Starting phenix.real_space_refine on Sun Feb 8 05:24:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ra2_53868/02_2026/9ra2_53868.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.033 sd= 0.164 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 324 5.16 5 C 25272 2.51 5 N 7101 2.21 5 O 7290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39987 Number of models: 1 Model: "" Number of chains: 27 Chain: "Aa" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ab" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ac" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ad" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ae" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Af" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ag" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ah" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ai" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Aj" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ak" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Al" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Am" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "An" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ao" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ap" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Aq" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ar" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "As" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "At" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Au" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Av" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Aw" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ax" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ay" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Az" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Chain: "Ba" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1481 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 167} Time building chain proxies: 9.20, per 1000 atoms: 0.23 Number of scatterers: 39987 At special positions: 0 Unit cell: (150.1, 150.1, 166.25, 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 324 16.00 O 7290 8.00 N 7101 7.00 C 25272 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9396 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 54 sheets defined 54.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'Aa' and resid 103 through 108 Processing helix chain 'Aa' and resid 123 through 139 Processing helix chain 'Aa' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAa 146 " --> pdb=" O ASPAa 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAa 147 " --> pdb=" O GLUAa 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAa 154 " --> pdb=" O ASNAa 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAa 158 " --> pdb=" O VALAa 154 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 192 through 198 Processing helix chain 'Aa' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAa 209 " --> pdb=" O GLUAa 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAa 214 " --> pdb=" O METAa 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAa 215 " --> pdb=" O ARGAa 211 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 219 through 224 Processing helix chain 'Aa' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAa 234 " --> pdb=" O SERAa 231 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAa 251 " --> pdb=" O PROAa 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAa 252 " --> pdb=" O ASNAa 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAa 256 " --> pdb=" O GLUAa 252 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 103 through 108 Processing helix chain 'Ab' and resid 123 through 139 Processing helix chain 'Ab' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAb 146 " --> pdb=" O ASPAb 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAb 147 " --> pdb=" O GLUAb 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAb 154 " --> pdb=" O ASNAb 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAb 158 " --> pdb=" O VALAb 154 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 188 Processing helix chain 'Ab' and resid 192 through 198 Processing helix chain 'Ab' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAb 209 " --> pdb=" O GLUAb 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAb 214 " --> pdb=" O METAb 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAb 215 " --> pdb=" O ARGAb 211 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 219 through 224 Processing helix chain 'Ab' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAb 234 " --> pdb=" O SERAb 231 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAb 251 " --> pdb=" O PROAb 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAb 252 " --> pdb=" O ASNAb 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAb 256 " --> pdb=" O GLUAb 252 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 103 through 108 Processing helix chain 'Ac' and resid 123 through 139 Processing helix chain 'Ac' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAc 146 " --> pdb=" O ASPAc 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAc 147 " --> pdb=" O GLUAc 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAc 154 " --> pdb=" O ASNAc 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAc 158 " --> pdb=" O VALAc 154 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 192 through 198 Processing helix chain 'Ac' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAc 209 " --> pdb=" O GLUAc 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAc 214 " --> pdb=" O METAc 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAc 215 " --> pdb=" O ARGAc 211 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 219 through 224 Processing helix chain 'Ac' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAc 234 " --> pdb=" O SERAc 231 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAc 251 " --> pdb=" O PROAc 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAc 252 " --> pdb=" O ASNAc 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAc 256 " --> pdb=" O GLUAc 252 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 103 through 108 Processing helix chain 'Ad' and resid 123 through 139 Processing helix chain 'Ad' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAd 146 " --> pdb=" O ASPAd 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAd 147 " --> pdb=" O GLUAd 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAd 154 " --> pdb=" O ASNAd 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAd 158 " --> pdb=" O VALAd 154 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 188 Processing helix chain 'Ad' and resid 192 through 198 Processing helix chain 'Ad' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAd 209 " --> pdb=" O GLUAd 205 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASPAd 214 " --> pdb=" O METAd 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAd 215 " --> pdb=" O ARGAd 211 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 219 through 224 Processing helix chain 'Ad' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAd 234 " --> pdb=" O SERAd 231 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAd 251 " --> pdb=" O PROAd 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAd 252 " --> pdb=" O ASNAd 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAd 256 " --> pdb=" O GLUAd 252 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 103 through 108 Processing helix chain 'Ae' and resid 123 through 139 Processing helix chain 'Ae' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAe 146 " --> pdb=" O ASPAe 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAe 147 " --> pdb=" O GLUAe 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAe 154 " --> pdb=" O ASNAe 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAe 158 " --> pdb=" O VALAe 154 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 192 through 198 Processing helix chain 'Ae' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAe 209 " --> pdb=" O GLUAe 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAe 214 " --> pdb=" O METAe 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAe 215 " --> pdb=" O ARGAe 211 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 219 through 224 Processing helix chain 'Ae' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAe 234 " --> pdb=" O SERAe 231 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAe 251 " --> pdb=" O PROAe 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAe 252 " --> pdb=" O ASNAe 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAe 256 " --> pdb=" O GLUAe 252 " (cutoff:3.500A) Processing helix chain 'Af' and resid 103 through 108 Processing helix chain 'Af' and resid 123 through 139 Processing helix chain 'Af' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAf 146 " --> pdb=" O ASPAf 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAf 147 " --> pdb=" O GLUAf 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAf 154 " --> pdb=" O ASNAf 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUAf 158 " --> pdb=" O VALAf 154 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 188 Processing helix chain 'Af' and resid 192 through 198 Processing helix chain 'Af' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAf 209 " --> pdb=" O GLUAf 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAf 214 " --> pdb=" O METAf 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAf 215 " --> pdb=" O ARGAf 211 " (cutoff:3.500A) Processing helix chain 'Af' and resid 219 through 224 Processing helix chain 'Af' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAf 234 " --> pdb=" O SERAf 231 " (cutoff:3.500A) Processing helix chain 'Af' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAf 251 " --> pdb=" O PROAf 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAf 252 " --> pdb=" O ASNAf 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAf 256 " --> pdb=" O GLUAf 252 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 103 through 108 Processing helix chain 'Ag' and resid 123 through 139 Processing helix chain 'Ag' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAg 146 " --> pdb=" O ASPAg 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAg 147 " --> pdb=" O GLUAg 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAg 154 " --> pdb=" O ASNAg 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAg 158 " --> pdb=" O VALAg 154 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 192 through 198 Processing helix chain 'Ag' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAg 209 " --> pdb=" O GLUAg 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAg 214 " --> pdb=" O METAg 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAg 215 " --> pdb=" O ARGAg 211 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 219 through 224 Processing helix chain 'Ag' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAg 234 " --> pdb=" O SERAg 231 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAg 251 " --> pdb=" O PROAg 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAg 252 " --> pdb=" O ASNAg 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAg 256 " --> pdb=" O GLUAg 252 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 103 through 108 Processing helix chain 'Ah' and resid 123 through 139 Processing helix chain 'Ah' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAh 146 " --> pdb=" O ASPAh 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAh 147 " --> pdb=" O GLUAh 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAh 154 " --> pdb=" O ASNAh 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAh 158 " --> pdb=" O VALAh 154 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 188 Processing helix chain 'Ah' and resid 192 through 198 Processing helix chain 'Ah' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAh 209 " --> pdb=" O GLUAh 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAh 214 " --> pdb=" O METAh 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAh 215 " --> pdb=" O ARGAh 211 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 219 through 224 Processing helix chain 'Ah' and resid 229 through 236 removed outlier: 4.733A pdb=" N ARGAh 234 " --> pdb=" O SERAh 231 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAh 251 " --> pdb=" O PROAh 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAh 252 " --> pdb=" O ASNAh 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAh 256 " --> pdb=" O GLUAh 252 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 103 through 108 Processing helix chain 'Ai' and resid 123 through 139 Processing helix chain 'Ai' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAi 146 " --> pdb=" O ASPAi 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAi 147 " --> pdb=" O GLUAi 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAi 154 " --> pdb=" O ASNAi 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUAi 158 " --> pdb=" O VALAi 154 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 192 through 198 Processing helix chain 'Ai' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAi 209 " --> pdb=" O GLUAi 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAi 214 " --> pdb=" O METAi 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAi 215 " --> pdb=" O ARGAi 211 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 219 through 224 Processing helix chain 'Ai' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAi 234 " --> pdb=" O SERAi 231 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAi 251 " --> pdb=" O PROAi 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAi 252 " --> pdb=" O ASNAi 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAi 256 " --> pdb=" O GLUAi 252 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 103 through 108 Processing helix chain 'Aj' and resid 123 through 139 Processing helix chain 'Aj' and resid 141 through 160 removed outlier: 3.948A pdb=" N ARGAj 146 " --> pdb=" O ASPAj 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAj 147 " --> pdb=" O GLUAj 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAj 154 " --> pdb=" O ASNAj 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAj 158 " --> pdb=" O VALAj 154 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 188 Processing helix chain 'Aj' and resid 192 through 198 Processing helix chain 'Aj' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAj 209 " --> pdb=" O GLUAj 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAj 214 " --> pdb=" O METAj 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAj 215 " --> pdb=" O ARGAj 211 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 219 through 224 Processing helix chain 'Aj' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAj 234 " --> pdb=" O SERAj 231 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAj 251 " --> pdb=" O PROAj 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAj 252 " --> pdb=" O ASNAj 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAj 256 " --> pdb=" O GLUAj 252 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 103 through 108 Processing helix chain 'Ak' and resid 123 through 139 Processing helix chain 'Ak' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAk 146 " --> pdb=" O ASPAk 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAk 147 " --> pdb=" O GLUAk 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAk 154 " --> pdb=" O ASNAk 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAk 158 " --> pdb=" O VALAk 154 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 188 Processing helix chain 'Ak' and resid 192 through 198 Processing helix chain 'Ak' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAk 209 " --> pdb=" O GLUAk 205 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASPAk 214 " --> pdb=" O METAk 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLUAk 215 " --> pdb=" O ARGAk 211 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 219 through 224 Processing helix chain 'Ak' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAk 234 " --> pdb=" O SERAk 231 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAk 251 " --> pdb=" O PROAk 247 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLUAk 252 " --> pdb=" O ASNAk 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAk 256 " --> pdb=" O GLUAk 252 " (cutoff:3.500A) Processing helix chain 'Al' and resid 103 through 108 Processing helix chain 'Al' and resid 123 through 139 Processing helix chain 'Al' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAl 146 " --> pdb=" O ASPAl 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAl 147 " --> pdb=" O GLUAl 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAl 154 " --> pdb=" O ASNAl 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAl 158 " --> pdb=" O VALAl 154 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 188 Processing helix chain 'Al' and resid 192 through 198 Processing helix chain 'Al' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAl 209 " --> pdb=" O GLUAl 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAl 214 " --> pdb=" O METAl 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAl 215 " --> pdb=" O ARGAl 211 " (cutoff:3.500A) Processing helix chain 'Al' and resid 219 through 224 Processing helix chain 'Al' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAl 234 " --> pdb=" O SERAl 231 " (cutoff:3.500A) Processing helix chain 'Al' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAl 251 " --> pdb=" O PROAl 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAl 252 " --> pdb=" O ASNAl 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAl 256 " --> pdb=" O GLUAl 252 " (cutoff:3.500A) Processing helix chain 'Am' and resid 103 through 108 Processing helix chain 'Am' and resid 123 through 139 Processing helix chain 'Am' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAm 146 " --> pdb=" O ASPAm 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAm 147 " --> pdb=" O GLUAm 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAm 154 " --> pdb=" O ASNAm 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLUAm 158 " --> pdb=" O VALAm 154 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 188 Processing helix chain 'Am' and resid 192 through 198 Processing helix chain 'Am' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAm 209 " --> pdb=" O GLUAm 205 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASPAm 214 " --> pdb=" O METAm 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAm 215 " --> pdb=" O ARGAm 211 " (cutoff:3.500A) Processing helix chain 'Am' and resid 219 through 224 Processing helix chain 'Am' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAm 234 " --> pdb=" O SERAm 231 " (cutoff:3.500A) Processing helix chain 'Am' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAm 251 " --> pdb=" O PROAm 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLUAm 252 " --> pdb=" O ASNAm 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAm 256 " --> pdb=" O GLUAm 252 " (cutoff:3.500A) Processing helix chain 'An' and resid 103 through 108 Processing helix chain 'An' and resid 123 through 139 Processing helix chain 'An' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAn 146 " --> pdb=" O ASPAn 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAn 147 " --> pdb=" O GLUAn 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAn 154 " --> pdb=" O ASNAn 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAn 158 " --> pdb=" O VALAn 154 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 188 Processing helix chain 'An' and resid 192 through 198 Processing helix chain 'An' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAn 209 " --> pdb=" O GLUAn 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAn 214 " --> pdb=" O METAn 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAn 215 " --> pdb=" O ARGAn 211 " (cutoff:3.500A) Processing helix chain 'An' and resid 219 through 224 Processing helix chain 'An' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAn 234 " --> pdb=" O SERAn 231 " (cutoff:3.500A) Processing helix chain 'An' and resid 247 through 256 removed outlier: 3.626A pdb=" N ARGAn 251 " --> pdb=" O PROAn 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAn 252 " --> pdb=" O ASNAn 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAn 256 " --> pdb=" O GLUAn 252 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 103 through 108 Processing helix chain 'Ao' and resid 123 through 139 Processing helix chain 'Ao' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAo 146 " --> pdb=" O ASPAo 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAo 147 " --> pdb=" O GLUAo 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAo 154 " --> pdb=" O ASNAo 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUAo 158 " --> pdb=" O VALAo 154 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 188 Processing helix chain 'Ao' and resid 192 through 198 Processing helix chain 'Ao' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAo 209 " --> pdb=" O GLUAo 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAo 214 " --> pdb=" O METAo 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAo 215 " --> pdb=" O ARGAo 211 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 219 through 224 Processing helix chain 'Ao' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAo 234 " --> pdb=" O SERAo 231 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAo 251 " --> pdb=" O PROAo 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAo 252 " --> pdb=" O ASNAo 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAo 256 " --> pdb=" O GLUAo 252 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 103 through 108 Processing helix chain 'Ap' and resid 123 through 139 Processing helix chain 'Ap' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAp 146 " --> pdb=" O ASPAp 142 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILEAp 147 " --> pdb=" O GLUAp 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAp 154 " --> pdb=" O ASNAp 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAp 158 " --> pdb=" O VALAp 154 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 188 Processing helix chain 'Ap' and resid 192 through 198 Processing helix chain 'Ap' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAp 209 " --> pdb=" O GLUAp 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAp 214 " --> pdb=" O METAp 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAp 215 " --> pdb=" O ARGAp 211 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 219 through 224 Processing helix chain 'Ap' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAp 234 " --> pdb=" O SERAp 231 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAp 251 " --> pdb=" O PROAp 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLUAp 252 " --> pdb=" O ASNAp 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAp 256 " --> pdb=" O GLUAp 252 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 103 through 108 Processing helix chain 'Aq' and resid 123 through 139 Processing helix chain 'Aq' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAq 146 " --> pdb=" O ASPAq 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAq 147 " --> pdb=" O GLUAq 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAq 154 " --> pdb=" O ASNAq 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAq 158 " --> pdb=" O VALAq 154 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 182 through 188 Processing helix chain 'Aq' and resid 192 through 198 Processing helix chain 'Aq' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAq 209 " --> pdb=" O GLUAq 205 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASPAq 214 " --> pdb=" O METAq 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAq 215 " --> pdb=" O ARGAq 211 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 219 through 224 Processing helix chain 'Aq' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAq 234 " --> pdb=" O SERAq 231 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAq 251 " --> pdb=" O PROAq 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAq 252 " --> pdb=" O ASNAq 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAq 256 " --> pdb=" O GLUAq 252 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 103 through 108 Processing helix chain 'Ar' and resid 123 through 139 Processing helix chain 'Ar' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAr 146 " --> pdb=" O ASPAr 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAr 147 " --> pdb=" O GLUAr 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAr 154 " --> pdb=" O ASNAr 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUAr 158 " --> pdb=" O VALAr 154 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 182 through 188 Processing helix chain 'Ar' and resid 192 through 198 Processing helix chain 'Ar' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAr 209 " --> pdb=" O GLUAr 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAr 214 " --> pdb=" O METAr 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAr 215 " --> pdb=" O ARGAr 211 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 219 through 224 Processing helix chain 'Ar' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAr 234 " --> pdb=" O SERAr 231 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAr 251 " --> pdb=" O PROAr 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLUAr 252 " --> pdb=" O ASNAr 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAr 256 " --> pdb=" O GLUAr 252 " (cutoff:3.500A) Processing helix chain 'As' and resid 103 through 108 Processing helix chain 'As' and resid 123 through 139 Processing helix chain 'As' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAs 146 " --> pdb=" O ASPAs 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAs 147 " --> pdb=" O GLUAs 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAs 154 " --> pdb=" O ASNAs 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAs 158 " --> pdb=" O VALAs 154 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 192 through 198 Processing helix chain 'As' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAs 209 " --> pdb=" O GLUAs 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAs 214 " --> pdb=" O METAs 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAs 215 " --> pdb=" O ARGAs 211 " (cutoff:3.500A) Processing helix chain 'As' and resid 219 through 224 Processing helix chain 'As' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAs 234 " --> pdb=" O SERAs 231 " (cutoff:3.500A) Processing helix chain 'As' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAs 251 " --> pdb=" O PROAs 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAs 252 " --> pdb=" O ASNAs 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAs 256 " --> pdb=" O GLUAs 252 " (cutoff:3.500A) Processing helix chain 'At' and resid 103 through 108 Processing helix chain 'At' and resid 123 through 139 Processing helix chain 'At' and resid 141 through 160 removed outlier: 3.948A pdb=" N ARGAt 146 " --> pdb=" O ASPAt 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAt 147 " --> pdb=" O GLUAt 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAt 154 " --> pdb=" O ASNAt 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAt 158 " --> pdb=" O VALAt 154 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 188 Processing helix chain 'At' and resid 192 through 198 Processing helix chain 'At' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAt 209 " --> pdb=" O GLUAt 205 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASPAt 214 " --> pdb=" O METAt 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAt 215 " --> pdb=" O ARGAt 211 " (cutoff:3.500A) Processing helix chain 'At' and resid 219 through 224 Processing helix chain 'At' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAt 234 " --> pdb=" O SERAt 231 " (cutoff:3.500A) Processing helix chain 'At' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAt 251 " --> pdb=" O PROAt 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAt 252 " --> pdb=" O ASNAt 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAt 256 " --> pdb=" O GLUAt 252 " (cutoff:3.500A) Processing helix chain 'Au' and resid 103 through 108 Processing helix chain 'Au' and resid 123 through 139 Processing helix chain 'Au' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAu 146 " --> pdb=" O ASPAu 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAu 147 " --> pdb=" O GLUAu 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAu 154 " --> pdb=" O ASNAu 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAu 158 " --> pdb=" O VALAu 154 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 192 through 198 Processing helix chain 'Au' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAu 209 " --> pdb=" O GLUAu 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAu 214 " --> pdb=" O METAu 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAu 215 " --> pdb=" O ARGAu 211 " (cutoff:3.500A) Processing helix chain 'Au' and resid 219 through 224 Processing helix chain 'Au' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAu 234 " --> pdb=" O SERAu 231 " (cutoff:3.500A) Processing helix chain 'Au' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAu 251 " --> pdb=" O PROAu 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAu 252 " --> pdb=" O ASNAu 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAu 256 " --> pdb=" O GLUAu 252 " (cutoff:3.500A) Processing helix chain 'Av' and resid 103 through 108 Processing helix chain 'Av' and resid 123 through 139 Processing helix chain 'Av' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAv 146 " --> pdb=" O ASPAv 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAv 147 " --> pdb=" O GLUAv 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAv 154 " --> pdb=" O ASNAv 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAv 158 " --> pdb=" O VALAv 154 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 188 Processing helix chain 'Av' and resid 192 through 198 Processing helix chain 'Av' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAv 209 " --> pdb=" O GLUAv 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAv 214 " --> pdb=" O METAv 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAv 215 " --> pdb=" O ARGAv 211 " (cutoff:3.500A) Processing helix chain 'Av' and resid 219 through 224 Processing helix chain 'Av' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAv 234 " --> pdb=" O SERAv 231 " (cutoff:3.500A) Processing helix chain 'Av' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAv 251 " --> pdb=" O PROAv 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAv 252 " --> pdb=" O ASNAv 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNAv 256 " --> pdb=" O GLUAv 252 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 103 through 108 Processing helix chain 'Aw' and resid 123 through 139 Processing helix chain 'Aw' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAw 146 " --> pdb=" O ASPAw 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAw 147 " --> pdb=" O GLUAw 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALAw 154 " --> pdb=" O ASNAw 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAw 158 " --> pdb=" O VALAw 154 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 192 through 198 Processing helix chain 'Aw' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUAw 209 " --> pdb=" O GLUAw 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAw 214 " --> pdb=" O METAw 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAw 215 " --> pdb=" O ARGAw 211 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 219 through 224 Processing helix chain 'Aw' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAw 234 " --> pdb=" O SERAw 231 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 247 through 256 removed outlier: 3.626A pdb=" N ARGAw 251 " --> pdb=" O PROAw 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAw 252 " --> pdb=" O ASNAw 248 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLNAw 256 " --> pdb=" O GLUAw 252 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 103 through 108 Processing helix chain 'Ax' and resid 123 through 139 Processing helix chain 'Ax' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGAx 146 " --> pdb=" O ASPAx 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILEAx 147 " --> pdb=" O GLUAx 143 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VALAx 154 " --> pdb=" O ASNAx 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUAx 158 " --> pdb=" O VALAx 154 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 182 through 188 Processing helix chain 'Ax' and resid 192 through 198 Processing helix chain 'Ax' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAx 209 " --> pdb=" O GLUAx 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPAx 214 " --> pdb=" O METAx 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAx 215 " --> pdb=" O ARGAx 211 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 219 through 224 Processing helix chain 'Ax' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGAx 234 " --> pdb=" O SERAx 231 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGAx 251 " --> pdb=" O PROAx 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAx 252 " --> pdb=" O ASNAx 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAx 256 " --> pdb=" O GLUAx 252 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 103 through 108 Processing helix chain 'Ay' and resid 123 through 139 Processing helix chain 'Ay' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAy 146 " --> pdb=" O ASPAy 142 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILEAy 147 " --> pdb=" O GLUAy 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAy 154 " --> pdb=" O ASNAy 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAy 158 " --> pdb=" O VALAy 154 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 192 through 198 Processing helix chain 'Ay' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAy 209 " --> pdb=" O GLUAy 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAy 214 " --> pdb=" O METAy 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUAy 215 " --> pdb=" O ARGAy 211 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 219 through 224 Processing helix chain 'Ay' and resid 229 through 236 removed outlier: 4.731A pdb=" N ARGAy 234 " --> pdb=" O SERAy 231 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAy 251 " --> pdb=" O PROAy 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLUAy 252 " --> pdb=" O ASNAy 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAy 256 " --> pdb=" O GLUAy 252 " (cutoff:3.500A) Processing helix chain 'Az' and resid 103 through 108 Processing helix chain 'Az' and resid 123 through 139 Processing helix chain 'Az' and resid 141 through 160 removed outlier: 3.950A pdb=" N ARGAz 146 " --> pdb=" O ASPAz 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEAz 147 " --> pdb=" O GLUAz 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALAz 154 " --> pdb=" O ASNAz 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUAz 158 " --> pdb=" O VALAz 154 " (cutoff:3.500A) Processing helix chain 'Az' and resid 182 through 188 Processing helix chain 'Az' and resid 192 through 198 Processing helix chain 'Az' and resid 200 through 215 removed outlier: 4.082A pdb=" N GLUAz 209 " --> pdb=" O GLUAz 205 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASPAz 214 " --> pdb=" O METAz 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUAz 215 " --> pdb=" O ARGAz 211 " (cutoff:3.500A) Processing helix chain 'Az' and resid 219 through 224 Processing helix chain 'Az' and resid 229 through 236 removed outlier: 4.733A pdb=" N ARGAz 234 " --> pdb=" O SERAz 231 " (cutoff:3.500A) Processing helix chain 'Az' and resid 247 through 256 removed outlier: 3.624A pdb=" N ARGAz 251 " --> pdb=" O PROAz 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAz 252 " --> pdb=" O ASNAz 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNAz 256 " --> pdb=" O GLUAz 252 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 103 through 108 Processing helix chain 'Ba' and resid 123 through 139 Processing helix chain 'Ba' and resid 141 through 160 removed outlier: 3.949A pdb=" N ARGBa 146 " --> pdb=" O ASPBa 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILEBa 147 " --> pdb=" O GLUBa 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALBa 154 " --> pdb=" O ASNBa 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUBa 158 " --> pdb=" O VALBa 154 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 192 through 198 Processing helix chain 'Ba' and resid 200 through 215 removed outlier: 4.081A pdb=" N GLUBa 209 " --> pdb=" O GLUBa 205 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASPBa 214 " --> pdb=" O METBa 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUBa 215 " --> pdb=" O ARGBa 211 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 219 through 224 Processing helix chain 'Ba' and resid 229 through 236 removed outlier: 4.732A pdb=" N ARGBa 234 " --> pdb=" O SERBa 231 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 247 through 256 removed outlier: 3.625A pdb=" N ARGBa 251 " --> pdb=" O PROBa 247 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUBa 252 " --> pdb=" O ASNBa 248 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLNBa 256 " --> pdb=" O GLUBa 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 95 through 96 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 168 through 171 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 95 through 96 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 168 through 171 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 95 through 96 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 168 through 171 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 168 through 171 Processing sheet with id=AB2, first strand: chain 'Af' and resid 95 through 96 Processing sheet with id=AB3, first strand: chain 'Af' and resid 168 through 171 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 95 through 96 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 168 through 171 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 95 through 96 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 168 through 171 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 168 through 171 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 95 through 96 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 168 through 171 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 95 through 96 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 168 through 171 Processing sheet with id=AC5, first strand: chain 'Al' and resid 95 through 96 Processing sheet with id=AC6, first strand: chain 'Al' and resid 168 through 171 Processing sheet with id=AC7, first strand: chain 'Am' and resid 95 through 96 Processing sheet with id=AC8, first strand: chain 'Am' and resid 168 through 171 Processing sheet with id=AC9, first strand: chain 'An' and resid 95 through 96 Processing sheet with id=AD1, first strand: chain 'An' and resid 168 through 171 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 95 through 96 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 168 through 171 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 95 through 96 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 168 through 171 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 95 through 96 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 168 through 171 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 95 through 96 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 168 through 171 Processing sheet with id=AE1, first strand: chain 'As' and resid 95 through 96 Processing sheet with id=AE2, first strand: chain 'As' and resid 168 through 171 Processing sheet with id=AE3, first strand: chain 'At' and resid 95 through 96 Processing sheet with id=AE4, first strand: chain 'At' and resid 168 through 171 Processing sheet with id=AE5, first strand: chain 'Au' and resid 95 through 96 Processing sheet with id=AE6, first strand: chain 'Au' and resid 168 through 171 Processing sheet with id=AE7, first strand: chain 'Av' and resid 95 through 96 Processing sheet with id=AE8, first strand: chain 'Av' and resid 168 through 171 Processing sheet with id=AE9, first strand: chain 'Aw' and resid 95 through 96 Processing sheet with id=AF1, first strand: chain 'Aw' and resid 168 through 171 Processing sheet with id=AF2, first strand: chain 'Ax' and resid 95 through 96 Processing sheet with id=AF3, first strand: chain 'Ax' and resid 168 through 171 Processing sheet with id=AF4, first strand: chain 'Ay' and resid 95 through 96 Processing sheet with id=AF5, first strand: chain 'Ay' and resid 168 through 171 Processing sheet with id=AF6, first strand: chain 'Az' and resid 95 through 96 Processing sheet with id=AF7, first strand: chain 'Az' and resid 168 through 171 Processing sheet with id=AF8, first strand: chain 'Ba' and resid 95 through 96 Processing sheet with id=AF9, first strand: chain 'Ba' and resid 168 through 171 1539 hydrogen bonds defined for protein. 4131 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: 7.58 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12412 1.34 - 1.45: 6761 1.45 - 1.57: 21192 1.57 - 1.69: 0 1.69 - 1.81: 594 Bond restraints: 40959 Sorted by residual: bond pdb=" C GLYAq 174 " pdb=" O GLYAq 174 " ideal model delta sigma weight residual 1.235 1.284 -0.049 1.35e-02 5.49e+03 1.33e+01 bond pdb=" C GLYAs 174 " pdb=" O GLYAs 174 " ideal model delta sigma weight residual 1.235 1.284 -0.049 1.35e-02 5.49e+03 1.32e+01 bond pdb=" C GLYAt 174 " pdb=" O GLYAt 174 " ideal model delta sigma weight residual 1.235 1.284 -0.049 1.35e-02 5.49e+03 1.32e+01 bond pdb=" C GLYAb 174 " pdb=" O GLYAb 174 " ideal model delta sigma weight residual 1.235 1.284 -0.049 1.35e-02 5.49e+03 1.31e+01 bond pdb=" C GLYAl 174 " pdb=" O GLYAl 174 " ideal model delta sigma weight residual 1.235 1.283 -0.049 1.35e-02 5.49e+03 1.30e+01 ... (remaining 40954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 48185 1.27 - 2.53: 4960 2.53 - 3.80: 1715 3.80 - 5.07: 401 5.07 - 6.33: 116 Bond angle restraints: 55377 Sorted by residual: angle pdb=" C THRAa 161 " pdb=" N SERAa 162 " pdb=" CA SERAa 162 " ideal model delta sigma weight residual 122.28 116.48 5.80 1.02e+00 9.61e-01 3.23e+01 angle pdb=" C THRAm 161 " pdb=" N SERAm 162 " pdb=" CA SERAm 162 " ideal model delta sigma weight residual 122.28 116.48 5.80 1.02e+00 9.61e-01 3.23e+01 angle pdb=" C THRAj 161 " pdb=" N SERAj 162 " pdb=" CA SERAj 162 " ideal model delta sigma weight residual 122.28 116.49 5.79 1.02e+00 9.61e-01 3.23e+01 angle pdb=" C THRAv 161 " pdb=" N SERAv 162 " pdb=" CA SERAv 162 " ideal model delta sigma weight residual 122.28 116.49 5.79 1.02e+00 9.61e-01 3.22e+01 angle pdb=" C THRAl 161 " pdb=" N SERAl 162 " pdb=" CA SERAl 162 " ideal model delta sigma weight residual 122.28 116.49 5.79 1.02e+00 9.61e-01 3.22e+01 ... (remaining 55372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 21776 13.96 - 27.93: 2484 27.93 - 41.89: 675 41.89 - 55.86: 229 55.86 - 69.82: 54 Dihedral angle restraints: 25218 sinusoidal: 10773 harmonic: 14445 Sorted by residual: dihedral pdb=" C ASPAq 173 " pdb=" N ASPAq 173 " pdb=" CA ASPAq 173 " pdb=" CB ASPAq 173 " ideal model delta harmonic sigma weight residual -122.60 -114.98 -7.62 0 2.50e+00 1.60e-01 9.29e+00 dihedral pdb=" C ASPBa 173 " pdb=" N ASPBa 173 " pdb=" CA ASPBa 173 " pdb=" CB ASPBa 173 " ideal model delta harmonic sigma weight residual -122.60 -115.01 -7.59 0 2.50e+00 1.60e-01 9.22e+00 dihedral pdb=" C ASPAz 173 " pdb=" N ASPAz 173 " pdb=" CA ASPAz 173 " pdb=" CB ASPAz 173 " ideal model delta harmonic sigma weight residual -122.60 -115.03 -7.57 0 2.50e+00 1.60e-01 9.18e+00 ... (remaining 25215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4479 0.057 - 0.114: 978 0.114 - 0.171: 186 0.171 - 0.228: 54 0.228 - 0.285: 54 Chirality restraints: 5751 Sorted by residual: chirality pdb=" CA ASPAw 173 " pdb=" N ASPAw 173 " pdb=" C ASPAw 173 " pdb=" CB ASPAw 173 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASPAl 173 " pdb=" N ASPAl 173 " pdb=" C ASPAl 173 " pdb=" CB ASPAl 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASPAc 173 " pdb=" N ASPAc 173 " pdb=" C ASPAc 173 " pdb=" CB ASPAc 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 5748 not shown) Planarity restraints: 7290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLYAj 174 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLYAj 174 " -0.024 2.00e-02 2.50e+03 pdb=" O GLYAj 174 " 0.009 2.00e-02 2.50e+03 pdb=" N ASNAj 175 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAu 174 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C GLYAu 174 " -0.024 2.00e-02 2.50e+03 pdb=" O GLYAu 174 " 0.009 2.00e-02 2.50e+03 pdb=" N ASNAu 175 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAs 174 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C GLYAs 174 " -0.024 2.00e-02 2.50e+03 pdb=" O GLYAs 174 " 0.009 2.00e-02 2.50e+03 pdb=" N ASNAs 175 " 0.008 2.00e-02 2.50e+03 ... (remaining 7287 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 16057 2.89 - 3.40: 39184 3.40 - 3.90: 64655 3.90 - 4.40: 71956 4.40 - 4.90: 119778 Nonbonded interactions: 311630 Sorted by model distance: nonbonded pdb=" OD1 ASNAv 159 " pdb=" N ASNAw 119 " model vdw 2.393 3.120 nonbonded pdb=" OD1 ASNAm 159 " pdb=" N ASNAn 119 " model vdw 2.425 3.120 nonbonded pdb=" OD1 ASNAd 159 " pdb=" N ASNAe 119 " model vdw 2.425 3.120 nonbonded pdb=" OD1 ASNAa 159 " pdb=" N ASNAb 119 " model vdw 2.425 3.120 nonbonded pdb=" N ASNAj 119 " pdb=" OD1 ASNAr 159 " model vdw 2.428 3.120 ... (remaining 311625 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: 0.15 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.150 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 40959 Z= 0.525 Angle : 0.986 6.333 55377 Z= 0.675 Chirality : 0.058 0.285 5751 Planarity : 0.004 0.023 7290 Dihedral : 13.692 69.821 15822 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.11), residues: 4779 helix: -1.66 (0.10), residues: 2268 sheet: -4.38 (0.15), residues: 270 loop : -1.33 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGAk 220 TYR 0.006 0.001 TYRBa 168 PHE 0.010 0.002 PHEAu 239 TRP 0.013 0.002 TRPAq 169 HIS 0.001 0.000 HISAt 124 Details of bonding type rmsd covalent geometry : bond 0.00870 (40959) covalent geometry : angle 0.98631 (55377) hydrogen bonds : bond 0.20501 ( 1539) hydrogen bonds : angle 7.59106 ( 4131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1663 time to evaluate : 1.638 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: Aa 210 MET cc_start: 0.7940 (tmm) cc_final: 0.7616 (tmm) REVERT: Ab 145 MET cc_start: 0.8148 (tpt) cc_final: 0.7948 (tpp) REVERT: Ab 179 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7380 (mt-10) REVERT: Ac 139 ASP cc_start: 0.7708 (t70) cc_final: 0.7388 (t70) REVERT: Ac 145 MET cc_start: 0.8379 (tpt) cc_final: 0.7911 (tpp) REVERT: Ac 221 TYR cc_start: 0.8434 (t80) cc_final: 0.8187 (t80) REVERT: Ad 145 MET cc_start: 0.8472 (tpt) cc_final: 0.7732 (tpp) REVERT: Ad 149 MET cc_start: 0.7991 (tpp) cc_final: 0.7706 (mmm) REVERT: Ad 218 MET cc_start: 0.7786 (ttm) cc_final: 0.7227 (ttp) REVERT: Ad 221 TYR cc_start: 0.8213 (t80) cc_final: 0.7865 (t80) REVERT: Ad 227 LEU cc_start: 0.9089 (tp) cc_final: 0.8878 (tt) REVERT: Ae 162 SER cc_start: 0.9075 (m) cc_final: 0.8747 (p) REVERT: Af 137 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8338 (mm-30) REVERT: Af 246 THR cc_start: 0.9279 (m) cc_final: 0.8801 (p) REVERT: Ag 186 VAL cc_start: 0.7651 (t) cc_final: 0.7404 (t) REVERT: Ag 196 CYS cc_start: 0.7359 (m) cc_final: 0.6628 (t) REVERT: Ag 230 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7538 (ttmt) REVERT: Ah 139 ASP cc_start: 0.6977 (t70) cc_final: 0.6710 (t0) REVERT: Ah 161 THR cc_start: 0.6452 (p) cc_final: 0.5854 (p) REVERT: Ah 197 MET cc_start: 0.7578 (tpp) cc_final: 0.7354 (mmm) REVERT: Ah 230 LYS cc_start: 0.7213 (mmtt) cc_final: 0.6974 (tttt) REVERT: Ai 99 LYS cc_start: 0.7639 (tttt) cc_final: 0.7083 (tptp) REVERT: Ai 144 GLN cc_start: 0.7573 (mt0) cc_final: 0.7302 (mp10) REVERT: Ai 172 VAL cc_start: 0.7624 (t) cc_final: 0.7412 (t) REVERT: Aj 210 MET cc_start: 0.7930 (tmm) cc_final: 0.7450 (tmm) REVERT: Al 139 ASP cc_start: 0.7669 (t70) cc_final: 0.7330 (t70) REVERT: Al 145 MET cc_start: 0.7894 (tpt) cc_final: 0.7619 (tpp) REVERT: Am 145 MET cc_start: 0.8144 (tpt) cc_final: 0.7367 (tpp) REVERT: Am 156 CYS cc_start: 0.8999 (m) cc_final: 0.8688 (m) REVERT: Am 218 MET cc_start: 0.7443 (ttm) cc_final: 0.6947 (ttp) REVERT: Am 226 ASN cc_start: 0.8770 (t0) cc_final: 0.8510 (p0) REVERT: Am 227 LEU cc_start: 0.9207 (tp) cc_final: 0.8867 (tt) REVERT: An 162 SER cc_start: 0.8934 (m) cc_final: 0.8732 (p) REVERT: Ao 153 MET cc_start: 0.8201 (ttp) cc_final: 0.7700 (ttp) REVERT: Ao 172 VAL cc_start: 0.8148 (t) cc_final: 0.7633 (t) REVERT: Ao 215 GLU cc_start: 0.7675 (pt0) cc_final: 0.7291 (pm20) REVERT: Ao 241 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6539 (mt-10) REVERT: Ap 186 VAL cc_start: 0.7487 (t) cc_final: 0.7267 (t) REVERT: Ap 230 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7524 (tttt) REVERT: Aq 196 CYS cc_start: 0.7448 (m) cc_final: 0.5998 (t) REVERT: Ar 144 GLN cc_start: 0.7583 (mt0) cc_final: 0.7371 (mm-40) REVERT: Ar 210 MET cc_start: 0.7791 (tmm) cc_final: 0.6932 (tmm) REVERT: Ar 215 GLU cc_start: 0.7735 (pt0) cc_final: 0.7412 (pm20) REVERT: As 99 LYS cc_start: 0.7437 (tttt) cc_final: 0.7216 (tptp) REVERT: As 210 MET cc_start: 0.7683 (tmm) cc_final: 0.6993 (tmm) REVERT: At 210 MET cc_start: 0.7879 (tmm) cc_final: 0.7472 (tmm) REVERT: Au 139 ASP cc_start: 0.7655 (t70) cc_final: 0.7384 (t70) REVERT: Au 142 ASP cc_start: 0.7219 (t70) cc_final: 0.6799 (t0) REVERT: Au 145 MET cc_start: 0.7242 (tpt) cc_final: 0.6968 (tpp) REVERT: Au 227 LEU cc_start: 0.8751 (tp) cc_final: 0.8432 (tt) REVERT: Av 145 MET cc_start: 0.7866 (tpt) cc_final: 0.7434 (tpp) REVERT: Av 156 CYS cc_start: 0.8759 (m) cc_final: 0.8444 (t) REVERT: Av 226 ASN cc_start: 0.8952 (t0) cc_final: 0.8692 (t0) REVERT: Aw 96 VAL cc_start: 0.6217 (p) cc_final: 0.5984 (m) REVERT: Aw 152 LEU cc_start: 0.9090 (tp) cc_final: 0.8597 (tp) REVERT: Aw 226 ASN cc_start: 0.8459 (t0) cc_final: 0.8235 (p0) REVERT: Ax 137 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8237 (mm-30) REVERT: Ax 153 MET cc_start: 0.8103 (ttp) cc_final: 0.7892 (ttp) REVERT: Ax 162 SER cc_start: 0.8779 (m) cc_final: 0.8484 (p) REVERT: Ax 172 VAL cc_start: 0.8150 (t) cc_final: 0.7914 (t) REVERT: Ay 186 VAL cc_start: 0.7597 (t) cc_final: 0.7363 (t) REVERT: Ay 188 ASN cc_start: 0.7928 (m-40) cc_final: 0.7608 (m-40) REVERT: Ay 230 LYS cc_start: 0.7461 (mmtt) cc_final: 0.7153 (ttmt) REVERT: Ay 246 THR cc_start: 0.8987 (m) cc_final: 0.8685 (p) REVERT: Az 159 ASN cc_start: 0.7551 (m-40) cc_final: 0.7254 (m-40) REVERT: Az 186 VAL cc_start: 0.6854 (t) cc_final: 0.6543 (t) REVERT: Az 196 CYS cc_start: 0.6604 (m) cc_final: 0.6019 (t) REVERT: Ba 148 LEU cc_start: 0.8332 (pp) cc_final: 0.7147 (mt) REVERT: Ba 172 VAL cc_start: 0.6808 (t) cc_final: 0.6413 (t) outliers start: 0 outliers final: 0 residues processed: 1663 average time/residue: 0.2354 time to fit residues: 638.6286 Evaluate side-chains 1039 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1039 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.5980 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0870 chunk 401 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 159 ASN Aa 199 HIS Aa 228 ASN Ac 109 GLN ** Ac 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 254 HIS ** Ae 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 106 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 254 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 254 HIS ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 254 HIS Ai 254 HIS ** Aj 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 159 ASN Aj 195 GLN Ak 175 ASN Al 109 GLN ** Al 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 254 HIS ** An 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 254 HIS ** Ap 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 254 HIS ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 254 HIS Ar 254 HIS As 159 ASN As 195 GLN As 254 HIS ** At 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 175 ASN At 228 ASN Au 199 HIS Au 254 HIS ** Av 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 254 HIS Aw 126 GLN Aw 254 HIS ** Ax 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 254 HIS Ay 254 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 114 GLN Ba 175 ASN Ba 254 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079458 restraints weight = 94799.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082744 restraints weight = 48063.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084962 restraints weight = 30590.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086459 restraints weight = 22066.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087481 restraints weight = 17219.732| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40959 Z= 0.124 Angle : 0.624 9.579 55377 Z= 0.316 Chirality : 0.038 0.283 5751 Planarity : 0.004 0.043 7290 Dihedral : 4.127 20.360 5400 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 15.71 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.12), residues: 4779 helix: -0.68 (0.10), residues: 2268 sheet: -3.25 (0.19), residues: 324 loop : -0.24 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAl 211 TYR 0.026 0.001 TYRAk 110 PHE 0.025 0.002 PHEAn 200 TRP 0.020 0.002 TRPAw 169 HIS 0.007 0.001 HISAg 254 Details of bonding type rmsd covalent geometry : bond 0.00274 (40959) covalent geometry : angle 0.62434 (55377) hydrogen bonds : bond 0.03550 ( 1539) hydrogen bonds : angle 4.71701 ( 4131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1178 time to evaluate : 1.751 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: Aa 109 GLN cc_start: 0.8728 (pp30) cc_final: 0.8475 (pp30) REVERT: Aa 205 GLU cc_start: 0.7774 (tt0) cc_final: 0.7452 (tt0) REVERT: Aa 210 MET cc_start: 0.7996 (tmm) cc_final: 0.7695 (tmm) REVERT: Ab 99 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7807 (tptp) REVERT: Ab 143 GLU cc_start: 0.8673 (tp30) cc_final: 0.8350 (tm-30) REVERT: Ab 145 MET cc_start: 0.8504 (tpt) cc_final: 0.8150 (tpp) REVERT: Ac 145 MET cc_start: 0.8472 (tpt) cc_final: 0.8096 (tpp) REVERT: Ac 158 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6734 (mt-10) REVERT: Ac 237 PHE cc_start: 0.7768 (p90) cc_final: 0.7251 (p90) REVERT: Ad 95 MET cc_start: 0.8087 (mmm) cc_final: 0.7681 (mmm) REVERT: Ad 145 MET cc_start: 0.8015 (tpt) cc_final: 0.7726 (tpp) REVERT: Ad 168 TYR cc_start: 0.7513 (m-80) cc_final: 0.7280 (m-10) REVERT: Ae 95 MET cc_start: 0.8397 (mmm) cc_final: 0.8034 (mmm) REVERT: Ae 162 SER cc_start: 0.9131 (m) cc_final: 0.8763 (p) REVERT: Af 95 MET cc_start: 0.8743 (mtp) cc_final: 0.8311 (mtt) REVERT: Af 110 TYR cc_start: 0.8680 (t80) cc_final: 0.7862 (t80) REVERT: Af 137 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8258 (mm-30) REVERT: Af 179 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8079 (tt0) REVERT: Af 246 THR cc_start: 0.9314 (m) cc_final: 0.8810 (p) REVERT: Ag 218 MET cc_start: 0.7544 (tpp) cc_final: 0.7263 (tpt) REVERT: Ah 110 TYR cc_start: 0.7347 (t80) cc_final: 0.7114 (t80) REVERT: Ah 124 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6762 (m90) REVERT: Ah 139 ASP cc_start: 0.6987 (t70) cc_final: 0.6648 (t0) REVERT: Ah 159 ASN cc_start: 0.6723 (m-40) cc_final: 0.6228 (m110) REVERT: Ah 197 MET cc_start: 0.7538 (tpp) cc_final: 0.7328 (tpp) REVERT: Ai 145 MET cc_start: 0.8652 (tpp) cc_final: 0.8185 (tpp) REVERT: Ai 159 ASN cc_start: 0.5460 (m-40) cc_final: 0.5050 (m110) REVERT: Ai 210 MET cc_start: 0.7819 (tmm) cc_final: 0.7416 (tmm) REVERT: Ai 235 TYR cc_start: 0.7955 (m-80) cc_final: 0.7632 (m-10) REVERT: Aj 109 GLN cc_start: 0.8227 (pp30) cc_final: 0.7779 (pp30) REVERT: Aj 110 TYR cc_start: 0.7696 (t80) cc_final: 0.7436 (t80) REVERT: Aj 205 GLU cc_start: 0.7943 (tt0) cc_final: 0.7533 (tt0) REVERT: Aj 210 MET cc_start: 0.7879 (tmm) cc_final: 0.7537 (tmm) REVERT: Aj 235 TYR cc_start: 0.8005 (m-80) cc_final: 0.7382 (m-80) REVERT: Ak 143 GLU cc_start: 0.8491 (tp30) cc_final: 0.8251 (tp30) REVERT: Ak 205 GLU cc_start: 0.7793 (tt0) cc_final: 0.7263 (tt0) REVERT: Al 90 LYS cc_start: 0.7901 (tttm) cc_final: 0.7540 (tptt) REVERT: Al 139 ASP cc_start: 0.7589 (t70) cc_final: 0.7302 (t70) REVERT: Al 145 MET cc_start: 0.8361 (tpt) cc_final: 0.8032 (tpp) REVERT: Al 241 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7144 (mt-10) REVERT: Am 95 MET cc_start: 0.7795 (mmm) cc_final: 0.7563 (mmm) REVERT: Am 145 MET cc_start: 0.7954 (tpt) cc_final: 0.7254 (tpp) REVERT: Am 218 MET cc_start: 0.7621 (ttm) cc_final: 0.7248 (ttp) REVERT: An 95 MET cc_start: 0.8189 (mmm) cc_final: 0.7802 (mmm) REVERT: An 126 GLN cc_start: 0.8615 (mt0) cc_final: 0.8395 (mt0) REVERT: Ao 215 GLU cc_start: 0.7676 (pt0) cc_final: 0.7455 (pm20) REVERT: Ap 95 MET cc_start: 0.8608 (mtp) cc_final: 0.8406 (mtp) REVERT: Aq 145 MET cc_start: 0.7665 (tpp) cc_final: 0.7255 (tpp) REVERT: Aq 196 CYS cc_start: 0.7251 (m) cc_final: 0.6405 (t) REVERT: Ar 159 ASN cc_start: 0.5918 (m-40) cc_final: 0.5238 (m110) REVERT: Ar 210 MET cc_start: 0.7883 (tmm) cc_final: 0.7591 (tmm) REVERT: Ar 218 MET cc_start: 0.6936 (ttm) cc_final: 0.6652 (ttm) REVERT: As 109 GLN cc_start: 0.8198 (pp30) cc_final: 0.7954 (pp30) REVERT: As 110 TYR cc_start: 0.7544 (t80) cc_final: 0.7313 (t80) REVERT: As 197 MET cc_start: 0.7080 (tpp) cc_final: 0.6754 (tpp) REVERT: As 210 MET cc_start: 0.7584 (tmm) cc_final: 0.7102 (tmm) REVERT: At 210 MET cc_start: 0.7883 (tmm) cc_final: 0.7600 (tmm) REVERT: Au 139 ASP cc_start: 0.7584 (t70) cc_final: 0.7382 (t70) REVERT: Au 145 MET cc_start: 0.7715 (tpt) cc_final: 0.7157 (tpp) REVERT: Au 227 LEU cc_start: 0.8764 (tp) cc_final: 0.8443 (tt) REVERT: Av 95 MET cc_start: 0.7908 (mmm) cc_final: 0.7596 (mmm) REVERT: Av 145 MET cc_start: 0.8167 (tpt) cc_final: 0.7713 (tpp) REVERT: Aw 95 MET cc_start: 0.7972 (mmm) cc_final: 0.7589 (mmm) REVERT: Aw 152 LEU cc_start: 0.8881 (tp) cc_final: 0.8432 (tp) REVERT: Aw 218 MET cc_start: 0.7543 (ttp) cc_final: 0.7242 (ttp) REVERT: Aw 226 ASN cc_start: 0.8393 (t0) cc_final: 0.8180 (p0) REVERT: Ax 95 MET cc_start: 0.8360 (mmm) cc_final: 0.7940 (mmm) REVERT: Ax 110 TYR cc_start: 0.8112 (t80) cc_final: 0.7508 (t80) REVERT: Ax 137 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7898 (mm-30) REVERT: Ax 162 SER cc_start: 0.8824 (m) cc_final: 0.8486 (p) REVERT: Ay 88 SER cc_start: 0.7430 (p) cc_final: 0.7037 (t) REVERT: Ay 95 MET cc_start: 0.8589 (mtp) cc_final: 0.8292 (mtt) REVERT: Ay 215 GLU cc_start: 0.7485 (pm20) cc_final: 0.7134 (pm20) REVERT: Ay 246 THR cc_start: 0.9130 (m) cc_final: 0.8886 (p) REVERT: Az 196 CYS cc_start: 0.6787 (m) cc_final: 0.6483 (t) REVERT: Ba 159 ASN cc_start: 0.5614 (m-40) cc_final: 0.4860 (m110) REVERT: Ba 218 MET cc_start: 0.6849 (ttp) cc_final: 0.6457 (ttt) outliers start: 138 outliers final: 73 residues processed: 1252 average time/residue: 0.2334 time to fit residues: 491.7030 Evaluate side-chains 1049 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 974 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 87 VAL Chi-restraints excluded: chain Aa residue 97 SER Chi-restraints excluded: chain Aa residue 123 THR Chi-restraints excluded: chain Aa residue 157 ILE Chi-restraints excluded: chain Ab residue 99 LYS Chi-restraints excluded: chain Ab residue 178 SER Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 84 LEU Chi-restraints excluded: chain Ac residue 224 LEU Chi-restraints excluded: chain Ad residue 78 THR Chi-restraints excluded: chain Ad residue 150 ASN Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Ad residue 196 CYS Chi-restraints excluded: chain Ae residue 161 THR Chi-restraints excluded: chain Af residue 152 LEU Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Ag residue 152 LEU Chi-restraints excluded: chain Ag residue 170 THR Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 148 LEU Chi-restraints excluded: chain Ah residue 157 ILE Chi-restraints excluded: chain Ah residue 170 THR Chi-restraints excluded: chain Ai residue 123 THR Chi-restraints excluded: chain Ai residue 157 ILE Chi-restraints excluded: chain Ai residue 170 THR Chi-restraints excluded: chain Ai residue 252 GLU Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 123 THR Chi-restraints excluded: chain Aj residue 157 ILE Chi-restraints excluded: chain Ak residue 123 THR Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 172 VAL Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 117 ILE Chi-restraints excluded: chain Ap residue 152 LEU Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Aq residue 84 LEU Chi-restraints excluded: chain Aq residue 157 ILE Chi-restraints excluded: chain Aq residue 170 THR Chi-restraints excluded: chain Ar residue 123 THR Chi-restraints excluded: chain Ar residue 157 ILE Chi-restraints excluded: chain Ar residue 170 THR Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain As residue 97 SER Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain As residue 157 ILE Chi-restraints excluded: chain As residue 170 THR Chi-restraints excluded: chain At residue 123 THR Chi-restraints excluded: chain Au residue 78 THR Chi-restraints excluded: chain Au residue 123 THR Chi-restraints excluded: chain Au residue 173 ASP Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 79 PHE Chi-restraints excluded: chain Av residue 84 LEU Chi-restraints excluded: chain Av residue 85 LYS Chi-restraints excluded: chain Av residue 126 GLN Chi-restraints excluded: chain Av residue 142 ASP Chi-restraints excluded: chain Av residue 198 MET Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Aw residue 78 THR Chi-restraints excluded: chain Aw residue 134 VAL Chi-restraints excluded: chain Aw residue 166 ASN Chi-restraints excluded: chain Ay residue 80 VAL Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Az residue 152 LEU Chi-restraints excluded: chain Az residue 156 CYS Chi-restraints excluded: chain Ba residue 101 ILE Chi-restraints excluded: chain Ba residue 157 ILE Chi-restraints excluded: chain Ba residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 347 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 359 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 144 GLN Ac 132 ASN Ad 150 ASN ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 195 GLN ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 114 GLN Ai 144 GLN Ai 254 HIS Aj 144 GLN Al 150 ASN Am 254 HIS Ao 106 HIS Ao 150 ASN ** Ap 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 254 HIS Aq 114 GLN ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 254 HIS Ar 188 ASN ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 114 GLN ** At 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 199 HIS Ax 106 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 254 HIS Az 126 GLN ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 254 HIS Ba 126 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074732 restraints weight = 91539.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077867 restraints weight = 47326.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079954 restraints weight = 30803.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081362 restraints weight = 22725.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082377 restraints weight = 18169.113| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 40959 Z= 0.188 Angle : 0.687 10.443 55377 Z= 0.352 Chirality : 0.042 0.343 5751 Planarity : 0.004 0.066 7290 Dihedral : 4.329 21.422 5400 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.34 % Allowed : 15.91 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4779 helix: -0.05 (0.11), residues: 2079 sheet: -2.50 (0.23), residues: 324 loop : 0.38 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARGAw 211 TYR 0.023 0.002 TYRAb 138 PHE 0.024 0.002 PHEAc 129 TRP 0.032 0.002 TRPAk 155 HIS 0.007 0.001 HISAh 254 Details of bonding type rmsd covalent geometry : bond 0.00442 (40959) covalent geometry : angle 0.68665 (55377) hydrogen bonds : bond 0.04147 ( 1539) hydrogen bonds : angle 4.69051 ( 4131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1074 time to evaluate : 1.634 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: Aa 171 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: Aa 205 GLU cc_start: 0.8116 (tt0) cc_final: 0.7882 (tt0) REVERT: Ab 113 ASP cc_start: 0.8114 (t0) cc_final: 0.7743 (t0) REVERT: Ab 145 MET cc_start: 0.8706 (tpt) cc_final: 0.8382 (tpp) REVERT: Ab 183 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8402 (ttpp) REVERT: Ab 221 TYR cc_start: 0.8693 (t80) cc_final: 0.8443 (t80) REVERT: Ab 229 ASP cc_start: 0.6898 (m-30) cc_final: 0.6333 (t70) REVERT: Ac 145 MET cc_start: 0.8733 (tpt) cc_final: 0.8499 (tpp) REVERT: Ac 205 GLU cc_start: 0.8372 (tt0) cc_final: 0.7964 (tt0) REVERT: Ac 218 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8050 (ttt) REVERT: Ad 95 MET cc_start: 0.8425 (mmm) cc_final: 0.7972 (mmm) REVERT: Ad 145 MET cc_start: 0.8522 (tpt) cc_final: 0.7956 (tpp) REVERT: Ad 149 MET cc_start: 0.7646 (mmm) cc_final: 0.7349 (mmm) REVERT: Ae 95 MET cc_start: 0.8656 (mmm) cc_final: 0.8353 (mmm) REVERT: Ae 162 SER cc_start: 0.9416 (m) cc_final: 0.8948 (p) REVERT: Ae 242 ILE cc_start: 0.9032 (mt) cc_final: 0.8802 (mt) REVERT: Af 215 GLU cc_start: 0.7951 (pm20) cc_final: 0.7559 (pm20) REVERT: Ag 196 CYS cc_start: 0.8851 (t) cc_final: 0.8490 (t) REVERT: Ag 215 GLU cc_start: 0.7962 (pm20) cc_final: 0.7730 (pm20) REVERT: Ag 218 MET cc_start: 0.8073 (tpp) cc_final: 0.7824 (tpt) REVERT: Ag 221 TYR cc_start: 0.8529 (t80) cc_final: 0.8097 (t80) REVERT: Ah 139 ASP cc_start: 0.7525 (t70) cc_final: 0.7319 (t70) REVERT: Ah 221 TYR cc_start: 0.8508 (t80) cc_final: 0.8303 (t80) REVERT: Ai 91 MET cc_start: 0.7890 (mmp) cc_final: 0.7669 (mtp) REVERT: Ai 145 MET cc_start: 0.8761 (tpp) cc_final: 0.8259 (tpp) REVERT: Ai 221 TYR cc_start: 0.8713 (t80) cc_final: 0.8507 (t80) REVERT: Aj 85 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7212 (pptt) REVERT: Aj 205 GLU cc_start: 0.7923 (tt0) cc_final: 0.7610 (tt0) REVERT: Aj 210 MET cc_start: 0.8387 (tmm) cc_final: 0.8100 (tmm) REVERT: Ak 143 GLU cc_start: 0.8671 (tp30) cc_final: 0.8390 (tp30) REVERT: Ak 205 GLU cc_start: 0.8092 (tt0) cc_final: 0.7771 (tt0) REVERT: Ak 235 TYR cc_start: 0.9242 (m-80) cc_final: 0.9013 (m-80) REVERT: Al 90 LYS cc_start: 0.7917 (tttm) cc_final: 0.7650 (tptp) REVERT: Al 139 ASP cc_start: 0.7615 (t70) cc_final: 0.7373 (t70) REVERT: Al 145 MET cc_start: 0.8646 (tpt) cc_final: 0.8349 (tpp) REVERT: Al 205 GLU cc_start: 0.8444 (tt0) cc_final: 0.8047 (tt0) REVERT: Al 218 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: Am 110 TYR cc_start: 0.8938 (t80) cc_final: 0.8663 (t80) REVERT: An 95 MET cc_start: 0.8472 (mmm) cc_final: 0.8059 (mmm) REVERT: An 137 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8241 (tm-30) REVERT: Ao 95 MET cc_start: 0.8856 (mmt) cc_final: 0.8113 (mmm) REVERT: Ao 198 MET cc_start: 0.9085 (ttm) cc_final: 0.8650 (ttm) REVERT: Ap 215 GLU cc_start: 0.7908 (pm20) cc_final: 0.7391 (pm20) REVERT: Aq 210 MET cc_start: 0.8384 (tmm) cc_final: 0.7936 (tmm) REVERT: Aq 215 GLU cc_start: 0.7835 (pt0) cc_final: 0.7514 (pm20) REVERT: Ar 81 ILE cc_start: 0.8711 (mm) cc_final: 0.8466 (mm) REVERT: Ar 145 MET cc_start: 0.8773 (tpp) cc_final: 0.8346 (tpp) REVERT: Ar 210 MET cc_start: 0.8216 (tmm) cc_final: 0.7838 (tmm) REVERT: Ar 218 MET cc_start: 0.8052 (ttm) cc_final: 0.7748 (ttt) REVERT: Ar 235 TYR cc_start: 0.9060 (m-80) cc_final: 0.8651 (m-10) REVERT: As 205 GLU cc_start: 0.8015 (tt0) cc_final: 0.7757 (tt0) REVERT: As 210 MET cc_start: 0.8307 (tmm) cc_final: 0.7898 (tmm) REVERT: As 245 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7819 (mtm-85) REVERT: At 218 MET cc_start: 0.8414 (ttm) cc_final: 0.8108 (ttt) REVERT: Au 128 GLN cc_start: 0.8331 (mt0) cc_final: 0.8117 (tt0) REVERT: Au 139 ASP cc_start: 0.7722 (t70) cc_final: 0.7498 (t70) REVERT: Au 145 MET cc_start: 0.8468 (tpt) cc_final: 0.8052 (tpp) REVERT: Au 205 GLU cc_start: 0.8206 (tt0) cc_final: 0.7951 (tt0) REVERT: Av 95 MET cc_start: 0.8210 (mmm) cc_final: 0.7999 (mmt) REVERT: Av 126 GLN cc_start: 0.8566 (tt0) cc_final: 0.8352 (mt0) REVERT: Av 145 MET cc_start: 0.8612 (tpt) cc_final: 0.8282 (tpp) REVERT: Aw 95 MET cc_start: 0.8380 (mmm) cc_final: 0.7853 (mmm) REVERT: Aw 149 MET cc_start: 0.7430 (tpp) cc_final: 0.7218 (tpp) REVERT: Ax 95 MET cc_start: 0.8723 (mmm) cc_final: 0.8190 (mmm) REVERT: Ax 143 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8466 (tp30) REVERT: Ay 137 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8546 (mm-30) REVERT: Ay 215 GLU cc_start: 0.7740 (pm20) cc_final: 0.7405 (pm20) REVERT: Az 143 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8384 (tp30) REVERT: Az 215 GLU cc_start: 0.7812 (pt0) cc_final: 0.7563 (pm20) REVERT: Az 218 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7634 (tpt) REVERT: Ba 81 ILE cc_start: 0.8763 (mm) cc_final: 0.8507 (mm) REVERT: Ba 198 MET cc_start: 0.9197 (ttm) cc_final: 0.8944 (mtp) outliers start: 190 outliers final: 81 residues processed: 1175 average time/residue: 0.2205 time to fit residues: 442.8888 Evaluate side-chains 986 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 899 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 123 THR Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 208 ILE Chi-restraints excluded: chain Ab residue 87 VAL Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ab residue 183 LYS Chi-restraints excluded: chain Ab residue 208 ILE Chi-restraints excluded: chain Ab residue 218 MET Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 165 ILE Chi-restraints excluded: chain Ac residue 170 THR Chi-restraints excluded: chain Ac residue 218 MET Chi-restraints excluded: chain Ad residue 78 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ad residue 209 GLU Chi-restraints excluded: chain Ae residue 161 THR Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Af residue 186 VAL Chi-restraints excluded: chain Af residue 208 ILE Chi-restraints excluded: chain Af residue 254 HIS Chi-restraints excluded: chain Ag residue 170 THR Chi-restraints excluded: chain Ag residue 208 ILE Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ah residue 148 LEU Chi-restraints excluded: chain Ah residue 170 THR Chi-restraints excluded: chain Ah residue 208 ILE Chi-restraints excluded: chain Ai residue 123 THR Chi-restraints excluded: chain Aj residue 85 LYS Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Ak residue 87 VAL Chi-restraints excluded: chain Ak residue 123 THR Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 170 THR Chi-restraints excluded: chain Al residue 218 MET Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 165 ILE Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain Am residue 172 VAL Chi-restraints excluded: chain Am residue 209 GLU Chi-restraints excluded: chain An residue 134 VAL Chi-restraints excluded: chain An residue 140 VAL Chi-restraints excluded: chain An residue 170 THR Chi-restraints excluded: chain An residue 209 GLU Chi-restraints excluded: chain Ao residue 101 ILE Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 246 THR Chi-restraints excluded: chain Ap residue 152 LEU Chi-restraints excluded: chain Ap residue 165 ILE Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 208 ILE Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Aq residue 170 THR Chi-restraints excluded: chain Aq residue 208 ILE Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain Ar residue 123 THR Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain As residue 124 HIS Chi-restraints excluded: chain As residue 223 LEU Chi-restraints excluded: chain At residue 123 THR Chi-restraints excluded: chain Au residue 123 THR Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 84 LEU Chi-restraints excluded: chain Av residue 170 THR Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Aw residue 78 THR Chi-restraints excluded: chain Aw residue 134 VAL Chi-restraints excluded: chain Aw residue 140 VAL Chi-restraints excluded: chain Aw residue 209 GLU Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ax residue 205 GLU Chi-restraints excluded: chain Ax residue 209 GLU Chi-restraints excluded: chain Ax residue 246 THR Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Ay residue 205 GLU Chi-restraints excluded: chain Ay residue 208 ILE Chi-restraints excluded: chain Az residue 164 ASP Chi-restraints excluded: chain Az residue 170 THR Chi-restraints excluded: chain Az residue 218 MET Chi-restraints excluded: chain Ba residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 296 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 208 optimal weight: 0.2980 chunk 121 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 124 HIS Ab 144 GLN Ab 226 ASN Ad 128 GLN Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS Ai 254 HIS ** Aj 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 114 GLN Aj 144 GLN Ak 226 ASN ** An 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 254 HIS ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 226 ASN Av 195 GLN Aw 195 GLN ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 124 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077517 restraints weight = 95363.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080708 restraints weight = 48429.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082900 restraints weight = 31109.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084361 restraints weight = 22657.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085371 restraints weight = 17969.753| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40959 Z= 0.113 Angle : 0.585 9.355 55377 Z= 0.294 Chirality : 0.039 0.228 5751 Planarity : 0.004 0.052 7290 Dihedral : 3.921 18.518 5400 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.72 % Allowed : 17.56 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4779 helix: 0.40 (0.12), residues: 2079 sheet: -1.79 (0.27), residues: 324 loop : 0.51 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAm 211 TYR 0.023 0.001 TYRAj 221 PHE 0.018 0.001 PHEAc 129 TRP 0.014 0.001 TRPAi 169 HIS 0.004 0.001 HISAu 254 Details of bonding type rmsd covalent geometry : bond 0.00262 (40959) covalent geometry : angle 0.58506 (55377) hydrogen bonds : bond 0.02960 ( 1539) hydrogen bonds : angle 4.23530 ( 4131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 999 time to evaluate : 1.687 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: Aa 113 ASP cc_start: 0.7653 (t0) cc_final: 0.7372 (t0) REVERT: Aa 161 THR cc_start: 0.8923 (p) cc_final: 0.8633 (t) REVERT: Aa 171 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: Ab 91 MET cc_start: 0.7367 (mmp) cc_final: 0.7053 (mtp) REVERT: Ab 145 MET cc_start: 0.8669 (tpt) cc_final: 0.8207 (tpp) REVERT: Ab 183 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8293 (ttpp) REVERT: Ab 221 TYR cc_start: 0.8649 (t80) cc_final: 0.8398 (t80) REVERT: Ab 229 ASP cc_start: 0.6949 (m-30) cc_final: 0.6518 (t70) REVERT: Ac 145 MET cc_start: 0.8716 (tpt) cc_final: 0.8492 (tpp) REVERT: Ac 205 GLU cc_start: 0.8270 (tt0) cc_final: 0.7876 (tt0) REVERT: Ac 218 MET cc_start: 0.8438 (ttm) cc_final: 0.8055 (ttt) REVERT: Ad 95 MET cc_start: 0.8424 (mmm) cc_final: 0.8188 (mmt) REVERT: Ad 125 THR cc_start: 0.9223 (m) cc_final: 0.8823 (p) REVERT: Ad 144 GLN cc_start: 0.8321 (mt0) cc_final: 0.8098 (mt0) REVERT: Ad 209 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8451 (pp20) REVERT: Ad 221 TYR cc_start: 0.8313 (t80) cc_final: 0.8038 (t80) REVERT: Ae 95 MET cc_start: 0.8715 (mmm) cc_final: 0.8431 (mmm) REVERT: Ae 162 SER cc_start: 0.9470 (m) cc_final: 0.8934 (p) REVERT: Ae 215 GLU cc_start: 0.7768 (pm20) cc_final: 0.7539 (pm20) REVERT: Af 179 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8204 (tt0) REVERT: Af 215 GLU cc_start: 0.7937 (pm20) cc_final: 0.7547 (pm20) REVERT: Ag 196 CYS cc_start: 0.8746 (t) cc_final: 0.8350 (t) REVERT: Ag 215 GLU cc_start: 0.7980 (pm20) cc_final: 0.7696 (pm20) REVERT: Ag 218 MET cc_start: 0.7999 (tpp) cc_final: 0.7646 (tpt) REVERT: Ah 215 GLU cc_start: 0.7565 (pm20) cc_final: 0.6983 (pm20) REVERT: Ah 245 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7883 (mpt180) REVERT: Ai 109 GLN cc_start: 0.8803 (pp30) cc_final: 0.8583 (pp30) REVERT: Ai 145 MET cc_start: 0.8701 (tpp) cc_final: 0.8200 (tpp) REVERT: Ai 205 GLU cc_start: 0.8118 (tt0) cc_final: 0.7835 (mt-10) REVERT: Aj 205 GLU cc_start: 0.7920 (tt0) cc_final: 0.7720 (tt0) REVERT: Aj 210 MET cc_start: 0.8428 (tmm) cc_final: 0.8146 (tmm) REVERT: Ak 143 GLU cc_start: 0.8700 (tp30) cc_final: 0.8224 (tm-30) REVERT: Ak 171 MET cc_start: 0.8498 (mtp) cc_final: 0.8243 (ttt) REVERT: Ak 205 GLU cc_start: 0.8093 (tt0) cc_final: 0.7747 (tt0) REVERT: Ak 235 TYR cc_start: 0.9188 (m-80) cc_final: 0.8984 (m-80) REVERT: Al 90 LYS cc_start: 0.7848 (tttm) cc_final: 0.7617 (tptp) REVERT: Al 139 ASP cc_start: 0.7682 (t70) cc_final: 0.7340 (t70) REVERT: Al 145 MET cc_start: 0.8631 (tpt) cc_final: 0.8326 (tpp) REVERT: Al 205 GLU cc_start: 0.8345 (tt0) cc_final: 0.8080 (mt-10) REVERT: Am 95 MET cc_start: 0.8428 (mmt) cc_final: 0.7864 (mmm) REVERT: Am 110 TYR cc_start: 0.8942 (t80) cc_final: 0.8723 (t80) REVERT: An 95 MET cc_start: 0.8484 (mmm) cc_final: 0.8076 (mmm) REVERT: An 209 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8511 (pp20) REVERT: Ao 215 GLU cc_start: 0.7883 (pm20) cc_final: 0.7674 (pm20) REVERT: Ap 81 ILE cc_start: 0.9289 (mm) cc_final: 0.8997 (mm) REVERT: Ap 88 SER cc_start: 0.7049 (p) cc_final: 0.6494 (t) REVERT: Ap 198 MET cc_start: 0.9066 (ttm) cc_final: 0.8853 (ttm) REVERT: Ap 215 GLU cc_start: 0.7877 (pm20) cc_final: 0.7314 (pm20) REVERT: Aq 165 ILE cc_start: 0.8568 (mm) cc_final: 0.8320 (tp) REVERT: Aq 210 MET cc_start: 0.8422 (tmm) cc_final: 0.7989 (tmm) REVERT: Aq 215 GLU cc_start: 0.7812 (pt0) cc_final: 0.7532 (pm20) REVERT: Aq 218 MET cc_start: 0.7650 (tpt) cc_final: 0.7371 (tpt) REVERT: Ar 81 ILE cc_start: 0.8793 (mm) cc_final: 0.8454 (mm) REVERT: Ar 109 GLN cc_start: 0.8364 (pm20) cc_final: 0.8125 (pm20) REVERT: Ar 145 MET cc_start: 0.8673 (tpp) cc_final: 0.8084 (tpp) REVERT: Ar 210 MET cc_start: 0.8293 (tmm) cc_final: 0.7957 (tmm) REVERT: Ar 218 MET cc_start: 0.8031 (ttm) cc_final: 0.7788 (ttt) REVERT: As 109 GLN cc_start: 0.8652 (pp30) cc_final: 0.8389 (pp30) REVERT: As 148 LEU cc_start: 0.8598 (tt) cc_final: 0.8292 (mp) REVERT: As 205 GLU cc_start: 0.8125 (tt0) cc_final: 0.7823 (mt-10) REVERT: As 210 MET cc_start: 0.8400 (tmm) cc_final: 0.8046 (tmm) REVERT: As 245 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7849 (mtm-85) REVERT: At 205 GLU cc_start: 0.8030 (tt0) cc_final: 0.7693 (mt-10) REVERT: At 210 MET cc_start: 0.8576 (tmm) cc_final: 0.8300 (tmm) REVERT: At 218 MET cc_start: 0.8267 (ttm) cc_final: 0.8012 (ttt) REVERT: At 237 PHE cc_start: 0.8700 (p90) cc_final: 0.8427 (p90) REVERT: Au 128 GLN cc_start: 0.8395 (mt0) cc_final: 0.8194 (tt0) REVERT: Au 143 GLU cc_start: 0.8767 (tp30) cc_final: 0.8418 (tm-30) REVERT: Au 145 MET cc_start: 0.8562 (tpt) cc_final: 0.8108 (tpp) REVERT: Au 205 GLU cc_start: 0.8277 (tt0) cc_final: 0.8027 (tt0) REVERT: Av 145 MET cc_start: 0.8604 (tpt) cc_final: 0.8304 (tpp) REVERT: Av 158 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7226 (mt-10) REVERT: Av 205 GLU cc_start: 0.8110 (tt0) cc_final: 0.7735 (tt0) REVERT: Av 218 MET cc_start: 0.7960 (ttp) cc_final: 0.7681 (ttt) REVERT: Aw 95 MET cc_start: 0.8490 (mmm) cc_final: 0.8265 (mmt) REVERT: Ax 95 MET cc_start: 0.8855 (mmm) cc_final: 0.8327 (mmm) REVERT: Ax 143 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8489 (tp30) REVERT: Ay 109 GLN cc_start: 0.8052 (pm20) cc_final: 0.7734 (pm20) REVERT: Ay 215 GLU cc_start: 0.7743 (pm20) cc_final: 0.7328 (pm20) REVERT: Ay 218 MET cc_start: 0.7899 (mmm) cc_final: 0.7603 (tpt) REVERT: Az 148 LEU cc_start: 0.8534 (pp) cc_final: 0.7947 (mt) REVERT: Az 215 GLU cc_start: 0.7784 (pt0) cc_final: 0.7538 (pm20) REVERT: Ba 81 ILE cc_start: 0.8800 (mm) cc_final: 0.8584 (mm) REVERT: Ba 148 LEU cc_start: 0.8385 (pp) cc_final: 0.8051 (mp) REVERT: Ba 159 ASN cc_start: 0.7783 (m-40) cc_final: 0.7578 (m110) REVERT: Ba 210 MET cc_start: 0.8158 (tmm) cc_final: 0.7861 (tmm) outliers start: 119 outliers final: 64 residues processed: 1063 average time/residue: 0.2188 time to fit residues: 400.4957 Evaluate side-chains 958 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 892 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 157 ILE Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Ab residue 87 VAL Chi-restraints excluded: chain Ab residue 183 LYS Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ad residue 78 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 117 ILE Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 101 ILE Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Af residue 208 ILE Chi-restraints excluded: chain Af residue 254 HIS Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ai residue 78 THR Chi-restraints excluded: chain Ai residue 123 THR Chi-restraints excluded: chain Aj residue 78 THR Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 196 CYS Chi-restraints excluded: chain Aj residue 218 MET Chi-restraints excluded: chain Ak residue 87 VAL Chi-restraints excluded: chain Ak residue 123 THR Chi-restraints excluded: chain Ak residue 170 THR Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 123 THR Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 165 ILE Chi-restraints excluded: chain An residue 134 VAL Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 208 ILE Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Ar residue 97 SER Chi-restraints excluded: chain Ar residue 123 THR Chi-restraints excluded: chain Ar residue 208 ILE Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain At residue 87 VAL Chi-restraints excluded: chain At residue 123 THR Chi-restraints excluded: chain Au residue 123 THR Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 196 CYS Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 84 LEU Chi-restraints excluded: chain Av residue 170 THR Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Av residue 227 LEU Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Ay residue 208 ILE Chi-restraints excluded: chain Ay residue 254 HIS Chi-restraints excluded: chain Az residue 170 THR Chi-restraints excluded: chain Ba residue 101 ILE Chi-restraints excluded: chain Ba residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 358 optimal weight: 8.9990 chunk 305 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 26 optimal weight: 0.0060 chunk 283 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 370 optimal weight: 9.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 124 HIS Aa 228 ASN Ab 144 GLN Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 254 HIS ** Ai 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS ** Aj 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 144 GLN An 126 GLN ** An 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 150 ASN Aq 124 HIS ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 254 HIS ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 254 HIS At 103 ASN At 114 GLN At 150 ASN Ax 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068035 restraints weight = 90110.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070835 restraints weight = 48171.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072754 restraints weight = 31821.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074073 restraints weight = 23700.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.075019 restraints weight = 19003.211| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.8968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 40959 Z= 0.239 Angle : 0.692 10.376 55377 Z= 0.354 Chirality : 0.043 0.342 5751 Planarity : 0.004 0.051 7290 Dihedral : 4.328 19.627 5400 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.93 % Allowed : 16.99 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.13), residues: 4779 helix: 0.16 (0.11), residues: 2268 sheet: -0.72 (0.32), residues: 270 loop : 0.46 (0.15), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAd 249 TYR 0.033 0.002 TYRAi 221 PHE 0.022 0.002 PHEAm 180 TRP 0.018 0.002 TRPBa 130 HIS 0.005 0.001 HISAa 254 Details of bonding type rmsd covalent geometry : bond 0.00560 (40959) covalent geometry : angle 0.69231 (55377) hydrogen bonds : bond 0.03862 ( 1539) hydrogen bonds : angle 4.63591 ( 4131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 953 time to evaluate : 1.543 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: Aa 113 ASP cc_start: 0.8170 (t0) cc_final: 0.7923 (t0) REVERT: Aa 171 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: Aa 218 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7783 (ttt) REVERT: Ab 161 THR cc_start: 0.9174 (p) cc_final: 0.8941 (t) REVERT: Ab 229 ASP cc_start: 0.7566 (m-30) cc_final: 0.7251 (t0) REVERT: Ac 145 MET cc_start: 0.8903 (tpt) cc_final: 0.8347 (tpp) REVERT: Ac 179 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8116 (mt-10) REVERT: Ac 218 MET cc_start: 0.8284 (ttm) cc_final: 0.8072 (ttt) REVERT: Ad 145 MET cc_start: 0.8577 (tpp) cc_final: 0.8160 (tpp) REVERT: Ad 209 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: Ad 221 TYR cc_start: 0.8756 (t80) cc_final: 0.8553 (t80) REVERT: Ae 81 ILE cc_start: 0.9240 (mt) cc_final: 0.8994 (mm) REVERT: Ae 95 MET cc_start: 0.8571 (mmm) cc_final: 0.8288 (mmm) REVERT: Ae 143 GLU cc_start: 0.8499 (tp30) cc_final: 0.8239 (tm-30) REVERT: Ae 215 GLU cc_start: 0.7999 (pm20) cc_final: 0.7735 (pm20) REVERT: Ae 221 TYR cc_start: 0.8750 (t80) cc_final: 0.8524 (t80) REVERT: Af 124 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8252 (t70) REVERT: Af 215 GLU cc_start: 0.8062 (pm20) cc_final: 0.7703 (pm20) REVERT: Af 221 TYR cc_start: 0.8726 (t80) cc_final: 0.8506 (t80) REVERT: Ag 145 MET cc_start: 0.8246 (tpp) cc_final: 0.8033 (tpp) REVERT: Ag 165 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8410 (tp) REVERT: Ag 196 CYS cc_start: 0.8829 (t) cc_final: 0.8478 (t) REVERT: Ag 221 TYR cc_start: 0.8809 (t80) cc_final: 0.8559 (t80) REVERT: Ah 145 MET cc_start: 0.8487 (tpp) cc_final: 0.8222 (tpp) REVERT: Ah 165 ILE cc_start: 0.9129 (mp) cc_final: 0.8891 (tt) REVERT: Ah 210 MET cc_start: 0.8644 (tmm) cc_final: 0.8318 (tmm) REVERT: Ah 215 GLU cc_start: 0.7714 (pm20) cc_final: 0.7333 (pm20) REVERT: Ah 218 MET cc_start: 0.8141 (tpp) cc_final: 0.7750 (tpt) REVERT: Ai 109 GLN cc_start: 0.8853 (pp30) cc_final: 0.8594 (pp30) REVERT: Ai 145 MET cc_start: 0.8531 (tpp) cc_final: 0.8084 (tpp) REVERT: Ai 168 TYR cc_start: 0.8659 (m-80) cc_final: 0.8242 (m-10) REVERT: Aj 109 GLN cc_start: 0.8795 (pp30) cc_final: 0.8526 (pp30) REVERT: Aj 149 MET cc_start: 0.8611 (tpp) cc_final: 0.8283 (tpp) REVERT: Aj 205 GLU cc_start: 0.8179 (tt0) cc_final: 0.7732 (tt0) REVERT: Aj 210 MET cc_start: 0.8468 (tmm) cc_final: 0.8057 (tmm) REVERT: Aj 230 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7440 (tttt) REVERT: Ak 139 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7904 (t0) REVERT: Ak 143 GLU cc_start: 0.8521 (tp30) cc_final: 0.8281 (tm-30) REVERT: Ak 171 MET cc_start: 0.8769 (mtp) cc_final: 0.8545 (ttt) REVERT: Ak 205 GLU cc_start: 0.8163 (tt0) cc_final: 0.7821 (tt0) REVERT: Ak 228 ASN cc_start: 0.7891 (m-40) cc_final: 0.7601 (p0) REVERT: Al 145 MET cc_start: 0.8774 (tpt) cc_final: 0.8293 (tpp) REVERT: Al 153 MET cc_start: 0.9259 (ttp) cc_final: 0.8991 (ttp) REVERT: Al 161 THR cc_start: 0.9164 (p) cc_final: 0.8840 (t) REVERT: Al 205 GLU cc_start: 0.8510 (tt0) cc_final: 0.8123 (tt0) REVERT: Al 235 TYR cc_start: 0.9422 (m-80) cc_final: 0.9171 (m-10) REVERT: Am 161 THR cc_start: 0.9174 (p) cc_final: 0.8806 (m) REVERT: Am 205 GLU cc_start: 0.8230 (tt0) cc_final: 0.7841 (tt0) REVERT: An 110 TYR cc_start: 0.9140 (t80) cc_final: 0.8915 (t80) REVERT: An 139 ASP cc_start: 0.7967 (t70) cc_final: 0.7610 (t70) REVERT: An 209 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8584 (pp20) REVERT: Ap 88 SER cc_start: 0.6689 (p) cc_final: 0.6042 (t) REVERT: Ap 164 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7594 (t70) REVERT: Ap 168 TYR cc_start: 0.8378 (m-80) cc_final: 0.8109 (m-10) REVERT: Ap 215 GLU cc_start: 0.7903 (pm20) cc_final: 0.7389 (pm20) REVERT: Aq 164 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7760 (t70) REVERT: Aq 165 ILE cc_start: 0.8835 (mm) cc_final: 0.8515 (tp) REVERT: Aq 210 MET cc_start: 0.8594 (tmm) cc_final: 0.8370 (tmm) REVERT: Aq 230 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7513 (ttmt) REVERT: Ar 81 ILE cc_start: 0.9193 (mm) cc_final: 0.8982 (mm) REVERT: Ar 145 MET cc_start: 0.8760 (tpp) cc_final: 0.8215 (tpp) REVERT: Ar 205 GLU cc_start: 0.8278 (tt0) cc_final: 0.7856 (tt0) REVERT: Ar 210 MET cc_start: 0.8401 (tmm) cc_final: 0.7948 (tmm) REVERT: As 109 GLN cc_start: 0.8718 (pp30) cc_final: 0.8089 (pp30) REVERT: As 171 MET cc_start: 0.8637 (mmm) cc_final: 0.8390 (mtp) REVERT: As 205 GLU cc_start: 0.8298 (tt0) cc_final: 0.8044 (mt-10) REVERT: As 210 MET cc_start: 0.8635 (tmm) cc_final: 0.8365 (tmm) REVERT: At 109 GLN cc_start: 0.8912 (pp30) cc_final: 0.8419 (pp30) REVERT: At 205 GLU cc_start: 0.8147 (tt0) cc_final: 0.7812 (mt-10) REVERT: Au 143 GLU cc_start: 0.8643 (tp30) cc_final: 0.8307 (tm-30) REVERT: Au 145 MET cc_start: 0.8571 (tpt) cc_final: 0.8199 (tpp) REVERT: Au 205 GLU cc_start: 0.8374 (tt0) cc_final: 0.7954 (mt-10) REVERT: Av 145 MET cc_start: 0.8746 (tpt) cc_final: 0.8273 (tpp) REVERT: Av 149 MET cc_start: 0.8286 (tpp) cc_final: 0.8030 (mpp) REVERT: Av 161 THR cc_start: 0.9217 (p) cc_final: 0.8797 (m) REVERT: Av 205 GLU cc_start: 0.8199 (tt0) cc_final: 0.7732 (tt0) REVERT: Aw 209 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8602 (pp20) REVERT: Ax 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8503 (mmt) REVERT: Ax 143 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8435 (tp30) REVERT: Ax 221 TYR cc_start: 0.8740 (t80) cc_final: 0.8540 (t80) REVERT: Ay 88 SER cc_start: 0.7034 (p) cc_final: 0.6534 (t) REVERT: Ay 109 GLN cc_start: 0.8321 (pm20) cc_final: 0.7979 (pm20) REVERT: Ay 215 GLU cc_start: 0.7924 (pm20) cc_final: 0.7575 (pm20) REVERT: Ay 218 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7660 (tpt) REVERT: Az 110 TYR cc_start: 0.8819 (t80) cc_final: 0.8540 (t80) REVERT: Az 210 MET cc_start: 0.8433 (tmm) cc_final: 0.8134 (tmm) REVERT: Az 215 GLU cc_start: 0.7686 (pt0) cc_final: 0.7339 (pm20) REVERT: Az 230 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7759 (ttmt) REVERT: Ba 148 LEU cc_start: 0.8514 (pp) cc_final: 0.8161 (mt) REVERT: Ba 168 TYR cc_start: 0.8668 (m-80) cc_final: 0.8407 (m-10) REVERT: Ba 205 GLU cc_start: 0.8079 (tt0) cc_final: 0.7701 (tt0) REVERT: Ba 210 MET cc_start: 0.8324 (tmm) cc_final: 0.8092 (tmm) outliers start: 172 outliers final: 90 residues processed: 1065 average time/residue: 0.2109 time to fit residues: 385.4052 Evaluate side-chains 938 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 837 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 124 HIS Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 156 CYS Chi-restraints excluded: chain Ac residue 170 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ad residue 209 GLU Chi-restraints excluded: chain Ae residue 170 THR Chi-restraints excluded: chain Af residue 124 HIS Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Af residue 208 ILE Chi-restraints excluded: chain Ag residue 165 ILE Chi-restraints excluded: chain Ag residue 208 ILE Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 148 LEU Chi-restraints excluded: chain Ah residue 208 ILE Chi-restraints excluded: chain Ai residue 78 THR Chi-restraints excluded: chain Ai residue 123 THR Chi-restraints excluded: chain Ai residue 196 CYS Chi-restraints excluded: chain Aj residue 78 THR Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 124 HIS Chi-restraints excluded: chain Aj residue 196 CYS Chi-restraints excluded: chain Aj residue 244 SER Chi-restraints excluded: chain Ak residue 124 HIS Chi-restraints excluded: chain Ak residue 139 ASP Chi-restraints excluded: chain Ak residue 156 CYS Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 170 THR Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 156 CYS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 170 THR Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 165 ILE Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain Am residue 209 GLU Chi-restraints excluded: chain Am residue 227 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain An residue 209 GLU Chi-restraints excluded: chain Ao residue 101 ILE Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 149 MET Chi-restraints excluded: chain Ao residue 208 ILE Chi-restraints excluded: chain Ap residue 149 MET Chi-restraints excluded: chain Ap residue 156 CYS Chi-restraints excluded: chain Ap residue 164 ASP Chi-restraints excluded: chain Ap residue 165 ILE Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 208 ILE Chi-restraints excluded: chain Ap residue 252 GLU Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Aq residue 164 ASP Chi-restraints excluded: chain Aq residue 208 ILE Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain Ar residue 148 LEU Chi-restraints excluded: chain Ar residue 196 CYS Chi-restraints excluded: chain Ar residue 208 ILE Chi-restraints excluded: chain As residue 78 THR Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 157 ILE Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 128 GLN Chi-restraints excluded: chain Av residue 165 ILE Chi-restraints excluded: chain Av residue 170 THR Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Av residue 209 GLU Chi-restraints excluded: chain Av residue 227 LEU Chi-restraints excluded: chain Av residue 254 HIS Chi-restraints excluded: chain Aw residue 91 MET Chi-restraints excluded: chain Aw residue 128 GLN Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Aw residue 209 GLU Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 109 GLN Chi-restraints excluded: chain Ax residue 156 CYS Chi-restraints excluded: chain Ax residue 170 THR Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ax residue 209 GLU Chi-restraints excluded: chain Ay residue 128 GLN Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Ay residue 205 GLU Chi-restraints excluded: chain Ay residue 208 ILE Chi-restraints excluded: chain Ay residue 218 MET Chi-restraints excluded: chain Az residue 170 THR Chi-restraints excluded: chain Ba residue 124 HIS Chi-restraints excluded: chain Ba residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 444 optimal weight: 1.9990 chunk 421 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 419 optimal weight: 0.0670 chunk 390 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 HIS Ac 132 ASN Ad 124 HIS ** Ad 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS Al 124 HIS Am 124 HIS Am 254 HIS ** An 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 124 HIS ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 159 ASN ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 124 HIS At 124 HIS ** Au 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 124 HIS Av 124 HIS Ax 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 124 HIS Az 124 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069211 restraints weight = 89618.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.072067 restraints weight = 47553.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074028 restraints weight = 31177.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.075375 restraints weight = 23094.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076310 restraints weight = 18436.026| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.9290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40959 Z= 0.173 Angle : 0.624 10.320 55377 Z= 0.319 Chirality : 0.041 0.273 5751 Planarity : 0.004 0.049 7290 Dihedral : 4.124 18.285 5400 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.72 % Allowed : 19.30 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4779 helix: 0.25 (0.11), residues: 2268 sheet: -0.23 (0.34), residues: 270 loop : 0.54 (0.15), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAs 245 TYR 0.032 0.002 TYRAq 221 PHE 0.014 0.002 PHEAn 200 TRP 0.014 0.001 TRPAw 169 HIS 0.004 0.001 HISAf 124 Details of bonding type rmsd covalent geometry : bond 0.00408 (40959) covalent geometry : angle 0.62365 (55377) hydrogen bonds : bond 0.03171 ( 1539) hydrogen bonds : angle 4.31293 ( 4131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 925 time to evaluate : 1.837 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: Aa 171 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: Aa 218 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7877 (ttt) REVERT: Ab 161 THR cc_start: 0.9174 (p) cc_final: 0.8961 (t) REVERT: Ab 218 MET cc_start: 0.8451 (ttt) cc_final: 0.8170 (ttt) REVERT: Ab 229 ASP cc_start: 0.7553 (m-30) cc_final: 0.7335 (t0) REVERT: Ac 145 MET cc_start: 0.8667 (tpt) cc_final: 0.8326 (tpp) REVERT: Ad 137 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7975 (tm-30) REVERT: Ad 145 MET cc_start: 0.8516 (tpp) cc_final: 0.8040 (tpp) REVERT: Ad 209 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8447 (pp20) REVERT: Ad 221 TYR cc_start: 0.8685 (t80) cc_final: 0.8483 (t80) REVERT: Ae 81 ILE cc_start: 0.9276 (mt) cc_final: 0.9025 (mm) REVERT: Ae 143 GLU cc_start: 0.8461 (tp30) cc_final: 0.8220 (tm-30) REVERT: Ae 215 GLU cc_start: 0.7975 (pm20) cc_final: 0.7667 (pm20) REVERT: Af 124 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7966 (t-90) REVERT: Af 215 GLU cc_start: 0.8004 (pm20) cc_final: 0.7623 (pm20) REVERT: Ag 196 CYS cc_start: 0.8801 (t) cc_final: 0.8403 (t) REVERT: Ag 221 TYR cc_start: 0.8744 (t80) cc_final: 0.8494 (t80) REVERT: Ah 145 MET cc_start: 0.8450 (tpp) cc_final: 0.8076 (tpp) REVERT: Ah 210 MET cc_start: 0.8684 (tmm) cc_final: 0.8397 (tmm) REVERT: Ah 215 GLU cc_start: 0.7610 (pm20) cc_final: 0.7270 (pm20) REVERT: Ah 218 MET cc_start: 0.8006 (tpp) cc_final: 0.7669 (tpt) REVERT: Ai 109 GLN cc_start: 0.8927 (pp30) cc_final: 0.8682 (pp30) REVERT: Ai 153 MET cc_start: 0.9073 (tmm) cc_final: 0.8699 (ttt) REVERT: Ai 168 TYR cc_start: 0.8632 (m-80) cc_final: 0.8242 (m-10) REVERT: Aj 109 GLN cc_start: 0.8881 (pp30) cc_final: 0.8607 (pp30) REVERT: Aj 145 MET cc_start: 0.8829 (tpp) cc_final: 0.8598 (tpp) REVERT: Aj 205 GLU cc_start: 0.8159 (tt0) cc_final: 0.7694 (tt0) REVERT: Aj 210 MET cc_start: 0.8494 (tmm) cc_final: 0.8232 (tmm) REVERT: Aj 230 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7311 (tttt) REVERT: Ak 171 MET cc_start: 0.8688 (mtp) cc_final: 0.8465 (ttt) REVERT: Ak 205 GLU cc_start: 0.8102 (tt0) cc_final: 0.7778 (tt0) REVERT: Ak 218 MET cc_start: 0.8221 (ttt) cc_final: 0.7768 (ttt) REVERT: Ak 227 LEU cc_start: 0.8972 (tt) cc_final: 0.8762 (tt) REVERT: Ak 228 ASN cc_start: 0.7850 (m-40) cc_final: 0.7530 (p0) REVERT: Al 145 MET cc_start: 0.8746 (tpt) cc_final: 0.8239 (tpp) REVERT: Al 161 THR cc_start: 0.9155 (p) cc_final: 0.8937 (m) REVERT: Al 205 GLU cc_start: 0.8439 (tt0) cc_final: 0.8101 (mt-10) REVERT: Am 161 THR cc_start: 0.9192 (p) cc_final: 0.8891 (m) REVERT: Am 171 MET cc_start: 0.8792 (ttt) cc_final: 0.8588 (ttt) REVERT: Am 205 GLU cc_start: 0.8230 (tt0) cc_final: 0.7822 (tt0) REVERT: An 139 ASP cc_start: 0.7983 (t70) cc_final: 0.7384 (t0) REVERT: An 209 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8497 (pp20) REVERT: An 215 GLU cc_start: 0.7712 (pm20) cc_final: 0.7369 (pm20) REVERT: Ap 81 ILE cc_start: 0.9259 (mm) cc_final: 0.9010 (mm) REVERT: Ap 109 GLN cc_start: 0.8698 (pp30) cc_final: 0.8109 (pp30) REVERT: Ap 215 GLU cc_start: 0.7890 (pm20) cc_final: 0.7397 (pm20) REVERT: Aq 165 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8476 (tp) REVERT: Aq 224 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8545 (mp) REVERT: Ar 145 MET cc_start: 0.8728 (tpp) cc_final: 0.8111 (tpp) REVERT: Ar 168 TYR cc_start: 0.8567 (m-80) cc_final: 0.8271 (m-10) REVERT: Ar 170 THR cc_start: 0.9395 (p) cc_final: 0.9182 (m) REVERT: Ar 198 MET cc_start: 0.9065 (ttm) cc_final: 0.8803 (mtp) REVERT: Ar 205 GLU cc_start: 0.8225 (tt0) cc_final: 0.7913 (tt0) REVERT: Ar 210 MET cc_start: 0.8411 (tmm) cc_final: 0.8143 (tmm) REVERT: As 109 GLN cc_start: 0.8770 (pp30) cc_final: 0.8135 (pp30) REVERT: As 143 GLU cc_start: 0.8550 (tp30) cc_final: 0.8342 (tp30) REVERT: As 148 LEU cc_start: 0.8806 (tt) cc_final: 0.8532 (mp) REVERT: As 210 MET cc_start: 0.8629 (tmm) cc_final: 0.8411 (tmm) REVERT: At 109 GLN cc_start: 0.8931 (pp30) cc_final: 0.8428 (pp30) REVERT: Au 109 GLN cc_start: 0.8969 (pp30) cc_final: 0.8768 (pp30) REVERT: Au 143 GLU cc_start: 0.8640 (tp30) cc_final: 0.8235 (tm-30) REVERT: Au 145 MET cc_start: 0.8528 (tpt) cc_final: 0.8232 (tpp) REVERT: Au 205 GLU cc_start: 0.8298 (tt0) cc_final: 0.7973 (mt-10) REVERT: Av 145 MET cc_start: 0.8690 (tpt) cc_final: 0.8200 (tpp) REVERT: Av 158 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7575 (mt-10) REVERT: Av 161 THR cc_start: 0.9312 (p) cc_final: 0.8879 (m) REVERT: Aw 95 MET cc_start: 0.8565 (mmt) cc_final: 0.8040 (mmm) REVERT: Aw 198 MET cc_start: 0.9002 (ttm) cc_final: 0.8632 (mtt) REVERT: Aw 209 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8536 (pp20) REVERT: Aw 218 MET cc_start: 0.8306 (ttt) cc_final: 0.7845 (ttt) REVERT: Ax 124 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8135 (t70) REVERT: Ax 143 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8341 (tp30) REVERT: Ax 221 TYR cc_start: 0.8578 (t80) cc_final: 0.8358 (t80) REVERT: Ay 88 SER cc_start: 0.7186 (p) cc_final: 0.6700 (t) REVERT: Ay 215 GLU cc_start: 0.7956 (pm20) cc_final: 0.7589 (pm20) REVERT: Az 210 MET cc_start: 0.8457 (tmm) cc_final: 0.8178 (tmm) REVERT: Az 215 GLU cc_start: 0.7690 (pt0) cc_final: 0.7283 (pm20) REVERT: Ba 205 GLU cc_start: 0.7999 (tt0) cc_final: 0.7700 (mt-10) REVERT: Ba 210 MET cc_start: 0.8333 (tmm) cc_final: 0.8091 (tmm) outliers start: 119 outliers final: 71 residues processed: 1011 average time/residue: 0.2207 time to fit residues: 385.0192 Evaluate side-chains 921 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 844 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 124 HIS Chi-restraints excluded: chain Ac residue 156 CYS Chi-restraints excluded: chain Ac residue 170 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Af residue 124 HIS Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Af residue 208 ILE Chi-restraints excluded: chain Ag residue 208 ILE Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 148 LEU Chi-restraints excluded: chain Ai residue 78 THR Chi-restraints excluded: chain Ai residue 123 THR Chi-restraints excluded: chain Aj residue 78 THR Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 166 ASN Chi-restraints excluded: chain Aj residue 196 CYS Chi-restraints excluded: chain Ak residue 87 VAL Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 170 THR Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 83 LYS Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 156 CYS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 165 ILE Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain Am residue 227 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain Ao residue 101 ILE Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 208 ILE Chi-restraints excluded: chain Ap residue 149 MET Chi-restraints excluded: chain Ap residue 156 CYS Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 208 ILE Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Aq residue 165 ILE Chi-restraints excluded: chain Aq residue 208 ILE Chi-restraints excluded: chain Aq residue 224 LEU Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain Ar residue 196 CYS Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 170 THR Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Aw residue 123 THR Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 109 GLN Chi-restraints excluded: chain Ax residue 124 HIS Chi-restraints excluded: chain Ax residue 170 THR Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ay residue 128 GLN Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Ay residue 208 ILE Chi-restraints excluded: chain Az residue 148 LEU Chi-restraints excluded: chain Az residue 241 GLU Chi-restraints excluded: chain Ba residue 139 ASP Chi-restraints excluded: chain Ba residue 156 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 65 optimal weight: 7.9990 chunk 398 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 124 HIS Ab 124 HIS Ac 124 HIS Ad 124 HIS ** Ad 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 124 HIS Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS Ag 150 ASN ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS Ak 124 HIS Ak 144 GLN Al 124 HIS Al 195 GLN Am 124 HIS Am 144 GLN Ap 124 HIS Aq 150 ASN ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 124 HIS Au 124 HIS Av 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 124 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.066103 restraints weight = 91280.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.068805 restraints weight = 49327.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.070660 restraints weight = 32865.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.071929 restraints weight = 24659.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072842 restraints weight = 19963.279| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.9730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 40959 Z= 0.301 Angle : 0.736 9.653 55377 Z= 0.379 Chirality : 0.045 0.291 5751 Planarity : 0.005 0.049 7290 Dihedral : 4.530 21.565 5400 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.96 % Allowed : 19.04 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4779 helix: 0.14 (0.11), residues: 2241 sheet: -0.07 (0.35), residues: 270 loop : 0.70 (0.15), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAm 225 TYR 0.032 0.002 TYRAt 235 PHE 0.022 0.002 PHEAn 200 TRP 0.015 0.002 TRPAw 169 HIS 0.006 0.001 HISAx 124 Details of bonding type rmsd covalent geometry : bond 0.00705 (40959) covalent geometry : angle 0.73629 (55377) hydrogen bonds : bond 0.03916 ( 1539) hydrogen bonds : angle 4.75480 ( 4131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 859 time to evaluate : 1.681 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: Aa 139 ASP cc_start: 0.8193 (t0) cc_final: 0.7764 (t70) REVERT: Aa 149 MET cc_start: 0.8518 (tpp) cc_final: 0.8074 (tpp) REVERT: Aa 171 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8527 (mtp) REVERT: Aa 218 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7984 (ttt) REVERT: Ab 109 GLN cc_start: 0.9229 (pp30) cc_final: 0.9022 (pp30) REVERT: Ab 161 THR cc_start: 0.9346 (p) cc_final: 0.9135 (m) REVERT: Ab 218 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (ttt) REVERT: Ab 229 ASP cc_start: 0.7784 (m-30) cc_final: 0.7433 (t0) REVERT: Ad 137 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8134 (tm-30) REVERT: Ad 209 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8551 (pp20) REVERT: Ae 81 ILE cc_start: 0.9229 (mt) cc_final: 0.8981 (mm) REVERT: Ae 143 GLU cc_start: 0.8576 (tp30) cc_final: 0.8348 (tm-30) REVERT: Ae 215 GLU cc_start: 0.8030 (pm20) cc_final: 0.7663 (pm20) REVERT: Af 124 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8302 (t70) REVERT: Af 215 GLU cc_start: 0.8104 (pm20) cc_final: 0.7703 (pm20) REVERT: Ag 95 MET cc_start: 0.8432 (mtp) cc_final: 0.8127 (mtt) REVERT: Ag 145 MET cc_start: 0.8624 (tpp) cc_final: 0.8189 (tpp) REVERT: Ag 164 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (t70) REVERT: Ag 168 TYR cc_start: 0.8792 (m-10) cc_final: 0.8418 (m-10) REVERT: Ag 196 CYS cc_start: 0.8955 (t) cc_final: 0.8570 (t) REVERT: Ag 221 TYR cc_start: 0.8803 (t80) cc_final: 0.8594 (t80) REVERT: Ah 145 MET cc_start: 0.8731 (tpp) cc_final: 0.8436 (tpp) REVERT: Ah 210 MET cc_start: 0.8834 (tmm) cc_final: 0.8532 (tmm) REVERT: Ah 215 GLU cc_start: 0.7812 (pm20) cc_final: 0.7453 (pm20) REVERT: Ah 218 MET cc_start: 0.8222 (tpp) cc_final: 0.7866 (tpt) REVERT: Ah 230 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7633 (ttmt) REVERT: Ai 109 GLN cc_start: 0.9107 (pp30) cc_final: 0.8879 (pp30) REVERT: Ai 153 MET cc_start: 0.9027 (tmm) cc_final: 0.8787 (ttt) REVERT: Ai 205 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8242 (mt-10) REVERT: Ai 230 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7403 (ttmt) REVERT: Aj 109 GLN cc_start: 0.9001 (pp30) cc_final: 0.8715 (pp30) REVERT: Aj 205 GLU cc_start: 0.8189 (tt0) cc_final: 0.7702 (tt0) REVERT: Aj 210 MET cc_start: 0.8574 (tmm) cc_final: 0.8341 (tmm) REVERT: Ak 158 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: Ak 171 MET cc_start: 0.8798 (mtp) cc_final: 0.8533 (ttt) REVERT: Ak 205 GLU cc_start: 0.8296 (tt0) cc_final: 0.7868 (tt0) REVERT: Al 145 MET cc_start: 0.8861 (tpt) cc_final: 0.8617 (tpp) REVERT: Al 153 MET cc_start: 0.9252 (ttp) cc_final: 0.9018 (ttp) REVERT: Al 205 GLU cc_start: 0.8510 (tt0) cc_final: 0.8085 (mt-10) REVERT: Am 205 GLU cc_start: 0.8292 (tt0) cc_final: 0.7871 (tt0) REVERT: An 209 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8543 (pp20) REVERT: An 215 GLU cc_start: 0.8003 (pm20) cc_final: 0.7752 (pm20) REVERT: An 218 MET cc_start: 0.8439 (ttp) cc_final: 0.8199 (ppp) REVERT: Ao 143 GLU cc_start: 0.8721 (tp30) cc_final: 0.8495 (tp30) REVERT: Ap 81 ILE cc_start: 0.9314 (mm) cc_final: 0.9063 (mm) REVERT: Ap 109 GLN cc_start: 0.8896 (pp30) cc_final: 0.8169 (pp30) REVERT: Ap 164 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7816 (t70) REVERT: Ap 171 MET cc_start: 0.8675 (mtp) cc_final: 0.8459 (ttt) REVERT: Ap 215 GLU cc_start: 0.7987 (pm20) cc_final: 0.7444 (pm20) REVERT: Aq 95 MET cc_start: 0.8473 (mtt) cc_final: 0.8186 (mtp) REVERT: Aq 143 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8504 (tp30) REVERT: Aq 165 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8680 (tp) REVERT: Aq 215 GLU cc_start: 0.7553 (pm20) cc_final: 0.7213 (pm20) REVERT: Aq 224 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8579 (mp) REVERT: Aq 235 TYR cc_start: 0.9307 (m-10) cc_final: 0.9025 (m-10) REVERT: Ar 145 MET cc_start: 0.8884 (tpp) cc_final: 0.8333 (tpp) REVERT: Ar 198 MET cc_start: 0.9187 (ttm) cc_final: 0.8931 (mtp) REVERT: Ar 205 GLU cc_start: 0.8305 (tt0) cc_final: 0.7798 (tt0) REVERT: Ar 210 MET cc_start: 0.8725 (tmm) cc_final: 0.8501 (tmm) REVERT: Ar 215 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: Ar 230 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7603 (ttmt) REVERT: As 109 GLN cc_start: 0.8902 (pp30) cc_final: 0.8668 (pp30) REVERT: As 168 TYR cc_start: 0.8573 (m-10) cc_final: 0.8360 (m-10) REVERT: As 230 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7575 (ttmt) REVERT: Au 109 GLN cc_start: 0.9094 (pp30) cc_final: 0.8869 (pp30) REVERT: Au 143 GLU cc_start: 0.8781 (tp30) cc_final: 0.8374 (tp30) REVERT: Au 205 GLU cc_start: 0.8396 (tt0) cc_final: 0.8011 (mt-10) REVERT: Av 205 GLU cc_start: 0.8161 (tt0) cc_final: 0.7794 (mt-10) REVERT: Aw 95 MET cc_start: 0.8681 (mmt) cc_final: 0.8134 (mmm) REVERT: Aw 209 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: Ax 124 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.8353 (m-70) REVERT: Ax 143 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8368 (tm-30) REVERT: Ay 88 SER cc_start: 0.7261 (p) cc_final: 0.6767 (t) REVERT: Ay 215 GLU cc_start: 0.8078 (pm20) cc_final: 0.7737 (pm20) REVERT: Ay 235 TYR cc_start: 0.9466 (m-80) cc_final: 0.9249 (m-10) REVERT: Az 164 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7884 (t70) REVERT: Ba 205 GLU cc_start: 0.8158 (tt0) cc_final: 0.7678 (tt0) REVERT: Ba 210 MET cc_start: 0.8398 (tmm) cc_final: 0.8178 (tmm) REVERT: Ba 218 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7984 (tpt) outliers start: 173 outliers final: 112 residues processed: 987 average time/residue: 0.2182 time to fit residues: 371.5075 Evaluate side-chains 945 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 818 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ab residue 218 MET Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 156 CYS Chi-restraints excluded: chain Ac residue 170 THR Chi-restraints excluded: chain Ad residue 78 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 124 HIS Chi-restraints excluded: chain Ad residue 134 VAL Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ae residue 78 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 124 HIS Chi-restraints excluded: chain Ae residue 170 THR Chi-restraints excluded: chain Af residue 124 HIS Chi-restraints excluded: chain Af residue 149 MET Chi-restraints excluded: chain Af residue 170 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Af residue 208 ILE Chi-restraints excluded: chain Ag residue 78 THR Chi-restraints excluded: chain Ag residue 124 HIS Chi-restraints excluded: chain Ag residue 164 ASP Chi-restraints excluded: chain Ag residue 172 VAL Chi-restraints excluded: chain Ag residue 208 ILE Chi-restraints excluded: chain Ag residue 252 GLU Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 148 LEU Chi-restraints excluded: chain Ah residue 156 CYS Chi-restraints excluded: chain Ah residue 208 ILE Chi-restraints excluded: chain Ai residue 78 THR Chi-restraints excluded: chain Ai residue 158 GLU Chi-restraints excluded: chain Ai residue 196 CYS Chi-restraints excluded: chain Aj residue 78 THR Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 124 HIS Chi-restraints excluded: chain Aj residue 166 ASN Chi-restraints excluded: chain Aj residue 244 SER Chi-restraints excluded: chain Ak residue 156 CYS Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 170 THR Chi-restraints excluded: chain Ak residue 224 LEU Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 83 LYS Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 156 CYS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 170 THR Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 124 HIS Chi-restraints excluded: chain Am residue 165 ILE Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain Am residue 209 GLU Chi-restraints excluded: chain Am residue 227 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain An residue 209 GLU Chi-restraints excluded: chain Ao residue 101 ILE Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 170 THR Chi-restraints excluded: chain Ao residue 208 ILE Chi-restraints excluded: chain Ap residue 149 MET Chi-restraints excluded: chain Ap residue 156 CYS Chi-restraints excluded: chain Ap residue 164 ASP Chi-restraints excluded: chain Ap residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 208 ILE Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Ap residue 252 GLU Chi-restraints excluded: chain Aq residue 78 THR Chi-restraints excluded: chain Aq residue 128 GLN Chi-restraints excluded: chain Aq residue 148 LEU Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Aq residue 165 ILE Chi-restraints excluded: chain Aq residue 208 ILE Chi-restraints excluded: chain Aq residue 224 LEU Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain Ar residue 148 LEU Chi-restraints excluded: chain Ar residue 196 CYS Chi-restraints excluded: chain Ar residue 215 GLU Chi-restraints excluded: chain Ar residue 244 SER Chi-restraints excluded: chain As residue 78 THR Chi-restraints excluded: chain As residue 123 THR Chi-restraints excluded: chain At residue 157 ILE Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 148 LEU Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 85 LYS Chi-restraints excluded: chain Av residue 170 THR Chi-restraints excluded: chain Av residue 208 ILE Chi-restraints excluded: chain Av residue 209 GLU Chi-restraints excluded: chain Av residue 227 LEU Chi-restraints excluded: chain Av residue 254 HIS Chi-restraints excluded: chain Aw residue 78 THR Chi-restraints excluded: chain Aw residue 123 THR Chi-restraints excluded: chain Aw residue 166 ASN Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Aw residue 209 GLU Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 109 GLN Chi-restraints excluded: chain Ax residue 124 HIS Chi-restraints excluded: chain Ax residue 156 CYS Chi-restraints excluded: chain Ax residue 170 THR Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ax residue 209 GLU Chi-restraints excluded: chain Ay residue 128 GLN Chi-restraints excluded: chain Ay residue 170 THR Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Ay residue 205 GLU Chi-restraints excluded: chain Ay residue 208 ILE Chi-restraints excluded: chain Az residue 148 LEU Chi-restraints excluded: chain Az residue 164 ASP Chi-restraints excluded: chain Az residue 172 VAL Chi-restraints excluded: chain Az residue 241 GLU Chi-restraints excluded: chain Ba residue 139 ASP Chi-restraints excluded: chain Ba residue 156 CYS Chi-restraints excluded: chain Ba residue 218 MET Chi-restraints excluded: chain Ba residue 244 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 238 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 374 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 152 optimal weight: 0.1980 chunk 410 optimal weight: 6.9990 chunk 282 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 124 HIS Ab 124 HIS Ac 124 HIS Ad 126 GLN Ad 150 ASN Ae 124 HIS Af 124 HIS Ah 254 HIS Ai 124 HIS ** Aj 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 124 HIS Ak 144 GLN Al 124 HIS Al 128 GLN Am 124 HIS ** Am 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 124 HIS ** Ap 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 124 HIS Aq 124 HIS ** Aq 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 188 ASN ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 124 HIS ** Au 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 124 HIS Av 124 HIS Ax 114 GLN Ax 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 124 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 124 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.073232 restraints weight = 89112.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.076207 restraints weight = 45916.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078237 restraints weight = 29550.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079623 restraints weight = 21499.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080620 restraints weight = 16897.563| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.9868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40959 Z= 0.122 Angle : 0.633 11.225 55377 Z= 0.324 Chirality : 0.040 0.201 5751 Planarity : 0.004 0.051 7290 Dihedral : 4.134 19.467 5400 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.08 % Allowed : 21.58 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4779 helix: 0.21 (0.11), residues: 2241 sheet: -0.87 (0.30), residues: 324 loop : 0.63 (0.15), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAs 245 TYR 0.032 0.002 TYRAb 235 PHE 0.012 0.001 PHEAv 129 TRP 0.016 0.001 TRPAg 169 HIS 0.016 0.001 HISAf 124 Details of bonding type rmsd covalent geometry : bond 0.00282 (40959) covalent geometry : angle 0.63313 (55377) hydrogen bonds : bond 0.02885 ( 1539) hydrogen bonds : angle 4.24738 ( 4131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 931 time to evaluate : 1.555 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: Aa 139 ASP cc_start: 0.8058 (t0) cc_final: 0.7495 (t70) REVERT: Aa 218 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7855 (ttt) REVERT: Ab 229 ASP cc_start: 0.7522 (m-30) cc_final: 0.7264 (t0) REVERT: Ad 209 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8450 (pp20) REVERT: Ae 81 ILE cc_start: 0.9267 (mt) cc_final: 0.9023 (mm) REVERT: Ae 143 GLU cc_start: 0.8468 (tp30) cc_final: 0.8206 (tm-30) REVERT: Ae 215 GLU cc_start: 0.7944 (pm20) cc_final: 0.7599 (pm20) REVERT: Af 150 ASN cc_start: 0.9172 (t0) cc_final: 0.8925 (t0) REVERT: Af 215 GLU cc_start: 0.7972 (pm20) cc_final: 0.7568 (pm20) REVERT: Ag 95 MET cc_start: 0.8308 (mtp) cc_final: 0.8031 (mtt) REVERT: Ag 145 MET cc_start: 0.8344 (tpp) cc_final: 0.7989 (tpp) REVERT: Ag 196 CYS cc_start: 0.8805 (t) cc_final: 0.8406 (t) REVERT: Ag 198 MET cc_start: 0.9011 (ttm) cc_final: 0.8747 (ttm) REVERT: Ag 221 TYR cc_start: 0.8608 (t80) cc_final: 0.8326 (t80) REVERT: Ah 210 MET cc_start: 0.8799 (tmm) cc_final: 0.8493 (tmm) REVERT: Ah 215 GLU cc_start: 0.7679 (pm20) cc_final: 0.7455 (pm20) REVERT: Ah 218 MET cc_start: 0.8176 (tpp) cc_final: 0.7932 (tpt) REVERT: Ai 109 GLN cc_start: 0.9071 (pp30) cc_final: 0.8844 (pp30) REVERT: Ai 145 MET cc_start: 0.8756 (tpp) cc_final: 0.8283 (tpp) REVERT: Ai 153 MET cc_start: 0.9036 (tmm) cc_final: 0.8717 (ttt) REVERT: Ai 168 TYR cc_start: 0.8369 (m-10) cc_final: 0.8052 (m-10) REVERT: Ai 196 CYS cc_start: 0.8825 (m) cc_final: 0.8515 (t) REVERT: Aj 109 GLN cc_start: 0.9015 (pp30) cc_final: 0.8715 (pp30) REVERT: Aj 205 GLU cc_start: 0.8126 (tt0) cc_final: 0.7771 (tt0) REVERT: Aj 210 MET cc_start: 0.8523 (tmm) cc_final: 0.8307 (tmm) REVERT: Aj 252 GLU cc_start: 0.8430 (pm20) cc_final: 0.8189 (pm20) REVERT: Ak 158 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: Ak 171 MET cc_start: 0.8650 (mtp) cc_final: 0.8424 (ttt) REVERT: Ak 205 GLU cc_start: 0.8000 (tt0) cc_final: 0.7676 (mt-10) REVERT: Al 114 GLN cc_start: 0.9082 (tp40) cc_final: 0.8814 (tp40) REVERT: Al 145 MET cc_start: 0.8610 (tpt) cc_final: 0.8260 (tpp) REVERT: Am 205 GLU cc_start: 0.8169 (tt0) cc_final: 0.7741 (mt-10) REVERT: Am 209 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8436 (pp20) REVERT: An 209 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8411 (pp20) REVERT: An 215 GLU cc_start: 0.7712 (pm20) cc_final: 0.7456 (pm20) REVERT: Ao 145 MET cc_start: 0.7647 (tpp) cc_final: 0.7230 (tpp) REVERT: Ao 150 ASN cc_start: 0.8966 (t0) cc_final: 0.8728 (t0) REVERT: Ap 109 GLN cc_start: 0.8844 (pp30) cc_final: 0.8113 (pp30) REVERT: Ap 215 GLU cc_start: 0.7906 (pm20) cc_final: 0.7367 (pm20) REVERT: Aq 109 GLN cc_start: 0.8506 (pm20) cc_final: 0.8016 (pp30) REVERT: Aq 124 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8166 (m-70) REVERT: Aq 153 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8800 (ttt) REVERT: Aq 162 SER cc_start: 0.9046 (m) cc_final: 0.8488 (t) REVERT: Ar 145 MET cc_start: 0.8698 (tpp) cc_final: 0.8015 (tpp) REVERT: Ar 168 TYR cc_start: 0.8318 (m-80) cc_final: 0.8078 (m-10) REVERT: Ar 198 MET cc_start: 0.9121 (ttm) cc_final: 0.8835 (mtp) REVERT: Ar 218 MET cc_start: 0.8251 (ttm) cc_final: 0.7892 (ttt) REVERT: As 109 GLN cc_start: 0.8922 (pp30) cc_final: 0.8699 (pp30) REVERT: As 143 GLU cc_start: 0.8528 (tp30) cc_final: 0.8318 (tp30) REVERT: As 230 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7317 (ttmt) REVERT: At 237 PHE cc_start: 0.8644 (p90) cc_final: 0.8363 (p90) REVERT: Au 218 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7769 (tpt) REVERT: Av 161 THR cc_start: 0.9224 (p) cc_final: 0.8884 (m) REVERT: Aw 95 MET cc_start: 0.8593 (mmt) cc_final: 0.8071 (mmm) REVERT: Aw 168 TYR cc_start: 0.8104 (m-80) cc_final: 0.7779 (m-10) REVERT: Aw 198 MET cc_start: 0.9015 (ttm) cc_final: 0.8621 (mtt) REVERT: Aw 209 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8516 (pp20) REVERT: Aw 218 MET cc_start: 0.8291 (ttt) cc_final: 0.8010 (ttt) REVERT: Ay 88 SER cc_start: 0.7159 (p) cc_final: 0.6667 (t) REVERT: Ay 145 MET cc_start: 0.8146 (tpp) cc_final: 0.7620 (tpp) REVERT: Ay 215 GLU cc_start: 0.7879 (pm20) cc_final: 0.7530 (pm20) REVERT: Ay 235 TYR cc_start: 0.9350 (m-80) cc_final: 0.9149 (m-10) REVERT: Az 205 GLU cc_start: 0.8042 (tt0) cc_final: 0.7599 (mt-10) REVERT: Az 235 TYR cc_start: 0.9142 (m-10) cc_final: 0.8847 (m-10) REVERT: Ba 205 GLU cc_start: 0.7996 (tt0) cc_final: 0.7713 (mt-10) REVERT: Ba 218 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7951 (tpt) outliers start: 91 outliers final: 49 residues processed: 997 average time/residue: 0.2078 time to fit residues: 360.1310 Evaluate side-chains 903 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 848 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 124 HIS Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 165 ILE Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ad residue 166 ASN Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ae residue 78 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 170 THR Chi-restraints excluded: chain Af residue 78 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Ag residue 78 THR Chi-restraints excluded: chain Ag residue 172 VAL Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 156 CYS Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 124 HIS Chi-restraints excluded: chain Aj residue 166 ASN Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 224 LEU Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 83 LYS Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 124 HIS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 224 LEU Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain Ao residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Ap residue 223 LEU Chi-restraints excluded: chain Aq residue 78 THR Chi-restraints excluded: chain Aq residue 124 HIS Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 218 MET Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 85 LYS Chi-restraints excluded: chain Av residue 254 HIS Chi-restraints excluded: chain Aw residue 166 ASN Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 124 HIS Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Az residue 241 GLU Chi-restraints excluded: chain Ba residue 139 ASP Chi-restraints excluded: chain Ba residue 156 CYS Chi-restraints excluded: chain Ba residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 18 optimal weight: 0.0980 chunk 194 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 124 HIS Ac 124 HIS Ad 124 HIS Ae 124 HIS Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS ** Aj 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 144 GLN Ak 195 GLN Al 124 HIS Am 124 HIS An 124 HIS An 195 GLN Ao 128 GLN ** Ap 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 124 HIS ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** As 128 GLN At 124 HIS Au 124 HIS Av 124 HIS Ax 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 124 HIS ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.070722 restraints weight = 90070.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073635 restraints weight = 46918.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075641 restraints weight = 30462.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076990 restraints weight = 22409.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077970 restraints weight = 17865.532| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.9952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40959 Z= 0.173 Angle : 0.677 10.947 55377 Z= 0.343 Chirality : 0.042 0.339 5751 Planarity : 0.004 0.052 7290 Dihedral : 4.173 21.137 5400 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.22 % Allowed : 22.27 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4779 helix: 0.27 (0.11), residues: 2241 sheet: -0.65 (0.30), residues: 324 loop : 0.71 (0.15), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAz 194 TYR 0.037 0.002 TYRAq 221 PHE 0.014 0.002 PHEAn 200 TRP 0.014 0.001 TRPAq 169 HIS 0.005 0.001 HISAx 124 Details of bonding type rmsd covalent geometry : bond 0.00413 (40959) covalent geometry : angle 0.67680 (55377) hydrogen bonds : bond 0.03220 ( 1539) hydrogen bonds : angle 4.29838 ( 4131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 878 time to evaluate : 1.217 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: Aa 139 ASP cc_start: 0.8054 (t0) cc_final: 0.7489 (t70) REVERT: Aa 171 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8185 (ttt) REVERT: Aa 218 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8051 (tpt) REVERT: Ab 229 ASP cc_start: 0.7652 (m-30) cc_final: 0.7335 (t0) REVERT: Ac 171 MET cc_start: 0.9070 (ttt) cc_final: 0.8790 (ttt) REVERT: Ad 209 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8539 (pp20) REVERT: Ae 81 ILE cc_start: 0.9264 (mt) cc_final: 0.9026 (mm) REVERT: Ae 143 GLU cc_start: 0.8504 (tp30) cc_final: 0.8250 (tm-30) REVERT: Ae 215 GLU cc_start: 0.7949 (pm20) cc_final: 0.7597 (pm20) REVERT: Af 215 GLU cc_start: 0.7962 (pm20) cc_final: 0.7604 (pm20) REVERT: Ag 95 MET cc_start: 0.8332 (mtp) cc_final: 0.8074 (mtt) REVERT: Ag 139 ASP cc_start: 0.7721 (t70) cc_final: 0.7332 (t0) REVERT: Ag 168 TYR cc_start: 0.8641 (m-10) cc_final: 0.8322 (m-10) REVERT: Ag 196 CYS cc_start: 0.8798 (t) cc_final: 0.8438 (t) REVERT: Ag 221 TYR cc_start: 0.8737 (t80) cc_final: 0.8437 (t80) REVERT: Ah 210 MET cc_start: 0.8838 (tmm) cc_final: 0.8539 (tmm) REVERT: Ah 218 MET cc_start: 0.8216 (tpp) cc_final: 0.8001 (tpt) REVERT: Ai 109 GLN cc_start: 0.9107 (pp30) cc_final: 0.8884 (pp30) REVERT: Ai 145 MET cc_start: 0.8821 (tpp) cc_final: 0.8459 (tpp) REVERT: Ai 153 MET cc_start: 0.9009 (tmm) cc_final: 0.8737 (ttt) REVERT: Ai 168 TYR cc_start: 0.8457 (m-10) cc_final: 0.8113 (m-10) REVERT: Aj 109 GLN cc_start: 0.9062 (pp30) cc_final: 0.8762 (pp30) REVERT: Aj 149 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (mpp) REVERT: Aj 205 GLU cc_start: 0.8090 (tt0) cc_final: 0.7742 (tt0) REVERT: Aj 210 MET cc_start: 0.8612 (tmm) cc_final: 0.8374 (tmm) REVERT: Aj 218 MET cc_start: 0.8470 (tpt) cc_final: 0.7543 (tpt) REVERT: Ak 158 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: Ak 171 MET cc_start: 0.8700 (mtp) cc_final: 0.8406 (ttt) REVERT: Ak 205 GLU cc_start: 0.8085 (tt0) cc_final: 0.7720 (tt0) REVERT: Al 114 GLN cc_start: 0.9134 (tp40) cc_final: 0.8771 (tp40) REVERT: Al 145 MET cc_start: 0.8708 (tpt) cc_final: 0.8445 (tpp) REVERT: Al 153 MET cc_start: 0.9218 (ttp) cc_final: 0.8928 (ttp) REVERT: Al 171 MET cc_start: 0.8749 (tpp) cc_final: 0.8220 (ttt) REVERT: Am 205 GLU cc_start: 0.8184 (tt0) cc_final: 0.7750 (tt0) REVERT: Am 209 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8485 (pp20) REVERT: An 209 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8434 (pp20) REVERT: An 215 GLU cc_start: 0.7805 (pm20) cc_final: 0.7552 (pm20) REVERT: Ap 109 GLN cc_start: 0.8937 (pp30) cc_final: 0.8215 (pp30) REVERT: Ap 215 GLU cc_start: 0.7981 (pm20) cc_final: 0.7442 (pm20) REVERT: Aq 109 GLN cc_start: 0.8582 (pm20) cc_final: 0.8140 (pp30) REVERT: Aq 145 MET cc_start: 0.8006 (tpp) cc_final: 0.7656 (tpp) REVERT: Aq 162 SER cc_start: 0.9059 (m) cc_final: 0.8686 (t) REVERT: Ar 145 MET cc_start: 0.8848 (tpp) cc_final: 0.8338 (tpp) REVERT: Ar 149 MET cc_start: 0.8056 (tpp) cc_final: 0.7393 (tpp) REVERT: Ar 168 TYR cc_start: 0.8470 (m-80) cc_final: 0.8187 (m-10) REVERT: Ar 198 MET cc_start: 0.9154 (ttm) cc_final: 0.8924 (mtp) REVERT: Ar 230 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7455 (ttmt) REVERT: As 109 GLN cc_start: 0.8969 (pp30) cc_final: 0.8754 (pp30) REVERT: As 143 GLU cc_start: 0.8601 (tp30) cc_final: 0.8339 (tp30) REVERT: At 218 MET cc_start: 0.8337 (ttt) cc_final: 0.8037 (ttt) REVERT: Au 158 GLU cc_start: 0.8595 (tt0) cc_final: 0.8165 (tt0) REVERT: Au 205 GLU cc_start: 0.8271 (tt0) cc_final: 0.7999 (mt-10) REVERT: Au 228 ASN cc_start: 0.7417 (m-40) cc_final: 0.7106 (p0) REVERT: Av 161 THR cc_start: 0.9207 (p) cc_final: 0.8851 (m) REVERT: Aw 95 MET cc_start: 0.8685 (mmt) cc_final: 0.8120 (mmm) REVERT: Aw 114 GLN cc_start: 0.8881 (tp40) cc_final: 0.8669 (tp40) REVERT: Aw 209 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8546 (pp20) REVERT: Aw 215 GLU cc_start: 0.7910 (pm20) cc_final: 0.7604 (pm20) REVERT: Aw 218 MET cc_start: 0.8325 (ttt) cc_final: 0.8105 (ttt) REVERT: Ax 91 MET cc_start: 0.7673 (mmp) cc_final: 0.7207 (tpp) REVERT: Ax 215 GLU cc_start: 0.7750 (pm20) cc_final: 0.7452 (pm20) REVERT: Ay 88 SER cc_start: 0.7173 (p) cc_final: 0.6673 (t) REVERT: Ay 145 MET cc_start: 0.8322 (tpp) cc_final: 0.7880 (tpp) REVERT: Ay 162 SER cc_start: 0.9155 (m) cc_final: 0.8670 (t) REVERT: Ay 215 GLU cc_start: 0.7932 (pm20) cc_final: 0.7631 (pm20) REVERT: Ay 235 TYR cc_start: 0.9374 (m-80) cc_final: 0.9095 (m-10) REVERT: Az 205 GLU cc_start: 0.8071 (tt0) cc_final: 0.7640 (mt-10) REVERT: Ba 205 GLU cc_start: 0.7984 (tt0) cc_final: 0.7684 (mt-10) REVERT: Ba 218 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7943 (tpt) outliers start: 97 outliers final: 64 residues processed: 943 average time/residue: 0.2068 time to fit residues: 336.8475 Evaluate side-chains 907 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 838 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 165 ILE Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 156 CYS Chi-restraints excluded: chain Ac residue 165 ILE Chi-restraints excluded: chain Ac residue 227 LEU Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ad residue 172 VAL Chi-restraints excluded: chain Ae residue 78 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 124 HIS Chi-restraints excluded: chain Ae residue 170 THR Chi-restraints excluded: chain Af residue 78 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Ag residue 78 THR Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 156 CYS Chi-restraints excluded: chain Ai residue 161 THR Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 124 HIS Chi-restraints excluded: chain Aj residue 149 MET Chi-restraints excluded: chain Aj residue 166 ASN Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 224 LEU Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 83 LYS Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 124 HIS Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain Ao residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Aq residue 78 THR Chi-restraints excluded: chain Aq residue 128 GLN Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain As residue 78 THR Chi-restraints excluded: chain As residue 170 THR Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 85 LYS Chi-restraints excluded: chain Av residue 227 LEU Chi-restraints excluded: chain Av residue 254 HIS Chi-restraints excluded: chain Aw residue 166 ASN Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 124 HIS Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Az residue 123 THR Chi-restraints excluded: chain Az residue 241 GLU Chi-restraints excluded: chain Ba residue 78 THR Chi-restraints excluded: chain Ba residue 139 ASP Chi-restraints excluded: chain Ba residue 156 CYS Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 218 MET Chi-restraints excluded: chain Ba residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 205 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 422 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 455 optimal weight: 0.0370 chunk 217 optimal weight: 4.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 124 HIS Ab 124 HIS Ac 124 HIS Ad 124 HIS Ae 124 HIS Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS Ai 195 GLN Ak 114 GLN Ak 144 GLN Al 124 HIS Am 124 HIS An 124 HIS ** Ap 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 124 HIS ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 HIS Au 124 HIS Av 114 GLN Av 124 HIS Ax 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.069155 restraints weight = 89724.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.071930 restraints weight = 48042.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073842 restraints weight = 31755.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.075114 restraints weight = 23610.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076079 restraints weight = 19048.483| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 1.0062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 40959 Z= 0.223 Angle : 0.717 10.589 55377 Z= 0.365 Chirality : 0.044 0.294 5751 Planarity : 0.004 0.054 7290 Dihedral : 4.321 22.048 5400 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.10 % Allowed : 22.68 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4779 helix: 0.18 (0.11), residues: 2268 sheet: -0.58 (0.31), residues: 324 loop : 0.79 (0.15), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAu 245 TYR 0.044 0.002 TYRAq 221 PHE 0.016 0.002 PHEAn 200 TRP 0.014 0.002 TRPAw 169 HIS 0.010 0.001 HISAm 124 Details of bonding type rmsd covalent geometry : bond 0.00528 (40959) covalent geometry : angle 0.71677 (55377) hydrogen bonds : bond 0.03468 ( 1539) hydrogen bonds : angle 4.50717 ( 4131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 852 time to evaluate : 1.723 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: Aa 139 ASP cc_start: 0.8050 (t0) cc_final: 0.7525 (t70) REVERT: Aa 143 GLU cc_start: 0.8556 (tp30) cc_final: 0.8351 (tp30) REVERT: Aa 149 MET cc_start: 0.8432 (tpp) cc_final: 0.7877 (tpp) REVERT: Aa 171 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8206 (ttt) REVERT: Aa 218 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (tpt) REVERT: Ab 171 MET cc_start: 0.8962 (ttt) cc_final: 0.8724 (ttt) REVERT: Ab 229 ASP cc_start: 0.7678 (m-30) cc_final: 0.7436 (t0) REVERT: Ac 171 MET cc_start: 0.9131 (ttt) cc_final: 0.8876 (ttt) REVERT: Ad 195 GLN cc_start: 0.9005 (mt0) cc_final: 0.8657 (mm-40) REVERT: Ad 209 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8582 (pp20) REVERT: Ad 215 GLU cc_start: 0.7838 (pm20) cc_final: 0.7433 (pm20) REVERT: Ae 81 ILE cc_start: 0.9253 (mt) cc_final: 0.9019 (mm) REVERT: Ae 215 GLU cc_start: 0.8002 (pm20) cc_final: 0.7662 (pm20) REVERT: Af 215 GLU cc_start: 0.7962 (pm20) cc_final: 0.7615 (pm20) REVERT: Ag 95 MET cc_start: 0.8245 (mtp) cc_final: 0.8003 (mtt) REVERT: Ag 139 ASP cc_start: 0.7755 (t70) cc_final: 0.7333 (t0) REVERT: Ag 168 TYR cc_start: 0.8625 (m-10) cc_final: 0.8302 (m-10) REVERT: Ag 171 MET cc_start: 0.8465 (mtp) cc_final: 0.8113 (ttt) REVERT: Ag 196 CYS cc_start: 0.8750 (t) cc_final: 0.8420 (t) REVERT: Ah 210 MET cc_start: 0.8888 (tmm) cc_final: 0.8607 (tmm) REVERT: Ah 218 MET cc_start: 0.8276 (tpp) cc_final: 0.8014 (tpt) REVERT: Ai 109 GLN cc_start: 0.9084 (pp30) cc_final: 0.8868 (pp30) REVERT: Ai 145 MET cc_start: 0.8808 (tpp) cc_final: 0.8451 (tpp) REVERT: Ai 153 MET cc_start: 0.9003 (tmm) cc_final: 0.8787 (ttt) REVERT: Ai 168 TYR cc_start: 0.8462 (m-10) cc_final: 0.8120 (m-10) REVERT: Ai 230 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7293 (tttt) REVERT: Aj 109 GLN cc_start: 0.9059 (pp30) cc_final: 0.8775 (pp30) REVERT: Aj 205 GLU cc_start: 0.8101 (tt0) cc_final: 0.7678 (tt0) REVERT: Aj 210 MET cc_start: 0.8676 (tmm) cc_final: 0.8428 (tmm) REVERT: Aj 218 MET cc_start: 0.8460 (tpt) cc_final: 0.8257 (tpt) REVERT: Ak 158 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: Ak 171 MET cc_start: 0.8723 (mtp) cc_final: 0.8426 (ttt) REVERT: Ak 205 GLU cc_start: 0.8169 (tt0) cc_final: 0.7787 (tt0) REVERT: Al 139 ASP cc_start: 0.7944 (t0) cc_final: 0.7721 (t70) REVERT: Al 145 MET cc_start: 0.8665 (tpt) cc_final: 0.8390 (tpp) REVERT: Al 153 MET cc_start: 0.9219 (ttp) cc_final: 0.8966 (ttp) REVERT: Al 171 MET cc_start: 0.8663 (tpp) cc_final: 0.8212 (ttt) REVERT: Al 205 GLU cc_start: 0.8441 (tt0) cc_final: 0.8114 (mt-10) REVERT: Am 205 GLU cc_start: 0.8219 (tt0) cc_final: 0.7825 (tt0) REVERT: An 209 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8469 (pp20) REVERT: An 215 GLU cc_start: 0.7792 (pm20) cc_final: 0.7570 (pm20) REVERT: Ao 145 MET cc_start: 0.8133 (tpp) cc_final: 0.7922 (tpp) REVERT: Ap 109 GLN cc_start: 0.8936 (pp30) cc_final: 0.8181 (pp30) REVERT: Ap 198 MET cc_start: 0.9096 (ttm) cc_final: 0.8891 (mtp) REVERT: Ap 215 GLU cc_start: 0.8043 (pm20) cc_final: 0.7514 (pm20) REVERT: Aq 109 GLN cc_start: 0.8557 (pm20) cc_final: 0.8171 (pp30) REVERT: Aq 162 SER cc_start: 0.9031 (m) cc_final: 0.8661 (t) REVERT: Aq 198 MET cc_start: 0.9125 (ttm) cc_final: 0.8901 (mtp) REVERT: Ar 145 MET cc_start: 0.8866 (tpp) cc_final: 0.8204 (tpp) REVERT: Ar 215 GLU cc_start: 0.7654 (pm20) cc_final: 0.7142 (pm20) REVERT: Ar 230 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7564 (ttmt) REVERT: At 218 MET cc_start: 0.8314 (ttt) cc_final: 0.8005 (ttt) REVERT: Au 205 GLU cc_start: 0.8312 (tt0) cc_final: 0.7965 (mt-10) REVERT: Aw 95 MET cc_start: 0.8672 (mmt) cc_final: 0.8131 (mmm) REVERT: Aw 209 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8533 (pp20) REVERT: Aw 215 GLU cc_start: 0.7973 (pm20) cc_final: 0.7714 (pm20) REVERT: Ax 91 MET cc_start: 0.7603 (mmp) cc_final: 0.7160 (tpp) REVERT: Ax 215 GLU cc_start: 0.7768 (pm20) cc_final: 0.7493 (pm20) REVERT: Ay 88 SER cc_start: 0.7129 (p) cc_final: 0.6613 (t) REVERT: Ay 145 MET cc_start: 0.8368 (tpp) cc_final: 0.7857 (tpp) REVERT: Ay 215 GLU cc_start: 0.7925 (pm20) cc_final: 0.7626 (pm20) REVERT: Ay 235 TYR cc_start: 0.9388 (m-80) cc_final: 0.9083 (m-10) REVERT: Az 205 GLU cc_start: 0.8074 (tt0) cc_final: 0.7602 (tt0) REVERT: Az 215 GLU cc_start: 0.7425 (pm20) cc_final: 0.7128 (pm20) REVERT: Ba 145 MET cc_start: 0.8089 (tpp) cc_final: 0.7650 (tpp) REVERT: Ba 149 MET cc_start: 0.8718 (tpp) cc_final: 0.8097 (mpp) REVERT: Ba 205 GLU cc_start: 0.8014 (tt0) cc_final: 0.7692 (mt-10) REVERT: Ba 218 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7991 (tpt) outliers start: 92 outliers final: 72 residues processed: 916 average time/residue: 0.2105 time to fit residues: 334.1372 Evaluate side-chains 906 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 830 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 166 ASN Chi-restraints excluded: chain Aa residue 171 MET Chi-restraints excluded: chain Aa residue 218 MET Chi-restraints excluded: chain Ab residue 170 THR Chi-restraints excluded: chain Ac residue 78 THR Chi-restraints excluded: chain Ac residue 156 CYS Chi-restraints excluded: chain Ac residue 165 ILE Chi-restraints excluded: chain Ac residue 227 LEU Chi-restraints excluded: chain Ad residue 170 THR Chi-restraints excluded: chain Ad residue 172 VAL Chi-restraints excluded: chain Ae residue 78 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 124 HIS Chi-restraints excluded: chain Ae residue 170 THR Chi-restraints excluded: chain Af residue 78 THR Chi-restraints excluded: chain Af residue 172 VAL Chi-restraints excluded: chain Ag residue 78 THR Chi-restraints excluded: chain Ag residue 124 HIS Chi-restraints excluded: chain Ah residue 124 HIS Chi-restraints excluded: chain Ah residue 156 CYS Chi-restraints excluded: chain Ai residue 78 THR Chi-restraints excluded: chain Ai residue 124 HIS Chi-restraints excluded: chain Ai residue 196 CYS Chi-restraints excluded: chain Aj residue 97 SER Chi-restraints excluded: chain Aj residue 124 HIS Chi-restraints excluded: chain Aj residue 166 ASN Chi-restraints excluded: chain Ak residue 158 GLU Chi-restraints excluded: chain Ak residue 224 LEU Chi-restraints excluded: chain Al residue 78 THR Chi-restraints excluded: chain Al residue 83 LYS Chi-restraints excluded: chain Al residue 85 LYS Chi-restraints excluded: chain Al residue 156 CYS Chi-restraints excluded: chain Al residue 165 ILE Chi-restraints excluded: chain Al residue 196 CYS Chi-restraints excluded: chain Al residue 224 LEU Chi-restraints excluded: chain Am residue 78 THR Chi-restraints excluded: chain Am residue 84 LEU Chi-restraints excluded: chain Am residue 85 LYS Chi-restraints excluded: chain Am residue 124 HIS Chi-restraints excluded: chain Am residue 170 THR Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 172 VAL Chi-restraints excluded: chain Ao residue 101 ILE Chi-restraints excluded: chain Ao residue 109 GLN Chi-restraints excluded: chain Ao residue 170 THR Chi-restraints excluded: chain Ap residue 172 VAL Chi-restraints excluded: chain Aq residue 78 THR Chi-restraints excluded: chain Aq residue 128 GLN Chi-restraints excluded: chain Aq residue 148 LEU Chi-restraints excluded: chain Aq residue 153 MET Chi-restraints excluded: chain Aq residue 244 SER Chi-restraints excluded: chain Ar residue 244 SER Chi-restraints excluded: chain As residue 170 THR Chi-restraints excluded: chain At residue 78 THR Chi-restraints excluded: chain At residue 124 HIS Chi-restraints excluded: chain At residue 166 ASN Chi-restraints excluded: chain Au residue 170 THR Chi-restraints excluded: chain Au residue 254 HIS Chi-restraints excluded: chain Av residue 78 THR Chi-restraints excluded: chain Av residue 85 LYS Chi-restraints excluded: chain Av residue 254 HIS Chi-restraints excluded: chain Aw residue 166 ASN Chi-restraints excluded: chain Aw residue 170 THR Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 101 ILE Chi-restraints excluded: chain Ax residue 124 HIS Chi-restraints excluded: chain Ax residue 172 VAL Chi-restraints excluded: chain Ax residue 209 GLU Chi-restraints excluded: chain Ay residue 172 VAL Chi-restraints excluded: chain Az residue 123 THR Chi-restraints excluded: chain Az residue 241 GLU Chi-restraints excluded: chain Ba residue 78 THR Chi-restraints excluded: chain Ba residue 156 CYS Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 218 MET Chi-restraints excluded: chain Ba residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 414 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 429 optimal weight: 10.0000 chunk 395 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 chunk 396 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 124 HIS Ab 124 HIS Ac 124 HIS Ad 124 HIS Ae 124 HIS Af 124 HIS ** Af 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 124 HIS ** Ag 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 HIS Ak 144 GLN Am 124 HIS An 124 HIS ** Ap 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 124 HIS ** As 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 HIS ** Au 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 124 HIS Av 124 HIS ** Ax 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 195 GLN ** Ay 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.069839 restraints weight = 89277.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072671 restraints weight = 47706.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074572 restraints weight = 31522.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075912 restraints weight = 23527.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076860 restraints weight = 18853.940| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 1.0128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40959 Z= 0.169 Angle : 0.694 10.814 55377 Z= 0.353 Chirality : 0.042 0.236 5751 Planarity : 0.004 0.056 7290 Dihedral : 4.258 21.635 5400 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.97 % Allowed : 22.59 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4779 helix: 0.20 (0.11), residues: 2241 sheet: -0.49 (0.31), residues: 324 loop : 0.76 (0.15), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAu 245 TYR 0.039 0.002 TYRAq 221 PHE 0.013 0.002 PHEAt 200 TRP 0.013 0.001 TRPAo 169 HIS 0.007 0.001 HISAx 124 Details of bonding type rmsd covalent geometry : bond 0.00404 (40959) covalent geometry : angle 0.69405 (55377) hydrogen bonds : bond 0.03292 ( 1539) hydrogen bonds : angle 4.41866 ( 4131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7893.74 seconds wall clock time: 136 minutes 49.85 seconds (8209.85 seconds total)