Starting phenix.real_space_refine on Mon Jan 20 21:07:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.map" model { file = "/net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opj_17062/01_2025/8opj_17062.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 600 5.16 5 C 41208 2.51 5 N 11256 2.21 5 O 12288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65352 Number of models: 1 Model: "" Number of chains: 48 Chain: "Aa" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ab" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ac" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ad" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ae" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Af" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ag" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ah" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ai" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Aj" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ak" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Al" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Am" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "An" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ao" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ap" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Aq" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ar" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "As" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "At" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Au" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Av" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Aw" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ax" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ay" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Az" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ba" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bb" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bc" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bd" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Be" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bf" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bg" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bh" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bi" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bj" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bk" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bl" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bm" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bn" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bo" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bp" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bq" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Br" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Bs" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bt" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bu" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Bv" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Time building chain proxies: 29.87, per 1000 atoms: 0.46 Number of scatterers: 65352 At special positions: 0 Unit cell: (180.018, 180.018, 180.018, 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 600 16.00 O 12288 8.00 N 11256 7.00 C 41208 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 - 3.00 Amino acid : True - 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: 12.83 Conformation dependent library (CDL) restraints added in 6.3 seconds 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15456 Finding SS restraints... Secondary structure from input PDB file: 480 helices and 48 sheets defined 57.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 Processing helix chain 'Aa' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAa 80 " --> pdb=" O GLNAa 76 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAa 92 " --> pdb=" O SERAa 88 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 122 Processing helix chain 'Aa' and resid 145 through 151 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 Processing helix chain 'Aa' and resid 182 through 187 Processing helix chain 'Aa' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEAb 80 " --> pdb=" O GLNAb 76 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAb 92 " --> pdb=" O SERAb 88 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 122 Processing helix chain 'Ab' and resid 145 through 151 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 176 Processing helix chain 'Ab' and resid 182 through 187 Processing helix chain 'Ab' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 Processing helix chain 'Ac' and resid 66 through 71 Processing helix chain 'Ac' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEAc 80 " --> pdb=" O GLNAc 76 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAc 92 " --> pdb=" O SERAc 88 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 122 Processing helix chain 'Ac' and resid 145 through 151 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 Processing helix chain 'Ac' and resid 182 through 187 Processing helix chain 'Ac' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAd 80 " --> pdb=" O GLNAd 76 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAd 92 " --> pdb=" O SERAd 88 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 122 Processing helix chain 'Ad' and resid 145 through 151 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 176 Processing helix chain 'Ad' and resid 182 through 187 Processing helix chain 'Ad' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 Processing helix chain 'Ae' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 Processing helix chain 'Ae' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAe 99 " --> pdb=" O GLUAe 95 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAe 121 " --> pdb=" O VALAe 117 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 174 Processing helix chain 'Ae' and resid 182 through 187 Processing helix chain 'Ae' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAf 72 " --> pdb=" O GLUAf 68 " (cutoff:3.500A) Processing helix chain 'Af' and resid 76 through 81 Processing helix chain 'Af' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAf 99 " --> pdb=" O GLUAf 95 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAf 121 " --> pdb=" O VALAf 117 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 174 Processing helix chain 'Af' and resid 182 through 187 Processing helix chain 'Af' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAf 218 " --> pdb=" O ARGAf 214 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 Processing helix chain 'Ag' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAg 99 " --> pdb=" O GLUAg 95 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAg 121 " --> pdb=" O VALAg 117 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 174 Processing helix chain 'Ag' and resid 182 through 187 Processing helix chain 'Ag' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAh 72 " --> pdb=" O GLUAh 68 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 76 through 81 Processing helix chain 'Ah' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAh 99 " --> pdb=" O GLUAh 95 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAh 121 " --> pdb=" O VALAh 117 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 174 Processing helix chain 'Ah' and resid 182 through 187 Processing helix chain 'Ah' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAh 218 " --> pdb=" O ARGAh 214 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 Processing helix chain 'Ai' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAi 80 " --> pdb=" O GLNAi 76 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRAi 92 " --> pdb=" O SERAi 88 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 122 Processing helix chain 'Ai' and resid 145 through 151 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 Processing helix chain 'Ai' and resid 182 through 187 Processing helix chain 'Ai' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAj 80 " --> pdb=" O GLNAj 76 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAj 92 " --> pdb=" O SERAj 88 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 122 Processing helix chain 'Aj' and resid 145 through 151 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 176 Processing helix chain 'Aj' and resid 182 through 187 Processing helix chain 'Aj' and resid 193 through 197 removed outlier: 4.113A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 Processing helix chain 'Ak' and resid 66 through 71 Processing helix chain 'Ak' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 76 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAk 92 " --> pdb=" O SERAk 88 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 122 Processing helix chain 'Ak' and resid 145 through 151 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 Processing helix chain 'Ak' and resid 182 through 187 Processing helix chain 'Ak' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAl 80 " --> pdb=" O GLNAl 76 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRAl 92 " --> pdb=" O SERAl 88 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 122 Processing helix chain 'Al' and resid 145 through 151 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 176 Processing helix chain 'Al' and resid 182 through 187 Processing helix chain 'Al' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 Processing helix chain 'Am' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 Processing helix chain 'Am' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAm 99 " --> pdb=" O GLUAm 95 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAm 121 " --> pdb=" O VALAm 117 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 174 Processing helix chain 'Am' and resid 182 through 187 Processing helix chain 'Am' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAn 72 " --> pdb=" O GLUAn 68 " (cutoff:3.500A) Processing helix chain 'An' and resid 76 through 81 Processing helix chain 'An' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUAn 99 " --> pdb=" O GLUAn 95 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAn 121 " --> pdb=" O VALAn 117 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 174 Processing helix chain 'An' and resid 182 through 187 Processing helix chain 'An' and resid 192 through 199 removed outlier: 4.541A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 removed outlier: 4.068A pdb=" N ILEAn 218 " --> pdb=" O ARGAn 214 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 Processing helix chain 'Ao' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAo 99 " --> pdb=" O GLUAo 95 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAo 121 " --> pdb=" O VALAo 117 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 174 Processing helix chain 'Ao' and resid 182 through 187 Processing helix chain 'Ao' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAp 72 " --> pdb=" O GLUAp 68 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 76 through 81 Processing helix chain 'Ap' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUAp 99 " --> pdb=" O GLUAp 95 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAp 121 " --> pdb=" O VALAp 117 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 174 Processing helix chain 'Ap' and resid 182 through 187 Processing helix chain 'Ap' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 removed outlier: 4.068A pdb=" N ILEAp 218 " --> pdb=" O ARGAp 214 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 66 through 71 Processing helix chain 'Aq' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAq 80 " --> pdb=" O GLNAq 76 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.663A pdb=" N THRAq 92 " --> pdb=" O SERAq 88 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 122 Processing helix chain 'Aq' and resid 145 through 151 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 176 Processing helix chain 'Aq' and resid 182 through 187 Processing helix chain 'Aq' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAq 197 " --> pdb=" O SERAq 194 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 221 Processing helix chain 'Ar' and resid 66 through 71 Processing helix chain 'Ar' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAr 80 " --> pdb=" O GLNAr 76 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAr 92 " --> pdb=" O SERAr 88 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 122 Processing helix chain 'Ar' and resid 145 through 151 Processing helix chain 'Ar' and resid 155 through 161 Processing helix chain 'Ar' and resid 163 through 176 Processing helix chain 'Ar' and resid 182 through 187 Processing helix chain 'Ar' and resid 193 through 197 removed outlier: 4.113A pdb=" N ARGAr 197 " --> pdb=" O SERAr 194 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 210 through 221 Processing helix chain 'As' and resid 66 through 71 Processing helix chain 'As' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEAs 80 " --> pdb=" O GLNAs 76 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAs 92 " --> pdb=" O SERAs 88 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 122 Processing helix chain 'As' and resid 145 through 151 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 176 Processing helix chain 'As' and resid 182 through 187 Processing helix chain 'As' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 221 Processing helix chain 'At' and resid 66 through 71 Processing helix chain 'At' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAt 80 " --> pdb=" O GLNAt 76 " (cutoff:3.500A) Processing helix chain 'At' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAt 92 " --> pdb=" O SERAt 88 " (cutoff:3.500A) Processing helix chain 'At' and resid 107 through 122 Processing helix chain 'At' and resid 145 through 151 Processing helix chain 'At' and resid 155 through 161 Processing helix chain 'At' and resid 163 through 176 Processing helix chain 'At' and resid 182 through 187 Processing helix chain 'At' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAt 197 " --> pdb=" O SERAt 194 " (cutoff:3.500A) Processing helix chain 'At' and resid 210 through 221 Processing helix chain 'Au' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAu 72 " --> pdb=" O GLUAu 68 " (cutoff:3.500A) Processing helix chain 'Au' and resid 76 through 81 Processing helix chain 'Au' and resid 86 through 101 removed outlier: 3.608A pdb=" N LEUAu 99 " --> pdb=" O GLUAu 95 " (cutoff:3.500A) Processing helix chain 'Au' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAu 121 " --> pdb=" O VALAu 117 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 174 Processing helix chain 'Au' and resid 182 through 187 Processing helix chain 'Au' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAu 218 " --> pdb=" O ARGAu 214 " (cutoff:3.500A) Processing helix chain 'Av' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAv 72 " --> pdb=" O GLUAv 68 " (cutoff:3.500A) Processing helix chain 'Av' and resid 76 through 81 Processing helix chain 'Av' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUAv 99 " --> pdb=" O GLUAv 95 " (cutoff:3.500A) Processing helix chain 'Av' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAv 121 " --> pdb=" O VALAv 117 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 151 Processing helix chain 'Av' and resid 155 through 161 Processing helix chain 'Av' and resid 163 through 174 Processing helix chain 'Av' and resid 182 through 187 Processing helix chain 'Av' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAv 197 " --> pdb=" O SERAv 194 " (cutoff:3.500A) Processing helix chain 'Av' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAv 218 " --> pdb=" O ARGAv 214 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAw 72 " --> pdb=" O GLUAw 68 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 76 through 81 Processing helix chain 'Aw' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUAw 99 " --> pdb=" O GLUAw 95 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 107 through 122 removed outlier: 3.629A pdb=" N GLUAw 121 " --> pdb=" O VALAw 117 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 174 Processing helix chain 'Aw' and resid 182 through 187 Processing helix chain 'Aw' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAw 218 " --> pdb=" O ARGAw 214 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAx 72 " --> pdb=" O GLUAx 68 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 76 through 81 Processing helix chain 'Ax' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAx 99 " --> pdb=" O GLUAx 95 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAx 121 " --> pdb=" O VALAx 117 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 145 through 151 Processing helix chain 'Ax' and resid 155 through 161 Processing helix chain 'Ax' and resid 163 through 174 Processing helix chain 'Ax' and resid 182 through 187 Processing helix chain 'Ax' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAx 197 " --> pdb=" O SERAx 194 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAx 218 " --> pdb=" O ARGAx 214 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 66 through 71 Processing helix chain 'Ay' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEAy 80 " --> pdb=" O GLNAy 76 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRAy 92 " --> pdb=" O SERAy 88 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 107 through 122 Processing helix chain 'Ay' and resid 145 through 151 Processing helix chain 'Ay' and resid 155 through 161 Processing helix chain 'Ay' and resid 163 through 176 Processing helix chain 'Ay' and resid 182 through 187 Processing helix chain 'Ay' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAy 197 " --> pdb=" O SERAy 194 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 210 through 221 Processing helix chain 'Az' and resid 66 through 71 Processing helix chain 'Az' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAz 80 " --> pdb=" O GLNAz 76 " (cutoff:3.500A) Processing helix chain 'Az' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAz 92 " --> pdb=" O SERAz 88 " (cutoff:3.500A) Processing helix chain 'Az' and resid 107 through 122 Processing helix chain 'Az' and resid 145 through 151 Processing helix chain 'Az' and resid 155 through 161 Processing helix chain 'Az' and resid 163 through 176 Processing helix chain 'Az' and resid 182 through 187 Processing helix chain 'Az' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAz 197 " --> pdb=" O SERAz 194 " (cutoff:3.500A) Processing helix chain 'Az' and resid 210 through 221 Processing helix chain 'Ba' and resid 66 through 71 Processing helix chain 'Ba' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBa 80 " --> pdb=" O GLNBa 76 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBa 92 " --> pdb=" O SERBa 88 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 107 through 122 Processing helix chain 'Ba' and resid 145 through 151 Processing helix chain 'Ba' and resid 155 through 161 Processing helix chain 'Ba' and resid 163 through 176 Processing helix chain 'Ba' and resid 182 through 187 Processing helix chain 'Ba' and resid 193 through 197 removed outlier: 4.113A pdb=" N ARGBa 197 " --> pdb=" O SERBa 194 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 210 through 221 Processing helix chain 'Bb' and resid 66 through 71 Processing helix chain 'Bb' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBb 80 " --> pdb=" O GLNBb 76 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBb 92 " --> pdb=" O SERBb 88 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 107 through 122 Processing helix chain 'Bb' and resid 145 through 151 Processing helix chain 'Bb' and resid 155 through 161 Processing helix chain 'Bb' and resid 163 through 176 Processing helix chain 'Bb' and resid 182 through 187 Processing helix chain 'Bb' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGBb 197 " --> pdb=" O SERBb 194 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 210 through 221 Processing helix chain 'Bc' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBc 72 " --> pdb=" O GLUBc 68 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 76 through 81 Processing helix chain 'Bc' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBc 99 " --> pdb=" O GLUBc 95 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBc 121 " --> pdb=" O VALBc 117 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 145 through 151 Processing helix chain 'Bc' and resid 155 through 161 Processing helix chain 'Bc' and resid 163 through 174 Processing helix chain 'Bc' and resid 182 through 187 Processing helix chain 'Bc' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGBc 197 " --> pdb=" O SERBc 194 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBc 218 " --> pdb=" O ARGBc 214 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBd 72 " --> pdb=" O GLUBd 68 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 76 through 81 Processing helix chain 'Bd' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUBd 99 " --> pdb=" O GLUBd 95 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBd 121 " --> pdb=" O VALBd 117 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 145 through 151 Processing helix chain 'Bd' and resid 155 through 161 Processing helix chain 'Bd' and resid 163 through 174 Processing helix chain 'Bd' and resid 182 through 187 Processing helix chain 'Bd' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGBd 197 " --> pdb=" O SERBd 194 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBd 218 " --> pdb=" O ARGBd 214 " (cutoff:3.500A) Processing helix chain 'Be' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBe 72 " --> pdb=" O GLUBe 68 " (cutoff:3.500A) Processing helix chain 'Be' and resid 76 through 81 Processing helix chain 'Be' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUBe 99 " --> pdb=" O GLUBe 95 " (cutoff:3.500A) Processing helix chain 'Be' and resid 107 through 122 removed outlier: 3.629A pdb=" N GLUBe 121 " --> pdb=" O VALBe 117 " (cutoff:3.500A) Processing helix chain 'Be' and resid 145 through 151 Processing helix chain 'Be' and resid 155 through 161 Processing helix chain 'Be' and resid 163 through 174 Processing helix chain 'Be' and resid 182 through 187 Processing helix chain 'Be' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGBe 197 " --> pdb=" O SERBe 194 " (cutoff:3.500A) Processing helix chain 'Be' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBe 218 " --> pdb=" O ARGBe 214 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBf 72 " --> pdb=" O GLUBf 68 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 76 through 81 Processing helix chain 'Bf' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBf 99 " --> pdb=" O GLUBf 95 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBf 121 " --> pdb=" O VALBf 117 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 145 through 151 Processing helix chain 'Bf' and resid 155 through 161 Processing helix chain 'Bf' and resid 163 through 174 Processing helix chain 'Bf' and resid 182 through 187 Processing helix chain 'Bf' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGBf 197 " --> pdb=" O SERBf 194 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEBf 218 " --> pdb=" O ARGBf 214 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 66 through 71 Processing helix chain 'Bg' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBg 80 " --> pdb=" O GLNBg 76 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBg 92 " --> pdb=" O SERBg 88 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 107 through 122 Processing helix chain 'Bg' and resid 145 through 151 Processing helix chain 'Bg' and resid 155 through 161 Processing helix chain 'Bg' and resid 163 through 176 Processing helix chain 'Bg' and resid 182 through 187 Processing helix chain 'Bg' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGBg 197 " --> pdb=" O SERBg 194 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 210 through 221 Processing helix chain 'Bh' and resid 66 through 71 Processing helix chain 'Bh' and resid 76 through 81 removed outlier: 3.790A pdb=" N ILEBh 80 " --> pdb=" O GLNBh 76 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRBh 92 " --> pdb=" O SERBh 88 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 107 through 122 Processing helix chain 'Bh' and resid 145 through 151 Processing helix chain 'Bh' and resid 155 through 161 Processing helix chain 'Bh' and resid 163 through 176 Processing helix chain 'Bh' and resid 182 through 187 Processing helix chain 'Bh' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGBh 197 " --> pdb=" O SERBh 194 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 210 through 221 Processing helix chain 'Bi' and resid 66 through 71 Processing helix chain 'Bi' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBi 80 " --> pdb=" O GLNBi 76 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRBi 92 " --> pdb=" O SERBi 88 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 107 through 122 Processing helix chain 'Bi' and resid 145 through 151 Processing helix chain 'Bi' and resid 155 through 161 Processing helix chain 'Bi' and resid 163 through 176 Processing helix chain 'Bi' and resid 182 through 187 Processing helix chain 'Bi' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGBi 197 " --> pdb=" O SERBi 194 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 210 through 221 Processing helix chain 'Bj' and resid 66 through 71 Processing helix chain 'Bj' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBj 80 " --> pdb=" O GLNBj 76 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBj 92 " --> pdb=" O SERBj 88 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 107 through 122 Processing helix chain 'Bj' and resid 145 through 151 Processing helix chain 'Bj' and resid 155 through 161 Processing helix chain 'Bj' and resid 163 through 176 Processing helix chain 'Bj' and resid 182 through 187 Processing helix chain 'Bj' and resid 193 through 197 removed outlier: 4.113A pdb=" N ARGBj 197 " --> pdb=" O SERBj 194 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 210 through 221 Processing helix chain 'Bk' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBk 72 " --> pdb=" O GLUBk 68 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 76 through 81 Processing helix chain 'Bk' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBk 99 " --> pdb=" O GLUBk 95 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBk 121 " --> pdb=" O VALBk 117 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 151 Processing helix chain 'Bk' and resid 155 through 161 Processing helix chain 'Bk' and resid 163 through 174 Processing helix chain 'Bk' and resid 182 through 187 Processing helix chain 'Bk' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGBk 197 " --> pdb=" O SERBk 194 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEBk 218 " --> pdb=" O ARGBk 214 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBl 72 " --> pdb=" O GLUBl 68 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 76 through 81 Processing helix chain 'Bl' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUBl 99 " --> pdb=" O GLUBl 95 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUBl 121 " --> pdb=" O VALBl 117 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 145 through 151 Processing helix chain 'Bl' and resid 155 through 161 Processing helix chain 'Bl' and resid 163 through 174 Processing helix chain 'Bl' and resid 182 through 187 Processing helix chain 'Bl' and resid 192 through 199 removed outlier: 4.541A pdb=" N ARGBl 197 " --> pdb=" O SERBl 194 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBl 218 " --> pdb=" O ARGBl 214 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBm 72 " --> pdb=" O GLUBm 68 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 76 through 81 Processing helix chain 'Bm' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUBm 99 " --> pdb=" O GLUBm 95 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBm 121 " --> pdb=" O VALBm 117 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 151 Processing helix chain 'Bm' and resid 155 through 161 Processing helix chain 'Bm' and resid 163 through 174 Processing helix chain 'Bm' and resid 182 through 187 Processing helix chain 'Bm' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGBm 197 " --> pdb=" O SERBm 194 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBm 218 " --> pdb=" O ARGBm 214 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBn 72 " --> pdb=" O GLUBn 68 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 76 through 81 Processing helix chain 'Bn' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBn 99 " --> pdb=" O GLUBn 95 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBn 121 " --> pdb=" O VALBn 117 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 145 through 151 Processing helix chain 'Bn' and resid 155 through 161 Processing helix chain 'Bn' and resid 163 through 174 Processing helix chain 'Bn' and resid 182 through 187 Processing helix chain 'Bn' and resid 192 through 199 removed outlier: 4.538A pdb=" N ARGBn 197 " --> pdb=" O SERBn 194 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBn 218 " --> pdb=" O ARGBn 214 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 66 through 71 Processing helix chain 'Bo' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEBo 80 " --> pdb=" O GLNBo 76 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBo 92 " --> pdb=" O SERBo 88 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 107 through 122 Processing helix chain 'Bo' and resid 145 through 151 Processing helix chain 'Bo' and resid 155 through 161 Processing helix chain 'Bo' and resid 163 through 176 Processing helix chain 'Bo' and resid 182 through 187 Processing helix chain 'Bo' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGBo 197 " --> pdb=" O SERBo 194 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 210 through 221 Processing helix chain 'Bp' and resid 66 through 71 Processing helix chain 'Bp' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEBp 80 " --> pdb=" O GLNBp 76 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBp 92 " --> pdb=" O SERBp 88 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 107 through 122 Processing helix chain 'Bp' and resid 145 through 151 Processing helix chain 'Bp' and resid 155 through 161 Processing helix chain 'Bp' and resid 163 through 176 Processing helix chain 'Bp' and resid 182 through 187 Processing helix chain 'Bp' and resid 193 through 197 removed outlier: 4.113A pdb=" N ARGBp 197 " --> pdb=" O SERBp 194 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 210 through 221 Processing helix chain 'Bq' and resid 66 through 71 Processing helix chain 'Bq' and resid 76 through 81 removed outlier: 3.788A pdb=" N ILEBq 80 " --> pdb=" O GLNBq 76 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRBq 92 " --> pdb=" O SERBq 88 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 107 through 122 Processing helix chain 'Bq' and resid 145 through 151 Processing helix chain 'Bq' and resid 155 through 161 Processing helix chain 'Bq' and resid 163 through 176 Processing helix chain 'Bq' and resid 182 through 187 Processing helix chain 'Bq' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGBq 197 " --> pdb=" O SERBq 194 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 210 through 221 Processing helix chain 'Br' and resid 66 through 71 Processing helix chain 'Br' and resid 76 through 81 removed outlier: 3.790A pdb=" N ILEBr 80 " --> pdb=" O GLNBr 76 " (cutoff:3.500A) Processing helix chain 'Br' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRBr 92 " --> pdb=" O SERBr 88 " (cutoff:3.500A) Processing helix chain 'Br' and resid 107 through 122 Processing helix chain 'Br' and resid 145 through 151 Processing helix chain 'Br' and resid 155 through 161 Processing helix chain 'Br' and resid 163 through 176 Processing helix chain 'Br' and resid 182 through 187 Processing helix chain 'Br' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGBr 197 " --> pdb=" O SERBr 194 " (cutoff:3.500A) Processing helix chain 'Br' and resid 210 through 221 Processing helix chain 'Bs' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBs 72 " --> pdb=" O GLUBs 68 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 76 through 81 Processing helix chain 'Bs' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBs 99 " --> pdb=" O GLUBs 95 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBs 121 " --> pdb=" O VALBs 117 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 145 through 151 Processing helix chain 'Bs' and resid 155 through 161 Processing helix chain 'Bs' and resid 163 through 174 Processing helix chain 'Bs' and resid 182 through 187 Processing helix chain 'Bs' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGBs 197 " --> pdb=" O SERBs 194 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEBs 218 " --> pdb=" O ARGBs 214 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBt 72 " --> pdb=" O GLUBt 68 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 76 through 81 Processing helix chain 'Bt' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUBt 99 " --> pdb=" O GLUBt 95 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUBt 121 " --> pdb=" O VALBt 117 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 145 through 151 Processing helix chain 'Bt' and resid 155 through 161 Processing helix chain 'Bt' and resid 163 through 174 Processing helix chain 'Bt' and resid 182 through 187 Processing helix chain 'Bt' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGBt 197 " --> pdb=" O SERBt 194 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEBt 218 " --> pdb=" O ARGBt 214 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUBu 72 " --> pdb=" O GLUBu 68 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 76 through 81 Processing helix chain 'Bu' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUBu 99 " --> pdb=" O GLUBu 95 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUBu 121 " --> pdb=" O VALBu 117 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 145 through 151 Processing helix chain 'Bu' and resid 155 through 161 Processing helix chain 'Bu' and resid 163 through 174 Processing helix chain 'Bu' and resid 182 through 187 Processing helix chain 'Bu' and resid 192 through 199 removed outlier: 4.541A pdb=" N ARGBu 197 " --> pdb=" O SERBu 194 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 210 through 221 removed outlier: 4.068A pdb=" N ILEBu 218 " --> pdb=" O ARGBu 214 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUBv 72 " --> pdb=" O GLUBv 68 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 76 through 81 Processing helix chain 'Bv' and resid 86 through 101 removed outlier: 3.608A pdb=" N LEUBv 99 " --> pdb=" O GLUBv 95 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUBv 121 " --> pdb=" O VALBv 117 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 145 through 151 Processing helix chain 'Bv' and resid 155 through 161 Processing helix chain 'Bv' and resid 163 through 174 Processing helix chain 'Bv' and resid 182 through 187 Processing helix chain 'Bv' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGBv 197 " --> pdb=" O SERBv 194 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEBv 218 " --> pdb=" O ARGBv 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 134 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 134 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 134 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 134 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAe 139 " --> pdb=" O ASPAe 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 136 removed outlier: 3.821A pdb=" N GLUAf 139 " --> pdb=" O ASPAf 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAg 139 " --> pdb=" O ASPAg 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAh 139 " --> pdb=" O ASPAh 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 134 Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 134 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 134 Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 134 Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAm 139 " --> pdb=" O ASPAm 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAn 139 " --> pdb=" O ASPAn 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAo 139 " --> pdb=" O ASPAo 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAp 139 " --> pdb=" O ASPAp 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Aq' and resid 131 through 134 Processing sheet with id=AB9, first strand: chain 'Ar' and resid 131 through 134 Processing sheet with id=AC1, first strand: chain 'As' and resid 131 through 134 Processing sheet with id=AC2, first strand: chain 'At' and resid 131 through 134 Processing sheet with id=AC3, first strand: chain 'Au' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAu 139 " --> pdb=" O ASPAu 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Av' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAv 139 " --> pdb=" O ASPAv 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Aw' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAw 139 " --> pdb=" O ASPAw 136 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Ax' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAx 139 " --> pdb=" O ASPAx 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Ay' and resid 131 through 134 Processing sheet with id=AC8, first strand: chain 'Az' and resid 131 through 134 Processing sheet with id=AC9, first strand: chain 'Ba' and resid 131 through 134 Processing sheet with id=AD1, first strand: chain 'Bb' and resid 131 through 134 Processing sheet with id=AD2, first strand: chain 'Bc' and resid 131 through 136 removed outlier: 3.821A pdb=" N GLUBc 139 " --> pdb=" O ASPBc 136 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Bd' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUBd 139 " --> pdb=" O ASPBd 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Be' and resid 131 through 136 removed outlier: 3.821A pdb=" N GLUBe 139 " --> pdb=" O ASPBe 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Bf' and resid 131 through 136 removed outlier: 3.824A pdb=" N GLUBf 139 " --> pdb=" O ASPBf 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Bg' and resid 131 through 134 Processing sheet with id=AD7, first strand: chain 'Bh' and resid 131 through 134 Processing sheet with id=AD8, first strand: chain 'Bi' and resid 131 through 134 Processing sheet with id=AD9, first strand: chain 'Bj' and resid 131 through 134 Processing sheet with id=AE1, first strand: chain 'Bk' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUBk 139 " --> pdb=" O ASPBk 136 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Bl' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUBl 139 " --> pdb=" O ASPBl 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Bm' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUBm 139 " --> pdb=" O ASPBm 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Bn' and resid 131 through 136 removed outlier: 3.824A pdb=" N GLUBn 139 " --> pdb=" O ASPBn 136 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Bo' and resid 131 through 134 Processing sheet with id=AE6, first strand: chain 'Bp' and resid 131 through 134 Processing sheet with id=AE7, first strand: chain 'Bq' and resid 131 through 134 Processing sheet with id=AE8, first strand: chain 'Br' and resid 131 through 134 Processing sheet with id=AE9, first strand: chain 'Bs' and resid 131 through 136 removed outlier: 3.821A pdb=" N GLUBs 139 " --> pdb=" O ASPBs 136 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Bt' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUBt 139 " --> pdb=" O ASPBt 136 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Bu' and resid 131 through 136 removed outlier: 3.821A pdb=" N GLUBu 139 " --> pdb=" O ASPBu 136 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Bv' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUBv 139 " --> pdb=" O ASPBv 136 " (cutoff:3.500A) 2784 hydrogen bonds defined for protein. 7920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.45 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13313 1.33 - 1.45: 15941 1.45 - 1.57: 36482 1.57 - 1.69: 0 1.69 - 1.81: 1104 Bond restraints: 66840 Sorted by residual: bond pdb=" CA LYSAv 58 " pdb=" C LYSAv 58 " ideal model delta sigma weight residual 1.521 1.457 0.064 1.28e-02 6.10e+03 2.47e+01 bond pdb=" CA LYSBn 58 " pdb=" C LYSBn 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.44e+01 bond pdb=" CA LYSBv 58 " pdb=" C LYSBv 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.44e+01 bond pdb=" CA LYSBl 58 " pdb=" C LYSBl 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.44e+01 bond pdb=" CA LYSAo 58 " pdb=" C LYSAo 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.44e+01 ... (remaining 66835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 86903 1.83 - 3.65: 2918 3.65 - 5.48: 522 5.48 - 7.30: 233 7.30 - 9.13: 72 Bond angle restraints: 90648 Sorted by residual: angle pdb=" N ASNAn 175 " pdb=" CA ASNAn 175 " pdb=" C ASNAn 175 " ideal model delta sigma weight residual 113.41 104.86 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N ASNBu 175 " pdb=" CA ASNBu 175 " pdb=" C ASNBu 175 " ideal model delta sigma weight residual 113.41 104.86 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N ASNBe 175 " pdb=" CA ASNBe 175 " pdb=" C ASNBe 175 " ideal model delta sigma weight residual 113.41 104.86 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N ASNBl 175 " pdb=" CA ASNBl 175 " pdb=" C ASNBl 175 " ideal model delta sigma weight residual 113.41 104.86 8.55 1.22e+00 6.72e-01 4.91e+01 angle pdb=" N ASNAw 175 " pdb=" CA ASNAw 175 " pdb=" C ASNAw 175 " ideal model delta sigma weight residual 113.41 104.90 8.51 1.22e+00 6.72e-01 4.87e+01 ... (remaining 90643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 35423 17.30 - 34.61: 3577 34.61 - 51.91: 1515 51.91 - 69.22: 213 69.22 - 86.52: 96 Dihedral angle restraints: 40824 sinusoidal: 16872 harmonic: 23952 Sorted by residual: dihedral pdb=" C ARGAo 191 " pdb=" N ARGAo 191 " pdb=" CA ARGAo 191 " pdb=" CB ARGAo 191 " ideal model delta harmonic sigma weight residual -122.60 -133.56 10.96 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" C ARGBn 191 " pdb=" N ARGBn 191 " pdb=" CA ARGBn 191 " pdb=" CB ARGBn 191 " ideal model delta harmonic sigma weight residual -122.60 -133.54 10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C ARGAu 191 " pdb=" N ARGAu 191 " pdb=" CA ARGAu 191 " pdb=" CB ARGAu 191 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 40821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 9049 0.086 - 0.172: 623 0.172 - 0.258: 48 0.258 - 0.343: 0 0.343 - 0.429: 24 Chirality restraints: 9744 Sorted by residual: chirality pdb=" CA ARGAo 191 " pdb=" N ARGAo 191 " pdb=" C ARGAo 191 " pdb=" CB ARGAo 191 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA ARGBn 191 " pdb=" N ARGBn 191 " pdb=" C ARGBn 191 " pdb=" CB ARGBn 191 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CA ARGAu 191 " pdb=" N ARGAu 191 " pdb=" C ARGAu 191 " pdb=" CB ARGAu 191 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 9741 not shown) Planarity restraints: 11856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARGAw 174 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ARGAw 174 " 0.039 2.00e-02 2.50e+03 pdb=" O ARGAw 174 " -0.015 2.00e-02 2.50e+03 pdb=" N ASNAw 175 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGBe 174 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARGBe 174 " -0.039 2.00e-02 2.50e+03 pdb=" O ARGBe 174 " 0.015 2.00e-02 2.50e+03 pdb=" N ASNBe 175 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGAh 174 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARGAh 174 " -0.039 2.00e-02 2.50e+03 pdb=" O ARGAh 174 " 0.015 2.00e-02 2.50e+03 pdb=" N ASNAh 175 " 0.013 2.00e-02 2.50e+03 ... (remaining 11853 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 23707 2.85 - 3.37: 64515 3.37 - 3.88: 110546 3.88 - 4.39: 136187 4.39 - 4.90: 216417 Nonbonded interactions: 551372 Sorted by model distance: nonbonded pdb=" OH TYRBi 101 " pdb=" O PROBi 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRBh 101 " pdb=" O PROBh 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRAs 101 " pdb=" O PROAs 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRAy 101 " pdb=" O PROAy 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRAc 101 " pdb=" O PROAc 144 " model vdw 2.342 3.040 ... (remaining 551367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.44 Found NCS groups: ncs_group { reference = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bc' selection = chain 'Bl' selection = chain 'Bm' selection = chain 'Bn' selection = chain 'Bk' selection = chain 'Bt' selection = chain 'Bu' selection = chain 'Bv' selection = chain 'Bs' selection = chain 'Ae' selection = chain 'Ag' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Am' selection = chain 'Ao' selection = chain 'An' selection = chain 'Ap' selection = chain 'Au' selection = chain 'Aw' selection = chain 'Av' selection = chain 'Ax' } ncs_group { reference = chain 'Bg' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bo' selection = chain 'Bh' selection = chain 'Bi' selection = chain 'Bj' selection = chain 'Bp' selection = chain 'Bq' selection = chain 'Br' selection = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' selection = chain 'Ad' selection = chain 'Ai' selection = chain 'Ak' selection = chain 'Aj' selection = chain 'Al' selection = chain 'Aq' selection = chain 'As' selection = chain 'Ar' selection = chain 'At' selection = chain 'Ay' selection = chain 'Az' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.100 Extract box with map and model: 2.140 Check model and map are aligned: 0.380 Set scattering table: 0.450 Process input model: 115.500 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: