Starting phenix.real_space_refine on Sun Feb 8 05:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ra1_53867/02_2026/9ra1_53867.map" } resolution = 4.02 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= 0.021 sd= 0.170 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 25164 2.51 5 N 7074 2.21 5 O 7236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.02s 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: 39798 Number of models: 1 Model: "" Number of chains: 27 Chain: "Aa" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ab" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ac" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ad" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ae" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Af" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ag" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ah" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ai" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Aj" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ak" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Al" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Am" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "An" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ao" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ap" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Aq" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ar" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "As" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "At" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Au" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Av" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Aw" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ax" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ay" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Az" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain: "Ba" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1474 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Time building chain proxies: 8.18, per 1000 atoms: 0.21 Number of scatterers: 39798 At special positions: 0 Unit cell: (153.9, 153.9, 201.4, 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 7236 8.00 N 7074 7.00 C 25164 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9342 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 54 sheets defined 50.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 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 158 removed outlier: 3.857A pdb=" N ARGAa 146 " --> pdb=" O ASPAa 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAa 147 " --> pdb=" O GLUAa 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAa 154 " --> pdb=" O ASNAa 150 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAa 188 " --> pdb=" O PROAa 184 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 192 through 198 Processing helix chain 'Aa' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAa 209 " --> pdb=" O GLUAa 205 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 219 through 225 Processing helix chain 'Aa' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAa 234 " --> pdb=" O SERAa 231 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAa 251 " --> pdb=" O PROAa 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAa 252 " --> pdb=" O ASNAa 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAb 146 " --> pdb=" O ASPAb 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAb 147 " --> pdb=" O GLUAb 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAb 154 " --> pdb=" O ASNAb 150 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAb 188 " --> pdb=" O PROAb 184 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 192 through 198 Processing helix chain 'Ab' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAb 209 " --> pdb=" O GLUAb 205 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 219 through 225 Processing helix chain 'Ab' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAb 234 " --> pdb=" O SERAb 231 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAb 251 " --> pdb=" O PROAb 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAb 252 " --> pdb=" O ASNAb 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAc 146 " --> pdb=" O ASPAc 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAc 147 " --> pdb=" O GLUAc 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAc 154 " --> pdb=" O ASNAc 150 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 183 through 188 removed outlier: 3.662A pdb=" N ASNAc 188 " --> pdb=" O PROAc 184 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 192 through 198 Processing helix chain 'Ac' and resid 200 through 211 removed outlier: 4.329A pdb=" N GLUAc 209 " --> pdb=" O GLUAc 205 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 219 through 225 Processing helix chain 'Ac' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAc 234 " --> pdb=" O SERAc 231 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAc 251 " --> pdb=" O PROAc 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAc 252 " --> pdb=" O ASNAc 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAd 146 " --> pdb=" O ASPAd 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAd 147 " --> pdb=" O GLUAd 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAd 154 " --> pdb=" O ASNAd 150 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAd 188 " --> pdb=" O PROAd 184 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 192 through 198 Processing helix chain 'Ad' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAd 209 " --> pdb=" O GLUAd 205 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 219 through 225 Processing helix chain 'Ad' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAd 234 " --> pdb=" O SERAd 231 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAd 251 " --> pdb=" O PROAd 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAd 252 " --> pdb=" O ASNAd 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAe 146 " --> pdb=" O ASPAe 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAe 147 " --> pdb=" O GLUAe 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAe 154 " --> pdb=" O ASNAe 150 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAe 188 " --> pdb=" O PROAe 184 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 192 through 198 Processing helix chain 'Ae' and resid 200 through 211 removed outlier: 4.329A pdb=" N GLUAe 209 " --> pdb=" O GLUAe 205 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 219 through 225 Processing helix chain 'Ae' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAe 234 " --> pdb=" O SERAe 231 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAe 251 " --> pdb=" O PROAe 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAe 252 " --> pdb=" O ASNAe 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAf 146 " --> pdb=" O ASPAf 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAf 147 " --> pdb=" O GLUAf 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAf 154 " --> pdb=" O ASNAf 150 " (cutoff:3.500A) Processing helix chain 'Af' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAf 188 " --> pdb=" O PROAf 184 " (cutoff:3.500A) Processing helix chain 'Af' and resid 192 through 198 Processing helix chain 'Af' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAf 209 " --> pdb=" O GLUAf 205 " (cutoff:3.500A) Processing helix chain 'Af' and resid 219 through 225 Processing helix chain 'Af' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAf 234 " --> pdb=" O SERAf 231 " (cutoff:3.500A) Processing helix chain 'Af' and resid 247 through 255 removed outlier: 3.749A pdb=" N ARGAf 251 " --> pdb=" O PROAf 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAf 252 " --> pdb=" O ASNAf 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAg 146 " --> pdb=" O ASPAg 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAg 147 " --> pdb=" O GLUAg 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAg 154 " --> pdb=" O ASNAg 150 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAg 188 " --> pdb=" O PROAg 184 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 192 through 198 Processing helix chain 'Ag' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAg 209 " --> pdb=" O GLUAg 205 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 219 through 225 Processing helix chain 'Ag' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAg 234 " --> pdb=" O SERAg 231 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAg 251 " --> pdb=" O PROAg 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAg 252 " --> pdb=" O ASNAg 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAh 146 " --> pdb=" O ASPAh 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAh 147 " --> pdb=" O GLUAh 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAh 154 " --> pdb=" O ASNAh 150 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAh 188 " --> pdb=" O PROAh 184 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 192 through 198 Processing helix chain 'Ah' and resid 200 through 211 removed outlier: 4.331A pdb=" N GLUAh 209 " --> pdb=" O GLUAh 205 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 219 through 225 Processing helix chain 'Ah' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAh 234 " --> pdb=" O SERAh 231 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAh 251 " --> pdb=" O PROAh 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAh 252 " --> pdb=" O ASNAh 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAi 146 " --> pdb=" O ASPAi 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAi 147 " --> pdb=" O GLUAi 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAi 154 " --> pdb=" O ASNAi 150 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAi 188 " --> pdb=" O PROAi 184 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 192 through 198 Processing helix chain 'Ai' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAi 209 " --> pdb=" O GLUAi 205 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 219 through 225 Processing helix chain 'Ai' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAi 234 " --> pdb=" O SERAi 231 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAi 251 " --> pdb=" O PROAi 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAi 252 " --> pdb=" O ASNAi 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAj 146 " --> pdb=" O ASPAj 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAj 147 " --> pdb=" O GLUAj 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAj 154 " --> pdb=" O ASNAj 150 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAj 188 " --> pdb=" O PROAj 184 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 192 through 198 Processing helix chain 'Aj' and resid 200 through 211 removed outlier: 4.331A pdb=" N GLUAj 209 " --> pdb=" O GLUAj 205 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 219 through 225 Processing helix chain 'Aj' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAj 234 " --> pdb=" O SERAj 231 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 247 through 255 removed outlier: 3.749A pdb=" N ARGAj 251 " --> pdb=" O PROAj 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAj 252 " --> pdb=" O ASNAj 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAk 146 " --> pdb=" O ASPAk 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAk 147 " --> pdb=" O GLUAk 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAk 154 " --> pdb=" O ASNAk 150 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAk 188 " --> pdb=" O PROAk 184 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 192 through 198 Processing helix chain 'Ak' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAk 209 " --> pdb=" O GLUAk 205 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 219 through 225 Processing helix chain 'Ak' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAk 234 " --> pdb=" O SERAk 231 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAk 251 " --> pdb=" O PROAk 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAk 252 " --> pdb=" O ASNAk 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAl 146 " --> pdb=" O ASPAl 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAl 147 " --> pdb=" O GLUAl 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAl 154 " --> pdb=" O ASNAl 150 " (cutoff:3.500A) Processing helix chain 'Al' and resid 183 through 188 removed outlier: 3.662A pdb=" N ASNAl 188 " --> pdb=" O PROAl 184 " (cutoff:3.500A) Processing helix chain 'Al' and resid 192 through 198 Processing helix chain 'Al' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAl 209 " --> pdb=" O GLUAl 205 " (cutoff:3.500A) Processing helix chain 'Al' and resid 219 through 225 Processing helix chain 'Al' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAl 234 " --> pdb=" O SERAl 231 " (cutoff:3.500A) Processing helix chain 'Al' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAl 251 " --> pdb=" O PROAl 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAl 252 " --> pdb=" O ASNAl 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAm 146 " --> pdb=" O ASPAm 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAm 147 " --> pdb=" O GLUAm 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAm 154 " --> pdb=" O ASNAm 150 " (cutoff:3.500A) Processing helix chain 'Am' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAm 188 " --> pdb=" O PROAm 184 " (cutoff:3.500A) Processing helix chain 'Am' and resid 192 through 198 Processing helix chain 'Am' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAm 209 " --> pdb=" O GLUAm 205 " (cutoff:3.500A) Processing helix chain 'Am' and resid 219 through 225 Processing helix chain 'Am' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAm 234 " --> pdb=" O SERAm 231 " (cutoff:3.500A) Processing helix chain 'Am' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAm 251 " --> pdb=" O PROAm 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAm 252 " --> pdb=" O ASNAm 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAn 146 " --> pdb=" O ASPAn 142 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILEAn 147 " --> pdb=" O GLUAn 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAn 154 " --> pdb=" O ASNAn 150 " (cutoff:3.500A) Processing helix chain 'An' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAn 188 " --> pdb=" O PROAn 184 " (cutoff:3.500A) Processing helix chain 'An' and resid 192 through 198 Processing helix chain 'An' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAn 209 " --> pdb=" O GLUAn 205 " (cutoff:3.500A) Processing helix chain 'An' and resid 219 through 225 Processing helix chain 'An' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAn 234 " --> pdb=" O SERAn 231 " (cutoff:3.500A) Processing helix chain 'An' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAn 251 " --> pdb=" O PROAn 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAn 252 " --> pdb=" O ASNAn 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAo 146 " --> pdb=" O ASPAo 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAo 147 " --> pdb=" O GLUAo 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAo 154 " --> pdb=" O ASNAo 150 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 183 through 188 removed outlier: 3.659A pdb=" N ASNAo 188 " --> pdb=" O PROAo 184 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 192 through 198 Processing helix chain 'Ao' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAo 209 " --> pdb=" O GLUAo 205 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 219 through 225 Processing helix chain 'Ao' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAo 234 " --> pdb=" O SERAo 231 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 247 through 255 removed outlier: 3.749A pdb=" N ARGAo 251 " --> pdb=" O PROAo 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAo 252 " --> pdb=" O ASNAo 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAp 146 " --> pdb=" O ASPAp 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAp 147 " --> pdb=" O GLUAp 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAp 154 " --> pdb=" O ASNAp 150 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAp 188 " --> pdb=" O PROAp 184 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 192 through 198 Processing helix chain 'Ap' and resid 200 through 211 removed outlier: 4.329A pdb=" N GLUAp 209 " --> pdb=" O GLUAp 205 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 219 through 225 Processing helix chain 'Ap' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAp 234 " --> pdb=" O SERAp 231 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 247 through 255 removed outlier: 3.749A pdb=" N ARGAp 251 " --> pdb=" O PROAp 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAp 252 " --> pdb=" O ASNAp 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAq 146 " --> pdb=" O ASPAq 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAq 147 " --> pdb=" O GLUAq 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAq 154 " --> pdb=" O ASNAq 150 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAq 188 " --> pdb=" O PROAq 184 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 192 through 198 Processing helix chain 'Aq' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAq 209 " --> pdb=" O GLUAq 205 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 219 through 225 Processing helix chain 'Aq' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAq 234 " --> pdb=" O SERAq 231 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAq 251 " --> pdb=" O PROAq 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAq 252 " --> pdb=" O ASNAq 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAr 146 " --> pdb=" O ASPAr 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAr 147 " --> pdb=" O GLUAr 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAr 154 " --> pdb=" O ASNAr 150 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAr 188 " --> pdb=" O PROAr 184 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 192 through 198 Processing helix chain 'Ar' and resid 200 through 211 removed outlier: 4.331A pdb=" N GLUAr 209 " --> pdb=" O GLUAr 205 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 219 through 225 Processing helix chain 'Ar' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAr 234 " --> pdb=" O SERAr 231 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAr 251 " --> pdb=" O PROAr 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAr 252 " --> pdb=" O ASNAr 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAs 146 " --> pdb=" O ASPAs 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAs 147 " --> pdb=" O GLUAs 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAs 154 " --> pdb=" O ASNAs 150 " (cutoff:3.500A) Processing helix chain 'As' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAs 188 " --> pdb=" O PROAs 184 " (cutoff:3.500A) Processing helix chain 'As' and resid 192 through 198 Processing helix chain 'As' and resid 200 through 211 removed outlier: 4.331A pdb=" N GLUAs 209 " --> pdb=" O GLUAs 205 " (cutoff:3.500A) Processing helix chain 'As' and resid 219 through 225 Processing helix chain 'As' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAs 234 " --> pdb=" O SERAs 231 " (cutoff:3.500A) Processing helix chain 'As' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAs 251 " --> pdb=" O PROAs 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAs 252 " --> pdb=" O ASNAs 248 " (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 158 removed outlier: 3.855A pdb=" N ARGAt 146 " --> pdb=" O ASPAt 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAt 147 " --> pdb=" O GLUAt 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAt 154 " --> pdb=" O ASNAt 150 " (cutoff:3.500A) Processing helix chain 'At' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAt 188 " --> pdb=" O PROAt 184 " (cutoff:3.500A) Processing helix chain 'At' and resid 192 through 198 Processing helix chain 'At' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAt 209 " --> pdb=" O GLUAt 205 " (cutoff:3.500A) Processing helix chain 'At' and resid 219 through 225 Processing helix chain 'At' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAt 234 " --> pdb=" O SERAt 231 " (cutoff:3.500A) Processing helix chain 'At' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAt 251 " --> pdb=" O PROAt 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAt 252 " --> pdb=" O ASNAt 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAu 146 " --> pdb=" O ASPAu 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAu 147 " --> pdb=" O GLUAu 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAu 154 " --> pdb=" O ASNAu 150 " (cutoff:3.500A) Processing helix chain 'Au' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAu 188 " --> pdb=" O PROAu 184 " (cutoff:3.500A) Processing helix chain 'Au' and resid 192 through 198 Processing helix chain 'Au' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAu 209 " --> pdb=" O GLUAu 205 " (cutoff:3.500A) Processing helix chain 'Au' and resid 219 through 225 Processing helix chain 'Au' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAu 234 " --> pdb=" O SERAu 231 " (cutoff:3.500A) Processing helix chain 'Au' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAu 251 " --> pdb=" O PROAu 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAu 252 " --> pdb=" O ASNAu 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAv 146 " --> pdb=" O ASPAv 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAv 147 " --> pdb=" O GLUAv 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAv 154 " --> pdb=" O ASNAv 150 " (cutoff:3.500A) Processing helix chain 'Av' and resid 183 through 188 removed outlier: 3.661A pdb=" N ASNAv 188 " --> pdb=" O PROAv 184 " (cutoff:3.500A) Processing helix chain 'Av' and resid 192 through 198 Processing helix chain 'Av' and resid 200 through 211 removed outlier: 4.329A pdb=" N GLUAv 209 " --> pdb=" O GLUAv 205 " (cutoff:3.500A) Processing helix chain 'Av' and resid 219 through 225 Processing helix chain 'Av' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAv 234 " --> pdb=" O SERAv 231 " (cutoff:3.500A) Processing helix chain 'Av' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAv 251 " --> pdb=" O PROAv 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAv 252 " --> pdb=" O ASNAv 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAw 146 " --> pdb=" O ASPAw 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAw 147 " --> pdb=" O GLUAw 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAw 154 " --> pdb=" O ASNAw 150 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 183 through 188 removed outlier: 3.659A pdb=" N ASNAw 188 " --> pdb=" O PROAw 184 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 192 through 198 Processing helix chain 'Aw' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAw 209 " --> pdb=" O GLUAw 205 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 219 through 225 Processing helix chain 'Aw' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAw 234 " --> pdb=" O SERAw 231 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAw 251 " --> pdb=" O PROAw 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAw 252 " --> pdb=" O ASNAw 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAx 146 " --> pdb=" O ASPAx 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAx 147 " --> pdb=" O GLUAx 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAx 154 " --> pdb=" O ASNAx 150 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAx 188 " --> pdb=" O PROAx 184 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 192 through 198 Processing helix chain 'Ax' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAx 209 " --> pdb=" O GLUAx 205 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 219 through 225 Processing helix chain 'Ax' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAx 234 " --> pdb=" O SERAx 231 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 247 through 255 removed outlier: 3.749A pdb=" N ARGAx 251 " --> pdb=" O PROAx 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAx 252 " --> pdb=" O ASNAx 248 " (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 158 removed outlier: 3.856A pdb=" N ARGAy 146 " --> pdb=" O ASPAy 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILEAy 147 " --> pdb=" O GLUAy 143 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAy 154 " --> pdb=" O ASNAy 150 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAy 188 " --> pdb=" O PROAy 184 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 192 through 198 Processing helix chain 'Ay' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAy 209 " --> pdb=" O GLUAy 205 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 219 through 225 Processing helix chain 'Ay' and resid 229 through 236 removed outlier: 4.958A pdb=" N ARGAy 234 " --> pdb=" O SERAy 231 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAy 251 " --> pdb=" O PROAy 247 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLUAy 252 " --> pdb=" O ASNAy 248 " (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 158 removed outlier: 3.857A pdb=" N ARGAz 146 " --> pdb=" O ASPAz 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAz 147 " --> pdb=" O GLUAz 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALAz 154 " --> pdb=" O ASNAz 150 " (cutoff:3.500A) Processing helix chain 'Az' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNAz 188 " --> pdb=" O PROAz 184 " (cutoff:3.500A) Processing helix chain 'Az' and resid 192 through 198 Processing helix chain 'Az' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUAz 209 " --> pdb=" O GLUAz 205 " (cutoff:3.500A) Processing helix chain 'Az' and resid 219 through 225 Processing helix chain 'Az' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGAz 234 " --> pdb=" O SERAz 231 " (cutoff:3.500A) Processing helix chain 'Az' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGAz 251 " --> pdb=" O PROAz 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUAz 252 " --> pdb=" O ASNAz 248 " (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 158 removed outlier: 3.856A pdb=" N ARGBa 146 " --> pdb=" O ASPBa 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEBa 147 " --> pdb=" O GLUBa 143 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALBa 154 " --> pdb=" O ASNBa 150 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 183 through 188 removed outlier: 3.660A pdb=" N ASNBa 188 " --> pdb=" O PROBa 184 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 192 through 198 Processing helix chain 'Ba' and resid 200 through 211 removed outlier: 4.330A pdb=" N GLUBa 209 " --> pdb=" O GLUBa 205 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 219 through 225 Processing helix chain 'Ba' and resid 229 through 236 removed outlier: 4.957A pdb=" N ARGBa 234 " --> pdb=" O SERBa 231 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 247 through 255 removed outlier: 3.748A pdb=" N ARGBa 251 " --> pdb=" O PROBa 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUBa 252 " --> pdb=" O ASNBa 248 " (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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 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 170 1377 hydrogen bonds defined for protein. 3726 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: 5.77 Time building geometry restraints manager: 4.47 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: 12604 1.34 - 1.45: 6681 1.45 - 1.57: 20891 1.57 - 1.69: 0 1.69 - 1.81: 594 Bond restraints: 40770 Sorted by residual: bond pdb=" N VALAm 172 " pdb=" CA VALAm 172 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" N VALAt 172 " pdb=" CA VALAt 172 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.19e-02 7.06e+03 1.22e+01 bond pdb=" N VALAb 172 " pdb=" CA VALAb 172 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N VALAy 172 " pdb=" CA VALAy 172 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.17e+01 bond pdb=" N VALAd 172 " pdb=" CA VALAd 172 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.19e-02 7.06e+03 1.16e+01 ... (remaining 40765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 51105 1.69 - 3.38: 3103 3.38 - 5.07: 764 5.07 - 6.76: 108 6.76 - 8.45: 27 Bond angle restraints: 55107 Sorted by residual: angle pdb=" N METAq 91 " pdb=" CA METAq 91 " pdb=" C METAq 91 " ideal model delta sigma weight residual 110.28 101.83 8.45 1.48e+00 4.57e-01 3.26e+01 angle pdb=" N METAn 91 " pdb=" CA METAn 91 " pdb=" C METAn 91 " ideal model delta sigma weight residual 110.28 101.84 8.44 1.48e+00 4.57e-01 3.25e+01 angle pdb=" N METAj 91 " pdb=" CA METAj 91 " pdb=" C METAj 91 " ideal model delta sigma weight residual 110.28 101.85 8.43 1.48e+00 4.57e-01 3.24e+01 angle pdb=" N METAy 91 " pdb=" CA METAy 91 " pdb=" C METAy 91 " ideal model delta sigma weight residual 110.28 101.85 8.43 1.48e+00 4.57e-01 3.24e+01 angle pdb=" N METAg 91 " pdb=" CA METAg 91 " pdb=" C METAg 91 " ideal model delta sigma weight residual 110.28 101.85 8.43 1.48e+00 4.57e-01 3.24e+01 ... (remaining 55102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.07: 20862 11.07 - 22.13: 2596 22.13 - 33.20: 1247 33.20 - 44.26: 351 44.26 - 55.33: 54 Dihedral angle restraints: 25110 sinusoidal: 10746 harmonic: 14364 Sorted by residual: dihedral pdb=" CA PHEBa 237 " pdb=" C PHEBa 237 " pdb=" N ASPBa 238 " pdb=" CA ASPBa 238 " ideal model delta harmonic sigma weight residual 180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHEAw 237 " pdb=" C PHEAw 237 " pdb=" N ASPAw 238 " pdb=" CA ASPAw 238 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHEAq 237 " pdb=" C PHEAq 237 " pdb=" N ASPAq 238 " pdb=" CA ASPAq 238 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 25107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3994 0.057 - 0.114: 1339 0.114 - 0.170: 229 0.170 - 0.227: 108 0.227 - 0.284: 27 Chirality restraints: 5697 Sorted by residual: chirality pdb=" CA METAq 91 " pdb=" N METAq 91 " pdb=" C METAq 91 " pdb=" CB METAq 91 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA METAn 91 " pdb=" N METAn 91 " pdb=" C METAn 91 " pdb=" CB METAn 91 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA METAw 91 " pdb=" N METAw 91 " pdb=" C METAw 91 " pdb=" CB METAw 91 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 5694 not shown) Planarity restraints: 7263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYSAk 90 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C LYSAk 90 " 0.058 2.00e-02 2.50e+03 pdb=" O LYSAk 90 " -0.022 2.00e-02 2.50e+03 pdb=" N METAk 91 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAf 90 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LYSAf 90 " 0.058 2.00e-02 2.50e+03 pdb=" O LYSAf 90 " -0.022 2.00e-02 2.50e+03 pdb=" N METAf 91 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAl 90 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LYSAl 90 " 0.058 2.00e-02 2.50e+03 pdb=" O LYSAl 90 " -0.022 2.00e-02 2.50e+03 pdb=" N METAl 91 " -0.021 2.00e-02 2.50e+03 ... (remaining 7260 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 17879 2.92 - 3.41: 38951 3.41 - 3.91: 60540 3.91 - 4.40: 69028 4.40 - 4.90: 109660 Nonbonded interactions: 296058 Sorted by model distance: nonbonded pdb=" OH TYRAm 138 " pdb=" O PROAm 181 " model vdw 2.419 3.040 nonbonded pdb=" OH TYRAp 138 " pdb=" O PROAp 181 " model vdw 2.419 3.040 nonbonded pdb=" OH TYRAk 138 " pdb=" O PROAk 181 " model vdw 2.419 3.040 nonbonded pdb=" OH TYRAt 138 " pdb=" O PROAt 181 " model vdw 2.420 3.040 nonbonded pdb=" OH TYRAb 138 " pdb=" O PROAb 181 " model vdw 2.420 3.040 ... (remaining 296053 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 32.040 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.130 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 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 : 0.008 0.042 40770 Z= 0.455 Angle : 0.981 8.452 55107 Z= 0.631 Chirality : 0.063 0.284 5697 Planarity : 0.006 0.063 7263 Dihedral : 12.559 55.327 15768 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % 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: -2.32 (0.12), residues: 4752 helix: -1.47 (0.11), residues: 2133 sheet: None (None), residues: 0 loop : -1.57 (0.13), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAn 220 TYR 0.023 0.002 TYRAp 217 PHE 0.019 0.002 PHEAm 237 TRP 0.014 0.002 TRPAn 130 HIS 0.003 0.001 HISAc 199 Details of bonding type rmsd covalent geometry : bond 0.00812 (40770) covalent geometry : angle 0.98059 (55107) hydrogen bonds : bond 0.16032 ( 1377) hydrogen bonds : angle 6.41955 ( 3726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1830 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1830 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 MET cc_start: 0.7857 (mmt) cc_final: 0.7266 (mmm) REVERT: Aa 147 ILE cc_start: 0.8434 (mm) cc_final: 0.8216 (mp) REVERT: Aa 173 ASP cc_start: 0.7480 (t70) cc_final: 0.6875 (p0) REVERT: Ab 159 ASN cc_start: 0.3636 (m-40) cc_final: 0.3210 (m-40) REVERT: Ab 173 ASP cc_start: 0.7731 (t70) cc_final: 0.7412 (t70) REVERT: Ad 111 LYS cc_start: 0.9047 (mttt) cc_final: 0.8784 (mtmt) REVERT: Ad 123 THR cc_start: 0.7747 (p) cc_final: 0.7280 (p) REVERT: Ad 208 ILE cc_start: 0.7634 (tt) cc_final: 0.7326 (tt) REVERT: Ae 123 THR cc_start: 0.8267 (p) cc_final: 0.7872 (p) REVERT: Ae 143 GLU cc_start: 0.8393 (tp30) cc_final: 0.8087 (tm-30) REVERT: Ae 145 MET cc_start: 0.8482 (tpt) cc_final: 0.8121 (tpt) REVERT: Ae 152 LEU cc_start: 0.8920 (tp) cc_final: 0.8512 (tt) REVERT: Ae 202 ASP cc_start: 0.8253 (m-30) cc_final: 0.8022 (m-30) REVERT: Af 141 ASP cc_start: 0.7889 (p0) cc_final: 0.7335 (p0) REVERT: Af 159 ASN cc_start: 0.8907 (m-40) cc_final: 0.8691 (m110) REVERT: Af 202 ASP cc_start: 0.8188 (m-30) cc_final: 0.7886 (m-30) REVERT: Ag 79 PHE cc_start: 0.7284 (p90) cc_final: 0.5865 (m-80) REVERT: Ag 128 GLN cc_start: 0.8587 (tt0) cc_final: 0.8344 (tt0) REVERT: Ag 159 ASN cc_start: 0.8022 (m-40) cc_final: 0.7777 (m110) REVERT: Ag 190 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8309 (mmmt) REVERT: Ag 225 ARG cc_start: 0.8895 (mpt180) cc_final: 0.8403 (ttp-170) REVERT: Ag 229 ASP cc_start: 0.8235 (m-30) cc_final: 0.7774 (t0) REVERT: Ah 156 CYS cc_start: 0.6518 (m) cc_final: 0.6114 (m) REVERT: Ah 186 VAL cc_start: 0.7436 (t) cc_final: 0.7168 (t) REVERT: Ah 231 SER cc_start: 0.7663 (p) cc_final: 0.7462 (t) REVERT: Ai 164 ASP cc_start: 0.8063 (t70) cc_final: 0.7703 (m-30) REVERT: Ai 180 PHE cc_start: 0.6002 (m-80) cc_final: 0.5787 (m-80) REVERT: Ai 195 GLN cc_start: 0.7214 (mt0) cc_final: 0.6990 (mt0) REVERT: Aj 142 ASP cc_start: 0.7707 (t70) cc_final: 0.7447 (t70) REVERT: Aj 164 ASP cc_start: 0.7659 (t70) cc_final: 0.6999 (t0) REVERT: Ak 178 SER cc_start: 0.8106 (m) cc_final: 0.7876 (p) REVERT: Al 87 VAL cc_start: 0.6895 (m) cc_final: 0.6644 (p) REVERT: Al 241 GLU cc_start: 0.7849 (tt0) cc_final: 0.7003 (tt0) REVERT: Am 123 THR cc_start: 0.7524 (p) cc_final: 0.6906 (p) REVERT: Am 208 ILE cc_start: 0.7591 (tt) cc_final: 0.7355 (tt) REVERT: Am 221 TYR cc_start: 0.7633 (t80) cc_final: 0.7330 (t80) REVERT: Am 241 GLU cc_start: 0.7079 (tt0) cc_final: 0.6692 (mt-10) REVERT: An 141 ASP cc_start: 0.7878 (p0) cc_final: 0.7497 (p0) REVERT: An 143 GLU cc_start: 0.8755 (tp30) cc_final: 0.8500 (tm-30) REVERT: An 209 GLU cc_start: 0.7796 (pt0) cc_final: 0.7327 (tt0) REVERT: An 234 ARG cc_start: 0.7762 (ptm160) cc_final: 0.7341 (ptm160) REVERT: Ao 123 THR cc_start: 0.8138 (p) cc_final: 0.7438 (p) REVERT: Ao 138 TYR cc_start: 0.7177 (m-10) cc_final: 0.6974 (m-10) REVERT: Ao 209 GLU cc_start: 0.8478 (pt0) cc_final: 0.7877 (tt0) REVERT: Ao 234 ARG cc_start: 0.8227 (ptm160) cc_final: 0.7933 (ptm160) REVERT: Ap 141 ASP cc_start: 0.7969 (p0) cc_final: 0.7448 (p0) REVERT: Ap 159 ASN cc_start: 0.8447 (m-40) cc_final: 0.8136 (m110) REVERT: Ap 183 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8423 (tttp) REVERT: Ap 208 ILE cc_start: 0.8843 (tt) cc_final: 0.8619 (tt) REVERT: Ap 225 ARG cc_start: 0.8908 (mpt180) cc_final: 0.8126 (ttp-170) REVERT: Ap 238 ASP cc_start: 0.8332 (t70) cc_final: 0.7998 (t0) REVERT: Aq 186 VAL cc_start: 0.7630 (t) cc_final: 0.7290 (t) REVERT: Aq 190 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8336 (mmmt) REVERT: Aq 217 TYR cc_start: 0.6662 (t80) cc_final: 0.5947 (t80) REVERT: Aq 225 ARG cc_start: 0.8745 (mpt180) cc_final: 0.8365 (ttp-170) REVERT: Aq 241 GLU cc_start: 0.7354 (tt0) cc_final: 0.6977 (tt0) REVERT: Ar 123 THR cc_start: 0.5645 (p) cc_final: 0.4119 (p) REVERT: Ar 168 TYR cc_start: 0.7261 (m-80) cc_final: 0.6950 (m-80) REVERT: As 142 ASP cc_start: 0.7855 (t70) cc_final: 0.7598 (t70) REVERT: At 144 GLN cc_start: 0.7386 (mt0) cc_final: 0.7166 (tm-30) REVERT: At 164 ASP cc_start: 0.7568 (t70) cc_final: 0.7062 (t0) REVERT: At 188 ASN cc_start: 0.8065 (m-40) cc_final: 0.7865 (m-40) REVERT: Au 147 ILE cc_start: 0.8058 (mm) cc_final: 0.7676 (mp) REVERT: Au 159 ASN cc_start: 0.3478 (m-40) cc_final: 0.2796 (m110) REVERT: Aw 123 THR cc_start: 0.7495 (p) cc_final: 0.6942 (p) REVERT: Aw 208 ILE cc_start: 0.7270 (tt) cc_final: 0.7018 (tt) REVERT: Ax 123 THR cc_start: 0.7615 (p) cc_final: 0.6927 (p) REVERT: Ax 126 GLN cc_start: 0.7194 (mt0) cc_final: 0.6906 (mt0) REVERT: Ax 141 ASP cc_start: 0.7626 (p0) cc_final: 0.6984 (p0) REVERT: Ax 145 MET cc_start: 0.7833 (tpt) cc_final: 0.7598 (tpp) REVERT: Ax 152 LEU cc_start: 0.8721 (tp) cc_final: 0.8414 (tt) REVERT: Ax 208 ILE cc_start: 0.7887 (tt) cc_final: 0.7594 (tt) REVERT: Ay 202 ASP cc_start: 0.8306 (m-30) cc_final: 0.7825 (t0) REVERT: Ay 208 ILE cc_start: 0.8749 (tt) cc_final: 0.8500 (tt) REVERT: Ay 225 ARG cc_start: 0.8947 (mpt180) cc_final: 0.7791 (ttp-170) REVERT: Ay 226 ASN cc_start: 0.8772 (t0) cc_final: 0.8382 (t0) REVERT: Ay 238 ASP cc_start: 0.8075 (t70) cc_final: 0.7626 (t70) REVERT: Az 141 ASP cc_start: 0.7869 (p0) cc_final: 0.7492 (p0) REVERT: Az 183 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8333 (tttp) REVERT: Az 215 GLU cc_start: 0.8167 (pt0) cc_final: 0.7844 (pm20) REVERT: Az 225 ARG cc_start: 0.8763 (mpt180) cc_final: 0.8324 (ttp-170) REVERT: Ba 183 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8137 (tttp) outliers start: 0 outliers final: 0 residues processed: 1830 average time/residue: 0.2531 time to fit residues: 733.4401 Evaluate side-chains 1326 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1326 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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: 0.9980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.2980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 98 ASN Ab 166 ASN Ac 159 ASN Af 106 HIS Ag 199 HIS Ah 98 ASN Ai 98 ASN ** Ai 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 98 ASN Al 159 ASN Al 199 HIS Am 132 ASN Am 159 ASN An 175 ASN An 199 HIS Ao 159 ASN Ao 188 ASN Ap 188 ASN ** Aq 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 159 ASN Ar 98 ASN Ar 128 GLN ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 175 ASN At 98 ASN ** Au 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 159 ASN Av 175 ASN Av 177 GLN Aw 159 ASN Aw 175 ASN Ax 159 ASN Ax 175 ASN Ay 106 HIS Ay 159 ASN Ay 188 ASN Az 159 ASN Az 188 ASN Az 199 HIS Ba 98 ASN Ba 199 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.099734 restraints weight = 65413.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102470 restraints weight = 42314.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104443 restraints weight = 30674.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105858 restraints weight = 24001.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106805 restraints weight = 19846.320| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40770 Z= 0.154 Angle : 0.648 11.667 55107 Z= 0.339 Chirality : 0.042 0.177 5697 Planarity : 0.006 0.062 7263 Dihedral : 4.910 22.252 5373 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.47 % 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: -1.26 (0.13), residues: 4752 helix: -0.77 (0.12), residues: 2106 sheet: -3.24 (0.28), residues: 270 loop : -0.43 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGBa 121 TYR 0.021 0.002 TYRAf 207 PHE 0.029 0.002 PHEAr 180 TRP 0.032 0.002 TRPAn 155 HIS 0.010 0.002 HISAz 199 Details of bonding type rmsd covalent geometry : bond 0.00342 (40770) covalent geometry : angle 0.64849 (55107) hydrogen bonds : bond 0.03908 ( 1377) hydrogen bonds : angle 4.58999 ( 3726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1694 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1689 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 MET cc_start: 0.7723 (mmt) cc_final: 0.7202 (mmm) REVERT: Aa 116 ASP cc_start: 0.7580 (m-30) cc_final: 0.7281 (t0) REVERT: Aa 152 LEU cc_start: 0.7216 (tp) cc_final: 0.6915 (tt) REVERT: Aa 180 PHE cc_start: 0.8046 (m-80) cc_final: 0.7769 (m-10) REVERT: Aa 249 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7392 (mtm110) REVERT: Ab 152 LEU cc_start: 0.7574 (tp) cc_final: 0.7100 (tt) REVERT: Ab 202 ASP cc_start: 0.7485 (m-30) cc_final: 0.7202 (m-30) REVERT: Ac 131 TYR cc_start: 0.8436 (t80) cc_final: 0.7983 (t80) REVERT: Ac 139 ASP cc_start: 0.7534 (m-30) cc_final: 0.7256 (t70) REVERT: Ac 156 CYS cc_start: 0.8042 (m) cc_final: 0.7405 (m) REVERT: Ac 173 ASP cc_start: 0.7327 (t70) cc_final: 0.7024 (t70) REVERT: Ac 208 ILE cc_start: 0.8343 (tt) cc_final: 0.8108 (tt) REVERT: Ad 109 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8308 (tm-30) REVERT: Ad 141 ASP cc_start: 0.7576 (p0) cc_final: 0.7201 (p0) REVERT: Ad 152 LEU cc_start: 0.8713 (tp) cc_final: 0.8330 (tt) REVERT: Ad 153 MET cc_start: 0.8785 (tmm) cc_final: 0.8481 (tmm) REVERT: Ad 208 ILE cc_start: 0.8623 (tt) cc_final: 0.8406 (tt) REVERT: Ae 105 ASP cc_start: 0.7532 (m-30) cc_final: 0.7331 (m-30) REVERT: Ae 143 GLU cc_start: 0.7697 (tp30) cc_final: 0.7390 (tm-30) REVERT: Ae 152 LEU cc_start: 0.8769 (tp) cc_final: 0.8378 (tt) REVERT: Ae 173 ASP cc_start: 0.7240 (t0) cc_final: 0.6981 (t0) REVERT: Af 140 VAL cc_start: 0.9263 (m) cc_final: 0.8973 (m) REVERT: Af 145 MET cc_start: 0.8313 (tpt) cc_final: 0.7693 (tpt) REVERT: Af 158 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7585 (mt-10) REVERT: Ag 158 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6780 (mt-10) REVERT: Ag 159 ASN cc_start: 0.7825 (m-40) cc_final: 0.7372 (m-40) REVERT: Ag 173 ASP cc_start: 0.6948 (t0) cc_final: 0.6630 (t0) REVERT: Ah 123 THR cc_start: 0.7533 (p) cc_final: 0.6709 (m) REVERT: Ah 210 MET cc_start: 0.8513 (ttp) cc_final: 0.8302 (tmm) REVERT: Ah 229 ASP cc_start: 0.8103 (m-30) cc_final: 0.7679 (t0) REVERT: Ai 108 ILE cc_start: 0.8904 (mm) cc_final: 0.8632 (mm) REVERT: Ai 158 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7262 (mm-30) REVERT: Ai 187 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6588 (tt0) REVERT: Ai 197 MET cc_start: 0.7182 (tpp) cc_final: 0.6902 (tpp) REVERT: Ai 231 SER cc_start: 0.7462 (p) cc_final: 0.7244 (t) REVERT: Ai 244 SER cc_start: 0.8558 (t) cc_final: 0.8336 (t) REVERT: Aj 130 TRP cc_start: 0.7683 (t60) cc_final: 0.7465 (t60) REVERT: Al 141 ASP cc_start: 0.7259 (p0) cc_final: 0.7051 (p0) REVERT: Al 197 MET cc_start: 0.6999 (tpp) cc_final: 0.6109 (tpt) REVERT: Al 227 LEU cc_start: 0.8830 (tp) cc_final: 0.8630 (mt) REVERT: Am 107 LEU cc_start: 0.7956 (tp) cc_final: 0.7593 (tp) REVERT: Am 141 ASP cc_start: 0.7764 (p0) cc_final: 0.7358 (p0) REVERT: Am 152 LEU cc_start: 0.8426 (tp) cc_final: 0.8027 (tt) REVERT: Am 202 ASP cc_start: 0.7626 (m-30) cc_final: 0.7409 (m-30) REVERT: An 109 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8259 (tm-30) REVERT: An 153 MET cc_start: 0.8804 (tmm) cc_final: 0.8476 (tmm) REVERT: An 156 CYS cc_start: 0.9051 (m) cc_final: 0.8333 (m) REVERT: An 173 ASP cc_start: 0.7410 (t0) cc_final: 0.7075 (t0) REVERT: An 202 ASP cc_start: 0.7966 (m-30) cc_final: 0.7626 (m-30) REVERT: Ao 159 ASN cc_start: 0.8665 (m-40) cc_final: 0.8399 (m110) REVERT: Ao 210 MET cc_start: 0.8558 (tmm) cc_final: 0.8356 (tmm) REVERT: Ap 156 CYS cc_start: 0.8346 (m) cc_final: 0.8073 (m) REVERT: Ap 208 ILE cc_start: 0.8963 (tt) cc_final: 0.8681 (tt) REVERT: Ap 225 ARG cc_start: 0.8392 (mpt180) cc_final: 0.8158 (mtp180) REVERT: Ap 242 ILE cc_start: 0.8696 (mt) cc_final: 0.8404 (mt) REVERT: Aq 110 TYR cc_start: 0.8098 (t80) cc_final: 0.7727 (t80) REVERT: Aq 141 ASP cc_start: 0.7364 (p0) cc_final: 0.6956 (p0) REVERT: Aq 147 ILE cc_start: 0.8628 (mm) cc_final: 0.8309 (mm) REVERT: Aq 183 LYS cc_start: 0.9085 (tmmt) cc_final: 0.8827 (tttm) REVERT: Aq 211 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8111 (tpt-90) REVERT: Aq 225 ARG cc_start: 0.8545 (mpt180) cc_final: 0.7914 (ttp-170) REVERT: Aq 228 ASN cc_start: 0.8239 (p0) cc_final: 0.8009 (p0) REVERT: Ar 147 ILE cc_start: 0.8741 (mm) cc_final: 0.8493 (mm) REVERT: Ar 152 LEU cc_start: 0.7623 (tp) cc_final: 0.7263 (tt) REVERT: Ar 228 ASN cc_start: 0.7801 (p0) cc_final: 0.7417 (p0) REVERT: Ar 241 GLU cc_start: 0.7656 (tt0) cc_final: 0.7363 (tt0) REVERT: As 244 SER cc_start: 0.8534 (t) cc_final: 0.8131 (t) REVERT: At 85 LYS cc_start: 0.7601 (ptpp) cc_final: 0.7277 (ptpp) REVERT: At 244 SER cc_start: 0.7779 (t) cc_final: 0.7373 (p) REVERT: Au 141 ASP cc_start: 0.7765 (p0) cc_final: 0.7460 (p0) REVERT: Au 173 ASP cc_start: 0.7388 (t70) cc_final: 0.6908 (t70) REVERT: Au 197 MET cc_start: 0.8342 (tpp) cc_final: 0.7886 (tpp) REVERT: Av 141 ASP cc_start: 0.7822 (p0) cc_final: 0.7499 (p0) REVERT: Av 173 ASP cc_start: 0.7635 (t0) cc_final: 0.7276 (t70) REVERT: Aw 108 ILE cc_start: 0.7637 (tp) cc_final: 0.7366 (tp) REVERT: Aw 141 ASP cc_start: 0.7720 (p0) cc_final: 0.7244 (p0) REVERT: Aw 202 ASP cc_start: 0.7604 (m-30) cc_final: 0.7346 (m-30) REVERT: Ax 107 LEU cc_start: 0.8787 (tp) cc_final: 0.8490 (tp) REVERT: Ax 123 THR cc_start: 0.8005 (p) cc_final: 0.7805 (p) REVERT: Ax 141 ASP cc_start: 0.7695 (p0) cc_final: 0.7099 (p0) REVERT: Ax 149 MET cc_start: 0.7907 (tpp) cc_final: 0.7621 (tpp) REVERT: Ax 152 LEU cc_start: 0.8693 (tp) cc_final: 0.8185 (tt) REVERT: Ax 156 CYS cc_start: 0.8799 (m) cc_final: 0.8394 (m) REVERT: Ax 202 ASP cc_start: 0.7696 (m-30) cc_final: 0.7372 (m-30) REVERT: Ax 209 GLU cc_start: 0.8575 (tt0) cc_final: 0.8223 (tt0) REVERT: Ay 107 LEU cc_start: 0.8702 (tp) cc_final: 0.8442 (tt) REVERT: Ay 145 MET cc_start: 0.7834 (tpt) cc_final: 0.7445 (tpt) REVERT: Ay 197 MET cc_start: 0.9142 (tpp) cc_final: 0.8927 (tpp) REVERT: Ay 208 ILE cc_start: 0.9069 (tt) cc_final: 0.8781 (tt) REVERT: Az 225 ARG cc_start: 0.8376 (mpt180) cc_final: 0.8141 (ttp-170) REVERT: Ba 183 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8424 (tttp) REVERT: Ba 228 ASN cc_start: 0.7663 (p0) cc_final: 0.7323 (p0) outliers start: 5 outliers final: 1 residues processed: 1694 average time/residue: 0.2320 time to fit residues: 644.3039 Evaluate side-chains 1412 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1411 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 70 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 419 optimal weight: 6.9990 chunk 314 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 327 optimal weight: 7.9990 chunk 414 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 175 ASN Ab 159 ASN Ac 126 GLN Ac 159 ASN Ac 226 ASN Ad 159 ASN Af 159 ASN ** Ag 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 159 ASN Al 175 ASN Am 159 ASN ** An 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 199 HIS ** Aq 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 175 ASN ** Ar 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 226 ASN As 188 ASN Au 159 ASN Av 159 ASN Ax 177 GLN Ay 159 ASN Az 188 ASN ** Ba 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 159 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091838 restraints weight = 68659.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.094326 restraints weight = 45643.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096130 restraints weight = 33877.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097425 restraints weight = 27061.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098393 restraints weight = 22772.031| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.7150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 40770 Z= 0.243 Angle : 0.744 12.037 55107 Z= 0.389 Chirality : 0.045 0.242 5697 Planarity : 0.006 0.057 7263 Dihedral : 5.332 24.884 5373 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % 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: -1.06 (0.13), residues: 4752 helix: -0.81 (0.11), residues: 2133 sheet: None (None), residues: 0 loop : -0.50 (0.13), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGAb 234 TYR 0.026 0.002 TYRAg 110 PHE 0.024 0.002 PHEAb 237 TRP 0.038 0.002 TRPAr 155 HIS 0.010 0.002 HISAz 106 Details of bonding type rmsd covalent geometry : bond 0.00565 (40770) covalent geometry : angle 0.74372 (55107) hydrogen bonds : bond 0.05112 ( 1377) hydrogen bonds : angle 4.87377 ( 3726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1651 time to evaluate : 1.704 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: Aa 161 THR cc_start: 0.9165 (p) cc_final: 0.8841 (p) REVERT: Aa 183 LYS cc_start: 0.9146 (tttp) cc_final: 0.8814 (ttpp) REVERT: Aa 205 GLU cc_start: 0.7655 (tt0) cc_final: 0.7413 (tt0) REVERT: Ab 116 ASP cc_start: 0.8195 (m-30) cc_final: 0.7953 (m-30) REVERT: Ab 139 ASP cc_start: 0.7613 (m-30) cc_final: 0.7129 (t70) REVERT: Ab 166 ASN cc_start: 0.8857 (p0) cc_final: 0.8511 (p0) REVERT: Ab 183 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8794 (ttpp) REVERT: Ab 205 GLU cc_start: 0.7838 (tt0) cc_final: 0.7635 (tp30) REVERT: Ac 161 THR cc_start: 0.9145 (p) cc_final: 0.8918 (p) REVERT: Ad 141 ASP cc_start: 0.7899 (p0) cc_final: 0.7586 (p0) REVERT: Ad 158 GLU cc_start: 0.8382 (tt0) cc_final: 0.7788 (tt0) REVERT: Af 80 VAL cc_start: 0.9054 (t) cc_final: 0.8794 (p) REVERT: Af 128 GLN cc_start: 0.8656 (tt0) cc_final: 0.8083 (tt0) REVERT: Af 145 MET cc_start: 0.8891 (tpt) cc_final: 0.8520 (tpt) REVERT: Af 158 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7658 (mt-10) REVERT: Ag 80 VAL cc_start: 0.9198 (t) cc_final: 0.8970 (p) REVERT: Ag 173 ASP cc_start: 0.7213 (t0) cc_final: 0.6933 (t0) REVERT: Ag 183 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8835 (ptmm) REVERT: Ag 202 ASP cc_start: 0.7006 (t70) cc_final: 0.5365 (t70) REVERT: Ag 205 GLU cc_start: 0.8208 (pt0) cc_final: 0.7945 (pt0) REVERT: Ag 209 GLU cc_start: 0.8464 (pp20) cc_final: 0.8058 (pp20) REVERT: Ag 232 LEU cc_start: 0.8995 (mp) cc_final: 0.8269 (tt) REVERT: Ah 159 ASN cc_start: 0.8328 (m-40) cc_final: 0.7862 (m110) REVERT: Ah 195 GLN cc_start: 0.8181 (tt0) cc_final: 0.7818 (mm-40) REVERT: Ah 197 MET cc_start: 0.9103 (tpp) cc_final: 0.8843 (mmm) REVERT: Ah 229 ASP cc_start: 0.8223 (m-30) cc_final: 0.7550 (t0) REVERT: Ai 158 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7778 (mm-30) REVERT: Ai 159 ASN cc_start: 0.7994 (m-40) cc_final: 0.7763 (m-40) REVERT: Aj 158 GLU cc_start: 0.8150 (tp30) cc_final: 0.7912 (tp30) REVERT: Aj 229 ASP cc_start: 0.8336 (m-30) cc_final: 0.7393 (t0) REVERT: Ak 109 GLN cc_start: 0.8494 (pp30) cc_final: 0.8275 (pp30) REVERT: Ak 116 ASP cc_start: 0.8056 (m-30) cc_final: 0.7848 (m-30) REVERT: Ak 123 THR cc_start: 0.7511 (p) cc_final: 0.7294 (p) REVERT: Ak 153 MET cc_start: 0.9423 (tmm) cc_final: 0.9060 (tmm) REVERT: Al 158 GLU cc_start: 0.8561 (tp30) cc_final: 0.7477 (tp30) REVERT: Al 197 MET cc_start: 0.8517 (tpp) cc_final: 0.8169 (tpp) REVERT: Am 123 THR cc_start: 0.8291 (p) cc_final: 0.7977 (p) REVERT: Am 141 ASP cc_start: 0.8186 (p0) cc_final: 0.7955 (p0) REVERT: Am 198 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7749 (tmm) REVERT: An 109 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8359 (tm-30) REVERT: An 141 ASP cc_start: 0.8097 (p0) cc_final: 0.7651 (p0) REVERT: An 173 ASP cc_start: 0.7624 (t0) cc_final: 0.7382 (t0) REVERT: An 177 GLN cc_start: 0.8071 (mt0) cc_final: 0.7852 (mt0) REVERT: Ao 80 VAL cc_start: 0.8877 (t) cc_final: 0.8580 (p) REVERT: Ao 141 ASP cc_start: 0.8000 (p0) cc_final: 0.7572 (p0) REVERT: Ao 171 MET cc_start: 0.8218 (ttp) cc_final: 0.7954 (ttp) REVERT: Ao 173 ASP cc_start: 0.7426 (t70) cc_final: 0.7206 (t0) REVERT: Ap 80 VAL cc_start: 0.9247 (t) cc_final: 0.8999 (p) REVERT: Ap 158 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7699 (mt-10) REVERT: Ap 159 ASN cc_start: 0.8477 (m-40) cc_final: 0.8270 (m110) REVERT: Ap 208 ILE cc_start: 0.9042 (tt) cc_final: 0.8827 (tt) REVERT: Ap 210 MET cc_start: 0.8674 (tmm) cc_final: 0.8451 (tmm) REVERT: Ap 228 ASN cc_start: 0.8498 (p0) cc_final: 0.8041 (p0) REVERT: Ap 230 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7419 (pttt) REVERT: Aq 128 GLN cc_start: 0.8514 (tt0) cc_final: 0.8288 (tp40) REVERT: Aq 141 ASP cc_start: 0.7607 (p0) cc_final: 0.7371 (p0) REVERT: Aq 158 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8076 (mm-30) REVERT: Aq 159 ASN cc_start: 0.8243 (m-40) cc_final: 0.7885 (m110) REVERT: Aq 173 ASP cc_start: 0.7096 (t0) cc_final: 0.6786 (t0) REVERT: Aq 225 ARG cc_start: 0.8675 (mpt180) cc_final: 0.7782 (ttp-170) REVERT: Aq 228 ASN cc_start: 0.8469 (p0) cc_final: 0.8056 (p0) REVERT: Ar 158 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8140 (mm-30) REVERT: Ar 197 MET cc_start: 0.8837 (tpp) cc_final: 0.8474 (tpp) REVERT: Ar 228 ASN cc_start: 0.8177 (p0) cc_final: 0.7888 (p0) REVERT: As 183 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8738 (ttpp) REVERT: At 108 ILE cc_start: 0.8595 (mm) cc_final: 0.8347 (mm) REVERT: At 171 MET cc_start: 0.8341 (mmm) cc_final: 0.8128 (mmm) REVERT: At 187 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7020 (mt-10) REVERT: At 229 ASP cc_start: 0.7816 (m-30) cc_final: 0.7068 (t0) REVERT: Au 109 GLN cc_start: 0.8653 (pp30) cc_final: 0.8338 (pp30) REVERT: Au 123 THR cc_start: 0.7638 (p) cc_final: 0.7184 (p) REVERT: Au 173 ASP cc_start: 0.7623 (t70) cc_final: 0.7264 (t70) REVERT: Av 95 MET cc_start: 0.7745 (mtm) cc_final: 0.7470 (mtt) REVERT: Av 114 GLN cc_start: 0.8516 (tp40) cc_final: 0.7413 (tp40) REVERT: Av 141 ASP cc_start: 0.8005 (p0) cc_final: 0.7727 (p0) REVERT: Av 241 GLU cc_start: 0.7950 (tt0) cc_final: 0.7737 (tt0) REVERT: Aw 80 VAL cc_start: 0.9071 (t) cc_final: 0.8849 (p) REVERT: Aw 141 ASP cc_start: 0.8087 (p0) cc_final: 0.7712 (p0) REVERT: Aw 158 GLU cc_start: 0.8204 (tt0) cc_final: 0.7923 (mt-10) REVERT: Aw 173 ASP cc_start: 0.7680 (t0) cc_final: 0.7367 (t0) REVERT: Aw 197 MET cc_start: 0.9002 (tpp) cc_final: 0.8722 (tpp) REVERT: Aw 202 ASP cc_start: 0.8164 (m-30) cc_final: 0.7897 (m-30) REVERT: Ax 80 VAL cc_start: 0.8975 (t) cc_final: 0.8668 (p) REVERT: Ax 110 TYR cc_start: 0.8621 (t80) cc_final: 0.8258 (t80) REVERT: Ax 141 ASP cc_start: 0.7943 (p0) cc_final: 0.7419 (p0) REVERT: Ax 156 CYS cc_start: 0.9001 (m) cc_final: 0.8323 (m) REVERT: Ay 80 VAL cc_start: 0.9109 (t) cc_final: 0.8839 (p) REVERT: Ay 128 GLN cc_start: 0.8439 (tt0) cc_final: 0.8139 (tt0) REVERT: Ay 141 ASP cc_start: 0.7730 (p0) cc_final: 0.7295 (p0) REVERT: Ay 159 ASN cc_start: 0.8633 (m-40) cc_final: 0.8230 (m110) REVERT: Ay 161 THR cc_start: 0.9049 (p) cc_final: 0.8827 (p) REVERT: Ay 173 ASP cc_start: 0.7377 (t70) cc_final: 0.7130 (t0) REVERT: Ay 209 GLU cc_start: 0.8814 (pp20) cc_final: 0.8398 (pp20) REVERT: Ay 218 MET cc_start: 0.7936 (ttp) cc_final: 0.7729 (ttp) REVERT: Az 80 VAL cc_start: 0.9330 (t) cc_final: 0.9016 (p) REVERT: Az 83 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8576 (tppt) REVERT: Az 141 ASP cc_start: 0.7426 (p0) cc_final: 0.7161 (p0) REVERT: Az 173 ASP cc_start: 0.7253 (t0) cc_final: 0.6761 (t0) REVERT: Az 183 LYS cc_start: 0.9230 (tttm) cc_final: 0.8880 (ptmm) REVERT: Az 202 ASP cc_start: 0.6880 (t70) cc_final: 0.6577 (t70) REVERT: Az 230 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7289 (pttt) REVERT: Ba 153 MET cc_start: 0.9208 (ttp) cc_final: 0.8725 (tmm) REVERT: Ba 159 ASN cc_start: 0.6854 (OUTLIER) cc_final: 0.6287 (t0) REVERT: Ba 183 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8867 (tttm) REVERT: Ba 228 ASN cc_start: 0.8034 (p0) cc_final: 0.7661 (p0) outliers start: 3 outliers final: 0 residues processed: 1651 average time/residue: 0.2308 time to fit residues: 635.6330 Evaluate side-chains 1422 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1420 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 392 optimal weight: 0.7980 chunk 149 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 383 optimal weight: 7.9990 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 Aa 159 ASN Aa 254 HIS Ab 254 HIS Ac 159 ASN Ad 175 ASN ** Ae 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 159 ASN Ag 159 ASN ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 226 ASN Aj 159 ASN Aj 226 ASN Ak 159 ASN Ak 226 ASN Al 226 ASN Am 132 ASN Ao 159 ASN Ar 195 GLN As 159 ASN ** At 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 159 ASN Au 126 GLN Av 126 GLN Ax 159 ASN Az 128 GLN Az 159 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095577 restraints weight = 66538.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098183 restraints weight = 43960.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100057 restraints weight = 32451.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101404 restraints weight = 25800.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102326 restraints weight = 21642.989| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40770 Z= 0.121 Angle : 0.609 7.889 55107 Z= 0.316 Chirality : 0.040 0.212 5697 Planarity : 0.005 0.043 7263 Dihedral : 4.796 23.244 5373 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % 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: -0.91 (0.13), residues: 4752 helix: -0.64 (0.11), residues: 2133 sheet: -2.54 (0.32), residues: 270 loop : -0.12 (0.14), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAu 211 TYR 0.024 0.001 TYRAn 110 PHE 0.027 0.002 PHEAg 237 TRP 0.022 0.002 TRPAr 155 HIS 0.006 0.001 HISAa 254 Details of bonding type rmsd covalent geometry : bond 0.00277 (40770) covalent geometry : angle 0.60869 (55107) hydrogen bonds : bond 0.03811 ( 1377) hydrogen bonds : angle 4.45529 ( 3726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1629 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: symmetry clash REVERT: Aa 83 LYS cc_start: 0.8129 (tppt) cc_final: 0.7828 (mmtt) REVERT: Aa 109 GLN cc_start: 0.8324 (pp30) cc_final: 0.7980 (pp30) REVERT: Aa 114 GLN cc_start: 0.8694 (tp40) cc_final: 0.8448 (tp-100) REVERT: Aa 159 ASN cc_start: 0.8064 (m-40) cc_final: 0.7754 (m110) REVERT: Aa 161 THR cc_start: 0.9046 (p) cc_final: 0.8718 (p) REVERT: Aa 180 PHE cc_start: 0.9044 (m-80) cc_final: 0.8832 (m-80) REVERT: Aa 183 LYS cc_start: 0.9176 (tttp) cc_final: 0.8878 (ttpp) REVERT: Aa 232 LEU cc_start: 0.8603 (mp) cc_final: 0.7944 (tt) REVERT: Ab 139 ASP cc_start: 0.7532 (m-30) cc_final: 0.7097 (t70) REVERT: Ab 158 GLU cc_start: 0.8683 (tp30) cc_final: 0.8251 (tp30) REVERT: Ab 161 THR cc_start: 0.8963 (p) cc_final: 0.8758 (p) REVERT: Ab 183 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8739 (ttpp) REVERT: Ab 205 GLU cc_start: 0.7714 (tt0) cc_final: 0.7468 (tp30) REVERT: Ad 119 ASN cc_start: 0.7865 (p0) cc_final: 0.7624 (t0) REVERT: Ad 152 LEU cc_start: 0.9002 (tp) cc_final: 0.8738 (tt) REVERT: Ad 158 GLU cc_start: 0.7751 (tt0) cc_final: 0.7329 (tt0) REVERT: Ae 128 GLN cc_start: 0.8712 (tp40) cc_final: 0.8417 (tp40) REVERT: Af 80 VAL cc_start: 0.8994 (t) cc_final: 0.8730 (p) REVERT: Af 128 GLN cc_start: 0.8677 (tt0) cc_final: 0.8063 (tt0) REVERT: Af 145 MET cc_start: 0.8839 (tpt) cc_final: 0.8597 (tpt) REVERT: Af 158 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7466 (mm-30) REVERT: Af 159 ASN cc_start: 0.8557 (m-40) cc_final: 0.8241 (m110) REVERT: Af 161 THR cc_start: 0.8913 (m) cc_final: 0.8420 (p) REVERT: Ag 80 VAL cc_start: 0.9183 (t) cc_final: 0.8963 (p) REVERT: Ag 152 LEU cc_start: 0.9086 (tp) cc_final: 0.8805 (tt) REVERT: Ag 159 ASN cc_start: 0.8287 (m-40) cc_final: 0.8026 (m110) REVERT: Ag 197 MET cc_start: 0.8889 (tpp) cc_final: 0.8661 (tpp) REVERT: Ag 209 GLU cc_start: 0.8600 (pp20) cc_final: 0.8127 (pp20) REVERT: Ag 232 LEU cc_start: 0.8955 (mp) cc_final: 0.8276 (tt) REVERT: Ah 140 VAL cc_start: 0.9169 (m) cc_final: 0.8942 (t) REVERT: Ah 159 ASN cc_start: 0.8061 (m-40) cc_final: 0.7653 (m110) REVERT: Ah 183 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8670 (tttp) REVERT: Ah 187 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6893 (mt-10) REVERT: Aj 116 ASP cc_start: 0.7908 (m-30) cc_final: 0.7685 (m-30) REVERT: Aj 158 GLU cc_start: 0.8122 (tp30) cc_final: 0.7791 (tp30) REVERT: Aj 159 ASN cc_start: 0.7841 (m-40) cc_final: 0.7431 (m110) REVERT: Aj 168 TYR cc_start: 0.8107 (m-80) cc_final: 0.7880 (m-10) REVERT: Aj 183 LYS cc_start: 0.9112 (tttm) cc_final: 0.8906 (ttpp) REVERT: Aj 202 ASP cc_start: 0.7863 (m-30) cc_final: 0.6846 (t0) REVERT: Aj 205 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7821 (tm-30) REVERT: Ak 109 GLN cc_start: 0.8552 (pp30) cc_final: 0.8246 (pp30) REVERT: Ak 153 MET cc_start: 0.9314 (tmm) cc_final: 0.8984 (tmm) REVERT: Ak 161 THR cc_start: 0.9064 (p) cc_final: 0.8796 (p) REVERT: Al 158 GLU cc_start: 0.8496 (tp30) cc_final: 0.8162 (tp30) REVERT: Al 173 ASP cc_start: 0.7481 (t70) cc_final: 0.7266 (p0) REVERT: Al 235 TYR cc_start: 0.8804 (m-80) cc_final: 0.8591 (m-80) REVERT: Am 141 ASP cc_start: 0.8134 (p0) cc_final: 0.7902 (p0) REVERT: Am 208 ILE cc_start: 0.9063 (tt) cc_final: 0.8855 (tt) REVERT: Am 209 GLU cc_start: 0.8495 (tt0) cc_final: 0.8265 (mt-10) REVERT: Am 223 LEU cc_start: 0.8659 (mm) cc_final: 0.8404 (mt) REVERT: An 95 MET cc_start: 0.7863 (mpp) cc_final: 0.7629 (mmt) REVERT: An 109 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8247 (tm-30) REVERT: An 197 MET cc_start: 0.8850 (tpp) cc_final: 0.8635 (tpp) REVERT: Ao 109 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8190 (tm-30) REVERT: Ao 131 TYR cc_start: 0.8980 (t80) cc_final: 0.8777 (t80) REVERT: Ao 141 ASP cc_start: 0.7880 (p0) cc_final: 0.7609 (p0) REVERT: Ao 159 ASN cc_start: 0.8717 (m-40) cc_final: 0.8392 (m110) REVERT: Ap 80 VAL cc_start: 0.9251 (t) cc_final: 0.9005 (p) REVERT: Ap 152 LEU cc_start: 0.8775 (tt) cc_final: 0.8423 (tt) REVERT: Ap 161 THR cc_start: 0.9048 (p) cc_final: 0.8742 (p) REVERT: Ap 228 ASN cc_start: 0.8551 (p0) cc_final: 0.8030 (p0) REVERT: Ap 230 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7271 (pttt) REVERT: Aq 149 MET cc_start: 0.8740 (tpp) cc_final: 0.8539 (tpp) REVERT: Aq 158 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8017 (mm-30) REVERT: Aq 159 ASN cc_start: 0.8135 (m-40) cc_final: 0.7686 (m110) REVERT: Aq 173 ASP cc_start: 0.7124 (t0) cc_final: 0.6832 (t0) REVERT: Aq 225 ARG cc_start: 0.8607 (mpt180) cc_final: 0.7818 (ttp-170) REVERT: Ar 158 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7952 (tp30) REVERT: Ar 197 MET cc_start: 0.8697 (tpp) cc_final: 0.8159 (mmm) REVERT: Ar 228 ASN cc_start: 0.8327 (p0) cc_final: 0.7993 (p0) REVERT: As 158 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7866 (mm-30) REVERT: As 183 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8836 (tttm) REVERT: As 197 MET cc_start: 0.8124 (tpp) cc_final: 0.7860 (tpp) REVERT: At 109 GLN cc_start: 0.8194 (pp30) cc_final: 0.7782 (pp30) REVERT: At 152 LEU cc_start: 0.8656 (tp) cc_final: 0.8433 (tt) REVERT: At 171 MET cc_start: 0.8055 (mmm) cc_final: 0.7712 (mmm) REVERT: At 187 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7111 (mt-10) REVERT: Au 109 GLN cc_start: 0.8625 (pp30) cc_final: 0.8401 (pp30) REVERT: Au 158 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6952 (mt-10) REVERT: Au 164 ASP cc_start: 0.7913 (t0) cc_final: 0.7708 (m-30) REVERT: Au 166 ASN cc_start: 0.8753 (p0) cc_final: 0.8339 (p0) REVERT: Au 173 ASP cc_start: 0.7444 (t70) cc_final: 0.7189 (t70) REVERT: Av 114 GLN cc_start: 0.8372 (tp40) cc_final: 0.7540 (tp40) REVERT: Av 141 ASP cc_start: 0.8130 (p0) cc_final: 0.7798 (p0) REVERT: Av 152 LEU cc_start: 0.8172 (tt) cc_final: 0.7745 (tt) REVERT: Av 205 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8266 (tm-30) REVERT: Av 208 ILE cc_start: 0.8835 (tt) cc_final: 0.8631 (tt) REVERT: Aw 80 VAL cc_start: 0.9073 (t) cc_final: 0.8832 (p) REVERT: Aw 128 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8077 (mm-40) REVERT: Aw 141 ASP cc_start: 0.7902 (p0) cc_final: 0.7689 (p0) REVERT: Aw 173 ASP cc_start: 0.7656 (t0) cc_final: 0.7387 (t0) REVERT: Aw 202 ASP cc_start: 0.8047 (m-30) cc_final: 0.7810 (m-30) REVERT: Ax 80 VAL cc_start: 0.9010 (t) cc_final: 0.8686 (p) REVERT: Ax 110 TYR cc_start: 0.8617 (t80) cc_final: 0.8367 (t80) REVERT: Ax 128 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8420 (tp40) REVERT: Ax 141 ASP cc_start: 0.7947 (p0) cc_final: 0.7451 (p0) REVERT: Ax 159 ASN cc_start: 0.8481 (m-40) cc_final: 0.8040 (m110) REVERT: Ax 173 ASP cc_start: 0.7375 (t0) cc_final: 0.7129 (t0) REVERT: Ax 209 GLU cc_start: 0.8622 (tt0) cc_final: 0.8278 (tt0) REVERT: Ay 80 VAL cc_start: 0.9151 (t) cc_final: 0.8918 (p) REVERT: Ay 128 GLN cc_start: 0.8454 (tt0) cc_final: 0.8161 (tt0) REVERT: Ay 141 ASP cc_start: 0.7602 (p0) cc_final: 0.7382 (p0) REVERT: Ay 159 ASN cc_start: 0.8520 (m-40) cc_final: 0.8213 (m110) REVERT: Ay 173 ASP cc_start: 0.7345 (t70) cc_final: 0.7047 (t0) REVERT: Ay 209 GLU cc_start: 0.8796 (pp20) cc_final: 0.8464 (pp20) REVERT: Ay 225 ARG cc_start: 0.8603 (mpt180) cc_final: 0.7920 (mtp180) REVERT: Az 141 ASP cc_start: 0.7333 (p0) cc_final: 0.7124 (p0) REVERT: Az 161 THR cc_start: 0.9014 (p) cc_final: 0.8601 (p) REVERT: Az 173 ASP cc_start: 0.7125 (t0) cc_final: 0.6811 (t0) REVERT: Az 183 LYS cc_start: 0.9192 (tttm) cc_final: 0.8951 (ptmm) REVERT: Ba 153 MET cc_start: 0.9143 (ttp) cc_final: 0.8752 (tmm) REVERT: Ba 183 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8800 (tttm) REVERT: Ba 228 ASN cc_start: 0.8166 (p0) cc_final: 0.7731 (p0) REVERT: Ba 232 LEU cc_start: 0.8847 (mp) cc_final: 0.8201 (tt) outliers start: 2 outliers final: 0 residues processed: 1629 average time/residue: 0.2221 time to fit residues: 608.3473 Evaluate side-chains 1417 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1417 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 183 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 435 optimal weight: 2.9990 chunk 414 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 243 optimal weight: 0.8980 chunk 336 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 159 ASN Ap 159 ASN Aq 128 GLN Ar 248 ASN ** At 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 159 ASN At 226 ASN Au 126 GLN Au 226 ASN Av 126 GLN Az 128 GLN Az 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.090501 restraints weight = 67206.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.092615 restraints weight = 46470.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094226 restraints weight = 35665.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.095419 restraints weight = 28992.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.096258 restraints weight = 24591.550| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40770 Z= 0.141 Angle : 0.617 8.088 55107 Z= 0.318 Chirality : 0.041 0.194 5697 Planarity : 0.004 0.049 7263 Dihedral : 4.596 22.452 5373 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.02 % Allowed : 1.86 % Favored : 98.11 % 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: -0.73 (0.13), residues: 4752 helix: -0.44 (0.12), residues: 2106 sheet: -2.42 (0.32), residues: 270 loop : -0.09 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAz 211 TYR 0.033 0.001 TYRAo 110 PHE 0.020 0.002 PHEAg 237 TRP 0.016 0.002 TRPAr 155 HIS 0.006 0.001 HISAy 199 Details of bonding type rmsd covalent geometry : bond 0.00332 (40770) covalent geometry : angle 0.61671 (55107) hydrogen bonds : bond 0.03681 ( 1377) hydrogen bonds : angle 4.33849 ( 3726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1608 time to evaluate : 2.388 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 83 LYS cc_start: 0.8209 (tppt) cc_final: 0.7964 (mmtt) REVERT: Aa 109 GLN cc_start: 0.8409 (pp30) cc_final: 0.7990 (pp30) REVERT: Aa 114 GLN cc_start: 0.8880 (tp40) cc_final: 0.8643 (tp-100) REVERT: Aa 139 ASP cc_start: 0.7786 (m-30) cc_final: 0.7244 (t0) REVERT: Aa 147 ILE cc_start: 0.9605 (mp) cc_final: 0.9402 (mp) REVERT: Aa 159 ASN cc_start: 0.7925 (m-40) cc_final: 0.7613 (m110) REVERT: Aa 183 LYS cc_start: 0.9222 (tttp) cc_final: 0.8946 (ttpp) REVERT: Aa 202 ASP cc_start: 0.7756 (m-30) cc_final: 0.6893 (t0) REVERT: Aa 232 LEU cc_start: 0.8751 (mp) cc_final: 0.8045 (tt) REVERT: Ab 139 ASP cc_start: 0.7628 (m-30) cc_final: 0.7217 (t70) REVERT: Ab 158 GLU cc_start: 0.8755 (tp30) cc_final: 0.8302 (tp30) REVERT: Ab 161 THR cc_start: 0.9115 (p) cc_final: 0.8881 (p) REVERT: Ab 183 LYS cc_start: 0.9114 (ttpp) cc_final: 0.8868 (ttpp) REVERT: Ab 205 GLU cc_start: 0.7855 (tt0) cc_final: 0.7369 (tp30) REVERT: Ab 237 PHE cc_start: 0.8954 (p90) cc_final: 0.8637 (p90) REVERT: Ac 109 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8563 (tm-30) REVERT: Ac 139 ASP cc_start: 0.7663 (m-30) cc_final: 0.7142 (t0) REVERT: Ac 158 GLU cc_start: 0.8680 (tp30) cc_final: 0.8160 (tp30) REVERT: Ad 139 ASP cc_start: 0.7990 (p0) cc_final: 0.7711 (p0) REVERT: Ad 158 GLU cc_start: 0.8059 (tt0) cc_final: 0.7852 (tt0) REVERT: Ad 209 GLU cc_start: 0.8814 (tt0) cc_final: 0.8442 (mt-10) REVERT: Ae 95 MET cc_start: 0.7885 (mtt) cc_final: 0.7625 (mtt) REVERT: Ae 110 TYR cc_start: 0.8521 (t80) cc_final: 0.8248 (t80) REVERT: Af 80 VAL cc_start: 0.9065 (t) cc_final: 0.8835 (p) REVERT: Af 128 GLN cc_start: 0.8718 (tt0) cc_final: 0.8089 (tt0) REVERT: Af 152 LEU cc_start: 0.9058 (tt) cc_final: 0.8833 (tt) REVERT: Ag 80 VAL cc_start: 0.9217 (t) cc_final: 0.9003 (p) REVERT: Ag 152 LEU cc_start: 0.9073 (tp) cc_final: 0.8771 (tt) REVERT: Ag 161 THR cc_start: 0.9073 (p) cc_final: 0.8745 (p) REVERT: Ag 197 MET cc_start: 0.8898 (tpp) cc_final: 0.8667 (tpp) REVERT: Ag 209 GLU cc_start: 0.8642 (pp20) cc_final: 0.8150 (pp20) REVERT: Ag 232 LEU cc_start: 0.8972 (mp) cc_final: 0.8210 (tt) REVERT: Ag 242 ILE cc_start: 0.9206 (mp) cc_final: 0.9006 (mp) REVERT: Ah 116 ASP cc_start: 0.8024 (m-30) cc_final: 0.7752 (m-30) REVERT: Ah 140 VAL cc_start: 0.9264 (m) cc_final: 0.9014 (t) REVERT: Ah 159 ASN cc_start: 0.8055 (m-40) cc_final: 0.7723 (m110) REVERT: Ah 197 MET cc_start: 0.8969 (tpp) cc_final: 0.8707 (tpp) REVERT: Ai 109 GLN cc_start: 0.8001 (pp30) cc_final: 0.7656 (pp30) REVERT: Aj 116 ASP cc_start: 0.8193 (m-30) cc_final: 0.7991 (m-30) REVERT: Aj 159 ASN cc_start: 0.7928 (m-40) cc_final: 0.7593 (m110) REVERT: Aj 171 MET cc_start: 0.8197 (mmm) cc_final: 0.7910 (mmm) REVERT: Aj 202 ASP cc_start: 0.7723 (m-30) cc_final: 0.7230 (t0) REVERT: Aj 205 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7367 (tm-30) REVERT: Aj 209 GLU cc_start: 0.8195 (tt0) cc_final: 0.7460 (tt0) REVERT: Aj 232 LEU cc_start: 0.8647 (mp) cc_final: 0.7805 (tt) REVERT: Aj 234 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8251 (ptm160) REVERT: Ak 91 MET cc_start: 0.7652 (mmp) cc_final: 0.6333 (mmp) REVERT: Ak 109 GLN cc_start: 0.8602 (pp30) cc_final: 0.8179 (pp30) REVERT: Ak 153 MET cc_start: 0.9345 (tmm) cc_final: 0.9062 (tmm) REVERT: Ak 217 TYR cc_start: 0.7511 (t80) cc_final: 0.7162 (t80) REVERT: Al 235 TYR cc_start: 0.8807 (m-80) cc_final: 0.8569 (m-80) REVERT: Am 173 ASP cc_start: 0.7637 (t70) cc_final: 0.7352 (t0) REVERT: An 109 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8275 (tm-30) REVERT: An 110 TYR cc_start: 0.8464 (t80) cc_final: 0.8189 (t80) REVERT: Ao 109 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8216 (tm-30) REVERT: Ao 141 ASP cc_start: 0.7905 (p0) cc_final: 0.7655 (p0) REVERT: Ao 159 ASN cc_start: 0.8409 (m-40) cc_final: 0.8085 (m110) REVERT: Ao 173 ASP cc_start: 0.7158 (t0) cc_final: 0.6956 (t0) REVERT: Ao 197 MET cc_start: 0.9019 (tpp) cc_final: 0.8805 (tpp) REVERT: Ap 80 VAL cc_start: 0.9260 (t) cc_final: 0.9048 (p) REVERT: Ap 156 CYS cc_start: 0.8794 (m) cc_final: 0.8361 (t) REVERT: Ap 161 THR cc_start: 0.9081 (p) cc_final: 0.8773 (p) REVERT: Ap 173 ASP cc_start: 0.6972 (t70) cc_final: 0.6686 (t0) REVERT: Ap 228 ASN cc_start: 0.8618 (p0) cc_final: 0.8101 (p0) REVERT: Ap 230 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7286 (pttt) REVERT: Aq 159 ASN cc_start: 0.8244 (m-40) cc_final: 0.7805 (m110) REVERT: Aq 173 ASP cc_start: 0.7224 (t0) cc_final: 0.6905 (t0) REVERT: Ar 197 MET cc_start: 0.8793 (tpp) cc_final: 0.8587 (tpp) REVERT: Ar 228 ASN cc_start: 0.8415 (p0) cc_final: 0.8083 (p0) REVERT: As 161 THR cc_start: 0.9438 (p) cc_final: 0.9174 (p) REVERT: As 197 MET cc_start: 0.8369 (tpp) cc_final: 0.7931 (tpp) REVERT: At 109 GLN cc_start: 0.8231 (pp30) cc_final: 0.7886 (pp30) REVERT: At 159 ASN cc_start: 0.7992 (m-40) cc_final: 0.7741 (m110) REVERT: At 202 ASP cc_start: 0.7918 (m-30) cc_final: 0.6962 (t0) REVERT: At 210 MET cc_start: 0.8191 (tmm) cc_final: 0.7848 (tmm) REVERT: Au 109 GLN cc_start: 0.8609 (pp30) cc_final: 0.8339 (pp30) REVERT: Au 152 LEU cc_start: 0.8764 (tp) cc_final: 0.8503 (tt) REVERT: Au 158 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7086 (mt-10) REVERT: Au 164 ASP cc_start: 0.8027 (t0) cc_final: 0.7817 (m-30) REVERT: Au 166 ASN cc_start: 0.8818 (p0) cc_final: 0.8421 (p0) REVERT: Av 114 GLN cc_start: 0.8502 (tp40) cc_final: 0.7894 (tp40) REVERT: Av 141 ASP cc_start: 0.8126 (p0) cc_final: 0.7910 (p0) REVERT: Av 152 LEU cc_start: 0.8219 (tt) cc_final: 0.7877 (tt) REVERT: Av 205 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8236 (tm-30) REVERT: Aw 141 ASP cc_start: 0.7540 (p0) cc_final: 0.7218 (p0) REVERT: Aw 156 CYS cc_start: 0.8915 (m) cc_final: 0.8650 (t) REVERT: Aw 202 ASP cc_start: 0.8158 (m-30) cc_final: 0.7943 (m-30) REVERT: Ax 80 VAL cc_start: 0.9051 (t) cc_final: 0.8777 (p) REVERT: Ax 83 LYS cc_start: 0.8483 (tppp) cc_final: 0.8216 (tppt) REVERT: Ax 141 ASP cc_start: 0.8021 (p0) cc_final: 0.7682 (p0) REVERT: Ax 156 CYS cc_start: 0.8969 (m) cc_final: 0.8643 (t) REVERT: Ax 173 ASP cc_start: 0.7336 (t0) cc_final: 0.7102 (t0) REVERT: Ax 209 GLU cc_start: 0.8667 (tt0) cc_final: 0.8249 (tt0) REVERT: Ay 128 GLN cc_start: 0.8516 (tt0) cc_final: 0.8261 (tt0) REVERT: Ay 141 ASP cc_start: 0.7710 (p0) cc_final: 0.7499 (p0) REVERT: Ay 173 ASP cc_start: 0.7318 (t70) cc_final: 0.6975 (t0) REVERT: Ay 209 GLU cc_start: 0.8917 (pp20) cc_final: 0.8520 (pp20) REVERT: Az 81 ILE cc_start: 0.9095 (mp) cc_final: 0.8728 (mm) REVERT: Az 95 MET cc_start: 0.8361 (mtp) cc_final: 0.8091 (mtt) REVERT: Az 158 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8128 (mm-30) REVERT: Az 161 THR cc_start: 0.9082 (p) cc_final: 0.8745 (p) REVERT: Az 173 ASP cc_start: 0.7225 (t0) cc_final: 0.6900 (t0) REVERT: Az 183 LYS cc_start: 0.9170 (tttm) cc_final: 0.8950 (ptmm) REVERT: Az 230 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7210 (pttt) REVERT: Ba 183 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8832 (tttm) REVERT: Ba 228 ASN cc_start: 0.8230 (p0) cc_final: 0.7871 (p0) REVERT: Ba 232 LEU cc_start: 0.8845 (mp) cc_final: 0.8240 (tt) outliers start: 1 outliers final: 0 residues processed: 1609 average time/residue: 0.2233 time to fit residues: 604.9477 Evaluate side-chains 1403 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1403 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 366 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 334 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 159 ASN Af 159 ASN Ag 159 ASN Ag 199 HIS ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 159 ASN Ak 159 ASN Al 159 ASN An 243 ASN Ap 159 ASN Au 126 GLN Av 126 GLN Ax 159 ASN Ay 159 ASN Az 159 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085308 restraints weight = 69306.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.087188 restraints weight = 50063.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.088543 restraints weight = 39307.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089595 restraints weight = 32683.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.090331 restraints weight = 28361.606| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.8931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40770 Z= 0.226 Angle : 0.703 8.714 55107 Z= 0.366 Chirality : 0.044 0.238 5697 Planarity : 0.005 0.083 7263 Dihedral : 4.913 26.384 5373 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.02 % Allowed : 1.50 % Favored : 98.48 % 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: -0.77 (0.13), residues: 4752 helix: -0.45 (0.12), residues: 2106 sheet: -2.35 (0.32), residues: 270 loop : -0.15 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAf 211 TYR 0.026 0.002 TYRAx 110 PHE 0.022 0.002 PHEAo 200 TRP 0.015 0.002 TRPAw 130 HIS 0.009 0.001 HISAy 199 Details of bonding type rmsd covalent geometry : bond 0.00528 (40770) covalent geometry : angle 0.70322 (55107) hydrogen bonds : bond 0.04350 ( 1377) hydrogen bonds : angle 4.60170 ( 3726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1598 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1597 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 LYS cc_start: 0.8406 (tppt) cc_final: 0.8155 (mmtt) REVERT: Aa 109 GLN cc_start: 0.8592 (pp30) cc_final: 0.8357 (pp30) REVERT: Aa 111 LYS cc_start: 0.8810 (mttt) cc_final: 0.8230 (tptt) REVERT: Aa 139 ASP cc_start: 0.7854 (m-30) cc_final: 0.7558 (t70) REVERT: Aa 159 ASN cc_start: 0.8598 (m-40) cc_final: 0.8331 (m110) REVERT: Aa 183 LYS cc_start: 0.9247 (tttp) cc_final: 0.8951 (ttpp) REVERT: Aa 202 ASP cc_start: 0.7854 (m-30) cc_final: 0.6850 (t0) REVERT: Aa 205 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7455 (tm-30) REVERT: Aa 227 LEU cc_start: 0.8861 (tp) cc_final: 0.8594 (tp) REVERT: Aa 230 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7466 (pttt) REVERT: Aa 232 LEU cc_start: 0.8904 (mp) cc_final: 0.8149 (tt) REVERT: Ab 139 ASP cc_start: 0.7860 (m-30) cc_final: 0.7453 (t70) REVERT: Ab 158 GLU cc_start: 0.8858 (tp30) cc_final: 0.8144 (tp30) REVERT: Ab 208 ILE cc_start: 0.8405 (tt) cc_final: 0.8165 (tt) REVERT: Ac 109 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8561 (tm-30) REVERT: Ac 139 ASP cc_start: 0.7805 (m-30) cc_final: 0.7307 (t0) REVERT: Ad 139 ASP cc_start: 0.8046 (p0) cc_final: 0.7795 (p0) REVERT: Ad 158 GLU cc_start: 0.8188 (tt0) cc_final: 0.7626 (tt0) REVERT: Ae 161 THR cc_start: 0.9147 (p) cc_final: 0.8885 (p) REVERT: Ae 172 VAL cc_start: 0.9356 (t) cc_final: 0.8556 (t) REVERT: Ae 173 ASP cc_start: 0.7617 (t70) cc_final: 0.7367 (t0) REVERT: Ae 197 MET cc_start: 0.8993 (mmm) cc_final: 0.8761 (tpp) REVERT: Af 128 GLN cc_start: 0.8776 (tt0) cc_final: 0.8216 (tt0) REVERT: Af 161 THR cc_start: 0.8813 (m) cc_final: 0.8582 (p) REVERT: Ag 159 ASN cc_start: 0.8652 (m-40) cc_final: 0.8338 (m110) REVERT: Ag 161 THR cc_start: 0.9182 (p) cc_final: 0.8856 (p) REVERT: Ag 173 ASP cc_start: 0.7225 (t70) cc_final: 0.6748 (t0) REVERT: Ag 197 MET cc_start: 0.8957 (tpp) cc_final: 0.8569 (tpp) REVERT: Ag 209 GLU cc_start: 0.8717 (pp20) cc_final: 0.8175 (pp20) REVERT: Ag 232 LEU cc_start: 0.9018 (mp) cc_final: 0.8230 (tt) REVERT: Ah 159 ASN cc_start: 0.8337 (m-40) cc_final: 0.8128 (m110) REVERT: Ah 161 THR cc_start: 0.9313 (p) cc_final: 0.9085 (p) REVERT: Ah 229 ASP cc_start: 0.8377 (m-30) cc_final: 0.7502 (t0) REVERT: Ai 109 GLN cc_start: 0.8261 (pp30) cc_final: 0.7926 (pp30) REVERT: Ai 229 ASP cc_start: 0.8549 (m-30) cc_final: 0.7630 (t0) REVERT: Aj 109 GLN cc_start: 0.8276 (pp30) cc_final: 0.8026 (pp30) REVERT: Aj 202 ASP cc_start: 0.7845 (m-30) cc_final: 0.7144 (t0) REVERT: Aj 205 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8099 (tm-30) REVERT: Ak 91 MET cc_start: 0.7731 (mmp) cc_final: 0.6166 (mmp) REVERT: Ak 109 GLN cc_start: 0.8774 (pp30) cc_final: 0.8312 (pp30) REVERT: Ak 110 TYR cc_start: 0.8861 (t80) cc_final: 0.8635 (t80) REVERT: Ak 156 CYS cc_start: 0.9096 (m) cc_final: 0.8891 (t) REVERT: Ak 202 ASP cc_start: 0.7902 (m-30) cc_final: 0.6992 (t0) REVERT: Ak 227 LEU cc_start: 0.9107 (tp) cc_final: 0.8800 (tp) REVERT: Ak 232 LEU cc_start: 0.8682 (mp) cc_final: 0.7882 (tt) REVERT: Al 210 MET cc_start: 0.8349 (tmm) cc_final: 0.7740 (tmm) REVERT: Am 156 CYS cc_start: 0.9211 (m) cc_final: 0.8745 (t) REVERT: Am 173 ASP cc_start: 0.7441 (t70) cc_final: 0.7234 (t0) REVERT: Am 197 MET cc_start: 0.9201 (mmm) cc_final: 0.8621 (mmm) REVERT: An 109 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8406 (tm-30) REVERT: An 116 ASP cc_start: 0.8068 (m-30) cc_final: 0.7626 (m-30) REVERT: An 208 ILE cc_start: 0.8788 (tt) cc_final: 0.8513 (tt) REVERT: Ao 159 ASN cc_start: 0.8618 (m-40) cc_final: 0.8387 (m110) REVERT: Ao 161 THR cc_start: 0.8956 (p) cc_final: 0.8669 (p) REVERT: Ap 156 CYS cc_start: 0.8883 (m) cc_final: 0.8562 (t) REVERT: Ap 161 THR cc_start: 0.9205 (p) cc_final: 0.8989 (p) REVERT: Ap 173 ASP cc_start: 0.7181 (t70) cc_final: 0.6888 (t0) REVERT: Ap 228 ASN cc_start: 0.8714 (p0) cc_final: 0.8204 (p0) REVERT: Ap 230 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7419 (pttt) REVERT: Aq 83 LYS cc_start: 0.8916 (tptt) cc_final: 0.8678 (tppt) REVERT: Aq 84 LEU cc_start: 0.8248 (tp) cc_final: 0.7937 (tp) REVERT: Aq 114 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7480 (tm-30) REVERT: Aq 159 ASN cc_start: 0.8397 (m-40) cc_final: 0.7970 (m110) REVERT: Aq 173 ASP cc_start: 0.7417 (t0) cc_final: 0.7074 (t0) REVERT: Aq 230 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7612 (pttt) REVERT: Ar 141 ASP cc_start: 0.7483 (p0) cc_final: 0.7273 (p0) REVERT: Ar 158 GLU cc_start: 0.8571 (tp30) cc_final: 0.8170 (tp30) REVERT: Ar 177 GLN cc_start: 0.8436 (tt0) cc_final: 0.8073 (tt0) REVERT: Ar 197 MET cc_start: 0.9103 (tpp) cc_final: 0.8771 (mmm) REVERT: Ar 228 ASN cc_start: 0.8596 (p0) cc_final: 0.8348 (p0) REVERT: As 83 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8621 (tppt) REVERT: As 159 ASN cc_start: 0.8640 (m-40) cc_final: 0.8366 (m110) REVERT: As 177 GLN cc_start: 0.8507 (tt0) cc_final: 0.8260 (tt0) REVERT: At 109 GLN cc_start: 0.8391 (pp30) cc_final: 0.7967 (pp30) REVERT: At 197 MET cc_start: 0.8792 (mmm) cc_final: 0.8420 (tpp) REVERT: At 202 ASP cc_start: 0.8054 (m-30) cc_final: 0.7150 (t0) REVERT: At 229 ASP cc_start: 0.7941 (m-30) cc_final: 0.7280 (t0) REVERT: Au 109 GLN cc_start: 0.8703 (pp30) cc_final: 0.8076 (pp30) REVERT: Au 137 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8299 (tm-30) REVERT: Au 158 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7314 (mt-10) REVERT: Au 197 MET cc_start: 0.8583 (tpp) cc_final: 0.8371 (tpp) REVERT: Au 209 GLU cc_start: 0.8502 (mt-10) cc_final: 0.7098 (mt-10) REVERT: Av 114 GLN cc_start: 0.8770 (tp40) cc_final: 0.8291 (tp40) REVERT: Aw 141 ASP cc_start: 0.7555 (p0) cc_final: 0.7267 (p0) REVERT: Aw 156 CYS cc_start: 0.9006 (m) cc_final: 0.8680 (t) REVERT: Ax 128 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8693 (tp40) REVERT: Ax 141 ASP cc_start: 0.7981 (p0) cc_final: 0.7699 (p0) REVERT: Ax 156 CYS cc_start: 0.9037 (m) cc_final: 0.8782 (t) REVERT: Ax 161 THR cc_start: 0.9094 (p) cc_final: 0.8862 (p) REVERT: Ax 173 ASP cc_start: 0.7613 (t0) cc_final: 0.7371 (t0) REVERT: Ax 209 GLU cc_start: 0.8753 (tt0) cc_final: 0.8292 (tt0) REVERT: Ay 128 GLN cc_start: 0.8655 (tt0) cc_final: 0.8365 (tt0) REVERT: Ay 161 THR cc_start: 0.9224 (m) cc_final: 0.8916 (p) REVERT: Ay 173 ASP cc_start: 0.7389 (t70) cc_final: 0.6990 (t0) REVERT: Ay 202 ASP cc_start: 0.7974 (m-30) cc_final: 0.7699 (t0) REVERT: Ay 209 GLU cc_start: 0.8972 (pp20) cc_final: 0.8501 (pp20) REVERT: Ay 230 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7316 (tttt) REVERT: Az 81 ILE cc_start: 0.9266 (mp) cc_final: 0.8874 (mm) REVERT: Az 91 MET cc_start: 0.7710 (mmp) cc_final: 0.5862 (mmt) REVERT: Az 95 MET cc_start: 0.8523 (mtp) cc_final: 0.8131 (mtt) REVERT: Az 159 ASN cc_start: 0.8633 (m-40) cc_final: 0.8420 (m110) REVERT: Az 161 THR cc_start: 0.9224 (p) cc_final: 0.8841 (p) REVERT: Az 173 ASP cc_start: 0.7430 (t0) cc_final: 0.7177 (t0) REVERT: Az 183 LYS cc_start: 0.9192 (tttm) cc_final: 0.8937 (ptmm) REVERT: Az 230 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7590 (tttt) REVERT: Az 232 LEU cc_start: 0.8867 (mp) cc_final: 0.8018 (tt) REVERT: Ba 228 ASN cc_start: 0.8320 (p0) cc_final: 0.7956 (p0) REVERT: Ba 232 LEU cc_start: 0.8916 (mp) cc_final: 0.8138 (tt) outliers start: 1 outliers final: 0 residues processed: 1598 average time/residue: 0.2245 time to fit residues: 598.7563 Evaluate side-chains 1341 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1341 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 274 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 447 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 384 optimal weight: 0.6980 chunk 377 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 421 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 159 ASN ** Ac 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 132 ASN Ae 114 GLN Ae 159 ASN ** Ag 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 256 GLN ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 132 ASN ** Ai 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 159 ASN Ak 159 ASN Aq 248 ASN At 159 ASN ** Au 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 126 GLN Av 126 GLN Ax 159 ASN Ay 159 ASN ** Ay 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 128 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.086137 restraints weight = 68341.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.088217 restraints weight = 48093.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.089729 restraints weight = 37110.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090841 restraints weight = 30545.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091689 restraints weight = 26201.760| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.9302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 40770 Z= 0.172 Angle : 0.656 7.627 55107 Z= 0.340 Chirality : 0.042 0.269 5697 Planarity : 0.005 0.085 7263 Dihedral : 4.795 24.639 5373 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % Favored : 98.27 % 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: -0.85 (0.13), residues: 4752 helix: -0.50 (0.12), residues: 2106 sheet: -2.48 (0.31), residues: 270 loop : -0.20 (0.14), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGAn 211 TYR 0.045 0.002 TYRAe 110 PHE 0.019 0.002 PHEAv 237 TRP 0.014 0.002 TRPAw 130 HIS 0.008 0.001 HISAn 199 Details of bonding type rmsd covalent geometry : bond 0.00404 (40770) covalent geometry : angle 0.65566 (55107) hydrogen bonds : bond 0.03863 ( 1377) hydrogen bonds : angle 4.50650 ( 3726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1587 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 LYS cc_start: 0.8409 (tppt) cc_final: 0.8181 (mmtt) REVERT: Aa 109 GLN cc_start: 0.8610 (pp30) cc_final: 0.8372 (pp30) REVERT: Aa 111 LYS cc_start: 0.8791 (mttt) cc_final: 0.8212 (tptt) REVERT: Aa 139 ASP cc_start: 0.7825 (m-30) cc_final: 0.7516 (t0) REVERT: Aa 183 LYS cc_start: 0.9151 (tttp) cc_final: 0.8923 (ttpp) REVERT: Aa 202 ASP cc_start: 0.7781 (m-30) cc_final: 0.6462 (t0) REVERT: Aa 205 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7463 (tm-30) REVERT: Aa 209 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8301 (mt-10) REVERT: Aa 210 MET cc_start: 0.8268 (tmm) cc_final: 0.7957 (tmm) REVERT: Aa 227 LEU cc_start: 0.8865 (tp) cc_final: 0.8610 (tp) REVERT: Aa 230 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7425 (pttt) REVERT: Aa 232 LEU cc_start: 0.8914 (mp) cc_final: 0.8163 (tt) REVERT: Ab 139 ASP cc_start: 0.7807 (m-30) cc_final: 0.7428 (t70) REVERT: Ab 232 LEU cc_start: 0.8886 (mp) cc_final: 0.8213 (tp) REVERT: Ac 83 LYS cc_start: 0.9089 (tptp) cc_final: 0.8648 (tppt) REVERT: Ac 95 MET cc_start: 0.7991 (mpp) cc_final: 0.7694 (mtt) REVERT: Ad 158 GLU cc_start: 0.8153 (tt0) cc_final: 0.7658 (tt0) REVERT: Ad 161 THR cc_start: 0.9074 (p) cc_final: 0.8710 (p) REVERT: Ad 183 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8676 (ttpp) REVERT: Ae 159 ASN cc_start: 0.8499 (m-40) cc_final: 0.8259 (m110) REVERT: Ae 161 THR cc_start: 0.9105 (p) cc_final: 0.8777 (p) REVERT: Ae 173 ASP cc_start: 0.7575 (t70) cc_final: 0.7312 (t0) REVERT: Ae 197 MET cc_start: 0.8930 (mmm) cc_final: 0.8706 (tpp) REVERT: Af 107 LEU cc_start: 0.9040 (tp) cc_final: 0.8695 (tp) REVERT: Af 128 GLN cc_start: 0.8713 (tt0) cc_final: 0.8164 (tt0) REVERT: Af 161 THR cc_start: 0.8742 (m) cc_final: 0.8446 (p) REVERT: Af 182 LEU cc_start: 0.9404 (tp) cc_final: 0.9063 (tp) REVERT: Ag 152 LEU cc_start: 0.9026 (tp) cc_final: 0.8689 (tt) REVERT: Ag 161 THR cc_start: 0.9071 (p) cc_final: 0.8738 (p) REVERT: Ag 209 GLU cc_start: 0.8635 (pp20) cc_final: 0.8178 (pp20) REVERT: Ag 232 LEU cc_start: 0.9011 (mp) cc_final: 0.8219 (tt) REVERT: Ah 109 GLN cc_start: 0.8360 (pt0) cc_final: 0.7716 (pp30) REVERT: Ah 161 THR cc_start: 0.9232 (p) cc_final: 0.9011 (p) REVERT: Ah 172 VAL cc_start: 0.8735 (m) cc_final: 0.7891 (m) REVERT: Ah 177 GLN cc_start: 0.8449 (tt0) cc_final: 0.8184 (tt0) REVERT: Ai 109 GLN cc_start: 0.8343 (pp30) cc_final: 0.7943 (pp30) REVERT: Ai 158 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8189 (mm-30) REVERT: Ai 177 GLN cc_start: 0.8465 (tt0) cc_final: 0.8215 (tt0) REVERT: Ai 229 ASP cc_start: 0.8488 (m-30) cc_final: 0.7571 (t0) REVERT: Aj 171 MET cc_start: 0.8302 (mmm) cc_final: 0.7925 (mmm) REVERT: Aj 205 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7937 (tm-30) REVERT: Aj 214 ASP cc_start: 0.8645 (m-30) cc_final: 0.8425 (m-30) REVERT: Ak 109 GLN cc_start: 0.8775 (pp30) cc_final: 0.8568 (pp30) REVERT: Ak 110 TYR cc_start: 0.8890 (t80) cc_final: 0.8644 (t80) REVERT: Ak 202 ASP cc_start: 0.7846 (m-30) cc_final: 0.6963 (t0) REVERT: Ak 227 LEU cc_start: 0.9215 (tp) cc_final: 0.8921 (tp) REVERT: Ak 230 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7550 (pttt) REVERT: Ak 232 LEU cc_start: 0.8558 (mp) cc_final: 0.7761 (tt) REVERT: Al 86 LYS cc_start: 0.8713 (tppp) cc_final: 0.8331 (mtpp) REVERT: Al 158 GLU cc_start: 0.8527 (tp30) cc_final: 0.8252 (tp30) REVERT: Al 209 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8479 (mt-10) REVERT: Al 210 MET cc_start: 0.8410 (tmm) cc_final: 0.7832 (tmm) REVERT: Am 177 GLN cc_start: 0.8107 (mt0) cc_final: 0.6800 (mt0) REVERT: Am 209 GLU cc_start: 0.8554 (tt0) cc_final: 0.8255 (mt-10) REVERT: An 109 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8364 (tm-30) REVERT: Ao 108 ILE cc_start: 0.9031 (tp) cc_final: 0.8698 (tp) REVERT: Ao 159 ASN cc_start: 0.8471 (m-40) cc_final: 0.8112 (m110) REVERT: Ao 161 THR cc_start: 0.8977 (p) cc_final: 0.8670 (p) REVERT: Ap 156 CYS cc_start: 0.8898 (m) cc_final: 0.8501 (t) REVERT: Ap 161 THR cc_start: 0.9120 (p) cc_final: 0.8887 (p) REVERT: Ap 173 ASP cc_start: 0.7194 (t70) cc_final: 0.6938 (t0) REVERT: Ap 228 ASN cc_start: 0.8688 (p0) cc_final: 0.8170 (p0) REVERT: Ap 230 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7394 (pttt) REVERT: Aq 83 LYS cc_start: 0.8942 (tptt) cc_final: 0.8734 (tppt) REVERT: Aq 84 LEU cc_start: 0.8146 (tp) cc_final: 0.7910 (tp) REVERT: Aq 114 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7656 (tm-30) REVERT: Aq 159 ASN cc_start: 0.8259 (m-40) cc_final: 0.7978 (m110) REVERT: Aq 171 MET cc_start: 0.7651 (mtm) cc_final: 0.7237 (mtm) REVERT: Aq 173 ASP cc_start: 0.7316 (t0) cc_final: 0.7018 (t0) REVERT: Aq 230 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7548 (pttt) REVERT: Ar 86 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8383 (mtpp) REVERT: Ar 158 GLU cc_start: 0.8586 (tp30) cc_final: 0.8246 (tp30) REVERT: Ar 161 THR cc_start: 0.9357 (p) cc_final: 0.9059 (p) REVERT: Ar 177 GLN cc_start: 0.8497 (tt0) cc_final: 0.8032 (tt0) REVERT: As 159 ASN cc_start: 0.8558 (m-40) cc_final: 0.8316 (m110) REVERT: At 83 LYS cc_start: 0.8979 (tppt) cc_final: 0.8668 (tppt) REVERT: At 109 GLN cc_start: 0.8408 (pp30) cc_final: 0.8104 (pp30) REVERT: At 110 TYR cc_start: 0.8801 (t80) cc_final: 0.8339 (t80) REVERT: At 116 ASP cc_start: 0.7848 (m-30) cc_final: 0.7553 (m-30) REVERT: At 197 MET cc_start: 0.8869 (mmm) cc_final: 0.8484 (tpp) REVERT: At 202 ASP cc_start: 0.7976 (m-30) cc_final: 0.7107 (t0) REVERT: At 229 ASP cc_start: 0.8046 (m-30) cc_final: 0.7438 (t0) REVERT: Au 109 GLN cc_start: 0.8649 (pp30) cc_final: 0.8090 (pp30) REVERT: Au 110 TYR cc_start: 0.8950 (t80) cc_final: 0.8363 (t80) REVERT: Au 137 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8293 (tm-30) REVERT: Au 209 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7803 (mt-10) REVERT: Av 114 GLN cc_start: 0.8770 (tp40) cc_final: 0.8234 (tm-30) REVERT: Av 173 ASP cc_start: 0.7528 (t70) cc_final: 0.7322 (t70) REVERT: Av 183 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8966 (ptmm) REVERT: Av 209 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7273 (mt-10) REVERT: Aw 141 ASP cc_start: 0.7394 (p0) cc_final: 0.7145 (p0) REVERT: Aw 156 CYS cc_start: 0.8950 (m) cc_final: 0.8505 (t) REVERT: Ax 116 ASP cc_start: 0.7990 (m-30) cc_final: 0.7405 (m-30) REVERT: Ax 141 ASP cc_start: 0.7849 (p0) cc_final: 0.7622 (p0) REVERT: Ax 156 CYS cc_start: 0.9125 (m) cc_final: 0.8739 (t) REVERT: Ax 161 THR cc_start: 0.9088 (p) cc_final: 0.8850 (p) REVERT: Ax 209 GLU cc_start: 0.8675 (tt0) cc_final: 0.8317 (tt0) REVERT: Ax 223 LEU cc_start: 0.8722 (mm) cc_final: 0.8339 (mt) REVERT: Ay 128 GLN cc_start: 0.8614 (tt0) cc_final: 0.8373 (tt0) REVERT: Ay 158 GLU cc_start: 0.7722 (tt0) cc_final: 0.7198 (tt0) REVERT: Ay 159 ASN cc_start: 0.8570 (m-40) cc_final: 0.8199 (m110) REVERT: Ay 161 THR cc_start: 0.9180 (m) cc_final: 0.8840 (p) REVERT: Ay 173 ASP cc_start: 0.7221 (t70) cc_final: 0.6913 (t0) REVERT: Ay 209 GLU cc_start: 0.8933 (pp20) cc_final: 0.8510 (pp20) REVERT: Ay 228 ASN cc_start: 0.8522 (p0) cc_final: 0.8198 (p0) REVERT: Ay 230 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7398 (tttt) REVERT: Az 81 ILE cc_start: 0.9215 (mp) cc_final: 0.8853 (mm) REVERT: Az 107 LEU cc_start: 0.9130 (tp) cc_final: 0.8889 (tp) REVERT: Az 161 THR cc_start: 0.9149 (p) cc_final: 0.8789 (p) REVERT: Az 173 ASP cc_start: 0.7478 (t0) cc_final: 0.7133 (t0) REVERT: Az 183 LYS cc_start: 0.9189 (tttm) cc_final: 0.8937 (ptmm) REVERT: Az 230 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7507 (tttt) REVERT: Ba 92 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8499 (ttm-80) REVERT: Ba 147 ILE cc_start: 0.9227 (mm) cc_final: 0.8978 (tp) REVERT: Ba 228 ASN cc_start: 0.8280 (p0) cc_final: 0.7680 (p0) REVERT: Ba 230 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7498 (pttt) REVERT: Ba 232 LEU cc_start: 0.8838 (mp) cc_final: 0.8101 (tt) outliers start: 2 outliers final: 0 residues processed: 1588 average time/residue: 0.2300 time to fit residues: 612.9305 Evaluate side-chains 1353 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1353 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 381 optimal weight: 0.9980 chunk 297 optimal weight: 0.4980 chunk 274 optimal weight: 10.0000 chunk 414 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 396 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 444 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 159 ASN Ac 159 ASN Ae 114 GLN Af 159 ASN Ag 159 ASN ** Ag 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 128 GLN Ah 159 ASN Ah 248 ASN Ai 159 ASN Ai 248 ASN ** Aj 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 159 ASN Ak 159 ASN An 159 ASN ** Ao 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 126 GLN Av 126 GLN ** Az 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 159 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089643 restraints weight = 66946.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091831 restraints weight = 46521.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093394 restraints weight = 35529.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094569 restraints weight = 29034.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.095350 restraints weight = 24756.440| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.9575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40770 Z= 0.134 Angle : 0.648 8.752 55107 Z= 0.333 Chirality : 0.041 0.250 5697 Planarity : 0.004 0.054 7263 Dihedral : 4.604 24.728 5373 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.07 % Allowed : 0.92 % Favored : 99.01 % 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: -0.72 (0.13), residues: 4752 helix: -0.46 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.38 (0.13), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAs 211 TYR 0.037 0.001 TYRAo 110 PHE 0.023 0.001 PHEAn 200 TRP 0.016 0.002 TRPAh 130 HIS 0.009 0.001 HISAh 199 Details of bonding type rmsd covalent geometry : bond 0.00315 (40770) covalent geometry : angle 0.64802 (55107) hydrogen bonds : bond 0.03635 ( 1377) hydrogen bonds : angle 4.41785 ( 3726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1578 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 109 GLN cc_start: 0.8593 (pp30) cc_final: 0.8389 (pp30) REVERT: Aa 111 LYS cc_start: 0.8780 (mttt) cc_final: 0.8246 (tptt) REVERT: Aa 183 LYS cc_start: 0.9137 (tttp) cc_final: 0.8850 (ttpp) REVERT: Aa 205 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7241 (tm-30) REVERT: Aa 210 MET cc_start: 0.8143 (tmm) cc_final: 0.7912 (tmm) REVERT: Aa 227 LEU cc_start: 0.8857 (tp) cc_final: 0.8635 (tp) REVERT: Aa 230 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7401 (pttt) REVERT: Aa 232 LEU cc_start: 0.8925 (mp) cc_final: 0.8173 (tt) REVERT: Ab 158 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8190 (tp30) REVERT: Ab 232 LEU cc_start: 0.8975 (mp) cc_final: 0.8357 (tp) REVERT: Ac 83 LYS cc_start: 0.9025 (tptp) cc_final: 0.8624 (tppt) REVERT: Ac 95 MET cc_start: 0.7951 (mpp) cc_final: 0.7531 (mtt) REVERT: Ac 113 ASP cc_start: 0.7918 (t70) cc_final: 0.7307 (t0) REVERT: Ac 139 ASP cc_start: 0.7797 (m-30) cc_final: 0.7379 (t0) REVERT: Ac 238 ASP cc_start: 0.8155 (t70) cc_final: 0.7695 (t0) REVERT: Ad 145 MET cc_start: 0.8973 (tpp) cc_final: 0.8770 (tpp) REVERT: Ad 158 GLU cc_start: 0.8056 (tt0) cc_final: 0.7483 (tt0) REVERT: Ad 161 THR cc_start: 0.9015 (p) cc_final: 0.8667 (p) REVERT: Ad 183 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8708 (ttpp) REVERT: Ad 230 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7297 (ttpt) REVERT: Ae 111 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8422 (mtmt) REVERT: Ae 161 THR cc_start: 0.8958 (p) cc_final: 0.8636 (p) REVERT: Ae 173 ASP cc_start: 0.7654 (t70) cc_final: 0.7431 (t0) REVERT: Ae 223 LEU cc_start: 0.8748 (mm) cc_final: 0.8513 (mt) REVERT: Af 91 MET cc_start: 0.7099 (mmp) cc_final: 0.6886 (mmt) REVERT: Af 128 GLN cc_start: 0.8622 (tt0) cc_final: 0.8095 (tt0) REVERT: Ag 152 LEU cc_start: 0.9084 (tp) cc_final: 0.8745 (tt) REVERT: Ag 159 ASN cc_start: 0.8337 (m-40) cc_final: 0.7931 (m110) REVERT: Ag 161 THR cc_start: 0.8973 (p) cc_final: 0.8692 (p) REVERT: Ag 209 GLU cc_start: 0.8661 (pp20) cc_final: 0.8147 (pp20) REVERT: Ag 232 LEU cc_start: 0.9015 (mp) cc_final: 0.8192 (tt) REVERT: Ah 139 ASP cc_start: 0.7634 (m-30) cc_final: 0.7383 (t0) REVERT: Ah 161 THR cc_start: 0.9202 (p) cc_final: 0.8975 (p) REVERT: Ah 172 VAL cc_start: 0.8944 (m) cc_final: 0.8348 (m) REVERT: Ai 109 GLN cc_start: 0.8254 (pp30) cc_final: 0.7907 (pp30) REVERT: Ai 158 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8090 (mm-30) REVERT: Ai 159 ASN cc_start: 0.8098 (m-40) cc_final: 0.7820 (m110) REVERT: Ai 232 LEU cc_start: 0.8852 (mt) cc_final: 0.7958 (tt) REVERT: Aj 139 ASP cc_start: 0.7530 (m-30) cc_final: 0.7260 (t0) REVERT: Aj 159 ASN cc_start: 0.8251 (m-40) cc_final: 0.7923 (m110) REVERT: Aj 205 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7745 (tm-30) REVERT: Ak 109 GLN cc_start: 0.8665 (pp30) cc_final: 0.8459 (pp30) REVERT: Ak 158 GLU cc_start: 0.8604 (tp30) cc_final: 0.8350 (tp30) REVERT: Ak 210 MET cc_start: 0.8160 (tmm) cc_final: 0.7622 (tmm) REVERT: Al 86 LYS cc_start: 0.8685 (tppp) cc_final: 0.8235 (mtpp) REVERT: Al 183 LYS cc_start: 0.9264 (ttpp) cc_final: 0.9035 (tttm) REVERT: Al 209 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8522 (mt-10) REVERT: Al 210 MET cc_start: 0.8507 (tmm) cc_final: 0.7944 (tmm) REVERT: Am 156 CYS cc_start: 0.9037 (m) cc_final: 0.8729 (t) REVERT: Am 197 MET cc_start: 0.9128 (tpp) cc_final: 0.8906 (tpp) REVERT: An 196 CYS cc_start: 0.8634 (t) cc_final: 0.8413 (t) REVERT: An 210 MET cc_start: 0.8720 (tmm) cc_final: 0.8323 (tmm) REVERT: Ao 159 ASN cc_start: 0.8333 (m-40) cc_final: 0.7717 (m110) REVERT: Ao 161 THR cc_start: 0.8872 (p) cc_final: 0.8608 (p) REVERT: Ap 156 CYS cc_start: 0.8898 (m) cc_final: 0.8411 (t) REVERT: Ap 161 THR cc_start: 0.9027 (p) cc_final: 0.8771 (p) REVERT: Ap 172 VAL cc_start: 0.8606 (t) cc_final: 0.7285 (t) REVERT: Ap 173 ASP cc_start: 0.7123 (t70) cc_final: 0.6902 (t0) REVERT: Ap 197 MET cc_start: 0.8948 (tpp) cc_final: 0.8273 (tpt) REVERT: Ap 228 ASN cc_start: 0.8646 (p0) cc_final: 0.8166 (p0) REVERT: Ap 230 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7374 (pttt) REVERT: Aq 114 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7639 (tm-30) REVERT: Aq 139 ASP cc_start: 0.7537 (t0) cc_final: 0.7314 (t0) REVERT: Aq 159 ASN cc_start: 0.8127 (m-40) cc_final: 0.7707 (m110) REVERT: Aq 173 ASP cc_start: 0.7142 (t0) cc_final: 0.6812 (t0) REVERT: Aq 230 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7407 (pttt) REVERT: Ar 158 GLU cc_start: 0.8344 (tp30) cc_final: 0.8035 (tp30) REVERT: Ar 161 THR cc_start: 0.9212 (p) cc_final: 0.8966 (p) REVERT: Ar 171 MET cc_start: 0.8361 (mmp) cc_final: 0.8128 (mmp) REVERT: Ar 177 GLN cc_start: 0.8376 (tt0) cc_final: 0.8143 (tt0) REVERT: Ar 183 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8767 (ttpp) REVERT: Ar 196 CYS cc_start: 0.8875 (t) cc_final: 0.8657 (t) REVERT: Ar 232 LEU cc_start: 0.8668 (mt) cc_final: 0.7881 (tt) REVERT: As 81 ILE cc_start: 0.9269 (mp) cc_final: 0.8920 (mm) REVERT: As 158 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8168 (mm-30) REVERT: As 159 ASN cc_start: 0.8297 (m-40) cc_final: 0.8039 (m-40) REVERT: As 165 ILE cc_start: 0.9349 (tt) cc_final: 0.9140 (tt) REVERT: At 83 LYS cc_start: 0.8944 (tppt) cc_final: 0.8657 (tppt) REVERT: At 197 MET cc_start: 0.8668 (mmm) cc_final: 0.8354 (tpp) REVERT: At 202 ASP cc_start: 0.7799 (m-30) cc_final: 0.7074 (t0) REVERT: At 229 ASP cc_start: 0.7979 (m-30) cc_final: 0.7346 (t0) REVERT: At 232 LEU cc_start: 0.8752 (mp) cc_final: 0.7989 (tt) REVERT: Au 109 GLN cc_start: 0.8564 (pp30) cc_final: 0.7977 (pp30) REVERT: Au 110 TYR cc_start: 0.8898 (t80) cc_final: 0.8320 (t80) REVERT: Au 205 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7823 (tm-30) REVERT: Au 210 MET cc_start: 0.8259 (tmm) cc_final: 0.7819 (tmm) REVERT: Au 227 LEU cc_start: 0.9071 (tt) cc_final: 0.8819 (tt) REVERT: Au 232 LEU cc_start: 0.9115 (mp) cc_final: 0.8392 (tp) REVERT: Au 235 TYR cc_start: 0.8379 (m-10) cc_final: 0.7573 (m-10) REVERT: Av 152 LEU cc_start: 0.8512 (tt) cc_final: 0.8132 (tt) REVERT: Av 183 LYS cc_start: 0.9219 (ttpp) cc_final: 0.8989 (ptmm) REVERT: Av 235 TYR cc_start: 0.8375 (m-10) cc_final: 0.7899 (m-10) REVERT: Ax 173 ASP cc_start: 0.7290 (t70) cc_final: 0.7059 (t0) REVERT: Ax 209 GLU cc_start: 0.8641 (tt0) cc_final: 0.8312 (tt0) REVERT: Ax 223 LEU cc_start: 0.8702 (mm) cc_final: 0.8396 (mt) REVERT: Ay 114 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7169 (tm-30) REVERT: Ay 158 GLU cc_start: 0.7707 (tt0) cc_final: 0.7497 (tt0) REVERT: Ay 159 ASN cc_start: 0.8260 (m-40) cc_final: 0.7958 (m110) REVERT: Ay 161 THR cc_start: 0.9162 (m) cc_final: 0.8835 (p) REVERT: Ay 173 ASP cc_start: 0.7232 (t70) cc_final: 0.6883 (t0) REVERT: Ay 223 LEU cc_start: 0.8832 (mm) cc_final: 0.8529 (mt) REVERT: Ay 228 ASN cc_start: 0.8452 (p0) cc_final: 0.8137 (p0) REVERT: Ay 230 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7306 (tttt) REVERT: Az 161 THR cc_start: 0.9054 (p) cc_final: 0.8720 (p) REVERT: Az 173 ASP cc_start: 0.7508 (t0) cc_final: 0.7269 (t0) REVERT: Az 183 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8797 (tttp) REVERT: Az 187 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7284 (mt-10) REVERT: Az 230 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7388 (tttt) REVERT: Ba 92 ARG cc_start: 0.8741 (mtp85) cc_final: 0.8493 (ttm-80) REVERT: Ba 161 THR cc_start: 0.9317 (p) cc_final: 0.9053 (p) REVERT: Ba 228 ASN cc_start: 0.8219 (p0) cc_final: 0.7961 (p0) REVERT: Ba 232 LEU cc_start: 0.8787 (mp) cc_final: 0.8147 (tt) outliers start: 3 outliers final: 0 residues processed: 1581 average time/residue: 0.2261 time to fit residues: 601.5189 Evaluate side-chains 1315 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1315 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 427 optimal weight: 6.9990 chunk 82 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 365 optimal weight: 0.7980 chunk 334 optimal weight: 0.0020 chunk 361 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 overall best weight: 0.9770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 159 ASN ** Aa 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 159 ASN Ad 254 HIS Ae 159 ASN ** Af 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 177 GLN Ah 124 HIS ** Ah 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 248 ASN ** Ai 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 159 ASN ** Al 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 199 HIS Ao 128 GLN Aq 132 ASN ** As 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 126 GLN Au 159 ASN Av 126 GLN Aw 177 GLN ** Ax 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 128 GLN ** Ay 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 159 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091419 restraints weight = 67223.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.093677 restraints weight = 46790.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.095294 restraints weight = 35729.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096370 restraints weight = 29151.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097365 restraints weight = 25053.234| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.9759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40770 Z= 0.128 Angle : 0.649 8.203 55107 Z= 0.332 Chirality : 0.041 0.241 5697 Planarity : 0.004 0.053 7263 Dihedral : 4.519 24.372 5373 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.07 % Allowed : 0.55 % Favored : 99.38 % 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: -0.65 (0.12), residues: 4752 helix: -0.37 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.36 (0.13), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAd 211 TYR 0.024 0.001 TYRAc 235 PHE 0.020 0.001 PHEBa 237 TRP 0.015 0.001 TRPAw 130 HIS 0.011 0.001 HISAn 199 Details of bonding type rmsd covalent geometry : bond 0.00299 (40770) covalent geometry : angle 0.64947 (55107) hydrogen bonds : bond 0.03568 ( 1377) hydrogen bonds : angle 4.38669 ( 3726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1522 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 109 GLN cc_start: 0.8610 (pp30) cc_final: 0.8398 (pp30) REVERT: Aa 111 LYS cc_start: 0.8776 (mttt) cc_final: 0.8270 (tptt) REVERT: Aa 139 ASP cc_start: 0.7755 (m-30) cc_final: 0.7477 (t0) REVERT: Aa 161 THR cc_start: 0.8724 (p) cc_final: 0.8405 (p) REVERT: Aa 183 LYS cc_start: 0.9141 (tttp) cc_final: 0.8883 (ttpp) REVERT: Aa 227 LEU cc_start: 0.8902 (tp) cc_final: 0.8645 (tp) REVERT: Aa 230 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7340 (pttt) REVERT: Aa 232 LEU cc_start: 0.8918 (mp) cc_final: 0.8232 (tt) REVERT: Ab 158 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8246 (tp30) REVERT: Ab 227 LEU cc_start: 0.9135 (tp) cc_final: 0.8930 (tp) REVERT: Ab 232 LEU cc_start: 0.8897 (mp) cc_final: 0.8272 (tp) REVERT: Ac 83 LYS cc_start: 0.9006 (tptp) cc_final: 0.8593 (tppt) REVERT: Ac 113 ASP cc_start: 0.7963 (t70) cc_final: 0.7380 (t0) REVERT: Ac 139 ASP cc_start: 0.7675 (m-30) cc_final: 0.7450 (t0) REVERT: Ad 161 THR cc_start: 0.8934 (p) cc_final: 0.8564 (p) REVERT: Ad 183 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8730 (ttpp) REVERT: Ad 230 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7333 (ttpt) REVERT: Ae 161 THR cc_start: 0.8863 (p) cc_final: 0.8553 (p) REVERT: Ae 223 LEU cc_start: 0.8719 (mm) cc_final: 0.8462 (mt) REVERT: Af 128 GLN cc_start: 0.8564 (tt0) cc_final: 0.8080 (tt0) REVERT: Af 182 LEU cc_start: 0.9395 (tp) cc_final: 0.9124 (tp) REVERT: Af 197 MET cc_start: 0.8765 (tpp) cc_final: 0.8530 (mmm) REVERT: Ag 161 THR cc_start: 0.8898 (p) cc_final: 0.8565 (p) REVERT: Ag 197 MET cc_start: 0.8834 (tpp) cc_final: 0.8601 (mmm) REVERT: Ag 209 GLU cc_start: 0.8642 (pp20) cc_final: 0.8149 (pp20) REVERT: Ag 232 LEU cc_start: 0.8953 (mp) cc_final: 0.8172 (tt) REVERT: Ah 109 GLN cc_start: 0.8527 (pp30) cc_final: 0.7999 (pp30) REVERT: Ah 139 ASP cc_start: 0.7703 (m-30) cc_final: 0.7460 (t0) REVERT: Ah 161 THR cc_start: 0.9183 (p) cc_final: 0.8951 (p) REVERT: Ai 109 GLN cc_start: 0.8196 (pp30) cc_final: 0.7778 (pp30) REVERT: Ai 156 CYS cc_start: 0.8975 (m) cc_final: 0.8655 (t) REVERT: Ai 158 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7951 (mm-30) REVERT: Ai 232 LEU cc_start: 0.8798 (mt) cc_final: 0.7986 (tt) REVERT: Aj 159 ASN cc_start: 0.8097 (m-40) cc_final: 0.7808 (m110) REVERT: Aj 197 MET cc_start: 0.8908 (mmm) cc_final: 0.8667 (tpt) REVERT: Ak 109 GLN cc_start: 0.8635 (pp30) cc_final: 0.8377 (pp30) REVERT: Ak 210 MET cc_start: 0.8143 (tmm) cc_final: 0.7670 (tmm) REVERT: Al 209 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8531 (mt-10) REVERT: Al 235 TYR cc_start: 0.8519 (m-10) cc_final: 0.8249 (m-10) REVERT: Am 156 CYS cc_start: 0.8980 (m) cc_final: 0.8624 (t) REVERT: An 158 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7620 (tt0) REVERT: An 172 VAL cc_start: 0.9397 (p) cc_final: 0.8770 (p) REVERT: An 177 GLN cc_start: 0.7771 (mt0) cc_final: 0.6243 (mt0) REVERT: An 183 LYS cc_start: 0.8830 (ttpp) cc_final: 0.8561 (ttpp) REVERT: An 193 LEU cc_start: 0.8313 (tt) cc_final: 0.7852 (tt) REVERT: Ao 158 GLU cc_start: 0.7577 (tt0) cc_final: 0.7131 (tt0) REVERT: Ao 197 MET cc_start: 0.8748 (tpp) cc_final: 0.8522 (tpp) REVERT: Ap 156 CYS cc_start: 0.8845 (m) cc_final: 0.8291 (t) REVERT: Ap 161 THR cc_start: 0.8923 (p) cc_final: 0.8668 (p) REVERT: Ap 171 MET cc_start: 0.7880 (mmm) cc_final: 0.7369 (tpt) REVERT: Ap 172 VAL cc_start: 0.8846 (t) cc_final: 0.8106 (t) REVERT: Ap 197 MET cc_start: 0.8909 (tpp) cc_final: 0.8203 (tpt) REVERT: Aq 114 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7671 (tm-30) REVERT: Aq 159 ASN cc_start: 0.8231 (m-40) cc_final: 0.7877 (m110) REVERT: Aq 173 ASP cc_start: 0.7102 (t0) cc_final: 0.6814 (t0) REVERT: Aq 232 LEU cc_start: 0.8842 (mt) cc_final: 0.7796 (tt) REVERT: Ar 158 GLU cc_start: 0.8216 (tp30) cc_final: 0.8000 (tp30) REVERT: Ar 161 THR cc_start: 0.9207 (p) cc_final: 0.8953 (p) REVERT: Ar 171 MET cc_start: 0.8285 (mmp) cc_final: 0.8011 (mmp) REVERT: Ar 183 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8711 (ttpp) REVERT: Ar 196 CYS cc_start: 0.8851 (t) cc_final: 0.8650 (t) REVERT: Ar 232 LEU cc_start: 0.8630 (mt) cc_final: 0.7862 (tt) REVERT: As 81 ILE cc_start: 0.9275 (mp) cc_final: 0.8955 (mm) REVERT: As 158 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8198 (mm-30) REVERT: As 159 ASN cc_start: 0.8231 (m-40) cc_final: 0.7966 (m110) REVERT: At 83 LYS cc_start: 0.8932 (tppt) cc_final: 0.8717 (tppt) REVERT: At 110 TYR cc_start: 0.8719 (t80) cc_final: 0.8474 (t80) REVERT: At 158 GLU cc_start: 0.8660 (tp30) cc_final: 0.8454 (mm-30) REVERT: At 197 MET cc_start: 0.8702 (mmm) cc_final: 0.8306 (tpp) REVERT: At 232 LEU cc_start: 0.8756 (mp) cc_final: 0.8426 (tp) REVERT: Au 109 GLN cc_start: 0.8502 (pp30) cc_final: 0.7931 (pp30) REVERT: Au 110 TYR cc_start: 0.8875 (t80) cc_final: 0.8265 (t80) REVERT: Au 173 ASP cc_start: 0.7296 (t70) cc_final: 0.6913 (t70) REVERT: Au 210 MET cc_start: 0.8409 (tmm) cc_final: 0.7914 (tmm) REVERT: Au 227 LEU cc_start: 0.9051 (tt) cc_final: 0.8786 (tp) REVERT: Au 232 LEU cc_start: 0.9004 (mp) cc_final: 0.8307 (tp) REVERT: Av 152 LEU cc_start: 0.8480 (tt) cc_final: 0.8095 (tt) REVERT: Av 183 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8952 (ptmm) REVERT: Av 209 GLU cc_start: 0.8436 (mt-10) cc_final: 0.6868 (mt-10) REVERT: Av 210 MET cc_start: 0.8444 (tmm) cc_final: 0.8188 (tmm) REVERT: Ax 209 GLU cc_start: 0.8538 (tt0) cc_final: 0.8260 (tt0) REVERT: Ax 223 LEU cc_start: 0.8648 (mm) cc_final: 0.8275 (mt) REVERT: Ay 159 ASN cc_start: 0.8213 (m-40) cc_final: 0.7888 (m110) REVERT: Ay 173 ASP cc_start: 0.7211 (t70) cc_final: 0.6949 (t70) REVERT: Ay 183 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8805 (ttpp) REVERT: Ay 223 LEU cc_start: 0.8830 (mm) cc_final: 0.8525 (mt) REVERT: Ay 228 ASN cc_start: 0.8400 (p0) cc_final: 0.8093 (p0) REVERT: Ay 230 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7292 (tttt) REVERT: Az 107 LEU cc_start: 0.9057 (tp) cc_final: 0.8833 (tp) REVERT: Az 173 ASP cc_start: 0.7604 (t0) cc_final: 0.7353 (t0) REVERT: Az 183 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8801 (tttp) REVERT: Az 187 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7191 (mt-10) REVERT: Az 197 MET cc_start: 0.8948 (mmm) cc_final: 0.8714 (tpp) REVERT: Az 209 GLU cc_start: 0.8827 (tt0) cc_final: 0.8423 (mt-10) REVERT: Ba 232 LEU cc_start: 0.8719 (mp) cc_final: 0.8128 (tt) outliers start: 3 outliers final: 0 residues processed: 1524 average time/residue: 0.2167 time to fit residues: 560.5795 Evaluate side-chains 1287 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1287 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 272 optimal weight: 5.9990 chunk 387 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 356 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 399 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 159 ASN ** Aa 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 159 ASN Ad 159 ASN Ae 159 ASN ** Ae 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 159 ASN ** Ag 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 248 ASN ** Ai 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 159 ASN Ak 159 ASN Al 159 ASN ** Al 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 254 HIS Ao 128 GLN ** As 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 126 GLN Av 126 GLN ** Ax 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 128 GLN Az 159 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.092200 restraints weight = 66491.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.094487 restraints weight = 46000.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096114 restraints weight = 35042.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097335 restraints weight = 28493.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098267 restraints weight = 24158.823| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.9940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40770 Z= 0.143 Angle : 0.675 9.777 55107 Z= 0.345 Chirality : 0.042 0.239 5697 Planarity : 0.004 0.081 7263 Dihedral : 4.550 26.644 5373 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.05 % Allowed : 0.16 % Favored : 99.79 % 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: -0.61 (0.12), residues: 4752 helix: -0.32 (0.11), residues: 2106 sheet: None (None), residues: 0 loop : -0.37 (0.13), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAb 194 TYR 0.034 0.002 TYRAx 110 PHE 0.021 0.001 PHEAn 237 TRP 0.015 0.002 TRPAu 169 HIS 0.010 0.001 HISAn 199 Details of bonding type rmsd covalent geometry : bond 0.00338 (40770) covalent geometry : angle 0.67461 (55107) hydrogen bonds : bond 0.03756 ( 1377) hydrogen bonds : angle 4.43006 ( 3726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1488 time to evaluate : 1.261 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: Aa 84 LEU cc_start: 0.7892 (tp) cc_final: 0.7660 (tp) REVERT: Aa 109 GLN cc_start: 0.8600 (pp30) cc_final: 0.8391 (pp30) REVERT: Aa 111 LYS cc_start: 0.8738 (mttt) cc_final: 0.8264 (tptt) REVERT: Aa 161 THR cc_start: 0.8646 (p) cc_final: 0.8254 (p) REVERT: Aa 183 LYS cc_start: 0.9135 (tttp) cc_final: 0.8843 (ttpp) REVERT: Aa 196 CYS cc_start: 0.8749 (t) cc_final: 0.8510 (t) REVERT: Aa 227 LEU cc_start: 0.8895 (tp) cc_final: 0.8610 (tp) REVERT: Aa 230 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7378 (pttt) REVERT: Aa 232 LEU cc_start: 0.8912 (mp) cc_final: 0.8187 (tt) REVERT: Ab 158 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8182 (tp30) REVERT: Ab 232 LEU cc_start: 0.8822 (mp) cc_final: 0.8236 (tp) REVERT: Ac 83 LYS cc_start: 0.9025 (tptp) cc_final: 0.8595 (tppt) REVERT: Ac 95 MET cc_start: 0.7802 (mpp) cc_final: 0.7590 (mtt) REVERT: Ac 113 ASP cc_start: 0.7916 (t70) cc_final: 0.7299 (t0) REVERT: Ac 238 ASP cc_start: 0.8081 (t70) cc_final: 0.7862 (t0) REVERT: Ad 161 THR cc_start: 0.9058 (p) cc_final: 0.8663 (p) REVERT: Ae 173 ASP cc_start: 0.7441 (t70) cc_final: 0.7235 (t0) REVERT: Ae 223 LEU cc_start: 0.8717 (mm) cc_final: 0.8456 (mt) REVERT: Af 128 GLN cc_start: 0.8535 (tt0) cc_final: 0.7995 (tt0) REVERT: Ag 159 ASN cc_start: 0.8405 (m-40) cc_final: 0.8138 (m110) REVERT: Ag 161 THR cc_start: 0.8870 (p) cc_final: 0.8549 (p) REVERT: Ag 209 GLU cc_start: 0.8620 (pp20) cc_final: 0.8073 (pp20) REVERT: Ag 232 LEU cc_start: 0.8976 (mp) cc_final: 0.8225 (tt) REVERT: Ah 109 GLN cc_start: 0.8535 (pp30) cc_final: 0.8128 (pp30) REVERT: Ah 139 ASP cc_start: 0.7623 (m-30) cc_final: 0.7368 (t0) REVERT: Ah 172 VAL cc_start: 0.9309 (p) cc_final: 0.8978 (p) REVERT: Ai 109 GLN cc_start: 0.8198 (pp30) cc_final: 0.7745 (pp30) REVERT: Ai 156 CYS cc_start: 0.8999 (m) cc_final: 0.8594 (t) REVERT: Ai 158 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8029 (mm-30) REVERT: Ai 161 THR cc_start: 0.8940 (p) cc_final: 0.8673 (p) REVERT: Ai 232 LEU cc_start: 0.8831 (mt) cc_final: 0.8051 (tt) REVERT: Aj 159 ASN cc_start: 0.8120 (m-40) cc_final: 0.7913 (m110) REVERT: Ak 109 GLN cc_start: 0.8608 (pp30) cc_final: 0.8333 (pp30) REVERT: Ak 110 TYR cc_start: 0.8847 (t80) cc_final: 0.8603 (t80) REVERT: Ak 210 MET cc_start: 0.8088 (tmm) cc_final: 0.7617 (tmm) REVERT: Al 209 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8490 (mt-10) REVERT: Al 235 TYR cc_start: 0.8509 (m-10) cc_final: 0.8261 (m-10) REVERT: An 172 VAL cc_start: 0.8971 (p) cc_final: 0.8752 (p) REVERT: An 173 ASP cc_start: 0.7492 (t70) cc_final: 0.7237 (p0) REVERT: An 183 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8663 (ttpp) REVERT: An 193 LEU cc_start: 0.8329 (tt) cc_final: 0.7885 (tt) REVERT: Ap 156 CYS cc_start: 0.8855 (m) cc_final: 0.8335 (t) REVERT: Ap 161 THR cc_start: 0.8841 (p) cc_final: 0.8577 (p) REVERT: Ap 172 VAL cc_start: 0.8756 (t) cc_final: 0.8163 (t) REVERT: Ap 197 MET cc_start: 0.8873 (tpp) cc_final: 0.8499 (mmm) REVERT: Aq 81 ILE cc_start: 0.9287 (mp) cc_final: 0.9078 (mm) REVERT: Aq 114 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7674 (tm-30) REVERT: Aq 159 ASN cc_start: 0.8230 (m-40) cc_final: 0.7828 (m110) REVERT: Aq 232 LEU cc_start: 0.8880 (mt) cc_final: 0.7849 (tt) REVERT: Ar 158 GLU cc_start: 0.8235 (tp30) cc_final: 0.7879 (tp30) REVERT: Ar 161 THR cc_start: 0.9173 (p) cc_final: 0.8952 (p) REVERT: Ar 171 MET cc_start: 0.8450 (mmp) cc_final: 0.8087 (mmp) REVERT: Ar 183 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8754 (ttpp) REVERT: Ar 232 LEU cc_start: 0.8666 (mt) cc_final: 0.7906 (tt) REVERT: As 81 ILE cc_start: 0.9302 (mp) cc_final: 0.9000 (mm) REVERT: As 158 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8115 (mm-30) REVERT: As 159 ASN cc_start: 0.8282 (m-40) cc_final: 0.7988 (m110) REVERT: As 232 LEU cc_start: 0.8783 (mp) cc_final: 0.8113 (tp) REVERT: At 83 LYS cc_start: 0.8890 (tppt) cc_final: 0.8681 (tppt) REVERT: At 110 TYR cc_start: 0.8768 (t80) cc_final: 0.8367 (t80) REVERT: At 197 MET cc_start: 0.8732 (mmm) cc_final: 0.8380 (tpp) REVERT: At 232 LEU cc_start: 0.8819 (mp) cc_final: 0.8500 (tp) REVERT: Au 109 GLN cc_start: 0.8479 (pp30) cc_final: 0.7868 (pp30) REVERT: Au 110 TYR cc_start: 0.8900 (t80) cc_final: 0.8291 (t80) REVERT: Au 173 ASP cc_start: 0.7426 (t70) cc_final: 0.7109 (t70) REVERT: Au 227 LEU cc_start: 0.9074 (tt) cc_final: 0.8843 (tp) REVERT: Au 232 LEU cc_start: 0.8915 (mp) cc_final: 0.8199 (tp) REVERT: Av 152 LEU cc_start: 0.8485 (tt) cc_final: 0.8149 (tt) REVERT: Av 156 CYS cc_start: 0.8683 (m) cc_final: 0.7810 (m) REVERT: Av 183 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8957 (ptmm) REVERT: Av 210 MET cc_start: 0.8249 (tmm) cc_final: 0.7919 (tmm) REVERT: Ax 210 MET cc_start: 0.9005 (tmm) cc_final: 0.8799 (tmm) REVERT: Ax 223 LEU cc_start: 0.8544 (mm) cc_final: 0.8250 (mt) REVERT: Ay 159 ASN cc_start: 0.8202 (m-40) cc_final: 0.7927 (m110) REVERT: Ay 173 ASP cc_start: 0.7278 (t70) cc_final: 0.7018 (t70) REVERT: Ay 183 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8786 (ttpp) REVERT: Ay 223 LEU cc_start: 0.8840 (mm) cc_final: 0.8545 (mt) REVERT: Ay 228 ASN cc_start: 0.8295 (p0) cc_final: 0.8005 (p0) REVERT: Ay 230 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7326 (tttt) REVERT: Az 159 ASN cc_start: 0.8390 (m-40) cc_final: 0.8153 (m110) REVERT: Az 161 THR cc_start: 0.9003 (p) cc_final: 0.8642 (p) REVERT: Az 183 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8781 (tttp) REVERT: Az 187 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7216 (mt-10) REVERT: Az 197 MET cc_start: 0.8969 (mmm) cc_final: 0.8742 (tpt) REVERT: Az 209 GLU cc_start: 0.8799 (tt0) cc_final: 0.8535 (mt-10) REVERT: Ba 139 ASP cc_start: 0.7327 (t0) cc_final: 0.7123 (t0) REVERT: Ba 232 LEU cc_start: 0.8708 (mp) cc_final: 0.8128 (tt) outliers start: 2 outliers final: 0 residues processed: 1490 average time/residue: 0.2140 time to fit residues: 542.2642 Evaluate side-chains 1258 residues out of total 4347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1258 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 196 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 457 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 98 ASN Ac 243 ASN Ad 199 HIS Ad 254 HIS ** Ag 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 248 ASN Ai 159 ASN ** Al 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 243 ASN An 132 ASN Ao 132 ASN Aq 248 ASN Au 126 GLN ** Au 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 126 GLN Aw 243 ASN Ay 132 ASN Ba 243 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102555 restraints weight = 70590.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105500 restraints weight = 48849.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107651 restraints weight = 37245.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109230 restraints weight = 30292.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110388 restraints weight = 25836.254| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 1.0287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.064 40770 Z= 0.418 Angle : 0.931 9.793 55107 Z= 0.483 Chirality : 0.053 0.297 5697 Planarity : 0.006 0.071 7263 Dihedral : 5.550 27.296 5373 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.09 % Allowed : 0.55 % Favored : 99.36 % 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: -0.92 (0.12), residues: 4752 helix: -0.57 (0.11), residues: 2079 sheet: None (None), residues: 0 loop : -0.55 (0.13), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAm 211 TYR 0.039 0.003 TYRAt 217 PHE 0.031 0.003 PHEBa 237 TRP 0.030 0.003 TRPAx 169 HIS 0.014 0.002 HISAq 124 Details of bonding type rmsd covalent geometry : bond 0.00968 (40770) covalent geometry : angle 0.93071 (55107) hydrogen bonds : bond 0.05416 ( 1377) hydrogen bonds : angle 5.33887 ( 3726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9890.35 seconds wall clock time: 170 minutes 8.89 seconds (10208.89 seconds total)