Starting phenix.real_space_refine on Tue Dec 31 04:14:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opj_17062/12_2024/8opj_17062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opj_17062/12_2024/8opj_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_17062/12_2024/8opj_17062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opj_17062/12_2024/8opj_17062.map" model { file = "/net/cci-nas-00/data/ceres_data/8opj_17062/12_2024/8opj_17062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opj_17062/12_2024/8opj_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 26.39, per 1000 atoms: 0.40 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: 12.42 Conformation dependent library (CDL) restraints added in 6.7 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: 5.09 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: 22.00 Time building geometry restraints manager: 14.68 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'Aa' and resid 55 through 222) selection = (chain 'Ab' and resid 55 through 222) selection = (chain 'Ac' and resid 55 through 222) selection = (chain 'Ad' and resid 55 through 222) selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = (chain 'Ai' and resid 55 through 222) selection = (chain 'Aj' and resid 55 through 222) selection = (chain 'Ak' and resid 55 through 222) selection = (chain 'Al' and resid 55 through 222) selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = (chain 'Aq' and resid 55 through 222) selection = (chain 'Ar' and resid 55 through 222) selection = (chain 'As' and resid 55 through 222) selection = (chain 'At' and resid 55 through 222) selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = (chain 'Ay' and resid 55 through 222) selection = (chain 'Az' and resid 55 through 222) selection = (chain 'Ba' and resid 55 through 222) selection = (chain 'Bb' and resid 55 through 222) selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = (chain 'Bg' and resid 55 through 222) selection = (chain 'Bh' and resid 55 through 222) selection = (chain 'Bi' and resid 55 through 222) selection = (chain 'Bj' and resid 55 through 222) selection = chain 'Bk' selection = chain 'Bl' selection = chain 'Bm' selection = chain 'Bn' selection = (chain 'Bo' and resid 55 through 222) selection = (chain 'Bp' and resid 55 through 222) selection = (chain 'Bq' and resid 55 through 222) selection = (chain 'Br' and resid 55 through 222) selection = chain 'Bs' selection = chain 'Bt' selection = chain 'Bu' selection = chain 'Bv' } 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: 12.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.920 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 109.140 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.007 0.066 66840 Z= 0.440 Angle : 0.844 9.131 90648 Z= 0.530 Chirality : 0.050 0.429 9744 Planarity : 0.006 0.047 11856 Dihedral : 16.833 86.524 25368 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.72 % Allowed : 19.37 % Favored : 79.90 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 10.00 % 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: -1.75 (0.10), residues: 8016 helix: -1.42 (0.08), residues: 3984 sheet: -0.44 (0.20), residues: 528 loop : -0.73 (0.12), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPBf 118 HIS 0.005 0.001 HISBp 69 PHE 0.021 0.002 PHEAd 202 TYR 0.020 0.002 TYRAn 73 ARG 0.006 0.001 ARGAn 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1863 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 1812 time to evaluate : 5.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 170 TYR cc_start: 0.8154 (t80) cc_final: 0.7881 (t80) REVERT: Ad 166 VAL cc_start: 0.8187 (t) cc_final: 0.7933 (m) REVERT: Ae 81 SER cc_start: 0.8785 (p) cc_final: 0.8481 (m) REVERT: Af 183 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6439 (ttp-170) REVERT: Ah 183 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6431 (ttp-170) REVERT: Ai 166 VAL cc_start: 0.8428 (t) cc_final: 0.8176 (m) REVERT: Ai 170 TYR cc_start: 0.8161 (t80) cc_final: 0.7552 (t80) REVERT: Ai 186 LEU cc_start: 0.8837 (mt) cc_final: 0.8629 (mp) REVERT: Aj 166 VAL cc_start: 0.8299 (t) cc_final: 0.8081 (m) REVERT: Ak 166 VAL cc_start: 0.8393 (t) cc_final: 0.8095 (m) REVERT: Ak 170 TYR cc_start: 0.8100 (t80) cc_final: 0.7755 (t80) REVERT: Al 56 MET cc_start: 0.8182 (mmm) cc_final: 0.7882 (mmm) REVERT: Al 209 THR cc_start: 0.8565 (m) cc_final: 0.7752 (m) REVERT: Al 214 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7368 (mtm-85) REVERT: Ao 204 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6673 (mt-10) REVERT: Ap 121 GLU cc_start: 0.6647 (mt-10) cc_final: 0.5604 (mt-10) REVERT: Ap 183 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.6787 (ttp-110) REVERT: As 170 TYR cc_start: 0.8054 (t80) cc_final: 0.7809 (t80) REVERT: At 186 LEU cc_start: 0.8773 (mt) cc_final: 0.8550 (mt) REVERT: Au 108 MET cc_start: 0.7473 (tpt) cc_final: 0.7256 (tpt) REVERT: Aw 181 MET cc_start: 0.7831 (tpt) cc_final: 0.7588 (tpp) REVERT: Ax 181 MET cc_start: 0.7816 (tpt) cc_final: 0.7463 (tpt) REVERT: Ax 204 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6857 (mt-10) REVERT: Ay 170 TYR cc_start: 0.8168 (t80) cc_final: 0.7808 (t80) REVERT: Az 56 MET cc_start: 0.8189 (mmm) cc_final: 0.7950 (mmm) REVERT: Bd 183 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.6544 (ttp-170) REVERT: Bg 170 TYR cc_start: 0.8112 (t80) cc_final: 0.7906 (t80) REVERT: Bi 186 LEU cc_start: 0.8803 (mt) cc_final: 0.8561 (mt) REVERT: Bj 166 VAL cc_start: 0.8285 (t) cc_final: 0.8054 (m) REVERT: Bj 170 TYR cc_start: 0.8081 (t80) cc_final: 0.7862 (t80) REVERT: Bm 181 MET cc_start: 0.7833 (tpt) cc_final: 0.7559 (tpt) REVERT: Bo 168 GLU cc_start: 0.6492 (pt0) cc_final: 0.6206 (pt0) REVERT: Bo 197 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6893 (ptm-80) REVERT: Bo 214 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7446 (mtm-85) REVERT: Bq 56 MET cc_start: 0.8168 (mmm) cc_final: 0.7864 (mmm) REVERT: Bq 166 VAL cc_start: 0.8354 (t) cc_final: 0.8109 (m) REVERT: Bs 181 MET cc_start: 0.7920 (tpt) cc_final: 0.7634 (tpt) outliers start: 51 outliers final: 5 residues processed: 1860 average time/residue: 1.7461 time to fit residues: 4006.6498 Evaluate side-chains 1788 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1783 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 159 ILE Chi-restraints excluded: chain Al residue 98 GLN Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain Bg residue 98 GLN Chi-restraints excluded: chain Bj residue 69 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 0.4980 chunk 600 optimal weight: 0.1980 chunk 333 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 404 optimal weight: 0.6980 chunk 320 optimal weight: 1.9990 chunk 620 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 0.5980 chunk 462 optimal weight: 0.1980 chunk 719 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 98 GLN Ab 98 GLN ** Ac 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 76 GLN Af 76 GLN Af 98 GLN Ag 98 GLN ** Ag 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 98 GLN ** Ah 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 98 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 98 GLN Ap 98 GLN Aq 175 ASN As 98 GLN As 175 ASN Au 98 GLN ** Au 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 GLN ** Ba 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 98 GLN Be 98 GLN Bf 98 GLN ** Bh 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 175 ASN ** Bi 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 69 HIS Bj 98 GLN Bk 98 GLN Bl 98 GLN Bm 98 GLN ** Bo 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 98 GLN ** Br 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN Bt 98 GLN ** Bt 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 98 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 66840 Z= 0.211 Angle : 0.623 8.465 90648 Z= 0.320 Chirality : 0.041 0.141 9744 Planarity : 0.006 0.058 11856 Dihedral : 4.607 47.611 9036 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.53 % Allowed : 22.97 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.33 (0.10), residues: 8016 helix: -1.06 (0.08), residues: 4296 sheet: -0.38 (0.18), residues: 576 loop : -0.42 (0.13), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAo 132 HIS 0.006 0.001 HISBj 69 PHE 0.016 0.002 PHEAz 200 TYR 0.030 0.002 TYRBm 73 ARG 0.008 0.001 ARGAp 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2293 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 2044 time to evaluate : 5.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.7736 (tpp) cc_final: 0.7503 (mmm) REVERT: Aa 214 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7043 (ttm-80) REVERT: Ab 98 GLN cc_start: 0.7371 (mm110) cc_final: 0.6849 (tp40) REVERT: Ab 214 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7048 (mtm-85) REVERT: Ac 55 ARG cc_start: 0.8559 (mtp180) cc_final: 0.8300 (mtp180) REVERT: Ac 156 LEU cc_start: 0.8742 (tp) cc_final: 0.8520 (tm) REVERT: Ad 77 GLN cc_start: 0.7451 (mt0) cc_final: 0.6868 (mt0) REVERT: Ad 156 LEU cc_start: 0.8773 (tp) cc_final: 0.8562 (tm) REVERT: Ae 121 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6550 (mt-10) REVERT: Ag 76 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6954 (mt0) REVERT: Ag 108 MET cc_start: 0.7122 (tpp) cc_final: 0.6795 (tpp) REVERT: Ah 108 MET cc_start: 0.7089 (tpp) cc_final: 0.6807 (tpp) REVERT: Ah 172 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6314 (tm-30) REVERT: Ai 214 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.7182 (mtm-85) REVERT: Aj 55 ARG cc_start: 0.8569 (mtp180) cc_final: 0.8331 (mtp180) REVERT: Aj 168 GLU cc_start: 0.6461 (pt0) cc_final: 0.6230 (pt0) REVERT: Ak 156 LEU cc_start: 0.8762 (tp) cc_final: 0.8523 (tm) REVERT: Al 209 THR cc_start: 0.8514 (m) cc_final: 0.7544 (m) REVERT: Al 214 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7192 (mtm-85) REVERT: An 197 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7841 (ttm-80) REVERT: Ao 84 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (ptm-80) REVERT: Ap 97 VAL cc_start: 0.8713 (p) cc_final: 0.8498 (t) REVERT: Ap 108 MET cc_start: 0.7047 (tpp) cc_final: 0.6834 (tpp) REVERT: Ap 172 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6564 (tm-30) REVERT: Ap 197 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7317 (mtp180) REVERT: Aq 55 ARG cc_start: 0.8528 (mtp180) cc_final: 0.8182 (mtp180) REVERT: Aq 168 GLU cc_start: 0.6626 (pt0) cc_final: 0.6032 (pt0) REVERT: Aq 197 ARG cc_start: 0.7126 (ptm160) cc_final: 0.6507 (ptm160) REVERT: Ar 55 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8222 (mtp180) REVERT: Ar 156 LEU cc_start: 0.8697 (tp) cc_final: 0.8491 (tm) REVERT: As 160 MET cc_start: 0.7691 (tpp) cc_final: 0.7484 (mmm) REVERT: At 55 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8239 (mmm160) REVERT: At 183 ARG cc_start: 0.7458 (mtp-110) cc_final: 0.7205 (mtp-110) REVERT: Au 73 TYR cc_start: 0.7744 (t80) cc_final: 0.7354 (t80) REVERT: Au 108 MET cc_start: 0.7222 (tpt) cc_final: 0.6941 (tpt) REVERT: Au 197 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7679 (ttm-80) REVERT: Ay 55 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8316 (mmm160) REVERT: Az 55 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8212 (mmm160) REVERT: Az 77 GLN cc_start: 0.7433 (mt0) cc_final: 0.7120 (mt0) REVERT: Az 168 GLU cc_start: 0.6455 (pt0) cc_final: 0.5678 (pt0) REVERT: Az 197 ARG cc_start: 0.7242 (ptm160) cc_final: 0.6460 (ptm-80) REVERT: Bb 55 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8321 (mtp180) REVERT: Bc 73 TYR cc_start: 0.7656 (t80) cc_final: 0.7394 (t80) REVERT: Bc 108 MET cc_start: 0.6980 (tpp) cc_final: 0.6758 (tpp) REVERT: Bd 97 VAL cc_start: 0.8652 (p) cc_final: 0.8437 (t) REVERT: Bd 172 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6783 (tm-30) REVERT: Bd 173 MET cc_start: 0.7407 (tpp) cc_final: 0.7146 (tpp) REVERT: Be 76 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: Bf 73 TYR cc_start: 0.7728 (t80) cc_final: 0.7379 (t80) REVERT: Bf 108 MET cc_start: 0.7051 (tpp) cc_final: 0.6831 (tpp) REVERT: Bf 172 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6489 (tm-30) REVERT: Bi 55 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8308 (mmm160) REVERT: Bi 77 GLN cc_start: 0.7353 (mt0) cc_final: 0.6968 (mt0) REVERT: Bi 98 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6445 (tp40) REVERT: Bk 108 MET cc_start: 0.7036 (tpp) cc_final: 0.6819 (tpp) REVERT: Bk 160 MET cc_start: 0.7920 (tpp) cc_final: 0.7499 (mmm) REVERT: Bk 172 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6457 (tm-30) REVERT: Bk 173 MET cc_start: 0.7272 (tpp) cc_final: 0.6985 (mpp) REVERT: Bl 108 MET cc_start: 0.6970 (tpp) cc_final: 0.6736 (tpp) REVERT: Bm 73 TYR cc_start: 0.7772 (t80) cc_final: 0.7345 (t80) REVERT: Bn 151 ASN cc_start: 0.8621 (m110) cc_final: 0.8421 (m110) REVERT: Bo 168 GLU cc_start: 0.6531 (pt0) cc_final: 0.6268 (pt0) REVERT: Bo 197 ARG cc_start: 0.7414 (ptm160) cc_final: 0.6990 (ptm-80) REVERT: Bp 197 ARG cc_start: 0.7188 (ptm160) cc_final: 0.6986 (ptm160) REVERT: Br 77 GLN cc_start: 0.7455 (mt0) cc_final: 0.7135 (mt0) REVERT: Br 197 ARG cc_start: 0.7093 (ptm160) cc_final: 0.6743 (ptm160) REVERT: Bs 172 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6868 (tm-30) REVERT: Bt 108 MET cc_start: 0.6986 (tpp) cc_final: 0.6778 (tpp) outliers start: 249 outliers final: 102 residues processed: 2151 average time/residue: 1.6028 time to fit residues: 4320.6796 Evaluate side-chains 2096 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1989 time to evaluate : 5.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 68 GLU Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 195 LEU Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 124 THR Chi-restraints excluded: chain Ab residue 183 ARG Chi-restraints excluded: chain Ab residue 195 LEU Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ad residue 124 THR Chi-restraints excluded: chain Ae residue 124 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Ag residue 76 GLN Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 159 ILE Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 195 LEU Chi-restraints excluded: chain Aj residue 219 GLN Chi-restraints excluded: chain Ak residue 68 GLU Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 219 GLN Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 195 LEU Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain An residue 197 ARG Chi-restraints excluded: chain Ao residue 84 ARG Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 159 ILE Chi-restraints excluded: chain Ap residue 197 ARG Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 124 THR Chi-restraints excluded: chain Aq residue 195 LEU Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 159 ILE Chi-restraints excluded: chain Ar residue 195 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain As residue 195 LEU Chi-restraints excluded: chain At residue 124 THR Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 159 ILE Chi-restraints excluded: chain Ay residue 86 THR Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 219 GLN Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 124 THR Chi-restraints excluded: chain Bb residue 183 ARG Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Be residue 76 GLN Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 159 ILE Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bg residue 71 LEU Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 219 GLN Chi-restraints excluded: chain Bh residue 68 GLU Chi-restraints excluded: chain Bh residue 124 THR Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 183 ARG Chi-restraints excluded: chain Bh residue 195 LEU Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 124 THR Chi-restraints excluded: chain Bj residue 195 LEU Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 159 ILE Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 159 ILE Chi-restraints excluded: chain Bo residue 68 GLU Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 124 THR Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 124 THR Chi-restraints excluded: chain Bp residue 195 LEU Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Br residue 124 THR Chi-restraints excluded: chain Br residue 195 LEU Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bs residue 159 ILE Chi-restraints excluded: chain Bt residue 124 THR Chi-restraints excluded: chain Bt residue 159 ILE Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bv residue 124 THR Chi-restraints excluded: chain Bv residue 159 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 598 optimal weight: 1.9990 chunk 489 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 720 optimal weight: 1.9990 chunk 778 optimal weight: 0.8980 chunk 641 optimal weight: 3.9990 chunk 714 optimal weight: 0.0050 chunk 245 optimal weight: 4.9990 chunk 578 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 89 GLN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 89 GLN ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 140 GLN Ah 140 GLN Ah 151 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN Aq 175 ASN ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 66 ASN ** Ay 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 98 GLN Be 98 GLN ** Bg 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Br 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 66840 Z= 0.229 Angle : 0.601 8.130 90648 Z= 0.304 Chirality : 0.041 0.181 9744 Planarity : 0.006 0.064 11856 Dihedral : 4.488 18.594 9024 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.74 % Allowed : 24.97 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.92 (0.10), residues: 8016 helix: -0.81 (0.08), residues: 4272 sheet: 0.09 (0.19), residues: 576 loop : -0.17 (0.13), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAo 132 HIS 0.006 0.001 HISBr 162 PHE 0.020 0.002 PHEAt 200 TYR 0.023 0.002 TYRAu 73 ARG 0.009 0.001 ARGBi 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2372 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 2108 time to evaluate : 5.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 112 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7528 (mmm) REVERT: Aa 197 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6789 (ptm160) REVERT: Aa 209 THR cc_start: 0.8428 (m) cc_final: 0.7730 (p) REVERT: Aa 214 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6849 (ttm-80) REVERT: Ab 55 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8413 (mtp180) REVERT: Ab 77 GLN cc_start: 0.7379 (mt0) cc_final: 0.7018 (mt0) REVERT: Ab 160 MET cc_start: 0.7502 (tpp) cc_final: 0.7152 (mmm) REVERT: Ac 55 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8367 (mtp180) REVERT: Ad 77 GLN cc_start: 0.7542 (mt0) cc_final: 0.7186 (mt0) REVERT: Ae 121 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6648 (mt-10) REVERT: Af 160 MET cc_start: 0.7668 (mmm) cc_final: 0.7368 (mmm) REVERT: Ag 76 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7064 (mt0) REVERT: Ag 108 MET cc_start: 0.7174 (tpp) cc_final: 0.6833 (tpp) REVERT: Ag 183 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6847 (ttp-110) REVERT: Ah 108 MET cc_start: 0.7149 (tpp) cc_final: 0.6867 (tpp) REVERT: Ah 172 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6429 (tm-30) REVERT: Ai 214 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7166 (mtm-85) REVERT: Aj 135 MET cc_start: 0.7243 (mmp) cc_final: 0.7025 (mmp) REVERT: Aj 168 GLU cc_start: 0.6728 (pt0) cc_final: 0.6509 (pt0) REVERT: Aj 197 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7017 (ptm-80) REVERT: Ak 156 LEU cc_start: 0.8812 (tp) cc_final: 0.8578 (tm) REVERT: Ak 214 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7112 (ttm-80) REVERT: Al 209 THR cc_start: 0.8545 (m) cc_final: 0.7428 (m) REVERT: Al 214 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7200 (mtm-85) REVERT: Am 160 MET cc_start: 0.7731 (mmm) cc_final: 0.7468 (mmm) REVERT: Am 172 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6543 (tm-30) REVERT: Ao 84 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8125 (ptm-80) REVERT: Ap 108 MET cc_start: 0.7162 (tpp) cc_final: 0.6912 (tpp) REVERT: Aq 55 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8345 (mtp180) REVERT: Aq 160 MET cc_start: 0.7641 (mmm) cc_final: 0.7201 (mmm) REVERT: Aq 197 ARG cc_start: 0.7346 (ptm160) cc_final: 0.6967 (ptm160) REVERT: Ar 160 MET cc_start: 0.7560 (mmm) cc_final: 0.7078 (mmm) REVERT: As 160 MET cc_start: 0.7635 (tpp) cc_final: 0.7225 (mmm) REVERT: At 55 ARG cc_start: 0.8528 (mtp180) cc_final: 0.8282 (mtp180) REVERT: At 77 GLN cc_start: 0.7465 (mt0) cc_final: 0.7126 (mt0) REVERT: At 183 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.7240 (mtp-110) REVERT: At 209 THR cc_start: 0.8450 (m) cc_final: 0.7966 (p) REVERT: Au 108 MET cc_start: 0.7190 (tpt) cc_final: 0.6868 (tpt) REVERT: Au 197 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7600 (ttm-80) REVERT: Ax 78 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7665 (pp) REVERT: Ay 55 ARG cc_start: 0.8653 (mtp180) cc_final: 0.8410 (mtp180) REVERT: Az 55 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8336 (mtp180) REVERT: Az 77 GLN cc_start: 0.7570 (mt0) cc_final: 0.7344 (mt0) REVERT: Az 157 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: Az 168 GLU cc_start: 0.6403 (pt0) cc_final: 0.5782 (pt0) REVERT: Az 197 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6675 (ptm-80) REVERT: Ba 77 GLN cc_start: 0.7411 (mt0) cc_final: 0.6863 (mt0) REVERT: Ba 160 MET cc_start: 0.7685 (mmm) cc_final: 0.7290 (mmm) REVERT: Bb 160 MET cc_start: 0.7517 (mmm) cc_final: 0.7064 (mmm) REVERT: Bb 175 ASN cc_start: 0.8155 (t0) cc_final: 0.7841 (t160) REVERT: Bc 108 MET cc_start: 0.7011 (tpp) cc_final: 0.6799 (tpp) REVERT: Bd 121 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6566 (mt-10) REVERT: Bd 173 MET cc_start: 0.7268 (tpp) cc_final: 0.6846 (mpp) REVERT: Be 151 ASN cc_start: 0.8512 (m-40) cc_final: 0.8283 (m110) REVERT: Bf 108 MET cc_start: 0.7196 (tpp) cc_final: 0.6842 (tpp) REVERT: Bf 183 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6636 (ttp-170) REVERT: Bi 77 GLN cc_start: 0.7432 (mt0) cc_final: 0.7195 (mt0) REVERT: Bk 172 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6410 (tm-30) REVERT: Bk 173 MET cc_start: 0.7254 (tpp) cc_final: 0.6923 (mpp) REVERT: Bl 108 MET cc_start: 0.7045 (tpp) cc_final: 0.6823 (tpp) REVERT: Bm 136 ASP cc_start: 0.7837 (t0) cc_final: 0.7564 (t0) REVERT: Bo 160 MET cc_start: 0.7644 (mmm) cc_final: 0.7190 (mmm) REVERT: Bp 55 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8320 (mtp180) REVERT: Bp 160 MET cc_start: 0.7550 (tpp) cc_final: 0.7121 (mmm) REVERT: Bp 188 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8048 (mtt90) REVERT: Bp 197 ARG cc_start: 0.7278 (ptm160) cc_final: 0.6948 (ptm160) REVERT: Bq 160 MET cc_start: 0.7756 (tpp) cc_final: 0.7398 (mmm) REVERT: Br 160 MET cc_start: 0.7590 (mmm) cc_final: 0.7116 (mmm) REVERT: Bt 108 MET cc_start: 0.7162 (tpp) cc_final: 0.6916 (tpp) REVERT: Bu 73 TYR cc_start: 0.8007 (t80) cc_final: 0.7695 (t80) REVERT: Bu 84 ARG cc_start: 0.8337 (ptp-170) cc_final: 0.8102 (ptp-170) REVERT: Bv 73 TYR cc_start: 0.7632 (t80) cc_final: 0.7393 (t80) REVERT: Bv 84 ARG cc_start: 0.8256 (ptp-170) cc_final: 0.8041 (ptp-170) outliers start: 264 outliers final: 142 residues processed: 2182 average time/residue: 1.6579 time to fit residues: 4515.9475 Evaluate side-chains 2235 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 2085 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 68 GLU Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 112 MET Chi-restraints excluded: chain Aa residue 127 ASN Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 195 LEU Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 205 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ab residue 183 ARG Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ad residue 68 GLU Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Ag residue 76 GLN Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 131 VAL Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 183 ARG Chi-restraints excluded: chain Aj residue 197 ARG Chi-restraints excluded: chain Aj residue 219 GLN Chi-restraints excluded: chain Ak residue 131 VAL Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Ak residue 219 GLN Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 84 ARG Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Aq residue 55 ARG Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 68 GLU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 159 ILE Chi-restraints excluded: chain As residue 68 GLU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain At residue 68 GLU Chi-restraints excluded: chain At residue 212 ARG Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Aw residue 166 VAL Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 159 ILE Chi-restraints excluded: chain Ay residue 68 GLU Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 86 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Az residue 68 GLU Chi-restraints excluded: chain Az residue 141 VAL Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Ba residue 68 GLU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 183 ARG Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 183 ARG Chi-restraints excluded: chain Bc residue 116 MET Chi-restraints excluded: chain Bc residue 124 THR Chi-restraints excluded: chain Bc residue 131 VAL Chi-restraints excluded: chain Bd residue 124 THR Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Bd residue 166 VAL Chi-restraints excluded: chain Bd residue 205 VAL Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 141 VAL Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 166 VAL Chi-restraints excluded: chain Bg residue 68 GLU Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 183 ARG Chi-restraints excluded: chain Bh residue 195 LEU Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 208 ARG Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 159 ILE Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bo residue 68 GLU Chi-restraints excluded: chain Bo residue 80 ILE Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 131 VAL Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 208 ARG Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bs residue 145 LEU Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 159 ILE Chi-restraints excluded: chain Bt residue 173 MET Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 0.3980 chunk 541 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 343 optimal weight: 0.7980 chunk 483 optimal weight: 0.5980 chunk 723 optimal weight: 1.9990 chunk 765 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 685 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 98 GLN Al 77 GLN Am 151 ASN Ar 89 GLN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 77 GLN ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 98 GLN Bi 98 GLN ** Bj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 98 GLN Bs 98 GLN Bu 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 66840 Z= 0.253 Angle : 0.598 9.461 90648 Z= 0.302 Chirality : 0.042 0.180 9744 Planarity : 0.006 0.067 11856 Dihedral : 4.502 18.650 9024 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.58 % Allowed : 26.11 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.64 (0.10), residues: 8016 helix: -0.64 (0.08), residues: 4272 sheet: 0.67 (0.20), residues: 576 loop : -0.03 (0.13), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAo 132 HIS 0.005 0.001 HISAt 162 PHE 0.017 0.002 PHEAd 163 TYR 0.037 0.002 TYRAs 73 ARG 0.010 0.001 ARGAd 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2444 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 323 poor density : 2121 time to evaluate : 5.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 SER cc_start: 0.8244 (t) cc_final: 0.8021 (m) REVERT: Aa 188 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.8095 (mtt90) REVERT: Aa 197 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6924 (ptm160) REVERT: Aa 209 THR cc_start: 0.8480 (m) cc_final: 0.7691 (p) REVERT: Aa 214 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.6837 (ttm-80) REVERT: Ab 55 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8510 (mtp180) REVERT: Ab 160 MET cc_start: 0.7483 (tpp) cc_final: 0.7172 (mmm) REVERT: Ab 209 THR cc_start: 0.8489 (m) cc_final: 0.7965 (p) REVERT: Ac 55 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8295 (mtp180) REVERT: Ac 160 MET cc_start: 0.7548 (tpp) cc_final: 0.7237 (mmm) REVERT: Ad 77 GLN cc_start: 0.7554 (mt0) cc_final: 0.7332 (mt0) REVERT: Ae 121 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6630 (mt-10) REVERT: Ag 76 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: Ag 183 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6922 (ttp-110) REVERT: Ah 108 MET cc_start: 0.7078 (tpp) cc_final: 0.6878 (tpp) REVERT: Ah 172 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6638 (tm-30) REVERT: Ai 117 VAL cc_start: 0.8785 (m) cc_final: 0.8542 (t) REVERT: Aj 135 MET cc_start: 0.7204 (mmp) cc_final: 0.6995 (mmp) REVERT: Aj 168 GLU cc_start: 0.6594 (pt0) cc_final: 0.6369 (pt0) REVERT: Aj 197 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7096 (ptm-80) REVERT: Ak 112 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: Ak 156 LEU cc_start: 0.8826 (tp) cc_final: 0.8576 (tm) REVERT: Ak 214 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7128 (ttm-80) REVERT: Al 68 GLU cc_start: 0.7150 (tp30) cc_final: 0.6806 (tp30) REVERT: Al 77 GLN cc_start: 0.7235 (mt0) cc_final: 0.6984 (mt0) REVERT: Al 209 THR cc_start: 0.8537 (m) cc_final: 0.7344 (m) REVERT: Am 79 ASP cc_start: 0.6867 (t0) cc_final: 0.6647 (t0) REVERT: Am 134 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7350 (ttp) REVERT: Am 172 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6928 (tm-30) REVERT: An 134 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7282 (ttp) REVERT: Ao 84 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (ptm-80) REVERT: Ap 108 MET cc_start: 0.7176 (tpp) cc_final: 0.6803 (tpp) REVERT: Ap 173 MET cc_start: 0.7579 (tpp) cc_final: 0.7269 (mpp) REVERT: Aq 160 MET cc_start: 0.7606 (mmm) cc_final: 0.7270 (mmm) REVERT: Aq 197 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7052 (ptm-80) REVERT: At 55 ARG cc_start: 0.8551 (mtp180) cc_final: 0.8329 (mtp180) REVERT: At 77 GLN cc_start: 0.7510 (mt0) cc_final: 0.6986 (mt0) REVERT: At 209 THR cc_start: 0.8409 (m) cc_final: 0.7925 (p) REVERT: Au 108 MET cc_start: 0.7362 (tpt) cc_final: 0.7039 (tpt) REVERT: Au 134 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7223 (ttp) REVERT: Au 197 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7504 (ttm-80) REVERT: Ax 78 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7590 (pp) REVERT: Ax 84 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: Ax 121 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6460 (mt-10) REVERT: Ay 55 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8480 (mtp180) REVERT: Ay 112 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7563 (mmm) REVERT: Az 55 ARG cc_start: 0.8669 (mtp180) cc_final: 0.8339 (mmm160) REVERT: Az 77 GLN cc_start: 0.7625 (mt0) cc_final: 0.7410 (mt0) REVERT: Az 157 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7556 (ttm-80) REVERT: Ba 160 MET cc_start: 0.7650 (mmm) cc_final: 0.7287 (mmm) REVERT: Bb 68 GLU cc_start: 0.7207 (tp30) cc_final: 0.6890 (tp30) REVERT: Bb 160 MET cc_start: 0.7445 (mmm) cc_final: 0.7012 (mmm) REVERT: Bb 175 ASN cc_start: 0.8140 (t0) cc_final: 0.7825 (t160) REVERT: Bb 209 THR cc_start: 0.8520 (m) cc_final: 0.8041 (p) REVERT: Bf 183 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6688 (ttp-170) REVERT: Bh 160 MET cc_start: 0.7731 (mmm) cc_final: 0.7158 (mmm) REVERT: Bk 108 MET cc_start: 0.7147 (tpp) cc_final: 0.6919 (tpp) REVERT: Bk 173 MET cc_start: 0.7198 (tpp) cc_final: 0.6860 (mpp) REVERT: Bm 136 ASP cc_start: 0.7839 (t0) cc_final: 0.7589 (t0) REVERT: Bm 183 ARG cc_start: 0.7312 (ttp-110) cc_final: 0.6648 (ttp-170) REVERT: Bn 160 MET cc_start: 0.7712 (mmm) cc_final: 0.7386 (mmm) REVERT: Bo 160 MET cc_start: 0.7656 (mmm) cc_final: 0.7316 (mmm) REVERT: Bp 55 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8319 (mtp180) REVERT: Bp 97 VAL cc_start: 0.8085 (p) cc_final: 0.7715 (t) REVERT: Bp 160 MET cc_start: 0.7503 (tpp) cc_final: 0.7071 (mmm) REVERT: Bq 160 MET cc_start: 0.7704 (tpp) cc_final: 0.7378 (mmm) REVERT: Br 160 MET cc_start: 0.7512 (mmm) cc_final: 0.7088 (mmm) REVERT: Br 197 ARG cc_start: 0.7312 (ptm160) cc_final: 0.7112 (ttp-170) REVERT: Bt 108 MET cc_start: 0.7308 (tpp) cc_final: 0.6919 (tpp) REVERT: Bt 134 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7268 (ttp) REVERT: Bt 183 ARG cc_start: 0.7441 (mtp-110) cc_final: 0.6964 (ttp-110) REVERT: Bu 117 VAL cc_start: 0.8764 (t) cc_final: 0.8506 (m) REVERT: Bu 183 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6794 (ttp-110) REVERT: Bu 197 ARG cc_start: 0.8235 (ptm160) cc_final: 0.8033 (ptm160) outliers start: 323 outliers final: 174 residues processed: 2205 average time/residue: 1.6665 time to fit residues: 4582.2461 Evaluate side-chains 2304 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 2116 time to evaluate : 5.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 127 ASN Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 68 GLU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ab residue 183 ARG Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 145 LEU Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 64 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 76 GLN Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 197 ARG Chi-restraints excluded: chain Ak residue 68 GLU Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 112 MET Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 131 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 219 GLN Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain Am residue 134 MET Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 134 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 84 ARG Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 159 ILE Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain At residue 212 ARG Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 134 MET Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Aw residue 116 MET Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 166 VAL Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 84 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 145 LEU Chi-restraints excluded: chain Ax residue 159 ILE Chi-restraints excluded: chain Ay residue 68 GLU Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 86 THR Chi-restraints excluded: chain Ay residue 112 MET Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Az residue 68 GLU Chi-restraints excluded: chain Az residue 141 VAL Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Az residue 209 THR Chi-restraints excluded: chain Az residue 219 GLN Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 183 ARG Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 131 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 183 ARG Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 124 THR Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Bd residue 205 VAL Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 141 VAL Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 181 MET Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 219 GLN Chi-restraints excluded: chain Bh residue 68 GLU Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 181 MET Chi-restraints excluded: chain Bh residue 183 ARG Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 71 LEU Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 181 MET Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 197 ARG Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 131 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 173 MET Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 166 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 131 VAL Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bs residue 166 VAL Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 124 THR Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bt residue 134 MET Chi-restraints excluded: chain Bt residue 159 ILE Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 145 LEU Chi-restraints excluded: chain Bu residue 166 VAL Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 0.3980 chunk 434 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 570 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 653 optimal weight: 3.9990 chunk 529 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 390 optimal weight: 0.5980 chunk 687 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 98 GLN Ad 69 HIS Ag 151 ASN An 98 GLN An 140 GLN As 89 GLN ** Ay 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 98 GLN Bf 140 GLN Bg 77 GLN ** Bg 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 98 GLN Bk 140 GLN Bm 98 GLN Bn 98 GLN Bp 77 GLN Bq 77 GLN Bq 98 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 66840 Z= 0.230 Angle : 0.607 12.058 90648 Z= 0.300 Chirality : 0.041 0.147 9744 Planarity : 0.006 0.069 11856 Dihedral : 4.466 19.417 9024 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.55 % Allowed : 27.47 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.37 (0.10), residues: 8016 helix: -0.45 (0.08), residues: 4128 sheet: 1.29 (0.21), residues: 528 loop : 0.01 (0.13), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAo 132 HIS 0.014 0.001 HISAs 69 PHE 0.015 0.002 PHEAt 200 TYR 0.032 0.002 TYRBm 73 ARG 0.010 0.001 ARGAz 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2439 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 321 poor density : 2118 time to evaluate : 5.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 SER cc_start: 0.8270 (t) cc_final: 0.8001 (m) REVERT: Aa 108 MET cc_start: 0.7348 (ttt) cc_final: 0.6757 (ttm) REVERT: Aa 138 ASP cc_start: 0.7825 (t70) cc_final: 0.7442 (t0) REVERT: Aa 197 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6985 (ptm160) REVERT: Aa 209 THR cc_start: 0.8449 (m) cc_final: 0.7620 (p) REVERT: Aa 214 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.6896 (mtm-85) REVERT: Ab 160 MET cc_start: 0.7431 (tpp) cc_final: 0.7157 (mmm) REVERT: Ab 181 MET cc_start: 0.7551 (tpp) cc_final: 0.7271 (tpp) REVERT: Ab 209 THR cc_start: 0.8465 (m) cc_final: 0.7917 (p) REVERT: Ac 55 ARG cc_start: 0.8634 (mtp180) cc_final: 0.8272 (mtp180) REVERT: Ac 160 MET cc_start: 0.7450 (tpp) cc_final: 0.7196 (mmm) REVERT: Ad 160 MET cc_start: 0.7602 (mmm) cc_final: 0.7281 (mmm) REVERT: Ae 121 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6592 (mt-10) REVERT: Ag 76 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6987 (mt0) REVERT: Ag 183 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6978 (ttp-110) REVERT: Ah 79 ASP cc_start: 0.6764 (t0) cc_final: 0.6345 (t0) REVERT: Ah 172 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6847 (tm-30) REVERT: Ah 173 MET cc_start: 0.7548 (tpp) cc_final: 0.7337 (mmp) REVERT: Ai 117 VAL cc_start: 0.8785 (m) cc_final: 0.8538 (t) REVERT: Ai 209 THR cc_start: 0.8571 (m) cc_final: 0.8035 (p) REVERT: Aj 97 VAL cc_start: 0.8280 (p) cc_final: 0.7999 (t) REVERT: Aj 160 MET cc_start: 0.7491 (tpp) cc_final: 0.7107 (mmm) REVERT: Aj 168 GLU cc_start: 0.6575 (pt0) cc_final: 0.6372 (pt0) REVERT: Aj 197 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7185 (ptm-80) REVERT: Ak 156 LEU cc_start: 0.8823 (tp) cc_final: 0.8585 (tm) REVERT: Ak 214 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7144 (ttm-80) REVERT: Al 68 GLU cc_start: 0.7125 (tp30) cc_final: 0.6822 (tp30) REVERT: Al 77 GLN cc_start: 0.7242 (mt0) cc_final: 0.6984 (mt0) REVERT: Al 160 MET cc_start: 0.7582 (mmm) cc_final: 0.7256 (mmm) REVERT: Am 79 ASP cc_start: 0.6892 (t0) cc_final: 0.6683 (t0) REVERT: Am 121 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6346 (mt-10) REVERT: Am 134 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7346 (ttp) REVERT: An 112 MET cc_start: 0.8588 (tpp) cc_final: 0.8359 (mmm) REVERT: Ao 84 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8160 (ptm-80) REVERT: Ap 108 MET cc_start: 0.7163 (tpp) cc_final: 0.6843 (tpp) REVERT: Ap 173 MET cc_start: 0.7521 (tpp) cc_final: 0.7304 (mpp) REVERT: Aq 160 MET cc_start: 0.7551 (mmm) cc_final: 0.7171 (mmm) REVERT: Aq 197 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7327 (ptm-80) REVERT: Ar 160 MET cc_start: 0.7586 (mmm) cc_final: 0.7108 (mmm) REVERT: As 160 MET cc_start: 0.7597 (mmm) cc_final: 0.7266 (mmm) REVERT: As 188 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7949 (mtt90) REVERT: At 77 GLN cc_start: 0.7491 (mt0) cc_final: 0.7144 (mt0) REVERT: Au 79 ASP cc_start: 0.6631 (t0) cc_final: 0.6412 (t0) REVERT: Au 108 MET cc_start: 0.7367 (tpt) cc_final: 0.7161 (tpt) REVERT: Au 134 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7273 (ttp) REVERT: Av 134 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7322 (ttp) REVERT: Aw 134 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7269 (ttp) REVERT: Ax 78 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7442 (pp) REVERT: Ax 84 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7449 (ptm-80) REVERT: Ay 160 MET cc_start: 0.7640 (mmm) cc_final: 0.7243 (mmm) REVERT: Az 55 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8335 (mmm160) REVERT: Az 157 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: Az 168 GLU cc_start: 0.6354 (pt0) cc_final: 0.6071 (pt0) REVERT: Ba 98 GLN cc_start: 0.7796 (tp40) cc_final: 0.7378 (tp40) REVERT: Ba 160 MET cc_start: 0.7619 (mmm) cc_final: 0.7376 (mmm) REVERT: Bb 68 GLU cc_start: 0.7218 (tp30) cc_final: 0.6926 (tp30) REVERT: Bb 160 MET cc_start: 0.7414 (mmm) cc_final: 0.6986 (mmm) REVERT: Bf 108 MET cc_start: 0.7166 (tpp) cc_final: 0.6891 (tpp) REVERT: Bg 157 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7546 (ttm-80) REVERT: Bh 160 MET cc_start: 0.7677 (mmm) cc_final: 0.7275 (mmm) REVERT: Bh 209 THR cc_start: 0.8561 (m) cc_final: 0.8073 (p) REVERT: Bi 77 GLN cc_start: 0.7418 (mt0) cc_final: 0.7200 (mt0) REVERT: Bj 160 MET cc_start: 0.7634 (tpp) cc_final: 0.7002 (mpp) REVERT: Bk 140 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7210 (mm-40) REVERT: Bk 160 MET cc_start: 0.7711 (mmm) cc_final: 0.7494 (mmm) REVERT: Bl 116 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: Bm 136 ASP cc_start: 0.7859 (t0) cc_final: 0.7592 (t0) REVERT: Bo 77 GLN cc_start: 0.7441 (mt0) cc_final: 0.7199 (mm-40) REVERT: Bo 160 MET cc_start: 0.7581 (mmm) cc_final: 0.7262 (mmm) REVERT: Bp 97 VAL cc_start: 0.8176 (p) cc_final: 0.7844 (t) REVERT: Bp 197 ARG cc_start: 0.7411 (ptm160) cc_final: 0.7087 (ptm160) REVERT: Bq 160 MET cc_start: 0.7678 (tpp) cc_final: 0.7328 (mmm) REVERT: Br 77 GLN cc_start: 0.7415 (mt0) cc_final: 0.7208 (mt0) REVERT: Br 160 MET cc_start: 0.7480 (mmm) cc_final: 0.7172 (mmm) REVERT: Br 197 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6945 (ptm160) REVERT: Bt 108 MET cc_start: 0.7249 (tpp) cc_final: 0.6983 (tpp) REVERT: Bt 183 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.6912 (ttp-110) REVERT: Bu 117 VAL cc_start: 0.8744 (t) cc_final: 0.8459 (m) REVERT: Bu 172 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6778 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6785 (ttp-110) outliers start: 321 outliers final: 201 residues processed: 2192 average time/residue: 1.7759 time to fit residues: 4950.2589 Evaluate side-chains 2315 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 2098 time to evaluate : 5.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 160 MET Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 68 GLU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 108 MET Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 124 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 64 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 145 LEU Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 76 GLN Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 159 ILE Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ah residue 145 LEU Chi-restraints excluded: chain Ah residue 166 VAL Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 183 ARG Chi-restraints excluded: chain Aj residue 197 ARG Chi-restraints excluded: chain Aj residue 219 GLN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Ak residue 219 GLN Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain Am residue 134 MET Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 140 GLN Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 84 ARG Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 197 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain As residue 68 GLU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 108 MET Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 134 MET Chi-restraints excluded: chain Au residue 140 GLN Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 134 MET Chi-restraints excluded: chain Av residue 166 VAL Chi-restraints excluded: chain Av residue 173 MET Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 84 ARG Chi-restraints excluded: chain Ax residue 116 MET Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 159 ILE Chi-restraints excluded: chain Ax residue 205 VAL Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Az residue 68 GLU Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 141 VAL Chi-restraints excluded: chain Az residue 173 MET Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Az residue 219 GLN Chi-restraints excluded: chain Ba residue 68 GLU Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 183 ARG Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 108 MET Chi-restraints excluded: chain Bb residue 131 VAL Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 183 ARG Chi-restraints excluded: chain Bb residue 191 ARG Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 124 THR Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 131 VAL Chi-restraints excluded: chain Bf residue 133 VAL Chi-restraints excluded: chain Bf residue 141 VAL Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 181 MET Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bh residue 68 GLU Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 181 MET Chi-restraints excluded: chain Bh residue 183 ARG Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 181 MET Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 181 MET Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 205 VAL Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 131 VAL Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 140 GLN Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 173 MET Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bk residue 220 MET Chi-restraints excluded: chain Bl residue 116 MET Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 141 VAL Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 131 VAL Chi-restraints excluded: chain Bp residue 141 VAL Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 77 GLN Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Br residue 197 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bt residue 159 ILE Chi-restraints excluded: chain Bt residue 173 MET Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 145 LEU Chi-restraints excluded: chain Bu residue 166 VAL Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bu residue 205 VAL Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 0.6980 chunk 689 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 449 optimal weight: 0.5980 chunk 188 optimal weight: 0.0980 chunk 766 optimal weight: 0.9980 chunk 636 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 253 optimal weight: 0.3980 chunk 402 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 98 GLN ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 89 GLN ** Ay 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 77 GLN Be 76 GLN ** Bg 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 98 GLN Bl 151 ASN Bp 98 GLN Bq 77 GLN Bq 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 66840 Z= 0.197 Angle : 0.607 13.285 90648 Z= 0.297 Chirality : 0.041 0.166 9744 Planarity : 0.006 0.066 11856 Dihedral : 4.402 18.715 9024 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.25 % Allowed : 28.94 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.22 (0.10), residues: 8016 helix: -0.21 (0.08), residues: 4080 sheet: 1.34 (0.21), residues: 528 loop : -0.09 (0.13), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAo 132 HIS 0.014 0.001 HISAs 69 PHE 0.014 0.002 PHEAc 200 TYR 0.039 0.002 TYRAs 73 ARG 0.011 0.001 ARGBs 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2428 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 2128 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 SER cc_start: 0.8253 (t) cc_final: 0.7965 (m) REVERT: Aa 138 ASP cc_start: 0.7846 (t70) cc_final: 0.7478 (t0) REVERT: Aa 197 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6967 (ptm160) REVERT: Aa 209 THR cc_start: 0.8422 (m) cc_final: 0.7435 (p) REVERT: Aa 214 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.6834 (mtm-85) REVERT: Ab 209 THR cc_start: 0.8440 (m) cc_final: 0.7875 (p) REVERT: Ac 55 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8233 (mtp180) REVERT: Ac 138 ASP cc_start: 0.7835 (t70) cc_final: 0.7460 (t0) REVERT: Ac 151 ASN cc_start: 0.7892 (m110) cc_final: 0.7683 (t0) REVERT: Ad 77 GLN cc_start: 0.7444 (mt0) cc_final: 0.7188 (mt0) REVERT: Ad 160 MET cc_start: 0.7590 (mmm) cc_final: 0.7254 (mmm) REVERT: Ae 145 LEU cc_start: 0.8953 (mm) cc_final: 0.8715 (mp) REVERT: Ag 76 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: Ag 173 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6985 (mpp) REVERT: Ag 183 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6937 (ttp-110) REVERT: Ai 117 VAL cc_start: 0.8783 (m) cc_final: 0.8550 (t) REVERT: Ai 160 MET cc_start: 0.7766 (mmm) cc_final: 0.7311 (mmm) REVERT: Aj 168 GLU cc_start: 0.6550 (pt0) cc_final: 0.6347 (pt0) REVERT: Aj 197 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7216 (ptm-80) REVERT: Ak 156 LEU cc_start: 0.8825 (tp) cc_final: 0.8602 (tm) REVERT: Ak 214 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7138 (mtm-85) REVERT: Al 68 GLU cc_start: 0.7075 (tp30) cc_final: 0.6836 (tp30) REVERT: Al 77 GLN cc_start: 0.7194 (mt0) cc_final: 0.6929 (mt0) REVERT: Al 160 MET cc_start: 0.7567 (mmm) cc_final: 0.7281 (mmm) REVERT: Am 121 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6242 (mt-10) REVERT: An 183 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6873 (ttp-110) REVERT: Ao 84 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (ptm-80) REVERT: Ao 145 LEU cc_start: 0.9002 (mm) cc_final: 0.8737 (mp) REVERT: Aq 55 ARG cc_start: 0.8662 (mtp180) cc_final: 0.8449 (mmm-85) REVERT: Aq 160 MET cc_start: 0.7550 (mmm) cc_final: 0.7272 (mmm) REVERT: Ar 160 MET cc_start: 0.7592 (mmm) cc_final: 0.7134 (mmm) REVERT: As 160 MET cc_start: 0.7577 (mmm) cc_final: 0.7252 (mmm) REVERT: As 188 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7932 (mtt90) REVERT: At 77 GLN cc_start: 0.7481 (mt0) cc_final: 0.7081 (mt0) REVERT: At 168 GLU cc_start: 0.6549 (pt0) cc_final: 0.6347 (pt0) REVERT: Au 108 MET cc_start: 0.7386 (tpt) cc_final: 0.7140 (tpt) REVERT: Au 134 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7247 (ttp) REVERT: Au 208 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7146 (mtm110) REVERT: Av 134 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7328 (ttp) REVERT: Aw 134 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7243 (ttp) REVERT: Ax 84 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8072 (ptp-170) REVERT: Ay 160 MET cc_start: 0.7613 (mmm) cc_final: 0.7269 (mmm) REVERT: Az 55 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8363 (mmm160) REVERT: Az 157 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: Az 160 MET cc_start: 0.7603 (mmm) cc_final: 0.7189 (mmm) REVERT: Ba 160 MET cc_start: 0.7604 (mmm) cc_final: 0.7384 (mmm) REVERT: Bb 160 MET cc_start: 0.7362 (mmm) cc_final: 0.7059 (mmm) REVERT: Bd 173 MET cc_start: 0.7718 (mpp) cc_final: 0.7446 (mpm) REVERT: Bg 55 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8188 (mmm160) REVERT: Bg 157 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7561 (ttm-80) REVERT: Bh 160 MET cc_start: 0.7702 (mmm) cc_final: 0.7290 (mmm) REVERT: Bh 209 THR cc_start: 0.8515 (m) cc_final: 0.8026 (p) REVERT: Bi 77 GLN cc_start: 0.7414 (mt0) cc_final: 0.7164 (mt0) REVERT: Bj 160 MET cc_start: 0.7614 (tpp) cc_final: 0.7050 (mpp) REVERT: Bj 168 GLU cc_start: 0.6445 (pt0) cc_final: 0.5908 (pt0) REVERT: Bj 197 ARG cc_start: 0.7449 (ptm160) cc_final: 0.7064 (ptm160) REVERT: Bm 136 ASP cc_start: 0.7844 (t0) cc_final: 0.7591 (t0) REVERT: Bm 183 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6654 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8228 (mtp180) REVERT: Bo 77 GLN cc_start: 0.7430 (mt0) cc_final: 0.7175 (mm-40) REVERT: Bo 160 MET cc_start: 0.7583 (mmm) cc_final: 0.7285 (mmm) REVERT: Bp 97 VAL cc_start: 0.8237 (p) cc_final: 0.7898 (t) REVERT: Bp 160 MET cc_start: 0.7396 (tpp) cc_final: 0.6993 (mmm) REVERT: Bp 197 ARG cc_start: 0.7390 (ptm160) cc_final: 0.7113 (ptm160) REVERT: Bq 160 MET cc_start: 0.7636 (tpp) cc_final: 0.7300 (mmm) REVERT: Br 77 GLN cc_start: 0.7384 (mt0) cc_final: 0.7178 (mt0) REVERT: Br 160 MET cc_start: 0.7443 (mmm) cc_final: 0.7089 (mmm) REVERT: Br 197 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7108 (ttp80) REVERT: Bt 108 MET cc_start: 0.7225 (tpp) cc_final: 0.6959 (tpp) REVERT: Bu 117 VAL cc_start: 0.8715 (t) cc_final: 0.8466 (m) REVERT: Bu 121 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6637 (mt-10) REVERT: Bu 172 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6767 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6743 (ttp-110) outliers start: 300 outliers final: 181 residues processed: 2201 average time/residue: 1.6246 time to fit residues: 4475.1254 Evaluate side-chains 2304 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 2109 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 160 MET Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 124 THR Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 64 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Af residue 145 LEU Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Ag residue 76 GLN Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 173 MET Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Aj residue 183 ARG Chi-restraints excluded: chain Aj residue 197 ARG Chi-restraints excluded: chain Aj residue 219 GLN Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Ak residue 219 GLN Chi-restraints excluded: chain Al residue 131 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 84 ARG Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain Ar residue 208 ARG Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 134 MET Chi-restraints excluded: chain Au residue 140 GLN Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 64 VAL Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 134 MET Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 173 MET Chi-restraints excluded: chain Ax residue 84 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ay residue 68 GLU Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Ay residue 212 ARG Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 131 VAL Chi-restraints excluded: chain Az residue 173 MET Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Az residue 219 GLN Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 191 ARG Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bb residue 212 ARG Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 124 THR Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Bd residue 141 VAL Chi-restraints excluded: chain Be residue 76 GLN Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 133 VAL Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 157 ARG Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 208 ARG Chi-restraints excluded: chain Bh residue 71 LEU Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 181 MET Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bk residue 220 MET Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 141 VAL Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 166 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 108 MET Chi-restraints excluded: chain Bp residue 131 VAL Chi-restraints excluded: chain Bp residue 141 VAL Chi-restraints excluded: chain Bp residue 212 ARG Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Br residue 197 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 133 VAL Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bu residue 205 VAL Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 436 optimal weight: 1.9990 chunk 559 optimal weight: 3.9990 chunk 433 optimal weight: 0.0050 chunk 645 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 chunk 763 optimal weight: 1.9990 chunk 477 optimal weight: 4.9990 chunk 465 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 89 GLN Aa 98 GLN ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 69 HIS ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 66 ASN At 89 GLN ** Ay 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 77 GLN Bb 89 GLN Bc 98 GLN ** Bg 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 89 GLN ** Bh 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 77 GLN Bl 98 GLN Bl 140 GLN ** Bn 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 66840 Z= 0.281 Angle : 0.651 11.750 90648 Z= 0.320 Chirality : 0.043 0.184 9744 Planarity : 0.006 0.094 11856 Dihedral : 4.587 19.070 9024 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.49 % Allowed : 29.12 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.26 (0.10), residues: 8016 helix: -0.31 (0.08), residues: 4152 sheet: 1.34 (0.21), residues: 528 loop : -0.01 (0.13), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPBh 93 HIS 0.012 0.001 HISAs 69 PHE 0.017 0.003 PHEAd 163 TYR 0.041 0.002 TYRAs 73 ARG 0.010 0.001 ARGBi 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2435 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 2118 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 SER cc_start: 0.8331 (t) cc_final: 0.8055 (m) REVERT: Aa 97 VAL cc_start: 0.8510 (p) cc_final: 0.8232 (t) REVERT: Aa 138 ASP cc_start: 0.7933 (t70) cc_final: 0.7613 (t0) REVERT: Aa 197 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6879 (ptm160) REVERT: Aa 209 THR cc_start: 0.8433 (m) cc_final: 0.7907 (p) REVERT: Ab 138 ASP cc_start: 0.7816 (t70) cc_final: 0.7396 (t0) REVERT: Ab 160 MET cc_start: 0.7409 (tpp) cc_final: 0.7068 (mmm) REVERT: Ab 209 THR cc_start: 0.8448 (m) cc_final: 0.7891 (p) REVERT: Ac 138 ASP cc_start: 0.7885 (t70) cc_final: 0.7528 (t0) REVERT: Ac 151 ASN cc_start: 0.7935 (m110) cc_final: 0.7711 (t0) REVERT: Ad 138 ASP cc_start: 0.7947 (t70) cc_final: 0.7618 (t0) REVERT: Ad 160 MET cc_start: 0.7625 (mmm) cc_final: 0.7357 (mmm) REVERT: Ae 145 LEU cc_start: 0.8977 (mm) cc_final: 0.8728 (mp) REVERT: Af 79 ASP cc_start: 0.6811 (t0) cc_final: 0.6434 (t0) REVERT: Ag 121 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6874 (mt-10) REVERT: Ag 183 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6965 (ttp-110) REVERT: Ah 79 ASP cc_start: 0.6799 (t0) cc_final: 0.6501 (t0) REVERT: Ai 117 VAL cc_start: 0.8783 (m) cc_final: 0.8541 (t) REVERT: Ai 160 MET cc_start: 0.7786 (mmm) cc_final: 0.7332 (mmm) REVERT: Ai 209 THR cc_start: 0.8598 (m) cc_final: 0.8073 (p) REVERT: Aj 209 THR cc_start: 0.8759 (m) cc_final: 0.8262 (p) REVERT: Aj 220 MET cc_start: 0.7086 (mtt) cc_final: 0.6882 (mtt) REVERT: Ak 156 LEU cc_start: 0.8852 (tp) cc_final: 0.8616 (tm) REVERT: Ak 160 MET cc_start: 0.7532 (mmm) cc_final: 0.7289 (mmm) REVERT: Al 68 GLU cc_start: 0.7094 (tp30) cc_final: 0.6842 (tp30) REVERT: Al 77 GLN cc_start: 0.7263 (mt0) cc_final: 0.6988 (mt0) REVERT: Al 160 MET cc_start: 0.7576 (mmm) cc_final: 0.7300 (mmm) REVERT: Am 121 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6185 (mt-10) REVERT: Am 134 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7413 (ttp) REVERT: Am 172 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6728 (tt0) REVERT: An 183 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7046 (ttp-110) REVERT: Ao 145 LEU cc_start: 0.9010 (mm) cc_final: 0.8719 (mp) REVERT: Aq 160 MET cc_start: 0.7491 (mmm) cc_final: 0.7202 (mmm) REVERT: Aq 197 ARG cc_start: 0.7541 (ptm-80) cc_final: 0.7289 (ptm-80) REVERT: Ar 160 MET cc_start: 0.7614 (mmm) cc_final: 0.7137 (mmm) REVERT: As 160 MET cc_start: 0.7577 (mmm) cc_final: 0.7180 (mmm) REVERT: At 77 GLN cc_start: 0.7533 (mt0) cc_final: 0.7184 (mt0) REVERT: At 138 ASP cc_start: 0.7888 (t70) cc_final: 0.7532 (t0) REVERT: At 209 THR cc_start: 0.8407 (m) cc_final: 0.7886 (p) REVERT: Au 108 MET cc_start: 0.7417 (tpt) cc_final: 0.7104 (tpt) REVERT: Au 134 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7284 (ttp) REVERT: Aw 134 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7258 (ttp) REVERT: Aw 173 MET cc_start: 0.7287 (tpp) cc_final: 0.6950 (mpp) REVERT: Ax 84 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7547 (ptm-80) REVERT: Ay 97 VAL cc_start: 0.8359 (p) cc_final: 0.7931 (t) REVERT: Ay 160 MET cc_start: 0.7670 (mmm) cc_final: 0.7241 (mmm) REVERT: Az 55 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8489 (mmm160) REVERT: Az 157 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: Ba 138 ASP cc_start: 0.7805 (t70) cc_final: 0.7416 (t0) REVERT: Ba 160 MET cc_start: 0.7576 (mmm) cc_final: 0.7319 (mmm) REVERT: Bb 160 MET cc_start: 0.7306 (mmm) cc_final: 0.7005 (mmm) REVERT: Bb 209 THR cc_start: 0.8450 (m) cc_final: 0.7901 (p) REVERT: Bc 79 ASP cc_start: 0.6743 (t0) cc_final: 0.6540 (t0) REVERT: Bg 157 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7597 (ttm-80) REVERT: Bh 97 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7477 (t) REVERT: Bh 138 ASP cc_start: 0.7863 (t70) cc_final: 0.7503 (t0) REVERT: Bh 160 MET cc_start: 0.7644 (mmm) cc_final: 0.7252 (mmm) REVERT: Bh 209 THR cc_start: 0.8578 (m) cc_final: 0.8050 (p) REVERT: Bi 77 GLN cc_start: 0.7531 (mt0) cc_final: 0.7311 (mt0) REVERT: Bi 97 VAL cc_start: 0.8359 (p) cc_final: 0.8072 (t) REVERT: Bj 139 GLU cc_start: 0.7145 (pt0) cc_final: 0.6941 (pt0) REVERT: Bj 191 ARG cc_start: 0.6809 (mtp85) cc_final: 0.6602 (mtp85) REVERT: Bj 209 THR cc_start: 0.8570 (m) cc_final: 0.8001 (p) REVERT: Bk 112 MET cc_start: 0.8331 (tpp) cc_final: 0.7842 (mmm) REVERT: Bk 173 MET cc_start: 0.6976 (mpp) cc_final: 0.6485 (mpp) REVERT: Bk 183 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6947 (ttp-110) REVERT: Bm 112 MET cc_start: 0.8526 (tpp) cc_final: 0.7905 (mmt) REVERT: Bm 183 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.6767 (ttp-170) REVERT: Bn 173 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6863 (mpp) REVERT: Bo 55 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8250 (mtp180) REVERT: Bo 77 GLN cc_start: 0.7470 (mt0) cc_final: 0.7240 (mm-40) REVERT: Bo 160 MET cc_start: 0.7533 (mmm) cc_final: 0.7241 (mmm) REVERT: Bp 160 MET cc_start: 0.7420 (tpp) cc_final: 0.7143 (mmm) REVERT: Bp 197 ARG cc_start: 0.7462 (ptm160) cc_final: 0.7204 (ptm160) REVERT: Bq 139 GLU cc_start: 0.7064 (pt0) cc_final: 0.6817 (pt0) REVERT: Br 160 MET cc_start: 0.7456 (mmm) cc_final: 0.7078 (mmm) REVERT: Bs 134 MET cc_start: 0.7729 (ttp) cc_final: 0.7515 (tpp) REVERT: Bt 183 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7007 (ttp-110) REVERT: Bu 117 VAL cc_start: 0.8737 (t) cc_final: 0.8494 (m) REVERT: Bu 121 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6601 (mt-10) REVERT: Bu 172 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6781 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6833 (ttp-110) outliers start: 317 outliers final: 209 residues processed: 2186 average time/residue: 1.6315 time to fit residues: 4459.1388 Evaluate side-chains 2332 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 2110 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Aa residue 160 MET Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 205 VAL Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 64 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 145 LEU Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 145 LEU Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ah residue 145 LEU Chi-restraints excluded: chain Ah residue 218 ILE Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Aj residue 159 ILE Chi-restraints excluded: chain Aj residue 183 ARG Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 131 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 134 MET Chi-restraints excluded: chain Am residue 135 MET Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 145 LEU Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 103 ILE Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 134 MET Chi-restraints excluded: chain Au residue 145 LEU Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 64 VAL Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 145 LEU Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Ax residue 84 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 145 LEU Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Az residue 68 GLU Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 141 VAL Chi-restraints excluded: chain Az residue 173 MET Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 183 ARG Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 168 GLU Chi-restraints excluded: chain Bb residue 191 ARG Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 124 THR Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Bc residue 145 LEU Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 124 THR Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Bd residue 145 LEU Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 145 LEU Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 133 VAL Chi-restraints excluded: chain Bf residue 140 GLN Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 63 THR Chi-restraints excluded: chain Bg residue 157 ARG Chi-restraints excluded: chain Bg residue 181 MET Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bh residue 71 LEU Chi-restraints excluded: chain Bh residue 97 VAL Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 168 GLU Chi-restraints excluded: chain Bh residue 181 MET Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 106 THR Chi-restraints excluded: chain Bi residue 159 ILE Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 168 GLU Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 71 LEU Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 131 VAL Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 145 LEU Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bk residue 220 MET Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 133 VAL Chi-restraints excluded: chain Bl residue 145 LEU Chi-restraints excluded: chain Bl residue 159 ILE Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 145 LEU Chi-restraints excluded: chain Bm residue 205 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 173 MET Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 166 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 141 VAL Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 77 GLN Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bs residue 145 LEU Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bt residue 183 ARG Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 133 VAL Chi-restraints excluded: chain Bu residue 145 LEU Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Chi-restraints excluded: chain Bv residue 145 LEU Chi-restraints excluded: chain Bv residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 0.0770 chunk 304 optimal weight: 0.9980 chunk 455 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 485 optimal weight: 0.9990 chunk 520 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 600 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ae 89 GLN Ah 89 GLN ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 98 GLN ** Ay 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 89 GLN ** Bg 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bl 89 GLN Bo 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 66840 Z= 0.262 Angle : 0.663 12.120 90648 Z= 0.323 Chirality : 0.043 0.214 9744 Planarity : 0.006 0.067 11856 Dihedral : 4.605 19.752 9024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.80 % Allowed : 30.73 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.34 (0.10), residues: 8016 helix: -0.29 (0.08), residues: 4128 sheet: 0.77 (0.21), residues: 576 loop : -0.08 (0.13), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAk 93 HIS 0.013 0.001 HISAs 69 PHE 0.016 0.002 PHEAd 163 TYR 0.048 0.002 TYRBf 198 ARG 0.011 0.001 ARGBk 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2367 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 2099 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 97 VAL cc_start: 0.8522 (p) cc_final: 0.8308 (t) REVERT: Aa 138 ASP cc_start: 0.7942 (t70) cc_final: 0.7522 (t0) REVERT: Aa 197 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6887 (ptm160) REVERT: Aa 209 THR cc_start: 0.8422 (m) cc_final: 0.7892 (p) REVERT: Ab 138 ASP cc_start: 0.7825 (t70) cc_final: 0.7386 (t0) REVERT: Ab 160 MET cc_start: 0.7370 (tpp) cc_final: 0.7023 (mmm) REVERT: Ab 209 THR cc_start: 0.8411 (m) cc_final: 0.7845 (p) REVERT: Ac 138 ASP cc_start: 0.7877 (t70) cc_final: 0.7499 (t0) REVERT: Ad 138 ASP cc_start: 0.7933 (t70) cc_final: 0.7608 (t0) REVERT: Ad 160 MET cc_start: 0.7585 (mmm) cc_final: 0.7325 (mmm) REVERT: Ae 145 LEU cc_start: 0.8944 (mm) cc_final: 0.8663 (mp) REVERT: Af 79 ASP cc_start: 0.6784 (t0) cc_final: 0.6421 (t0) REVERT: Ag 121 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6885 (mt-10) REVERT: Ag 183 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6962 (ttp-110) REVERT: Ah 79 ASP cc_start: 0.6705 (t0) cc_final: 0.6383 (t0) REVERT: Ai 97 VAL cc_start: 0.8401 (p) cc_final: 0.7931 (t) REVERT: Ai 117 VAL cc_start: 0.8780 (m) cc_final: 0.8538 (t) REVERT: Ai 160 MET cc_start: 0.7779 (mmm) cc_final: 0.7319 (mmm) REVERT: Ai 209 THR cc_start: 0.8560 (m) cc_final: 0.8017 (p) REVERT: Aj 209 THR cc_start: 0.8734 (m) cc_final: 0.8234 (p) REVERT: Aj 220 MET cc_start: 0.7009 (mtt) cc_final: 0.6806 (mtt) REVERT: Ak 160 MET cc_start: 0.7522 (mmm) cc_final: 0.7276 (mmm) REVERT: Al 68 GLU cc_start: 0.7066 (tp30) cc_final: 0.6859 (tp30) REVERT: Al 77 GLN cc_start: 0.7245 (mt0) cc_final: 0.6860 (mt0) REVERT: Al 160 MET cc_start: 0.7562 (mmm) cc_final: 0.7210 (mmm) REVERT: An 183 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6953 (ttp-110) REVERT: Ao 145 LEU cc_start: 0.8971 (mm) cc_final: 0.8659 (mp) REVERT: Ap 183 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.6778 (ttp-170) REVERT: Aq 160 MET cc_start: 0.7361 (mmm) cc_final: 0.7126 (mmm) REVERT: Aq 197 ARG cc_start: 0.7551 (ptm-80) cc_final: 0.7228 (ptm-80) REVERT: Ar 55 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8338 (mtp180) REVERT: Ar 77 GLN cc_start: 0.7476 (mt0) cc_final: 0.7218 (mt0) REVERT: Ar 160 MET cc_start: 0.7595 (mmm) cc_final: 0.7099 (mmm) REVERT: Ar 220 MET cc_start: 0.7234 (mtm) cc_final: 0.7033 (mtm) REVERT: As 97 VAL cc_start: 0.8300 (p) cc_final: 0.8053 (t) REVERT: As 160 MET cc_start: 0.7543 (mmm) cc_final: 0.7140 (mmm) REVERT: At 77 GLN cc_start: 0.7505 (mt0) cc_final: 0.7287 (mt0) REVERT: At 138 ASP cc_start: 0.7927 (t70) cc_final: 0.7529 (t0) REVERT: At 209 THR cc_start: 0.8393 (m) cc_final: 0.7868 (p) REVERT: Au 134 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7255 (ttp) REVERT: Av 134 MET cc_start: 0.7627 (ttp) cc_final: 0.7381 (tpp) REVERT: Aw 79 ASP cc_start: 0.6954 (t0) cc_final: 0.6596 (t0) REVERT: Aw 134 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7276 (ttp) REVERT: Aw 173 MET cc_start: 0.7326 (tpp) cc_final: 0.6998 (mpp) REVERT: Ax 84 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7544 (ptm-80) REVERT: Ay 97 VAL cc_start: 0.8414 (p) cc_final: 0.8068 (t) REVERT: Ay 108 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6885 (mtt) REVERT: Ay 160 MET cc_start: 0.7623 (mmm) cc_final: 0.7276 (mmm) REVERT: Az 55 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8479 (mmm160) REVERT: Az 116 MET cc_start: 0.8252 (tmm) cc_final: 0.7898 (ttp) REVERT: Az 157 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: Ba 138 ASP cc_start: 0.7809 (t70) cc_final: 0.7437 (t0) REVERT: Ba 160 MET cc_start: 0.7552 (mmm) cc_final: 0.7207 (mmm) REVERT: Bb 160 MET cc_start: 0.7274 (mmm) cc_final: 0.6902 (mmm) REVERT: Bb 209 THR cc_start: 0.8425 (m) cc_final: 0.7878 (p) REVERT: Bc 79 ASP cc_start: 0.6741 (t0) cc_final: 0.6522 (t0) REVERT: Bg 157 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7575 (ttm-80) REVERT: Bh 138 ASP cc_start: 0.7850 (t70) cc_final: 0.7502 (t0) REVERT: Bh 160 MET cc_start: 0.7664 (mmm) cc_final: 0.7236 (mmm) REVERT: Bh 209 THR cc_start: 0.8568 (m) cc_final: 0.8042 (p) REVERT: Bi 97 VAL cc_start: 0.8276 (p) cc_final: 0.7955 (t) REVERT: Bj 138 ASP cc_start: 0.7860 (t70) cc_final: 0.7459 (t0) REVERT: Bj 139 GLU cc_start: 0.7125 (pt0) cc_final: 0.6924 (pt0) REVERT: Bj 160 MET cc_start: 0.7604 (tpp) cc_final: 0.7191 (mmm) REVERT: Bj 209 THR cc_start: 0.8545 (m) cc_final: 0.7950 (p) REVERT: Bk 173 MET cc_start: 0.7088 (mpp) cc_final: 0.6874 (mpp) REVERT: Bk 181 MET cc_start: 0.7468 (mmm) cc_final: 0.7264 (tpp) REVERT: Bk 183 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6898 (ttp-110) REVERT: Bm 183 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.6766 (ttp-170) REVERT: Bo 55 ARG cc_start: 0.8569 (mtp180) cc_final: 0.8304 (mtp85) REVERT: Bo 77 GLN cc_start: 0.7470 (mt0) cc_final: 0.7223 (mm-40) REVERT: Bo 138 ASP cc_start: 0.7737 (t70) cc_final: 0.7325 (t0) REVERT: Bo 160 MET cc_start: 0.7544 (mmm) cc_final: 0.7259 (mmm) REVERT: Bp 160 MET cc_start: 0.7378 (tpp) cc_final: 0.7129 (mmm) REVERT: Bp 197 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7228 (ptm160) REVERT: Bq 139 GLU cc_start: 0.7066 (pt0) cc_final: 0.6811 (pt0) REVERT: Bq 160 MET cc_start: 0.7642 (tpp) cc_final: 0.7289 (mmm) REVERT: Br 160 MET cc_start: 0.7435 (mmm) cc_final: 0.7149 (mmm) REVERT: Bs 134 MET cc_start: 0.7728 (ttp) cc_final: 0.7492 (tpp) REVERT: Bs 208 ARG cc_start: 0.7417 (mtm110) cc_final: 0.7203 (mtm110) REVERT: Bu 117 VAL cc_start: 0.8708 (t) cc_final: 0.8459 (m) REVERT: Bu 121 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6771 (mt-10) REVERT: Bu 172 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6561 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6872 (ttp-110) outliers start: 268 outliers final: 201 residues processed: 2153 average time/residue: 1.6415 time to fit residues: 4415.8582 Evaluate side-chains 2298 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 2087 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 68 GLU Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 195 LEU Chi-restraints excluded: chain Ac residue 212 ARG Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 205 VAL Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 64 VAL Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 145 LEU Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 56 MET Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Aj residue 159 ILE Chi-restraints excluded: chain Aj residue 183 ARG Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 197 ARG Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 131 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 135 MET Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 173 MET Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain At residue 181 MET Chi-restraints excluded: chain At residue 212 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 103 ILE Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 134 MET Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 64 VAL Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 145 LEU Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Ax residue 84 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 205 VAL Chi-restraints excluded: chain Ay residue 68 GLU Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 108 MET Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Az residue 68 GLU Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Ba residue 63 THR Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 191 ARG Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 124 THR Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Bd residue 145 LEU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 140 GLN Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 63 THR Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 157 ARG Chi-restraints excluded: chain Bg residue 183 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 71 LEU Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 181 MET Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 127 ASN Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 145 LEU Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 205 VAL Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 172 GLU Chi-restraints excluded: chain Bm residue 205 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 166 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 141 VAL Chi-restraints excluded: chain Bp residue 212 ARG Chi-restraints excluded: chain Bp residue 219 GLN Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 77 GLN Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bs residue 145 LEU Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 133 VAL Chi-restraints excluded: chain Bu residue 145 LEU Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Chi-restraints excluded: chain Bv residue 145 LEU Chi-restraints excluded: chain Bv residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 0.1980 chunk 731 optimal weight: 0.5980 chunk 667 optimal weight: 0.4980 chunk 711 optimal weight: 0.9990 chunk 428 optimal weight: 0.0870 chunk 309 optimal weight: 0.5980 chunk 558 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 642 optimal weight: 0.9990 chunk 672 optimal weight: 0.8980 chunk 708 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aj 151 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 151 ASN Bg 151 ASN ** Bh 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66840 Z= 0.191 Angle : 0.649 11.825 90648 Z= 0.313 Chirality : 0.041 0.221 9744 Planarity : 0.006 0.116 11856 Dihedral : 4.517 23.667 9024 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.27 % Allowed : 31.76 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.26 (0.10), residues: 8016 helix: -0.19 (0.08), residues: 4104 sheet: 1.29 (0.22), residues: 528 loop : -0.20 (0.13), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPBh 93 HIS 0.013 0.001 HISAs 69 PHE 0.015 0.002 PHEAl 200 TYR 0.046 0.002 TYRBf 198 ARG 0.010 0.001 ARGBk 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2291 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 2060 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 97 VAL cc_start: 0.8382 (p) cc_final: 0.8082 (t) REVERT: Aa 138 ASP cc_start: 0.7898 (t70) cc_final: 0.7532 (t0) REVERT: Aa 197 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6905 (ptm160) REVERT: Aa 209 THR cc_start: 0.8382 (m) cc_final: 0.7845 (p) REVERT: Ab 117 VAL cc_start: 0.8853 (m) cc_final: 0.8631 (t) REVERT: Ab 138 ASP cc_start: 0.7858 (t70) cc_final: 0.7381 (t0) REVERT: Ab 160 MET cc_start: 0.7322 (tpp) cc_final: 0.6990 (mmm) REVERT: Ab 188 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8112 (mtt90) REVERT: Ac 138 ASP cc_start: 0.7874 (t70) cc_final: 0.7503 (t0) REVERT: Ac 160 MET cc_start: 0.7328 (mmm) cc_final: 0.7111 (mmm) REVERT: Ad 138 ASP cc_start: 0.7925 (t70) cc_final: 0.7606 (t0) REVERT: Ad 160 MET cc_start: 0.7507 (mmm) cc_final: 0.7187 (mmm) REVERT: Af 79 ASP cc_start: 0.6710 (t0) cc_final: 0.6487 (t0) REVERT: Ag 121 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6765 (mt-10) REVERT: Ag 183 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6929 (ttp-110) REVERT: Ah 79 ASP cc_start: 0.6713 (t0) cc_final: 0.6513 (t0) REVERT: Ai 160 MET cc_start: 0.7755 (mmm) cc_final: 0.7334 (mmm) REVERT: Aj 209 THR cc_start: 0.8698 (m) cc_final: 0.8178 (p) REVERT: Aj 220 MET cc_start: 0.6990 (mtt) cc_final: 0.6787 (mtt) REVERT: Ak 160 MET cc_start: 0.7467 (mmm) cc_final: 0.7147 (mmm) REVERT: Al 77 GLN cc_start: 0.7243 (mt0) cc_final: 0.6888 (mt0) REVERT: Al 160 MET cc_start: 0.7542 (mmm) cc_final: 0.7278 (mmm) REVERT: An 183 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6847 (ttp-110) REVERT: Ap 183 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6718 (ttp-170) REVERT: Aq 160 MET cc_start: 0.7356 (mmm) cc_final: 0.7128 (mmm) REVERT: Aq 197 ARG cc_start: 0.7562 (ptm-80) cc_final: 0.7296 (ptm-80) REVERT: Ar 55 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8285 (mtp180) REVERT: Ar 77 GLN cc_start: 0.7419 (mt0) cc_final: 0.7161 (mt0) REVERT: As 97 VAL cc_start: 0.8256 (p) cc_final: 0.8053 (t) REVERT: As 160 MET cc_start: 0.7544 (mmm) cc_final: 0.7163 (mmm) REVERT: At 77 GLN cc_start: 0.7506 (mt0) cc_final: 0.7156 (mt0) REVERT: At 138 ASP cc_start: 0.7959 (t70) cc_final: 0.7604 (t0) REVERT: At 139 GLU cc_start: 0.6902 (pt0) cc_final: 0.6639 (pt0) REVERT: Aw 79 ASP cc_start: 0.6915 (t0) cc_final: 0.6619 (t0) REVERT: Aw 134 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7216 (ttp) REVERT: Ay 97 VAL cc_start: 0.8354 (p) cc_final: 0.8087 (t) REVERT: Ay 160 MET cc_start: 0.7594 (mmm) cc_final: 0.7269 (mmm) REVERT: Az 116 MET cc_start: 0.8244 (tmm) cc_final: 0.7889 (ttp) REVERT: Az 157 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7530 (ttm-80) REVERT: Az 160 MET cc_start: 0.7588 (mmm) cc_final: 0.7207 (mmm) REVERT: Ba 138 ASP cc_start: 0.7800 (t70) cc_final: 0.7426 (t0) REVERT: Ba 160 MET cc_start: 0.7569 (mmm) cc_final: 0.7253 (mmm) REVERT: Bb 55 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8255 (mtp180) REVERT: Bb 160 MET cc_start: 0.7270 (mmm) cc_final: 0.7008 (mmm) REVERT: Be 145 LEU cc_start: 0.8688 (mp) cc_final: 0.8482 (mt) REVERT: Bg 157 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7539 (ttm-80) REVERT: Bh 64 VAL cc_start: 0.8284 (m) cc_final: 0.8077 (m) REVERT: Bh 138 ASP cc_start: 0.7830 (t70) cc_final: 0.7477 (t0) REVERT: Bh 160 MET cc_start: 0.7650 (mmm) cc_final: 0.7164 (mmm) REVERT: Bh 209 THR cc_start: 0.8519 (m) cc_final: 0.7989 (p) REVERT: Bi 64 VAL cc_start: 0.7567 (t) cc_final: 0.7356 (t) REVERT: Bj 138 ASP cc_start: 0.7860 (t70) cc_final: 0.7536 (t0) REVERT: Bj 160 MET cc_start: 0.7556 (tpp) cc_final: 0.7150 (mmm) REVERT: Bk 112 MET cc_start: 0.8075 (tpp) cc_final: 0.7874 (mmm) REVERT: Bk 183 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6866 (ttp-110) REVERT: Bm 108 MET cc_start: 0.7140 (tpp) cc_final: 0.6706 (ttp) REVERT: Bo 55 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8197 (mtp180) REVERT: Bo 77 GLN cc_start: 0.7460 (mt0) cc_final: 0.7192 (mt0) REVERT: Bo 138 ASP cc_start: 0.7715 (t70) cc_final: 0.7284 (t0) REVERT: Bo 160 MET cc_start: 0.7524 (mmm) cc_final: 0.7255 (mmm) REVERT: Bp 97 VAL cc_start: 0.8186 (p) cc_final: 0.7979 (t) REVERT: Bp 160 MET cc_start: 0.7355 (tpp) cc_final: 0.7101 (mmm) REVERT: Bq 139 GLU cc_start: 0.7038 (pt0) cc_final: 0.6779 (pt0) REVERT: Bq 160 MET cc_start: 0.7572 (tpp) cc_final: 0.7249 (mmm) REVERT: Br 160 MET cc_start: 0.7412 (mmm) cc_final: 0.7149 (mmm) REVERT: Bs 134 MET cc_start: 0.7715 (ttp) cc_final: 0.7443 (tpp) REVERT: Bs 208 ARG cc_start: 0.7368 (mtm110) cc_final: 0.7138 (mtm110) REVERT: Bt 173 MET cc_start: 0.7282 (tpp) cc_final: 0.6924 (mpp) REVERT: Bt 183 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7043 (ttp-110) REVERT: Bu 117 VAL cc_start: 0.8684 (t) cc_final: 0.8460 (m) REVERT: Bu 121 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6811 (mt-10) REVERT: Bu 172 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6640 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6770 (ttp-110) REVERT: Bv 112 MET cc_start: 0.8631 (tpp) cc_final: 0.8405 (mmm) outliers start: 231 outliers final: 168 residues processed: 2116 average time/residue: 1.6308 time to fit residues: 4328.9559 Evaluate side-chains 2210 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 2034 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 183 ARG Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ac residue 212 ARG Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 205 VAL Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 168 GLU Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 56 MET Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 131 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 197 ARG Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 131 VAL Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain At residue 181 MET Chi-restraints excluded: chain At residue 212 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 64 VAL Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Aw residue 212 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Ay residue 212 ARG Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 141 VAL Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 64 VAL Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 133 VAL Chi-restraints excluded: chain Bf residue 140 GLN Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 71 LEU Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 157 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 106 THR Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 71 LEU Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 127 ASN Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 145 LEU Chi-restraints excluded: chain Bm residue 205 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bp residue 212 ARG Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 80 ILE Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 159 ILE Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bt residue 64 VAL Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bt residue 159 ILE Chi-restraints excluded: chain Bt residue 183 ARG Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 133 VAL Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 0.6980 chunk 752 optimal weight: 0.9990 chunk 459 optimal weight: 0.9990 chunk 356 optimal weight: 0.2980 chunk 522 optimal weight: 1.9990 chunk 789 optimal weight: 3.9990 chunk 726 optimal weight: 0.4980 chunk 628 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 485 optimal weight: 0.7980 chunk 385 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 77 GLN Ar 66 ASN Bg 69 HIS Bi 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 66840 Z= 0.228 Angle : 0.680 14.387 90648 Z= 0.326 Chirality : 0.043 0.279 9744 Planarity : 0.006 0.112 11856 Dihedral : 4.561 24.436 9024 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.89 % Allowed : 32.72 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.28 (0.10), residues: 8016 helix: -0.15 (0.08), residues: 4080 sheet: 1.25 (0.22), residues: 528 loop : -0.27 (0.12), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPBh 93 HIS 0.016 0.002 HISAn 69 PHE 0.016 0.002 PHEAa 200 TYR 0.040 0.002 TYRAs 73 ARG 0.011 0.001 ARGBk 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16032 Ramachandran restraints generated. 8016 Oldfield, 0 Emsley, 8016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2262 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 2058 time to evaluate : 5.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.8168 (mtt) cc_final: 0.7928 (mtt) REVERT: Aa 138 ASP cc_start: 0.7918 (t70) cc_final: 0.7598 (t0) REVERT: Aa 197 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6914 (ptm160) REVERT: Aa 209 THR cc_start: 0.8383 (m) cc_final: 0.7847 (p) REVERT: Ab 138 ASP cc_start: 0.7853 (t70) cc_final: 0.7419 (t0) REVERT: Ab 160 MET cc_start: 0.7351 (tpp) cc_final: 0.6985 (mmm) REVERT: Ab 209 THR cc_start: 0.8379 (m) cc_final: 0.7788 (p) REVERT: Ac 138 ASP cc_start: 0.7899 (t70) cc_final: 0.7642 (t70) REVERT: Ad 138 ASP cc_start: 0.7942 (t70) cc_final: 0.7611 (t0) REVERT: Ad 160 MET cc_start: 0.7562 (mmm) cc_final: 0.7242 (mmm) REVERT: Ae 145 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8611 (mp) REVERT: Af 79 ASP cc_start: 0.6760 (t0) cc_final: 0.6503 (t0) REVERT: Ag 121 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6727 (mt-10) REVERT: Ag 183 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6936 (ttp-110) REVERT: Ah 79 ASP cc_start: 0.6689 (t0) cc_final: 0.6440 (t0) REVERT: Ai 160 MET cc_start: 0.7754 (mmm) cc_final: 0.7339 (mmm) REVERT: Aj 209 THR cc_start: 0.8700 (m) cc_final: 0.8166 (p) REVERT: Aj 220 MET cc_start: 0.6987 (mtt) cc_final: 0.6778 (mtt) REVERT: Al 77 GLN cc_start: 0.7248 (mt0) cc_final: 0.6892 (mt0) REVERT: Al 160 MET cc_start: 0.7560 (mmm) cc_final: 0.7301 (mmm) REVERT: Al 168 GLU cc_start: 0.6807 (pt0) cc_final: 0.6152 (pt0) REVERT: An 112 MET cc_start: 0.8553 (tpp) cc_final: 0.8318 (mmm) REVERT: An 183 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6887 (ttp-110) REVERT: Ao 145 LEU cc_start: 0.8914 (mm) cc_final: 0.8621 (mp) REVERT: Ap 183 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.6745 (ttp-170) REVERT: Aq 160 MET cc_start: 0.7324 (mmm) cc_final: 0.7122 (mmm) REVERT: Ar 77 GLN cc_start: 0.7462 (mt0) cc_final: 0.7198 (mt0) REVERT: Ar 160 MET cc_start: 0.7562 (mmm) cc_final: 0.7095 (mmm) REVERT: As 97 VAL cc_start: 0.8252 (p) cc_final: 0.8036 (t) REVERT: As 160 MET cc_start: 0.7523 (mmm) cc_final: 0.7148 (mmm) REVERT: At 77 GLN cc_start: 0.7505 (mt0) cc_final: 0.7149 (mt0) REVERT: At 138 ASP cc_start: 0.7973 (t70) cc_final: 0.7755 (t70) REVERT: Av 112 MET cc_start: 0.8415 (tpp) cc_final: 0.7884 (mmm) REVERT: Av 134 MET cc_start: 0.7697 (ttp) cc_final: 0.7460 (tpp) REVERT: Aw 79 ASP cc_start: 0.6952 (t0) cc_final: 0.6655 (t0) REVERT: Aw 134 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7187 (ttp) REVERT: Ay 97 VAL cc_start: 0.8321 (p) cc_final: 0.8026 (t) REVERT: Ay 160 MET cc_start: 0.7632 (mmm) cc_final: 0.7318 (mmm) REVERT: Az 55 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8262 (mtp85) REVERT: Az 157 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7530 (ttm-80) REVERT: Az 160 MET cc_start: 0.7586 (mmm) cc_final: 0.7227 (mmm) REVERT: Ba 138 ASP cc_start: 0.7847 (t70) cc_final: 0.7403 (t0) REVERT: Ba 160 MET cc_start: 0.7574 (mmm) cc_final: 0.7234 (mmm) REVERT: Bb 116 MET cc_start: 0.8252 (tmm) cc_final: 0.8010 (ttp) REVERT: Bb 160 MET cc_start: 0.7268 (mmm) cc_final: 0.7009 (mmm) REVERT: Bg 138 ASP cc_start: 0.7730 (t70) cc_final: 0.7372 (t0) REVERT: Bg 157 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7569 (ttm-80) REVERT: Bh 64 VAL cc_start: 0.8307 (m) cc_final: 0.8094 (m) REVERT: Bh 138 ASP cc_start: 0.7851 (t70) cc_final: 0.7514 (t0) REVERT: Bh 160 MET cc_start: 0.7645 (mmm) cc_final: 0.7219 (mmm) REVERT: Bh 209 THR cc_start: 0.8528 (m) cc_final: 0.7995 (p) REVERT: Bj 138 ASP cc_start: 0.7855 (t70) cc_final: 0.7563 (t0) REVERT: Bj 160 MET cc_start: 0.7552 (tpp) cc_final: 0.7158 (mmm) REVERT: Bk 112 MET cc_start: 0.8259 (tpp) cc_final: 0.7902 (mmm) REVERT: Bk 183 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6887 (ttp-110) REVERT: Bl 108 MET cc_start: 0.7069 (tpp) cc_final: 0.6535 (ttp) REVERT: Bm 112 MET cc_start: 0.8410 (mpp) cc_final: 0.7947 (mmt) REVERT: Bo 55 ARG cc_start: 0.8544 (mtp180) cc_final: 0.8281 (mtp85) REVERT: Bo 77 GLN cc_start: 0.7443 (mt0) cc_final: 0.7193 (mt0) REVERT: Bo 138 ASP cc_start: 0.7706 (t70) cc_final: 0.7290 (t0) REVERT: Bo 160 MET cc_start: 0.7516 (mmm) cc_final: 0.7245 (mmm) REVERT: Bo 220 MET cc_start: 0.7045 (mtt) cc_final: 0.6815 (mtt) REVERT: Bp 160 MET cc_start: 0.7362 (tpp) cc_final: 0.7116 (mmm) REVERT: Bp 220 MET cc_start: 0.7090 (mtt) cc_final: 0.6850 (mtt) REVERT: Bq 160 MET cc_start: 0.7583 (tpp) cc_final: 0.7266 (mmm) REVERT: Br 116 MET cc_start: 0.8385 (tmm) cc_final: 0.8054 (ttp) REVERT: Br 160 MET cc_start: 0.7403 (mmm) cc_final: 0.7054 (mmm) REVERT: Bs 134 MET cc_start: 0.7705 (ttp) cc_final: 0.7486 (tpp) REVERT: Bs 208 ARG cc_start: 0.7379 (mtm110) cc_final: 0.7152 (mtm110) REVERT: Bt 183 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7111 (ttp-110) REVERT: Bu 117 VAL cc_start: 0.8687 (t) cc_final: 0.8446 (m) REVERT: Bu 172 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6674 (tm-30) REVERT: Bu 183 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6782 (ttp-110) REVERT: Bv 121 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6637 (mt-10) outliers start: 204 outliers final: 169 residues processed: 2097 average time/residue: 1.6204 time to fit residues: 4260.9388 Evaluate side-chains 2223 residues out of total 7056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 2045 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 166 VAL Chi-restraints excluded: chain Ac residue 183 ARG Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 183 ARG Chi-restraints excluded: chain Ad residue 197 ARG Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 145 LEU Chi-restraints excluded: chain Ae residue 218 ILE Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 145 LEU Chi-restraints excluded: chain Af residue 159 ILE Chi-restraints excluded: chain Af residue 168 GLU Chi-restraints excluded: chain Af residue 205 VAL Chi-restraints excluded: chain Af residue 218 ILE Chi-restraints excluded: chain Ag residue 56 MET Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 183 ARG Chi-restraints excluded: chain Ag residue 220 MET Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 131 VAL Chi-restraints excluded: chain Ai residue 183 ARG Chi-restraints excluded: chain Ai residue 197 ARG Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Aj residue 159 ILE Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 197 ARG Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 131 VAL Chi-restraints excluded: chain Al residue 183 ARG Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 135 MET Chi-restraints excluded: chain Am residue 159 ILE Chi-restraints excluded: chain An residue 64 VAL Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 183 ARG Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 159 ILE Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 71 LEU Chi-restraints excluded: chain Aq residue 183 ARG Chi-restraints excluded: chain Aq residue 212 ARG Chi-restraints excluded: chain Ar residue 71 LEU Chi-restraints excluded: chain Ar residue 157 ARG Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 86 THR Chi-restraints excluded: chain As residue 159 ILE Chi-restraints excluded: chain As residue 197 ARG Chi-restraints excluded: chain At residue 71 LEU Chi-restraints excluded: chain At residue 181 MET Chi-restraints excluded: chain At residue 212 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 116 MET Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Au residue 183 ARG Chi-restraints excluded: chain Av residue 64 VAL Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 145 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 134 MET Chi-restraints excluded: chain Aw residue 183 ARG Chi-restraints excluded: chain Aw residue 212 ARG Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ay residue 71 LEU Chi-restraints excluded: chain Ay residue 131 VAL Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 183 ARG Chi-restraints excluded: chain Ay residue 197 ARG Chi-restraints excluded: chain Az residue 71 LEU Chi-restraints excluded: chain Az residue 183 ARG Chi-restraints excluded: chain Ba residue 71 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 166 VAL Chi-restraints excluded: chain Ba residue 212 ARG Chi-restraints excluded: chain Bb residue 71 LEU Chi-restraints excluded: chain Bb residue 80 ILE Chi-restraints excluded: chain Bb residue 166 VAL Chi-restraints excluded: chain Bb residue 197 ARG Chi-restraints excluded: chain Bc residue 141 VAL Chi-restraints excluded: chain Bc residue 205 VAL Chi-restraints excluded: chain Bd residue 133 VAL Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 133 VAL Chi-restraints excluded: chain Be residue 220 MET Chi-restraints excluded: chain Bf residue 124 THR Chi-restraints excluded: chain Bf residue 133 VAL Chi-restraints excluded: chain Bf residue 140 GLN Chi-restraints excluded: chain Bf residue 145 LEU Chi-restraints excluded: chain Bf residue 205 VAL Chi-restraints excluded: chain Bg residue 71 LEU Chi-restraints excluded: chain Bg residue 86 THR Chi-restraints excluded: chain Bg residue 157 ARG Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 208 ARG Chi-restraints excluded: chain Bh residue 71 LEU Chi-restraints excluded: chain Bh residue 141 VAL Chi-restraints excluded: chain Bh residue 166 VAL Chi-restraints excluded: chain Bh residue 197 ARG Chi-restraints excluded: chain Bi residue 71 LEU Chi-restraints excluded: chain Bi residue 77 GLN Chi-restraints excluded: chain Bi residue 106 THR Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 166 VAL Chi-restraints excluded: chain Bi residue 183 ARG Chi-restraints excluded: chain Bi residue 197 ARG Chi-restraints excluded: chain Bj residue 71 LEU Chi-restraints excluded: chain Bj residue 80 ILE Chi-restraints excluded: chain Bj residue 86 THR Chi-restraints excluded: chain Bj residue 131 VAL Chi-restraints excluded: chain Bj residue 141 VAL Chi-restraints excluded: chain Bj residue 183 ARG Chi-restraints excluded: chain Bj residue 219 GLN Chi-restraints excluded: chain Bk residue 124 THR Chi-restraints excluded: chain Bk residue 127 ASN Chi-restraints excluded: chain Bk residue 133 VAL Chi-restraints excluded: chain Bk residue 141 VAL Chi-restraints excluded: chain Bk residue 183 ARG Chi-restraints excluded: chain Bl residue 124 THR Chi-restraints excluded: chain Bl residue 218 ILE Chi-restraints excluded: chain Bm residue 116 MET Chi-restraints excluded: chain Bm residue 124 THR Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 145 LEU Chi-restraints excluded: chain Bm residue 205 VAL Chi-restraints excluded: chain Bn residue 124 THR Chi-restraints excluded: chain Bn residue 205 VAL Chi-restraints excluded: chain Bn residue 212 ARG Chi-restraints excluded: chain Bo residue 71 LEU Chi-restraints excluded: chain Bo residue 131 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 183 ARG Chi-restraints excluded: chain Bo residue 212 ARG Chi-restraints excluded: chain Bp residue 71 LEU Chi-restraints excluded: chain Bp residue 86 THR Chi-restraints excluded: chain Bq residue 71 LEU Chi-restraints excluded: chain Bq residue 159 ILE Chi-restraints excluded: chain Bq residue 183 ARG Chi-restraints excluded: chain Br residue 71 LEU Chi-restraints excluded: chain Br residue 131 VAL Chi-restraints excluded: chain Br residue 183 ARG Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 124 THR Chi-restraints excluded: chain Bt residue 64 VAL Chi-restraints excluded: chain Bt residue 116 MET Chi-restraints excluded: chain Bt residue 133 VAL Chi-restraints excluded: chain Bt residue 183 ARG Chi-restraints excluded: chain Bu residue 124 THR Chi-restraints excluded: chain Bu residue 133 VAL Chi-restraints excluded: chain Bu residue 183 ARG Chi-restraints excluded: chain Bv residue 64 VAL Chi-restraints excluded: chain Bv residue 116 MET Chi-restraints excluded: chain Bv residue 124 THR Chi-restraints excluded: chain Bv residue 212 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 0.9980 chunk 669 optimal weight: 0.5980 chunk 192 optimal weight: 0.2980 chunk 579 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 629 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 646 optimal weight: 0.0000 chunk 79 optimal weight: 1.9990 chunk 115 optimal weight: 0.0040 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ar 66 ASN Bi 77 GLN ** Bk 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130004 restraints weight = 98159.086| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.31 r_work: 0.3610 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 66840 Z= 0.181 Angle : 0.665 13.827 90648 Z= 0.318 Chirality : 0.041 0.276 9744 Planarity : 0.006 0.112 11856 Dihedral : 4.495 23.568 9024 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.75 % Allowed : 32.95 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.17 (0.10), residues: 8016 helix: -0.05 (0.08), residues: 4080 sheet: 1.26 (0.22), residues: 528 loop : -0.22 (0.13), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPBh 93 HIS 0.018 0.002 HISAn 69 PHE 0.016 0.002 PHEBi 200 TYR 0.042 0.002 TYRBf 198 ARG 0.011 0.001 ARGAp 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49414.79 seconds wall clock time: 844 minutes 7.43 seconds (50647.43 seconds total)