bu" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bv" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Bw" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bx" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "By" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Bz" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ca" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cb" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Cc" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cd" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ce" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cf" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Cg" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Ch" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ci" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cj" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Ck" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cl" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Cm" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cn" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Chain: "Co" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1466 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "Cp" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1243 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 1, 'TRANS': 158} Time building chain proxies: 33.46, per 1000 atoms: 0.36 Number of scatterers: 92106 At special positions: 0 Unit cell: (259.2, 261.6, 177.6, 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 680 16.00 O 17476 8.00 N 16184 7.00 C 57766 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: 27.81 Conformation dependent library (CDL) restraints added in 11.9 seconds 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22644 Finding SS restraints... Secondary structure from input PDB file: 510 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'Aa' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUAa 11 " --> pdb=" O LYSAa 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAa 45 " --> pdb=" O ALAAa 41 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALAAa 52 " --> pdb=" O LYSAa 48 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNAa 87 " --> pdb=" O PHEAa 83 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 98 through 106 Processing helix chain 'Aa' and resid 106 through 111 Processing helix chain 'Aa' and resid 115 through 126 Processing helix chain 'Aa' and resid 133 through 141 Processing helix chain 'Aa' and resid 145 through 153 Processing helix chain 'Aa' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAa 162 " --> pdb=" O PROAa 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAa 173 " --> pdb=" O ILEAa 169 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 180 through 186 removed outlier: 3.771A pdb=" N METAa 184 " --> pdb=" O ASPAa 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALAAa 185 " --> pdb=" O SERAa 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUAa 186 " --> pdb=" O VALAa 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 180 through 186' Processing helix chain 'Ab' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAb 39 " --> pdb=" O LYSAb 35 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRAb 102 " --> pdb=" O ALAAb 98 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEAb 108 " --> pdb=" O ASNAb 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRAb 137 " --> pdb=" O METAb 133 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 138 through 141 Processing helix chain 'Ab' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAb 146 " --> pdb=" O PROAb 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUAb 156 " --> pdb=" O GLUAb 152 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUAc 11 " --> pdb=" O LYSAc 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALAAc 45 " --> pdb=" O ALAAc 41 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAc 52 " --> pdb=" O LYSAc 48 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNAc 87 " --> pdb=" O PHEAc 83 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 98 through 106 Processing helix chain 'Ac' and resid 106 through 111 Processing helix chain 'Ac' and resid 115 through 126 Processing helix chain 'Ac' and resid 133 through 141 Processing helix chain 'Ac' and resid 145 through 153 Processing helix chain 'Ac' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAc 162 " --> pdb=" O PROAc 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAc 173 " --> pdb=" O ILEAc 169 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 180 through 186 removed outlier: 3.769A pdb=" N METAc 184 " --> pdb=" O ASPAc 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALAAc 185 " --> pdb=" O SERAc 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUAc 186 " --> pdb=" O VALAc 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 180 through 186' Processing helix chain 'Ad' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSAd 39 " --> pdb=" O LYSAd 35 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRAd 102 " --> pdb=" O ALAAd 98 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEAd 108 " --> pdb=" O ASNAd 104 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THRAd 137 " --> pdb=" O METAd 133 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 138 through 141 Processing helix chain 'Ad' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALAd 146 " --> pdb=" O PROAd 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUAd 156 " --> pdb=" O GLUAd 152 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUAe 11 " --> pdb=" O LYSAe 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALAAe 45 " --> pdb=" O ALAAe 41 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 48 through 82 removed outlier: 4.202A pdb=" N ALAAe 52 " --> pdb=" O LYSAe 48 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNAe 87 " --> pdb=" O PHEAe 83 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 98 through 106 Processing helix chain 'Ae' and resid 106 through 111 Processing helix chain 'Ae' and resid 115 through 126 Processing helix chain 'Ae' and resid 133 through 141 Processing helix chain 'Ae' and resid 145 through 153 Processing helix chain 'Ae' and resid 158 through 173 removed outlier: 3.579A pdb=" N VALAe 162 " --> pdb=" O PROAe 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAe 173 " --> pdb=" O ILEAe 169 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 180 through 186 removed outlier: 3.769A pdb=" N METAe 184 " --> pdb=" O ASPAe 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALAAe 185 " --> pdb=" O SERAe 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUAe 186 " --> pdb=" O VALAe 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 180 through 186' Processing helix chain 'Af' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSAf 39 " --> pdb=" O LYSAf 35 " (cutoff:3.500A) Processing helix chain 'Af' and resid 43 through 102 removed outlier: 4.191A pdb=" N THRAf 102 " --> pdb=" O ALAAf 98 " (cutoff:3.500A) Processing helix chain 'Af' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEAf 108 " --> pdb=" O ASNAf 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRAf 137 " --> pdb=" O METAf 133 " (cutoff:3.500A) Processing helix chain 'Af' and resid 138 through 141 Processing helix chain 'Af' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAf 146 " --> pdb=" O PROAf 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAf 156 " --> pdb=" O GLUAf 152 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUAg 11 " --> pdb=" O LYSAg 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAg 45 " --> pdb=" O ALAAg 41 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAg 52 " --> pdb=" O LYSAg 48 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNAg 87 " --> pdb=" O PHEAg 83 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 98 through 106 Processing helix chain 'Ag' and resid 106 through 111 Processing helix chain 'Ag' and resid 115 through 126 Processing helix chain 'Ag' and resid 133 through 141 Processing helix chain 'Ag' and resid 145 through 153 Processing helix chain 'Ag' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAg 162 " --> pdb=" O PROAg 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAg 173 " --> pdb=" O ILEAg 169 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 180 through 186 removed outlier: 3.770A pdb=" N METAg 184 " --> pdb=" O ASPAg 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALAAg 185 " --> pdb=" O SERAg 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUAg 186 " --> pdb=" O VALAg 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 180 through 186' Processing helix chain 'Ah' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSAh 39 " --> pdb=" O LYSAh 35 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRAh 102 " --> pdb=" O ALAAh 98 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILEAh 108 " --> pdb=" O ASNAh 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRAh 137 " --> pdb=" O METAh 133 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 138 through 141 Processing helix chain 'Ah' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAh 146 " --> pdb=" O PROAh 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUAh 156 " --> pdb=" O GLUAh 152 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 7 through 45 removed outlier: 3.773A pdb=" N LEUAi 11 " --> pdb=" O LYSAi 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAi 45 " --> pdb=" O ALAAi 41 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALAAi 52 " --> pdb=" O LYSAi 48 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNAi 87 " --> pdb=" O PHEAi 83 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 98 through 106 Processing helix chain 'Ai' and resid 106 through 111 Processing helix chain 'Ai' and resid 115 through 126 Processing helix chain 'Ai' and resid 133 through 141 Processing helix chain 'Ai' and resid 145 through 153 Processing helix chain 'Ai' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAi 162 " --> pdb=" O PROAi 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAi 173 " --> pdb=" O ILEAi 169 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 180 through 186 removed outlier: 3.772A pdb=" N METAi 184 " --> pdb=" O ASPAi 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALAAi 185 " --> pdb=" O SERAi 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUAi 186 " --> pdb=" O VALAi 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ai' and resid 180 through 186' Processing helix chain 'Aj' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAj 39 " --> pdb=" O LYSAj 35 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRAj 102 " --> pdb=" O ALAAj 98 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 104 through 137 removed outlier: 3.810A pdb=" N ILEAj 108 " --> pdb=" O ASNAj 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRAj 137 " --> pdb=" O METAj 133 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 138 through 141 Processing helix chain 'Aj' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALAj 146 " --> pdb=" O PROAj 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAj 156 " --> pdb=" O GLUAj 152 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 45 removed outlier: 3.769A pdb=" N LEUAk 11 " --> pdb=" O LYSAk 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALAAk 45 " --> pdb=" O ALAAk 41 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 48 through 82 removed outlier: 4.199A pdb=" N ALAAk 52 " --> pdb=" O LYSAk 48 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNAk 87 " --> pdb=" O PHEAk 83 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 98 through 106 Processing helix chain 'Ak' and resid 106 through 111 Processing helix chain 'Ak' and resid 115 through 126 Processing helix chain 'Ak' and resid 133 through 141 Processing helix chain 'Ak' and resid 145 through 153 Processing helix chain 'Ak' and resid 158 through 173 removed outlier: 3.579A pdb=" N VALAk 162 " --> pdb=" O PROAk 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAk 173 " --> pdb=" O ILEAk 169 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 180 through 186 removed outlier: 3.770A pdb=" N METAk 184 " --> pdb=" O ASPAk 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAAk 185 " --> pdb=" O SERAk 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUAk 186 " --> pdb=" O VALAk 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 180 through 186' Processing helix chain 'Al' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSAl 39 " --> pdb=" O LYSAl 35 " (cutoff:3.500A) Processing helix chain 'Al' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRAl 102 " --> pdb=" O ALAAl 98 " (cutoff:3.500A) Processing helix chain 'Al' and resid 104 through 137 removed outlier: 3.810A pdb=" N ILEAl 108 " --> pdb=" O ASNAl 104 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THRAl 137 " --> pdb=" O METAl 133 " (cutoff:3.500A) Processing helix chain 'Al' and resid 138 through 141 Processing helix chain 'Al' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALAl 146 " --> pdb=" O PROAl 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAl 156 " --> pdb=" O GLUAl 152 " (cutoff:3.500A) Processing helix chain 'Am' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUAm 11 " --> pdb=" O LYSAm 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALAAm 45 " --> pdb=" O ALAAm 41 " (cutoff:3.500A) Processing helix chain 'Am' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALAAm 52 " --> pdb=" O LYSAm 48 " (cutoff:3.500A) Processing helix chain 'Am' and resid 82 through 87 removed outlier: 3.745A pdb=" N GLNAm 87 " --> pdb=" O PHEAm 83 " (cutoff:3.500A) Processing helix chain 'Am' and resid 98 through 106 Processing helix chain 'Am' and resid 106 through 111 Processing helix chain 'Am' and resid 115 through 126 Processing helix chain 'Am' and resid 133 through 141 Processing helix chain 'Am' and resid 145 through 153 Processing helix chain 'Am' and resid 158 through 173 removed outlier: 3.582A pdb=" N VALAm 162 " --> pdb=" O PROAm 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAm 173 " --> pdb=" O ILEAm 169 " (cutoff:3.500A) Processing helix chain 'Am' and resid 180 through 186 removed outlier: 3.770A pdb=" N METAm 184 " --> pdb=" O ASPAm 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALAAm 185 " --> pdb=" O SERAm 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUAm 186 " --> pdb=" O VALAm 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Am' and resid 180 through 186' Processing helix chain 'An' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAn 39 " --> pdb=" O LYSAn 35 " (cutoff:3.500A) Processing helix chain 'An' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRAn 102 " --> pdb=" O ALAAn 98 " (cutoff:3.500A) Processing helix chain 'An' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILEAn 108 " --> pdb=" O ASNAn 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRAn 137 " --> pdb=" O METAn 133 " (cutoff:3.500A) Processing helix chain 'An' and resid 138 through 141 Processing helix chain 'An' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAn 146 " --> pdb=" O PROAn 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUAn 156 " --> pdb=" O GLUAn 152 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUAo 11 " --> pdb=" O LYSAo 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAo 45 " --> pdb=" O ALAAo 41 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAo 52 " --> pdb=" O LYSAo 48 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNAo 87 " --> pdb=" O PHEAo 83 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 98 through 106 Processing helix chain 'Ao' and resid 106 through 111 Processing helix chain 'Ao' and resid 115 through 126 Processing helix chain 'Ao' and resid 133 through 141 Processing helix chain 'Ao' and resid 145 through 153 Processing helix chain 'Ao' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALAo 162 " --> pdb=" O PROAo 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAo 173 " --> pdb=" O ILEAo 169 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 180 through 186 removed outlier: 3.771A pdb=" N METAo 184 " --> pdb=" O ASPAo 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAAo 185 " --> pdb=" O SERAo 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUAo 186 " --> pdb=" O VALAo 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ao' and resid 180 through 186' Processing helix chain 'Ap' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSAp 39 " --> pdb=" O LYSAp 35 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 43 through 102 removed outlier: 4.191A pdb=" N THRAp 102 " --> pdb=" O ALAAp 98 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILEAp 108 " --> pdb=" O ASNAp 104 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THRAp 137 " --> pdb=" O METAp 133 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 138 through 141 Processing helix chain 'Ap' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAp 146 " --> pdb=" O PROAp 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAp 156 " --> pdb=" O GLUAp 152 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUAq 11 " --> pdb=" O LYSAq 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALAAq 45 " --> pdb=" O ALAAq 41 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALAAq 52 " --> pdb=" O LYSAq 48 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNAq 87 " --> pdb=" O PHEAq 83 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 98 through 106 Processing helix chain 'Aq' and resid 106 through 111 Processing helix chain 'Aq' and resid 115 through 126 Processing helix chain 'Aq' and resid 133 through 141 Processing helix chain 'Aq' and resid 145 through 153 Processing helix chain 'Aq' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAq 162 " --> pdb=" O PROAq 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAq 173 " --> pdb=" O ILEAq 169 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 180 through 186 removed outlier: 3.772A pdb=" N METAq 184 " --> pdb=" O ASPAq 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAAq 185 " --> pdb=" O SERAq 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUAq 186 " --> pdb=" O VALAq 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aq' and resid 180 through 186' Processing helix chain 'Ar' and resid 2 through 39 removed outlier: 3.914A pdb=" N LYSAr 39 " --> pdb=" O LYSAr 35 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRAr 102 " --> pdb=" O ALAAr 98 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 104 through 137 removed outlier: 3.810A pdb=" N ILEAr 108 " --> pdb=" O ASNAr 104 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THRAr 137 " --> pdb=" O METAr 133 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 138 through 141 Processing helix chain 'Ar' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAr 146 " --> pdb=" O PROAr 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUAr 156 " --> pdb=" O GLUAr 152 " (cutoff:3.500A) Processing helix chain 'As' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUAs 11 " --> pdb=" O LYSAs 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAs 45 " --> pdb=" O ALAAs 41 " (cutoff:3.500A) Processing helix chain 'As' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALAAs 52 " --> pdb=" O LYSAs 48 " (cutoff:3.500A) Processing helix chain 'As' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNAs 87 " --> pdb=" O PHEAs 83 " (cutoff:3.500A) Processing helix chain 'As' and resid 98 through 106 Processing helix chain 'As' and resid 106 through 111 Processing helix chain 'As' and resid 115 through 126 Processing helix chain 'As' and resid 133 through 141 Processing helix chain 'As' and resid 145 through 153 Processing helix chain 'As' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALAs 162 " --> pdb=" O PROAs 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAs 173 " --> pdb=" O ILEAs 169 " (cutoff:3.500A) Processing helix chain 'As' and resid 180 through 186 removed outlier: 3.772A pdb=" N METAs 184 " --> pdb=" O ASPAs 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAAs 185 " --> pdb=" O SERAs 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUAs 186 " --> pdb=" O VALAs 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'As' and resid 180 through 186' Processing helix chain 'At' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSAt 39 " --> pdb=" O LYSAt 35 " (cutoff:3.500A) Processing helix chain 'At' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRAt 102 " --> pdb=" O ALAAt 98 " (cutoff:3.500A) Processing helix chain 'At' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEAt 108 " --> pdb=" O ASNAt 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRAt 137 " --> pdb=" O METAt 133 " (cutoff:3.500A) Processing helix chain 'At' and resid 138 through 141 Processing helix chain 'At' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAt 146 " --> pdb=" O PROAt 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAt 156 " --> pdb=" O GLUAt 152 " (cutoff:3.500A) Processing helix chain 'Au' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUAu 11 " --> pdb=" O LYSAu 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALAAu 45 " --> pdb=" O ALAAu 41 " (cutoff:3.500A) Processing helix chain 'Au' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAu 52 " --> pdb=" O LYSAu 48 " (cutoff:3.500A) Processing helix chain 'Au' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNAu 87 " --> pdb=" O PHEAu 83 " (cutoff:3.500A) Processing helix chain 'Au' and resid 98 through 106 Processing helix chain 'Au' and resid 106 through 111 Processing helix chain 'Au' and resid 115 through 126 Processing helix chain 'Au' and resid 133 through 141 Processing helix chain 'Au' and resid 145 through 153 Processing helix chain 'Au' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALAu 162 " --> pdb=" O PROAu 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAu 173 " --> pdb=" O ILEAu 169 " (cutoff:3.500A) Processing helix chain 'Au' and resid 180 through 186 removed outlier: 3.771A pdb=" N METAu 184 " --> pdb=" O ASPAu 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALAAu 185 " --> pdb=" O SERAu 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUAu 186 " --> pdb=" O VALAu 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Au' and resid 180 through 186' Processing helix chain 'Av' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAv 39 " --> pdb=" O LYSAv 35 " (cutoff:3.500A) Processing helix chain 'Av' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRAv 102 " --> pdb=" O ALAAv 98 " (cutoff:3.500A) Processing helix chain 'Av' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEAv 108 " --> pdb=" O ASNAv 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRAv 137 " --> pdb=" O METAv 133 " (cutoff:3.500A) Processing helix chain 'Av' and resid 138 through 141 Processing helix chain 'Av' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAv 146 " --> pdb=" O PROAv 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUAv 156 " --> pdb=" O GLUAv 152 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUAw 11 " --> pdb=" O LYSAw 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAw 45 " --> pdb=" O ALAAw 41 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAw 52 " --> pdb=" O LYSAw 48 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNAw 87 " --> pdb=" O PHEAw 83 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 98 through 106 Processing helix chain 'Aw' and resid 106 through 111 Processing helix chain 'Aw' and resid 115 through 126 Processing helix chain 'Aw' and resid 133 through 141 Processing helix chain 'Aw' and resid 145 through 153 Processing helix chain 'Aw' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALAw 162 " --> pdb=" O PROAw 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRAw 173 " --> pdb=" O ILEAw 169 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 180 through 186 removed outlier: 3.771A pdb=" N METAw 184 " --> pdb=" O ASPAw 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALAAw 185 " --> pdb=" O SERAw 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUAw 186 " --> pdb=" O VALAw 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aw' and resid 180 through 186' Processing helix chain 'Ax' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAx 39 " --> pdb=" O LYSAx 35 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRAx 102 " --> pdb=" O ALAAx 98 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEAx 108 " --> pdb=" O ASNAx 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRAx 137 " --> pdb=" O METAx 133 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 138 through 141 Processing helix chain 'Ax' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALAx 146 " --> pdb=" O PROAx 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUAx 156 " --> pdb=" O GLUAx 152 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUAy 11 " --> pdb=" O LYSAy 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALAAy 45 " --> pdb=" O ALAAy 41 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALAAy 52 " --> pdb=" O LYSAy 48 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNAy 87 " --> pdb=" O PHEAy 83 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 98 through 106 Processing helix chain 'Ay' and resid 106 through 111 Processing helix chain 'Ay' and resid 115 through 126 Processing helix chain 'Ay' and resid 133 through 141 Processing helix chain 'Ay' and resid 145 through 153 Processing helix chain 'Ay' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALAy 162 " --> pdb=" O PROAy 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRAy 173 " --> pdb=" O ILEAy 169 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 180 through 186 removed outlier: 3.771A pdb=" N METAy 184 " --> pdb=" O ASPAy 180 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALAAy 185 " --> pdb=" O SERAy 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUAy 186 " --> pdb=" O VALAy 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ay' and resid 180 through 186' Processing helix chain 'Az' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSAz 39 " --> pdb=" O LYSAz 35 " (cutoff:3.500A) Processing helix chain 'Az' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRAz 102 " --> pdb=" O ALAAz 98 " (cutoff:3.500A) Processing helix chain 'Az' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEAz 108 " --> pdb=" O ASNAz 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRAz 137 " --> pdb=" O METAz 133 " (cutoff:3.500A) Processing helix chain 'Az' and resid 138 through 141 Processing helix chain 'Az' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALAz 146 " --> pdb=" O PROAz 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUAz 156 " --> pdb=" O GLUAz 152 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBa 11 " --> pdb=" O LYSBa 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABa 45 " --> pdb=" O ALABa 41 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABa 52 " --> pdb=" O LYSBa 48 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNBa 87 " --> pdb=" O PHEBa 83 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 98 through 106 Processing helix chain 'Ba' and resid 106 through 111 Processing helix chain 'Ba' and resid 115 through 126 Processing helix chain 'Ba' and resid 133 through 141 Processing helix chain 'Ba' and resid 145 through 153 Processing helix chain 'Ba' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALBa 162 " --> pdb=" O PROBa 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRBa 173 " --> pdb=" O ILEBa 169 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 180 through 186 removed outlier: 3.769A pdb=" N METBa 184 " --> pdb=" O ASPBa 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALABa 185 " --> pdb=" O SERBa 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUBa 186 " --> pdb=" O VALBa 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 180 through 186' Processing helix chain 'Bb' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBb 39 " --> pdb=" O LYSBb 35 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRBb 102 " --> pdb=" O ALABb 98 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILEBb 108 " --> pdb=" O ASNBb 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBb 137 " --> pdb=" O METBb 133 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 138 through 141 Processing helix chain 'Bb' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBb 146 " --> pdb=" O PROBb 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUBb 156 " --> pdb=" O GLUBb 152 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBc 11 " --> pdb=" O LYSBc 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALABc 45 " --> pdb=" O ALABc 41 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABc 52 " --> pdb=" O LYSBc 48 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBc 87 " --> pdb=" O PHEBc 83 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 98 through 106 Processing helix chain 'Bc' and resid 106 through 111 Processing helix chain 'Bc' and resid 115 through 126 Processing helix chain 'Bc' and resid 133 through 141 Processing helix chain 'Bc' and resid 145 through 153 Processing helix chain 'Bc' and resid 158 through 173 removed outlier: 3.582A pdb=" N VALBc 162 " --> pdb=" O PROBc 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBc 173 " --> pdb=" O ILEBc 169 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 180 through 186 removed outlier: 3.771A pdb=" N METBc 184 " --> pdb=" O ASPBc 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALABc 185 " --> pdb=" O SERBc 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBc 186 " --> pdb=" O VALBc 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 180 through 186' Processing helix chain 'Bd' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSBd 39 " --> pdb=" O LYSBd 35 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 43 through 102 removed outlier: 4.187A pdb=" N THRBd 102 " --> pdb=" O ALABd 98 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBd 108 " --> pdb=" O ASNBd 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBd 137 " --> pdb=" O METBd 133 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 138 through 141 Processing helix chain 'Bd' and resid 142 through 156 removed outlier: 3.710A pdb=" N VALBd 146 " --> pdb=" O PROBd 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBd 156 " --> pdb=" O GLUBd 152 " (cutoff:3.500A) Processing helix chain 'Be' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBe 11 " --> pdb=" O LYSBe 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABe 45 " --> pdb=" O ALABe 41 " (cutoff:3.500A) Processing helix chain 'Be' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALABe 52 " --> pdb=" O LYSBe 48 " (cutoff:3.500A) Processing helix chain 'Be' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBe 87 " --> pdb=" O PHEBe 83 " (cutoff:3.500A) Processing helix chain 'Be' and resid 98 through 106 Processing helix chain 'Be' and resid 106 through 111 Processing helix chain 'Be' and resid 115 through 126 Processing helix chain 'Be' and resid 133 through 141 Processing helix chain 'Be' and resid 145 through 153 Processing helix chain 'Be' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALBe 162 " --> pdb=" O PROBe 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBe 173 " --> pdb=" O ILEBe 169 " (cutoff:3.500A) Processing helix chain 'Be' and resid 180 through 186 removed outlier: 3.770A pdb=" N METBe 184 " --> pdb=" O ASPBe 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALABe 185 " --> pdb=" O SERBe 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBe 186 " --> pdb=" O VALBe 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Be' and resid 180 through 186' Processing helix chain 'Bf' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSBf 39 " --> pdb=" O LYSBf 35 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRBf 102 " --> pdb=" O ALABf 98 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 104 through 137 removed outlier: 3.810A pdb=" N ILEBf 108 " --> pdb=" O ASNBf 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBf 137 " --> pdb=" O METBf 133 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 138 through 141 Processing helix chain 'Bf' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBf 146 " --> pdb=" O PROBf 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUBf 156 " --> pdb=" O GLUBf 152 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUBg 11 " --> pdb=" O LYSBg 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABg 45 " --> pdb=" O ALABg 41 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALABg 52 " --> pdb=" O LYSBg 48 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBg 87 " --> pdb=" O PHEBg 83 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 98 through 106 Processing helix chain 'Bg' and resid 106 through 111 Processing helix chain 'Bg' and resid 115 through 126 Processing helix chain 'Bg' and resid 133 through 141 Processing helix chain 'Bg' and resid 145 through 153 Processing helix chain 'Bg' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALBg 162 " --> pdb=" O PROBg 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBg 173 " --> pdb=" O ILEBg 169 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 180 through 186 removed outlier: 3.771A pdb=" N METBg 184 " --> pdb=" O ASPBg 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALABg 185 " --> pdb=" O SERBg 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBg 186 " --> pdb=" O VALBg 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 180 through 186' Processing helix chain 'Bh' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSBh 39 " --> pdb=" O LYSBh 35 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRBh 102 " --> pdb=" O ALABh 98 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEBh 108 " --> pdb=" O ASNBh 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRBh 137 " --> pdb=" O METBh 133 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 138 through 141 Processing helix chain 'Bh' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALBh 146 " --> pdb=" O PROBh 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBh 156 " --> pdb=" O GLUBh 152 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBi 11 " --> pdb=" O LYSBi 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABi 45 " --> pdb=" O ALABi 41 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALABi 52 " --> pdb=" O LYSBi 48 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBi 87 " --> pdb=" O PHEBi 83 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 98 through 106 Processing helix chain 'Bi' and resid 106 through 111 Processing helix chain 'Bi' and resid 115 through 126 Processing helix chain 'Bi' and resid 133 through 141 Processing helix chain 'Bi' and resid 145 through 153 Processing helix chain 'Bi' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALBi 162 " --> pdb=" O PROBi 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBi 173 " --> pdb=" O ILEBi 169 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 180 through 186 removed outlier: 3.771A pdb=" N METBi 184 " --> pdb=" O ASPBi 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALABi 185 " --> pdb=" O SERBi 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUBi 186 " --> pdb=" O VALBi 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bi' and resid 180 through 186' Processing helix chain 'Bj' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBj 39 " --> pdb=" O LYSBj 35 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRBj 102 " --> pdb=" O ALABj 98 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILEBj 108 " --> pdb=" O ASNBj 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBj 137 " --> pdb=" O METBj 133 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 138 through 141 Processing helix chain 'Bj' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALBj 146 " --> pdb=" O PROBj 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUBj 156 " --> pdb=" O GLUBj 152 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBk 11 " --> pdb=" O LYSBk 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALABk 45 " --> pdb=" O ALABk 41 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 48 through 82 removed outlier: 4.202A pdb=" N ALABk 52 " --> pdb=" O LYSBk 48 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBk 87 " --> pdb=" O PHEBk 83 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 98 through 106 Processing helix chain 'Bk' and resid 106 through 111 Processing helix chain 'Bk' and resid 115 through 126 Processing helix chain 'Bk' and resid 133 through 141 Processing helix chain 'Bk' and resid 145 through 153 Processing helix chain 'Bk' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALBk 162 " --> pdb=" O PROBk 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBk 173 " --> pdb=" O ILEBk 169 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 180 through 186 removed outlier: 3.770A pdb=" N METBk 184 " --> pdb=" O ASPBk 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALABk 185 " --> pdb=" O SERBk 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBk 186 " --> pdb=" O VALBk 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bk' and resid 180 through 186' Processing helix chain 'Bl' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSBl 39 " --> pdb=" O LYSBl 35 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRBl 102 " --> pdb=" O ALABl 98 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBl 108 " --> pdb=" O ASNBl 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRBl 137 " --> pdb=" O METBl 133 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 138 through 141 Processing helix chain 'Bl' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBl 146 " --> pdb=" O PROBl 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUBl 156 " --> pdb=" O GLUBl 152 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBm 11 " --> pdb=" O LYSBm 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALABm 45 " --> pdb=" O ALABm 41 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABm 52 " --> pdb=" O LYSBm 48 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBm 87 " --> pdb=" O PHEBm 83 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 98 through 106 Processing helix chain 'Bm' and resid 106 through 111 Processing helix chain 'Bm' and resid 115 through 126 Processing helix chain 'Bm' and resid 133 through 141 Processing helix chain 'Bm' and resid 145 through 153 Processing helix chain 'Bm' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALBm 162 " --> pdb=" O PROBm 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRBm 173 " --> pdb=" O ILEBm 169 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 180 through 186 removed outlier: 3.772A pdb=" N METBm 184 " --> pdb=" O ASPBm 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALABm 185 " --> pdb=" O SERBm 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUBm 186 " --> pdb=" O VALBm 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bm' and resid 180 through 186' Processing helix chain 'Bn' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBn 39 " --> pdb=" O LYSBn 35 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRBn 102 " --> pdb=" O ALABn 98 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBn 108 " --> pdb=" O ASNBn 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRBn 137 " --> pdb=" O METBn 133 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 138 through 141 Processing helix chain 'Bn' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBn 146 " --> pdb=" O PROBn 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUBn 156 " --> pdb=" O GLUBn 152 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUBo 11 " --> pdb=" O LYSBo 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABo 45 " --> pdb=" O ALABo 41 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABo 52 " --> pdb=" O LYSBo 48 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBo 87 " --> pdb=" O PHEBo 83 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 98 through 106 Processing helix chain 'Bo' and resid 106 through 111 Processing helix chain 'Bo' and resid 115 through 126 Processing helix chain 'Bo' and resid 133 through 141 Processing helix chain 'Bo' and resid 145 through 153 Processing helix chain 'Bo' and resid 158 through 173 removed outlier: 3.582A pdb=" N VALBo 162 " --> pdb=" O PROBo 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBo 173 " --> pdb=" O ILEBo 169 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 180 through 186 removed outlier: 3.772A pdb=" N METBo 184 " --> pdb=" O ASPBo 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALABo 185 " --> pdb=" O SERBo 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUBo 186 " --> pdb=" O VALBo 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bo' and resid 180 through 186' Processing helix chain 'Bp' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBp 39 " --> pdb=" O LYSBp 35 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRBp 102 " --> pdb=" O ALABp 98 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBp 108 " --> pdb=" O ASNBp 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRBp 137 " --> pdb=" O METBp 133 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 138 through 141 Processing helix chain 'Bp' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBp 146 " --> pdb=" O PROBp 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBp 156 " --> pdb=" O GLUBp 152 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUBq 11 " --> pdb=" O LYSBq 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALABq 45 " --> pdb=" O ALABq 41 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABq 52 " --> pdb=" O LYSBq 48 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBq 87 " --> pdb=" O PHEBq 83 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 98 through 106 Processing helix chain 'Bq' and resid 106 through 111 Processing helix chain 'Bq' and resid 115 through 126 Processing helix chain 'Bq' and resid 133 through 141 Processing helix chain 'Bq' and resid 145 through 153 Processing helix chain 'Bq' and resid 158 through 173 removed outlier: 3.579A pdb=" N VALBq 162 " --> pdb=" O PROBq 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRBq 173 " --> pdb=" O ILEBq 169 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 180 through 186 removed outlier: 3.772A pdb=" N METBq 184 " --> pdb=" O ASPBq 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALABq 185 " --> pdb=" O SERBq 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBq 186 " --> pdb=" O VALBq 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 180 through 186' Processing helix chain 'Br' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSBr 39 " --> pdb=" O LYSBr 35 " (cutoff:3.500A) Processing helix chain 'Br' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRBr 102 " --> pdb=" O ALABr 98 " (cutoff:3.500A) Processing helix chain 'Br' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEBr 108 " --> pdb=" O ASNBr 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBr 137 " --> pdb=" O METBr 133 " (cutoff:3.500A) Processing helix chain 'Br' and resid 138 through 141 Processing helix chain 'Br' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBr 146 " --> pdb=" O PROBr 142 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLUBr 156 " --> pdb=" O GLUBr 152 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUBs 11 " --> pdb=" O LYSBs 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALABs 45 " --> pdb=" O ALABs 41 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABs 52 " --> pdb=" O LYSBs 48 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBs 87 " --> pdb=" O PHEBs 83 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 98 through 106 Processing helix chain 'Bs' and resid 106 through 111 Processing helix chain 'Bs' and resid 115 through 126 Processing helix chain 'Bs' and resid 133 through 141 Processing helix chain 'Bs' and resid 145 through 153 Processing helix chain 'Bs' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALBs 162 " --> pdb=" O PROBs 158 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYRBs 173 " --> pdb=" O ILEBs 169 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 180 through 186 removed outlier: 3.770A pdb=" N METBs 184 " --> pdb=" O ASPBs 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALABs 185 " --> pdb=" O SERBs 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUBs 186 " --> pdb=" O VALBs 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bs' and resid 180 through 186' Processing helix chain 'Bt' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSBt 39 " --> pdb=" O LYSBt 35 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRBt 102 " --> pdb=" O ALABt 98 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEBt 108 " --> pdb=" O ASNBt 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRBt 137 " --> pdb=" O METBt 133 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 138 through 141 Processing helix chain 'Bt' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALBt 146 " --> pdb=" O PROBt 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBt 156 " --> pdb=" O GLUBt 152 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 7 through 45 removed outlier: 3.773A pdb=" N LEUBu 11 " --> pdb=" O LYSBu 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALABu 45 " --> pdb=" O ALABu 41 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 48 through 82 removed outlier: 4.199A pdb=" N ALABu 52 " --> pdb=" O LYSBu 48 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBu 87 " --> pdb=" O PHEBu 83 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 98 through 106 Processing helix chain 'Bu' and resid 106 through 111 Processing helix chain 'Bu' and resid 115 through 126 Processing helix chain 'Bu' and resid 133 through 141 Processing helix chain 'Bu' and resid 145 through 153 Processing helix chain 'Bu' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALBu 162 " --> pdb=" O PROBu 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRBu 173 " --> pdb=" O ILEBu 169 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 180 through 186 removed outlier: 3.771A pdb=" N METBu 184 " --> pdb=" O ASPBu 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALABu 185 " --> pdb=" O SERBu 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBu 186 " --> pdb=" O VALBu 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 180 through 186' Processing helix chain 'Bv' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBv 39 " --> pdb=" O LYSBv 35 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRBv 102 " --> pdb=" O ALABv 98 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILEBv 108 " --> pdb=" O ASNBv 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRBv 137 " --> pdb=" O METBv 133 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 138 through 141 Processing helix chain 'Bv' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALBv 146 " --> pdb=" O PROBv 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBv 156 " --> pdb=" O GLUBv 152 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUBw 11 " --> pdb=" O LYSBw 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALABw 45 " --> pdb=" O ALABw 41 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 48 through 82 removed outlier: 4.199A pdb=" N ALABw 52 " --> pdb=" O LYSBw 48 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNBw 87 " --> pdb=" O PHEBw 83 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 98 through 106 Processing helix chain 'Bw' and resid 106 through 111 Processing helix chain 'Bw' and resid 115 through 126 Processing helix chain 'Bw' and resid 133 through 141 Processing helix chain 'Bw' and resid 145 through 153 Processing helix chain 'Bw' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALBw 162 " --> pdb=" O PROBw 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRBw 173 " --> pdb=" O ILEBw 169 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 180 through 186 removed outlier: 3.770A pdb=" N METBw 184 " --> pdb=" O ASPBw 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALABw 185 " --> pdb=" O SERBw 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUBw 186 " --> pdb=" O VALBw 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bw' and resid 180 through 186' Processing helix chain 'Bx' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBx 39 " --> pdb=" O LYSBx 35 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRBx 102 " --> pdb=" O ALABx 98 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBx 108 " --> pdb=" O ASNBx 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRBx 137 " --> pdb=" O METBx 133 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 138 through 141 Processing helix chain 'Bx' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALBx 146 " --> pdb=" O PROBx 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUBx 156 " --> pdb=" O GLUBx 152 " (cutoff:3.500A) Processing helix chain 'By' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUBy 11 " --> pdb=" O LYSBy 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALABy 45 " --> pdb=" O ALABy 41 " (cutoff:3.500A) Processing helix chain 'By' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALABy 52 " --> pdb=" O LYSBy 48 " (cutoff:3.500A) Processing helix chain 'By' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNBy 87 " --> pdb=" O PHEBy 83 " (cutoff:3.500A) Processing helix chain 'By' and resid 98 through 106 Processing helix chain 'By' and resid 106 through 111 Processing helix chain 'By' and resid 115 through 126 Processing helix chain 'By' and resid 133 through 141 Processing helix chain 'By' and resid 145 through 153 Processing helix chain 'By' and resid 158 through 173 removed outlier: 3.579A pdb=" N VALBy 162 " --> pdb=" O PROBy 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRBy 173 " --> pdb=" O ILEBy 169 " (cutoff:3.500A) Processing helix chain 'By' and resid 180 through 186 removed outlier: 3.770A pdb=" N METBy 184 " --> pdb=" O ASPBy 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALABy 185 " --> pdb=" O SERBy 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLUBy 186 " --> pdb=" O VALBy 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'By' and resid 180 through 186' Processing helix chain 'Bz' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSBz 39 " --> pdb=" O LYSBz 35 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 43 through 102 removed outlier: 4.188A pdb=" N THRBz 102 " --> pdb=" O ALABz 98 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILEBz 108 " --> pdb=" O ASNBz 104 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRBz 137 " --> pdb=" O METBz 133 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 138 through 141 Processing helix chain 'Bz' and resid 142 through 156 removed outlier: 3.710A pdb=" N VALBz 146 " --> pdb=" O PROBz 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUBz 156 " --> pdb=" O GLUBz 152 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCa 11 " --> pdb=" O LYSCa 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALACa 45 " --> pdb=" O ALACa 41 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 48 through 82 removed outlier: 4.199A pdb=" N ALACa 52 " --> pdb=" O LYSCa 48 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNCa 87 " --> pdb=" O PHECa 83 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 98 through 106 Processing helix chain 'Ca' and resid 106 through 111 Processing helix chain 'Ca' and resid 115 through 126 Processing helix chain 'Ca' and resid 133 through 141 Processing helix chain 'Ca' and resid 145 through 153 Processing helix chain 'Ca' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALCa 162 " --> pdb=" O PROCa 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRCa 173 " --> pdb=" O ILECa 169 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 180 through 186 removed outlier: 3.771A pdb=" N METCa 184 " --> pdb=" O ASPCa 180 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALACa 185 " --> pdb=" O SERCa 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUCa 186 " --> pdb=" O VALCa 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ca' and resid 180 through 186' Processing helix chain 'Cb' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSCb 39 " --> pdb=" O LYSCb 35 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRCb 102 " --> pdb=" O ALACb 98 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILECb 108 " --> pdb=" O ASNCb 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRCb 137 " --> pdb=" O METCb 133 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 138 through 141 Processing helix chain 'Cb' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALCb 146 " --> pdb=" O PROCb 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUCb 156 " --> pdb=" O GLUCb 152 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCc 11 " --> pdb=" O LYSCc 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALACc 45 " --> pdb=" O ALACc 41 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALACc 52 " --> pdb=" O LYSCc 48 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNCc 87 " --> pdb=" O PHECc 83 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 98 through 106 Processing helix chain 'Cc' and resid 106 through 111 Processing helix chain 'Cc' and resid 115 through 126 Processing helix chain 'Cc' and resid 133 through 141 Processing helix chain 'Cc' and resid 145 through 153 Processing helix chain 'Cc' and resid 158 through 173 removed outlier: 3.582A pdb=" N VALCc 162 " --> pdb=" O PROCc 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRCc 173 " --> pdb=" O ILECc 169 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 180 through 186 removed outlier: 3.770A pdb=" N METCc 184 " --> pdb=" O ASPCc 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALACc 185 " --> pdb=" O SERCc 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUCc 186 " --> pdb=" O VALCc 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cc' and resid 180 through 186' Processing helix chain 'Cd' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSCd 39 " --> pdb=" O LYSCd 35 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRCd 102 " --> pdb=" O ALACd 98 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILECd 108 " --> pdb=" O ASNCd 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRCd 137 " --> pdb=" O METCd 133 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 138 through 141 Processing helix chain 'Cd' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALCd 146 " --> pdb=" O PROCd 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUCd 156 " --> pdb=" O GLUCd 152 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCe 11 " --> pdb=" O LYSCe 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALACe 45 " --> pdb=" O ALACe 41 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 48 through 82 removed outlier: 4.202A pdb=" N ALACe 52 " --> pdb=" O LYSCe 48 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 82 through 87 removed outlier: 3.743A pdb=" N GLNCe 87 " --> pdb=" O PHECe 83 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 98 through 106 Processing helix chain 'Ce' and resid 106 through 111 Processing helix chain 'Ce' and resid 115 through 126 Processing helix chain 'Ce' and resid 133 through 141 Processing helix chain 'Ce' and resid 145 through 153 Processing helix chain 'Ce' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALCe 162 " --> pdb=" O PROCe 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRCe 173 " --> pdb=" O ILECe 169 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 180 through 186 removed outlier: 3.771A pdb=" N METCe 184 " --> pdb=" O ASPCe 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALACe 185 " --> pdb=" O SERCe 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUCe 186 " --> pdb=" O VALCe 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ce' and resid 180 through 186' Processing helix chain 'Cf' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSCf 39 " --> pdb=" O LYSCf 35 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRCf 102 " --> pdb=" O ALACf 98 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILECf 108 " --> pdb=" O ASNCf 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRCf 137 " --> pdb=" O METCf 133 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 138 through 141 Processing helix chain 'Cf' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALCf 146 " --> pdb=" O PROCf 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUCf 156 " --> pdb=" O GLUCf 152 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCg 11 " --> pdb=" O LYSCg 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALACg 45 " --> pdb=" O ALACg 41 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALACg 52 " --> pdb=" O LYSCg 48 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNCg 87 " --> pdb=" O PHECg 83 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 98 through 106 Processing helix chain 'Cg' and resid 106 through 111 Processing helix chain 'Cg' and resid 115 through 126 Processing helix chain 'Cg' and resid 133 through 141 Processing helix chain 'Cg' and resid 145 through 153 Processing helix chain 'Cg' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALCg 162 " --> pdb=" O PROCg 158 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYRCg 173 " --> pdb=" O ILECg 169 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 180 through 186 removed outlier: 3.771A pdb=" N METCg 184 " --> pdb=" O ASPCg 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALACg 185 " --> pdb=" O SERCg 181 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLUCg 186 " --> pdb=" O VALCg 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cg' and resid 180 through 186' Processing helix chain 'Ch' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSCh 39 " --> pdb=" O LYSCh 35 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 43 through 102 removed outlier: 4.191A pdb=" N THRCh 102 " --> pdb=" O ALACh 98 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 104 through 137 removed outlier: 3.811A pdb=" N ILECh 108 " --> pdb=" O ASNCh 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRCh 137 " --> pdb=" O METCh 133 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 138 through 141 Processing helix chain 'Ch' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALCh 146 " --> pdb=" O PROCh 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUCh 156 " --> pdb=" O GLUCh 152 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCi 11 " --> pdb=" O LYSCi 7 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALACi 45 " --> pdb=" O ALACi 41 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 48 through 82 removed outlier: 4.201A pdb=" N ALACi 52 " --> pdb=" O LYSCi 48 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 82 through 87 removed outlier: 3.744A pdb=" N GLNCi 87 " --> pdb=" O PHECi 83 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 98 through 106 Processing helix chain 'Ci' and resid 106 through 111 Processing helix chain 'Ci' and resid 115 through 126 Processing helix chain 'Ci' and resid 133 through 141 Processing helix chain 'Ci' and resid 145 through 153 Processing helix chain 'Ci' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALCi 162 " --> pdb=" O PROCi 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRCi 173 " --> pdb=" O ILECi 169 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 180 through 186 removed outlier: 3.771A pdb=" N METCi 184 " --> pdb=" O ASPCi 180 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALACi 185 " --> pdb=" O SERCi 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUCi 186 " --> pdb=" O VALCi 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ci' and resid 180 through 186' Processing helix chain 'Cj' and resid 2 through 39 removed outlier: 3.917A pdb=" N LYSCj 39 " --> pdb=" O LYSCj 35 " (cutoff:3.500A) Processing helix chain 'Cj' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRCj 102 " --> pdb=" O ALACj 98 " (cutoff:3.500A) Processing helix chain 'Cj' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILECj 108 " --> pdb=" O ASNCj 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THRCj 137 " --> pdb=" O METCj 133 " (cutoff:3.500A) Processing helix chain 'Cj' and resid 138 through 141 Processing helix chain 'Cj' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALCj 146 " --> pdb=" O PROCj 142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLUCj 156 " --> pdb=" O GLUCj 152 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 7 through 45 removed outlier: 3.771A pdb=" N LEUCk 11 " --> pdb=" O LYSCk 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALACk 45 " --> pdb=" O ALACk 41 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALACk 52 " --> pdb=" O LYSCk 48 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNCk 87 " --> pdb=" O PHECk 83 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 98 through 106 Processing helix chain 'Ck' and resid 106 through 111 Processing helix chain 'Ck' and resid 115 through 126 Processing helix chain 'Ck' and resid 133 through 141 Processing helix chain 'Ck' and resid 145 through 153 Processing helix chain 'Ck' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALCk 162 " --> pdb=" O PROCk 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRCk 173 " --> pdb=" O ILECk 169 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 180 through 186 removed outlier: 3.773A pdb=" N METCk 184 " --> pdb=" O ASPCk 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALACk 185 " --> pdb=" O SERCk 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUCk 186 " --> pdb=" O VALCk 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ck' and resid 180 through 186' Processing helix chain 'Cl' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSCl 39 " --> pdb=" O LYSCl 35 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRCl 102 " --> pdb=" O ALACl 98 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 104 through 137 removed outlier: 3.813A pdb=" N ILECl 108 " --> pdb=" O ASNCl 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRCl 137 " --> pdb=" O METCl 133 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 138 through 141 Processing helix chain 'Cl' and resid 142 through 156 removed outlier: 3.711A pdb=" N VALCl 146 " --> pdb=" O PROCl 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUCl 156 " --> pdb=" O GLUCl 152 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 7 through 45 removed outlier: 3.772A pdb=" N LEUCm 11 " --> pdb=" O LYSCm 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALACm 45 " --> pdb=" O ALACm 41 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALACm 52 " --> pdb=" O LYSCm 48 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNCm 87 " --> pdb=" O PHECm 83 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 98 through 106 Processing helix chain 'Cm' and resid 106 through 111 Processing helix chain 'Cm' and resid 115 through 126 Processing helix chain 'Cm' and resid 133 through 141 Processing helix chain 'Cm' and resid 145 through 153 Processing helix chain 'Cm' and resid 158 through 173 removed outlier: 3.581A pdb=" N VALCm 162 " --> pdb=" O PROCm 158 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYRCm 173 " --> pdb=" O ILECm 169 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 180 through 186 removed outlier: 3.771A pdb=" N METCm 184 " --> pdb=" O ASPCm 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALACm 185 " --> pdb=" O SERCm 181 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLUCm 186 " --> pdb=" O VALCm 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cm' and resid 180 through 186' Processing helix chain 'Cn' and resid 2 through 39 removed outlier: 3.915A pdb=" N LYSCn 39 " --> pdb=" O LYSCn 35 " (cutoff:3.500A) Processing helix chain 'Cn' and resid 43 through 102 removed outlier: 4.190A pdb=" N THRCn 102 " --> pdb=" O ALACn 98 " (cutoff:3.500A) Processing helix chain 'Cn' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILECn 108 " --> pdb=" O ASNCn 104 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THRCn 137 " --> pdb=" O METCn 133 " (cutoff:3.500A) Processing helix chain 'Cn' and resid 138 through 141 Processing helix chain 'Cn' and resid 142 through 156 removed outlier: 3.712A pdb=" N VALCn 146 " --> pdb=" O PROCn 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLUCn 156 " --> pdb=" O GLUCn 152 " (cutoff:3.500A) Processing helix chain 'Co' and resid 7 through 45 removed outlier: 3.770A pdb=" N LEUCo 11 " --> pdb=" O LYSCo 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALACo 45 " --> pdb=" O ALACo 41 " (cutoff:3.500A) Processing helix chain 'Co' and resid 48 through 82 removed outlier: 4.200A pdb=" N ALACo 52 " --> pdb=" O LYSCo 48 " (cutoff:3.500A) Processing helix chain 'Co' and resid 82 through 87 removed outlier: 3.742A pdb=" N GLNCo 87 " --> pdb=" O PHECo 83 " (cutoff:3.500A) Processing helix chain 'Co' and resid 98 through 106 Processing helix chain 'Co' and resid 106 through 111 Processing helix chain 'Co' and resid 115 through 126 Processing helix chain 'Co' and resid 133 through 141 Processing helix chain 'Co' and resid 145 through 153 Processing helix chain 'Co' and resid 158 through 173 removed outlier: 3.580A pdb=" N VALCo 162 " --> pdb=" O PROCo 158 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYRCo 173 " --> pdb=" O ILECo 169 " (cutoff:3.500A) Processing helix chain 'Co' and resid 180 through 186 removed outlier: 3.772A pdb=" N METCo 184 " --> pdb=" O ASPCo 180 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALACo 185 " --> pdb=" O SERCo 181 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLUCo 186 " --> pdb=" O VALCo 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Co' and resid 180 through 186' Processing helix chain 'Cp' and resid 2 through 39 removed outlier: 3.916A pdb=" N LYSCp 39 " --> pdb=" O LYSCp 35 " (cutoff:3.500A) Processing helix chain 'Cp' and resid 43 through 102 removed outlier: 4.189A pdb=" N THRCp 102 " --> pdb=" O ALACp 98 " (cutoff:3.500A) Processing helix chain 'Cp' and resid 104 through 137 removed outlier: 3.812A pdb=" N ILECp 108 " --> pdb=" O ASNCp 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THRCp 137 " --> pdb=" O METCp 133 " (cutoff:3.500A) Processing helix chain 'Cp' and resid 138 through 141 Processing helix chain 'Cp' and resid 142 through 156 removed outlier: 3.713A pdb=" N VALCp 146 " --> pdb=" O PROCp 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUCp 156 " --> pdb=" O GLUCp 152 " (cutoff:3.500A) 7650 hydrogen bonds defined for protein. 22848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.29 Time building geometry restraints manager: 30.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 30737 1.33 - 1.45: 8222 1.45 - 1.57: 52807 1.57 - 1.69: 0 1.69 - 1.81: 1224 Bond restraints: 92990 Sorted by residual: bond pdb=" CA ILECb 53 " pdb=" CB ILECb 53 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.11e-02 8.12e+03 1.10e+01 bond pdb=" CA ILECf 53 " pdb=" CB ILECf 53 " ideal model delta sigma weight residual 1.540 1.503 0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" CA ILEBx 53 " pdb=" CB ILEBx 53 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" CA ILEBb 53 " pdb=" CB ILEBb 53 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.11e-02 8.12e+03 1.05e+01 bond pdb=" CA ILEBn 53 " pdb=" CB ILEBn 53 " ideal model delta sigma weight residual 1.540 1.504 0.036 1.11e-02 8.12e+03 1.03e+01 ... (remaining 92985 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.58: 1327 105.58 - 112.67: 50691 112.67 - 119.76: 31687 119.76 - 126.85: 40615 126.85 - 133.93: 392 Bond angle restraints: 124712 Sorted by residual: angle pdb=" O PROBq 157 " pdb=" C PROBq 157 " pdb=" N PROBq 158 " ideal model delta sigma weight residual 121.31 123.57 -2.26 4.60e-01 4.73e+00 2.40e+01 angle pdb=" O PROCe 157 " pdb=" C PROCe 157 " pdb=" N PROCe 158 " ideal model delta sigma weight residual 121.31 123.53 -2.22 4.60e-01 4.73e+00 2.34e+01 angle pdb=" O PROAy 157 " pdb=" C PROAy 157 " pdb=" N PROAy 158 " ideal model delta sigma weight residual 121.31 123.53 -2.22 4.60e-01 4.73e+00 2.33e+01 angle pdb=" O PROBa 157 " pdb=" C PROBa 157 " pdb=" N PROBa 158 " ideal model delta sigma weight residual 121.31 123.53 -2.22 4.60e-01 4.73e+00 2.33e+01 angle pdb=" O PROAs 157 " pdb=" C PROAs 157 " pdb=" N PROAs 158 " ideal model delta sigma weight residual 121.31 123.52 -2.21 4.60e-01 4.73e+00 2.32e+01 ... (remaining 124707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 57149 16.41 - 32.82: 1263 32.82 - 49.24: 442 49.24 - 65.65: 204 65.65 - 82.06: 136 Dihedral angle restraints: 59194 sinusoidal: 24718 harmonic: 34476 Sorted by residual: dihedral pdb=" CA ASNBt 104 " pdb=" C ASNBt 104 " pdb=" N LEUBt 105 " pdb=" CA LEUBt 105 " ideal model delta harmonic sigma weight residual 180.00 -158.74 -21.26 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ASNAn 104 " pdb=" C ASNAn 104 " pdb=" N LEUAn 105 " pdb=" CA LEUAn 105 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ASNAb 104 " pdb=" C ASNAb 104 " pdb=" N LEUAb 105 " pdb=" CA LEUAb 105 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 59191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 7518 0.035 - 0.071: 4799 0.071 - 0.106: 1657 0.106 - 0.141: 543 0.141 - 0.177: 103 Chirality restraints: 14620 Sorted by residual: chirality pdb=" CG LEUBx 122 " pdb=" CB LEUBx 122 " pdb=" CD1 LEUBx 122 " pdb=" CD2 LEUBx 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CG LEUCj 122 " pdb=" CB LEUCj 122 " pdb=" CD1 LEUCj 122 " pdb=" CD2 LEUCj 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CG LEUAv 122 " pdb=" CB LEUAv 122 " pdb=" CD1 LEUAv 122 " pdb=" CD2 LEUAv 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 14617 not shown) Planarity restraints: 15878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRCe 64 " -0.013 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYRCe 64 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYRCe 64 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYRCe 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYRCe 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRCe 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYRCe 64 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRCe 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAg 64 " 0.014 2.00e-02 2.50e+03 1.11e-02 2.48e+00 pdb=" CG TYRAg 64 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYRAg 64 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYRAg 64 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYRAg 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRAg 64 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYRAg 64 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYRAg 64 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBi 64 " -0.014 2.00e-02 2.50e+03 1.11e-02 2.46e+00 pdb=" CG TYRBi 64 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYRBi 64 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYRBi 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYRBi 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRBi 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYRBi 64 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRBi 64 " -0.002 2.00e-02 2.50e+03 ... (remaining 15875 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 24457 2.81 - 3.33: 102715 3.33 - 3.86: 144557 3.86 - 4.38: 164672 4.38 - 4.90: 269989 Nonbonded interactions: 706390 Sorted by model distance: nonbonded pdb=" O ILEBe 86 " pdb=" NZ LYSBe 127 " model vdw 2.291 2.520 nonbonded pdb=" O ILEAm 86 " pdb=" NZ LYSAm 127 " model vdw 2.291 2.520 nonbonded pdb=" O ILEAc 86 " pdb=" NZ LYSAc 127 " model vdw 2.291 2.520 nonbonded pdb=" O ILEAi 86 " pdb=" NZ LYSAi 127 " model vdw 2.291 2.520 nonbonded pdb=" O ILECa 86 " pdb=" NZ LYSCa 127 " model vdw 2.291 2.520 ... (remaining 706385 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 'Aa' selection = chain 'Ac' selection = chain 'Ae' selection = chain 'Ag' selection = chain 'Ai' selection = chain 'Ak' selection = chain 'Am' selection = chain 'Ao' selection = chain 'Aq' selection = chain 'As' selection = chain 'Au' selection = chain 'Aw' selection = chain 'Ay' selection = chain 'Ba' selection = chain 'Bc' selection = chain 'Be' selection = chain 'Bg' selection = chain 'Bi' selection = chain 'Bk' selection = chain 'Bm' selection = chain 'Bo' selection = chain 'Bq' selection = chain 'Bs' selection = chain 'Bu' selection = chain 'Bw' selection = chain 'By' selection = chain 'Ca' selection = chain 'Cc' selection = chain 'Ce' selection = chain 'Cg' selection = chain 'Ci' selection = chain 'Ck' selection = chain 'Cm' selection = chain 'Co' } ncs_group { reference = chain 'Ab' selection = chain 'Ad' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Aj' selection = chain 'Al' selection = chain 'An' selection = chain 'Ap' selection = chain 'Ar' selection = chain 'At' selection = chain 'Av' selection = chain 'Ax' selection = chain 'Az' selection = chain 'Bb' selection = chain 'Bd' selection = chain 'Bf' selection = chain 'Bh' selection = chain 'Bj' selection = chain 'Bl' selection = chain 'Bn' selection = chain 'Bp' selection = chain 'Br' selection = chain 'Bt' selection = chain 'Bv' selection = chain 'Bx' selection = chain 'Bz' selection = chain 'Cb' selection = chain 'Cd' selection = chain 'Cf' selection = chain 'Ch' selection = chain 'Cj' selection = chain 'Cl' selection = chain 'Cn' selection = chain 'Cp' } 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 11.220 Check model and map are aligned: 1.040 Set scattering table: 0.620 Process input model: 174.390 Find NCS groups from input model: 5.240 Set up NCS constraints: 1.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 92990 Z= 0.573 Angle : 1.191 9.025 124712 Z= 0.827 Chirality : 0.051 0.177 14620 Planarity : 0.004 0.019 15878 Dihedral : 10.367 82.059 36550 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.06), residues: 11492 helix: -2.71 (0.04), residues: 9044 sheet: None (None), residues: 0 loop : -0.93 (0.10), residues: 2448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2276 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2276 time to evaluate : 7.707 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 outliers start: 0 outliers final: 0 residues processed: 2276 average time/residue: 0.8311 time to fit residues: 3235.4339 Evaluate side-chains 1479 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1479 time to evaluate : 7.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.2538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 976 optimal weight: 0.8980 chunk 876 optimal weight: 0.7980 chunk 486 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 591 optimal weight: 8.9990 chunk 468 optimal weight: 5.9990 chunk 906 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 550 optimal weight: 7.9990 chunk 674 optimal weight: 0.6980 chunk 1049 optimal weight: 4.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 140 GLN ** Ab 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 41 ASN ** Ab 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 140 GLN ** Ad 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 58 GLN Ad 118 GLN ** Ae 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 123 GLN Ae 140 GLN ** Af 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 58 GLN Af 125 GLN Ag 123 GLN Ag 140 GLN ** Ah 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 58 GLN ** Ah 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 111 GLN Ai 123 GLN Ai 140 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 57 ASN Aj 58 GLN Aj 118 GLN Ak 140 GLN Al 57 ASN Al 58 GLN An 57 ASN An 58 GLN ** An 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 123 GLN Ap 57 ASN Ap 58 GLN Aq 123 GLN Aq 140 GLN Ar 57 ASN Ar 58 GLN Ar 118 GLN As 123 GLN As 140 GLN At 58 GLN ** At 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 123 GLN Au 140 GLN ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 58 GLN Av 118 GLN Aw 123 GLN Aw 140 GLN ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 58 GLN Ay 123 GLN Ay 140 GLN ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 118 GLN Ba 123 GLN Ba 140 GLN ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 118 GLN Bc 123 GLN Bc 140 GLN ** Bd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 118 GLN Be 123 GLN Be 140 GLN ** Bf 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 123 GLN Bg 140 GLN ** Bh 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 51 ASN Bh 58 GLN Bh 118 GLN Bi 140 GLN Bj 4 HIS Bj 41 ASN Bk 111 GLN Bk 140 GLN ** Bl 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 58 GLN Bl 118 GLN Bm 123 GLN Bm 140 GLN ** Bn 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 58 GLN ** Bn 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 123 GLN Bo 140 GLN ** Bp 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 58 GLN Bq 140 GLN ** Br 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Br 57 ASN Br 58 GLN Br 118 GLN Bs 140 GLN Bt 58 GLN Bt 118 GLN Bu 111 GLN Bv 58 GLN Bv 118 GLN Bw 123 GLN Bx 57 ASN Bx 58 GLN Bz 58 GLN Bz 118 GLN ** Ca 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 140 GLN Cb 58 GLN Cb 118 GLN ** Cc 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 58 HIS Cc 123 GLN Cc 140 GLN ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Cd 118 GLN Ce 140 GLN ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 58 GLN Cf 118 GLN Cg 140 GLN ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 58 GLN ** Ch 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ci 123 GLN Ci 140 GLN ** Cj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 41 ASN Cj 58 GLN Cj 118 GLN ** Ck 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 123 GLN Ck 140 GLN ** Cl 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 58 GLN Cl 118 GLN Cm 123 GLN Cm 140 GLN ** Cn 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 41 ASN Cn 58 GLN Cn 118 GLN ** Co 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 140 GLN ** Cp 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 41 ASN Cp 58 GLN Total number of N/Q/H flips: 115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 92990 Z= 0.287 Angle : 0.677 9.826 124712 Z= 0.359 Chirality : 0.039 0.229 14620 Planarity : 0.004 0.053 15878 Dihedral : 4.253 22.604 12512 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.48 % Allowed : 6.91 % Favored : 90.61 % 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: 0.93 (0.07), residues: 11492 helix: 0.95 (0.05), residues: 9112 sheet: None (None), residues: 0 loop : -0.39 (0.12), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1597 time to evaluate : 7.695 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 outliers start: 248 outliers final: 125 residues processed: 1721 average time/residue: 0.8035 time to fit residues: 2437.0239 Evaluate side-chains 1504 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1379 time to evaluate : 8.009 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 0 residues processed: 125 average time/residue: 0.6587 time to fit residues: 168.3640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 583 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 873 optimal weight: 0.9990 chunk 714 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 1051 optimal weight: 7.9990 chunk 1136 optimal weight: 10.0000 chunk 936 optimal weight: 3.9990 chunk 1042 optimal weight: 0.9990 chunk 358 optimal weight: 0.2980 chunk 843 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 118 GLN Ad 125 GLN ** Ae 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 118 GLN Af 125 GLN Ah 118 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 123 GLN Aq 123 GLN Aq 140 GLN As 123 GLN At 118 GLN ** Au 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 123 GLN ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 143 GLN ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 123 GLN ** Bd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 123 GLN Bf 48 HIS Bf 55 GLN Bf 118 GLN ** Bh 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 41 ASN Bh 128 GLN Bi 123 GLN Bp 143 GLN Bq 140 GLN ** Br 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 140 GLN Bw 14 ASN Bw 123 GLN ** Cc 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 123 GLN ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 57 ASN Ce 123 GLN ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 118 GLN ** Cj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 41 ASN Cj 128 GLN Cl 4 HIS ** Cn 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 128 GLN ** Cp 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 92990 Z= 0.195 Angle : 0.561 10.569 124712 Z= 0.294 Chirality : 0.036 0.259 14620 Planarity : 0.003 0.044 15878 Dihedral : 3.886 22.119 12512 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.45 % Favored : 98.54 % Rotamer: Outliers : 1.72 % Allowed : 8.97 % Favored : 89.31 % 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: 2.56 (0.08), residues: 11492 helix: 2.19 (0.05), residues: 9146 sheet: None (None), residues: 0 loop : -0.28 (0.12), residues: 2346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1529 time to evaluate : 7.655 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: 172 outliers final: 78 residues processed: 1614 average time/residue: 0.7789 time to fit residues: 2224.3568 Evaluate side-chains 1424 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1346 time to evaluate : 7.632 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.6388 time to fit residues: 107.3607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 1039 optimal weight: 7.9990 chunk 790 optimal weight: 8.9990 chunk 545 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 501 optimal weight: 5.9990 chunk 706 optimal weight: 5.9990 chunk 1055 optimal weight: 6.9990 chunk 1117 optimal weight: 8.9990 chunk 551 optimal weight: 0.9980 chunk 1000 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 48 HIS Ab 58 GLN Ad 48 HIS ** Ad 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 123 GLN Af 118 GLN Ag 123 GLN Ah 118 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 38 GLN ** An 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 38 GLN Ap 77 GLN ** Ap 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 140 GLN Ar 38 GLN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 38 GLN At 77 GLN Au 140 GLN ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 38 GLN Av 77 GLN Av 143 GLN ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 38 GLN Ax 77 GLN Ax 118 GLN ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 77 GLN ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 77 GLN ** Bc 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 48 HIS Bd 55 GLN Bd 77 GLN Be 123 GLN Bh 4 HIS Bh 48 HIS Bh 58 GLN Bh 128 GLN Bj 48 HIS Bj 57 ASN Bl 48 HIS Bl 55 GLN Bl 57 ASN Bm 123 GLN Bn 48 HIS Bn 55 GLN Bp 48 HIS Bq 140 GLN Br 4 HIS Bv 38 GLN Bv 58 GLN Bv 77 GLN Bw 14 ASN Bx 38 GLN Bx 77 GLN Bz 38 GLN Bz 77 GLN Cb 38 GLN Cb 77 GLN ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 38 GLN Cd 77 GLN Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 38 GLN Cf 77 GLN Cf 118 GLN Cf 143 GLN ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 38 GLN Ch 48 HIS Ch 77 GLN ** Cj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 125 GLN Cl 38 GLN Cl 48 HIS Cl 77 GLN Cn 4 HIS Cn 48 HIS Cn 55 GLN ** Cn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 48 HIS Cp 57 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.170 92990 Z= 0.396 Angle : 0.830 12.109 124712 Z= 0.433 Chirality : 0.046 0.275 14620 Planarity : 0.005 0.063 15878 Dihedral : 4.446 20.408 12512 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.78 % Allowed : 12.13 % Favored : 84.08 % 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: 1.74 (0.07), residues: 11492 helix: 1.59 (0.05), residues: 9112 sheet: None (None), residues: 0 loop : -0.42 (0.12), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1942 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1564 time to evaluate : 7.712 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 378 outliers final: 238 residues processed: 1848 average time/residue: 0.7701 time to fit residues: 2523.0651 Evaluate side-chains 1563 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1325 time to evaluate : 7.637 Switching outliers to nearest non-outliers outliers start: 238 outliers final: 0 residues processed: 238 average time/residue: 0.6340 time to fit residues: 301.4227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 930 optimal weight: 6.9990 chunk 634 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 831 optimal weight: 0.8980 chunk 461 optimal weight: 5.9990 chunk 953 optimal weight: 0.9980 chunk 772 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 570 optimal weight: 0.9990 chunk 1002 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 58 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 111 GLN ** Af 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 123 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 118 GLN Ak 140 GLN ** Am 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 123 GLN ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 125 GLN Bc 58 HIS ** Bd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 55 GLN Bd 125 GLN Bd 128 GLN Be 111 GLN Bf 77 GLN Bh 77 GLN ** Bi 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bl 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 123 GLN ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 4 HIS ** Bp 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 140 GLN Br 55 GLN Bv 58 GLN Bx 118 GLN ** Ca 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 118 GLN Cg 111 GLN ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 77 GLN Cn 55 GLN Cn 77 GLN Cp 4 HIS Cp 77 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 92990 Z= 0.193 Angle : 0.560 10.091 124712 Z= 0.288 Chirality : 0.035 0.272 14620 Planarity : 0.003 0.039 15878 Dihedral : 3.917 19.313 12512 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.33 % Allowed : 14.92 % Favored : 83.75 % 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: 2.92 (0.08), residues: 11492 helix: 2.50 (0.05), residues: 9112 sheet: None (None), residues: 0 loop : -0.36 (0.12), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1438 time to evaluate : 7.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 66 residues processed: 1511 average time/residue: 0.7902 time to fit residues: 2109.2899 Evaluate side-chains 1378 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1312 time to evaluate : 7.983 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.6545 time to fit residues: 93.1906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 375 optimal weight: 0.9990 chunk 1006 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 656 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 1118 optimal weight: 1.9990 chunk 928 optimal weight: 5.9990 chunk 517 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 369 optimal weight: 2.9990 chunk 587 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 58 GLN ** Ad 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 111 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 118 GLN ** Am 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 77 GLN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 143 GLN Au 140 GLN ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 41 ASN ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 128 GLN Bd 55 GLN Be 111 GLN Bj 128 GLN Bn 4 HIS ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 57 ASN Cc 174 ASN ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 58 HIS Ce 140 GLN ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 55 GLN Co 123 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.7244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 92990 Z= 0.189 Angle : 0.542 9.613 124712 Z= 0.278 Chirality : 0.035 0.291 14620 Planarity : 0.003 0.054 15878 Dihedral : 3.735 18.609 12512 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.47 % Allowed : 16.06 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.08), residues: 11492 helix: 2.82 (0.05), residues: 9112 sheet: None (None), residues: 0 loop : -0.35 (0.12), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1402 time to evaluate : 7.641 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 70 residues processed: 1477 average time/residue: 0.8058 time to fit residues: 2112.9250 Evaluate side-chains 1364 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1294 time to evaluate : 7.674 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.6600 time to fit residues: 99.5870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 1078 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 637 optimal weight: 4.9990 chunk 816 optimal weight: 9.9990 chunk 632 optimal weight: 9.9990 chunk 941 optimal weight: 3.9990 chunk 624 optimal weight: 8.9990 chunk 1114 optimal weight: 0.8980 chunk 697 optimal weight: 5.9990 chunk 679 optimal weight: 0.0670 chunk 514 optimal weight: 2.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 58 GLN Ad 77 GLN Af 118 GLN ** Ai 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 118 GLN Al 38 GLN Ap 143 GLN Aq 111 GLN ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 140 GLN ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 58 GLN ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 128 GLN Bd 55 GLN Bm 123 GLN ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 77 GLN Bz 125 GLN Ca 174 ASN ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 57 ASN Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 128 GLN Cl 128 GLN Cn 38 GLN Cn 55 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 92990 Z= 0.223 Angle : 0.572 11.221 124712 Z= 0.289 Chirality : 0.036 0.301 14620 Planarity : 0.003 0.038 15878 Dihedral : 3.687 19.077 12512 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.21 % Allowed : 17.40 % Favored : 81.39 % 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: 3.43 (0.08), residues: 11492 helix: 2.94 (0.05), residues: 9010 sheet: None (None), residues: 0 loop : -0.41 (0.12), residues: 2482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1348 time to evaluate : 10.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 63 residues processed: 1402 average time/residue: 0.7863 time to fit residues: 1962.9308 Evaluate side-chains 1341 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1278 time to evaluate : 7.878 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.6628 time to fit residues: 90.5987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 689 optimal weight: 4.9990 chunk 444 optimal weight: 0.9990 chunk 665 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 708 optimal weight: 0.0010 chunk 759 optimal weight: 8.9990 chunk 550 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 875 optimal weight: 2.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 58 GLN Ab 77 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 55 GLN Ad 118 GLN ** Ad 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 123 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 41 ASN ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 128 GLN Bd 55 GLN Bf 128 GLN Bh 55 GLN ** Bi 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 77 GLN ** Bl 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bz 125 GLN ** Ca 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 125 GLN Cn 55 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.7854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 92990 Z= 0.187 Angle : 0.554 10.452 124712 Z= 0.278 Chirality : 0.035 0.326 14620 Planarity : 0.003 0.049 15878 Dihedral : 3.630 17.580 12512 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.80 % Allowed : 18.08 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.08), residues: 11492 helix: 3.07 (0.05), residues: 9010 sheet: None (None), residues: 0 loop : -0.41 (0.12), residues: 2482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1433 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1353 time to evaluate : 7.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 31 residues processed: 1392 average time/residue: 0.7816 time to fit residues: 1931.3129 Evaluate side-chains 1313 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1282 time to evaluate : 7.659 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6885 time to fit residues: 52.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 1013 optimal weight: 7.9990 chunk 1067 optimal weight: 2.9990 chunk 973 optimal weight: 0.6980 chunk 1038 optimal weight: 4.9990 chunk 624 optimal weight: 6.9990 chunk 452 optimal weight: 8.9990 chunk 815 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 chunk 938 optimal weight: 4.9990 chunk 982 optimal weight: 0.9990 chunk 1034 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 58 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 123 GLN Af 55 GLN ** Af 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 123 GLN Aq 140 GLN Ar 77 GLN ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 128 GLN Bd 55 GLN Bf 128 GLN Bg 123 GLN Bh 55 GLN Bh 58 GLN Bl 77 GLN ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 38 GLN Bv 48 HIS ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 125 GLN Cn 55 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.8122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 92990 Z= 0.212 Angle : 0.588 12.157 124712 Z= 0.292 Chirality : 0.036 0.354 14620 Planarity : 0.003 0.042 15878 Dihedral : 3.621 17.769 12512 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.70 % Allowed : 18.82 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.08), residues: 11492 helix: 3.04 (0.05), residues: 8976 sheet: None (None), residues: 0 loop : -0.45 (0.12), residues: 2516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1348 time to evaluate : 7.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 36 residues processed: 1379 average time/residue: 0.7845 time to fit residues: 1920.7655 Evaluate side-chains 1318 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1282 time to evaluate : 7.696 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.6622 time to fit residues: 56.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 681 optimal weight: 6.9990 chunk 1097 optimal weight: 4.9990 chunk 670 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 763 optimal weight: 0.0060 chunk 1151 optimal weight: 0.9990 chunk 1059 optimal weight: 8.9990 chunk 917 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 708 optimal weight: 10.0000 chunk 562 optimal weight: 0.5980 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 58 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 38 GLN ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 48 HIS ** Am 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 125 GLN Bd 55 GLN Bf 125 GLN Bf 128 GLN Bh 55 GLN Bh 128 GLN ** Bi 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bl 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 77 GLN ** Bl 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Br 38 GLN Bt 48 HIS ** Cc 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 57 ASN Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 20 ASN Cn 55 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.8331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 92990 Z= 0.191 Angle : 0.574 13.730 124712 Z= 0.284 Chirality : 0.036 0.381 14620 Planarity : 0.003 0.040 15878 Dihedral : 3.589 16.904 12512 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.35 % Allowed : 19.17 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.08), residues: 11492 helix: 3.09 (0.05), residues: 9044 sheet: None (None), residues: 0 loop : -0.42 (0.12), residues: 2448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22984 Ramachandran restraints generated. 11492 Oldfield, 0 Emsley, 11492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1352 time to evaluate : 8.094 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 1370 average time/residue: 0.8155 time to fit residues: 1979.1587 Evaluate side-chains 1307 residues out of total 9996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1293 time to evaluate : 7.953 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.8145 time to fit residues: 34.2158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1156 random chunks: chunk 728 optimal weight: 9.9990 chunk 976 optimal weight: 1.9990 chunk 280 optimal weight: 0.0040 chunk 845 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 918 optimal weight: 6.9990 chunk 384 optimal weight: 9.9990 chunk 943 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 169 optimal weight: 0.0970 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 58 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 143 GLN ** Af 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 128 GLN Bd 55 GLN Bh 55 GLN Bh 128 GLN Bl 48 HIS ** Bn 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 58 HIS ** Cf 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 55 GLN Co 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.199188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.180409 restraints weight = 108922.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178510 restraints weight = 116437.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.179279 restraints weight = 87027.259| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.8481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 92990 Z= 0.190 Angle : 0.577 12.714 124712 Z= 0.284 Chirality : 0.036 0.350 14620 Planarity : 0.003 0.040 15878 Dihedral : 3.553 16.595 12512 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.39 % Allowed : 19.54 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.08), residues: 11492 helix: 3.15 (0.05), residues: 8976 sheet: None (None), residues: 0 loop : -0.44 (0.12), residues: 2516 =============================================================================== Job complete usr+sys time: 29267.23 seconds wall clock time: 510 minutes 27.10 seconds (30627.10 seconds total)