Starting phenix.real_space_refine on Wed Jun 3 11:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.map" model { file = "/net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h7u_51914/06_2026/9h7u_51914.cif" } resolution = 2.96 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= 0.000 sd= 0.000 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 54 5.16 5 C 2430 2.51 5 N 702 2.21 5 O 702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3888 Number of models: 1 Model: "" Number of chains: 54 Chain: "Aa" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ab" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ac" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ad" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ae" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Af" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ag" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ah" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ai" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Aj" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ak" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Al" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Am" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "An" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ao" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ap" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Aq" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ar" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ci" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cj" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ck" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cl" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cm" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cn" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Co" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cp" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cq" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cr" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cs" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ct" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cu" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cv" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cw" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cx" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cy" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cz" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Eq" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Er" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Es" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Et" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Eu" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ev" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ew" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ex" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ey" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ez" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fa" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fb" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fc" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fd" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fe" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ff" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fg" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Fh" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Time building chain proxies: 1.17, per 1000 atoms: 0.30 Number of scatterers: 3888 At special positions: 0 Unit cell: (126.025, 138.45, 28.4, 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 54 16.00 O 702 8.00 N 702 7.00 C 2430 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: 0.30 Conformation dependent library (CDL) restraints added in 144.7 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'Ci' and resid 218 through 224 removed outlier: 6.489A pdb=" N VALAa 110 " --> pdb=" O LYSEq 3 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SEREq 5 " --> pdb=" O VALAa 110 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAa 112 " --> pdb=" O SEREq 5 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILEEq 7 " --> pdb=" O VALAa 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNAa 114 " --> pdb=" O ILEEq 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Cj' and resid 227 through 233 removed outlier: 6.489A pdb=" N VALAb 119 " --> pdb=" O LYSEr 12 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SEREr 14 " --> pdb=" O VALAb 119 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAb 121 " --> pdb=" O SEREr 14 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILEEr 16 " --> pdb=" O VALAb 121 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNAb 123 " --> pdb=" O ILEEr 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ck' and resid 236 through 242 removed outlier: 6.488A pdb=" N VALAc 128 " --> pdb=" O LYSEs 21 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SEREs 23 " --> pdb=" O VALAc 128 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VALAc 130 " --> pdb=" O SEREs 23 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILEEs 25 " --> pdb=" O VALAc 130 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNAc 132 " --> pdb=" O ILEEs 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Cl' and resid 245 through 251 removed outlier: 6.489A pdb=" N VALAd 137 " --> pdb=" O LYSEt 30 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SEREt 32 " --> pdb=" O VALAd 137 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAd 139 " --> pdb=" O SEREt 32 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILEEt 34 " --> pdb=" O VALAd 139 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNAd 141 " --> pdb=" O ILEEt 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Cm' and resid 254 through 260 removed outlier: 6.489A pdb=" N VALAe 146 " --> pdb=" O LYSEu 39 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SEREu 41 " --> pdb=" O VALAe 146 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VALAe 148 " --> pdb=" O SEREu 41 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILEEu 43 " --> pdb=" O VALAe 148 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLNAe 150 " --> pdb=" O ILEEu 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Cn' and resid 263 through 269 removed outlier: 6.489A pdb=" N VALAf 155 " --> pdb=" O LYSEv 48 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SEREv 50 " --> pdb=" O VALAf 155 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAf 157 " --> pdb=" O SEREv 50 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILEEv 52 " --> pdb=" O VALAf 157 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLNAf 159 " --> pdb=" O ILEEv 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Co' and resid 227 through 233 removed outlier: 6.769A pdb=" N LYSAg 120 " --> pdb=" O VALCo 229 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLNCo 231 " --> pdb=" O LYSAg 120 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAg 122 " --> pdb=" O GLNCo 231 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASNCo 233 " --> pdb=" O SERAg 122 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILEAg 124 " --> pdb=" O ASNCo 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Cp' and resid 236 through 242 removed outlier: 6.769A pdb=" N LYSAh 129 " --> pdb=" O VALCp 238 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLNCp 240 " --> pdb=" O LYSAh 129 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAh 131 " --> pdb=" O GLNCp 240 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASNCp 242 " --> pdb=" O SERAh 131 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILEAh 133 " --> pdb=" O ASNCp 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Cq' and resid 245 through 251 removed outlier: 6.770A pdb=" N LYSAi 138 " --> pdb=" O VALCq 247 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLNCq 249 " --> pdb=" O LYSAi 138 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAi 140 " --> pdb=" O GLNCq 249 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASNCq 251 " --> pdb=" O SERAi 140 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILEAi 142 " --> pdb=" O ASNCq 251 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Cr' and resid 254 through 260 removed outlier: 6.769A pdb=" N LYSAj 147 " --> pdb=" O VALCr 256 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLNCr 258 " --> pdb=" O LYSAj 147 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAj 149 " --> pdb=" O GLNCr 258 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASNCr 260 " --> pdb=" O SERAj 149 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILEAj 151 " --> pdb=" O ASNCr 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Cs' and resid 263 through 269 removed outlier: 6.769A pdb=" N LYSAk 156 " --> pdb=" O VALCs 265 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLNCs 267 " --> pdb=" O LYSAk 156 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAk 158 " --> pdb=" O GLNCs 267 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASNCs 269 " --> pdb=" O SERAk 158 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILEAk 160 " --> pdb=" O ASNCs 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ct' and resid 272 through 278 removed outlier: 6.769A pdb=" N LYSAl 165 " --> pdb=" O VALCt 274 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLNCt 276 " --> pdb=" O LYSAl 165 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SERAl 167 " --> pdb=" O GLNCt 276 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASNCt 278 " --> pdb=" O SERAl 167 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILEAl 169 " --> pdb=" O ASNCt 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Cu' and resid 237 through 242 removed outlier: 6.732A pdb=" N LYSAm 129 " --> pdb=" O VALCu 238 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCu 240 " --> pdb=" O LYSAm 129 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SERAm 131 " --> pdb=" O GLNCu 240 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASNCu 242 " --> pdb=" O SERAm 131 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILEAm 133 " --> pdb=" O ASNCu 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Cv' and resid 246 through 251 removed outlier: 6.732A pdb=" N LYSAn 138 " --> pdb=" O VALCv 247 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCv 249 " --> pdb=" O LYSAn 138 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SERAn 140 " --> pdb=" O GLNCv 249 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASNCv 251 " --> pdb=" O SERAn 140 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILEAn 142 " --> pdb=" O ASNCv 251 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Cw' and resid 255 through 260 removed outlier: 6.732A pdb=" N LYSAo 147 " --> pdb=" O VALCw 256 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCw 258 " --> pdb=" O LYSAo 147 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SERAo 149 " --> pdb=" O GLNCw 258 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASNCw 260 " --> pdb=" O SERAo 149 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILEAo 151 " --> pdb=" O ASNCw 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Cx' and resid 264 through 269 removed outlier: 6.732A pdb=" N LYSAp 156 " --> pdb=" O VALCx 265 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCx 267 " --> pdb=" O LYSAp 156 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SERAp 158 " --> pdb=" O GLNCx 267 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASNCx 269 " --> pdb=" O SERAp 158 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILEAp 160 " --> pdb=" O ASNCx 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Cy' and resid 273 through 278 removed outlier: 6.732A pdb=" N LYSAq 165 " --> pdb=" O VALCy 274 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCy 276 " --> pdb=" O LYSAq 165 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SERAq 167 " --> pdb=" O GLNCy 276 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASNCy 278 " --> pdb=" O SERAq 167 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILEAq 169 " --> pdb=" O ASNCy 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Cz' and resid 282 through 287 removed outlier: 6.732A pdb=" N LYSAr 174 " --> pdb=" O VALCz 283 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLNCz 285 " --> pdb=" O LYSAr 174 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SERAr 176 " --> pdb=" O GLNCz 285 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASNCz 287 " --> pdb=" O SERAr 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILEAr 178 " --> pdb=" O ASNCz 287 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 306 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: 0.46 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 702 1.32 - 1.44: 543 1.44 - 1.57: 2445 1.57 - 1.69: 36 1.69 - 1.82: 108 Bond restraints: 3834 Sorted by residual: bond pdb=" N LYSAn 138 " pdb=" CA LYSAn 138 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.17e-02 7.31e+03 1.65e+01 bond pdb=" N LYSAq 165 " pdb=" CA LYSAq 165 " ideal model delta sigma weight residual 1.460 1.508 -0.048 1.17e-02 7.31e+03 1.65e+01 bond pdb=" N LYSAp 156 " pdb=" CA LYSAp 156 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.17e-02 7.31e+03 1.63e+01 bond pdb=" N LYSAm 129 " pdb=" CA LYSAm 129 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.17e-02 7.31e+03 1.63e+01 bond pdb=" N LYSAr 174 " pdb=" CA LYSAr 174 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.17e-02 7.31e+03 1.62e+01 ... (remaining 3829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 2374 1.52 - 3.03: 1715 3.03 - 4.55: 715 4.55 - 6.07: 128 6.07 - 7.58: 90 Bond angle restraints: 5022 Sorted by residual: angle pdb=" C VALAr 175 " pdb=" CA VALAr 175 " pdb=" CB VALAr 175 " ideal model delta sigma weight residual 110.42 118.00 -7.58 1.35e+00 5.49e-01 3.15e+01 angle pdb=" C VALAq 166 " pdb=" CA VALAq 166 " pdb=" CB VALAq 166 " ideal model delta sigma weight residual 110.42 117.97 -7.55 1.35e+00 5.49e-01 3.13e+01 angle pdb=" C VALFh 67 " pdb=" CA VALFh 67 " pdb=" CB VALFh 67 " ideal model delta sigma weight residual 110.42 117.96 -7.54 1.35e+00 5.49e-01 3.12e+01 angle pdb=" C VALCz 283 " pdb=" CA VALCz 283 " pdb=" CB VALCz 283 " ideal model delta sigma weight residual 110.42 117.96 -7.54 1.35e+00 5.49e-01 3.12e+01 angle pdb=" C VALAm 130 " pdb=" CA VALAm 130 " pdb=" CB VALAm 130 " ideal model delta sigma weight residual 110.42 117.96 -7.54 1.35e+00 5.49e-01 3.12e+01 ... (remaining 5017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2142 16.35 - 32.71: 306 32.71 - 49.06: 72 49.06 - 65.41: 18 65.41 - 81.76: 54 Dihedral angle restraints: 2592 sinusoidal: 1188 harmonic: 1404 Sorted by residual: dihedral pdb=" CA LYSFe 39 " pdb=" C LYSFe 39 " pdb=" N VALFe 40 " pdb=" CA VALFe 40 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYSAq 165 " pdb=" C LYSAq 165 " pdb=" N VALAq 166 " pdb=" CA VALAq 166 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LYSAr 174 " pdb=" C LYSAr 174 " pdb=" N VALAr 175 " pdb=" CA VALAr 175 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 2589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 137 0.052 - 0.105: 205 0.105 - 0.157: 175 0.157 - 0.210: 59 0.210 - 0.262: 72 Chirality restraints: 648 Sorted by residual: chirality pdb=" CA METAb 126 " pdb=" N METAb 126 " pdb=" C METAb 126 " pdb=" CB METAb 126 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA METEr 18 " pdb=" N METEr 18 " pdb=" C METEr 18 " pdb=" CB METEr 18 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA METAa 117 " pdb=" N METAa 117 " pdb=" C METAa 117 " pdb=" CB METAa 117 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 645 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METAe 153 " -0.046 2.00e-02 2.50e+03 9.38e-02 8.80e+01 pdb=" C METAe 153 " 0.162 2.00e-02 2.50e+03 pdb=" O METAe 153 " -0.058 2.00e-02 2.50e+03 pdb=" OXT METAe 153 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAa 117 " -0.046 2.00e-02 2.50e+03 9.38e-02 8.80e+01 pdb=" C METAa 117 " 0.162 2.00e-02 2.50e+03 pdb=" O METAa 117 " -0.058 2.00e-02 2.50e+03 pdb=" OXT METAa 117 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAd 144 " -0.046 2.00e-02 2.50e+03 9.38e-02 8.80e+01 pdb=" C METAd 144 " 0.162 2.00e-02 2.50e+03 pdb=" O METAd 144 " -0.058 2.00e-02 2.50e+03 pdb=" OXT METAd 144 " -0.058 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 659 2.82 - 3.34: 2887 3.34 - 3.86: 6082 3.86 - 4.38: 6428 4.38 - 4.90: 12558 Nonbonded interactions: 28614 Sorted by model distance: nonbonded pdb=" OE1 GLNAj 150 " pdb=" N LYSCk 235 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLNAg 123 " pdb=" N LYSCn 262 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLNAh 132 " pdb=" N LYSCi 217 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLNAi 141 " pdb=" N LYSCj 226 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLNAl 168 " pdb=" N LYSCm 253 " model vdw 2.295 3.120 ... (remaining 28609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'Aa' 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 'Ci' selection = chain 'Cj' selection = chain 'Ck' selection = chain 'Cl' selection = chain 'Cm' selection = chain 'Cn' selection = chain 'Co' selection = chain 'Cp' selection = chain 'Cq' selection = chain 'Cr' selection = chain 'Cs' selection = chain 'Ct' selection = chain 'Cu' selection = chain 'Cv' selection = chain 'Cw' selection = chain 'Cx' selection = chain 'Cy' selection = chain 'Cz' selection = chain 'Eq' selection = chain 'Er' selection = chain 'Es' selection = chain 'Et' selection = chain 'Eu' selection = chain 'Ev' selection = chain 'Ew' selection = chain 'Ex' selection = chain 'Ey' selection = chain 'Ez' selection = chain 'Fa' selection = chain 'Fb' selection = chain 'Fc' selection = chain 'Fd' selection = chain 'Fe' selection = chain 'Ff' selection = chain 'Fg' selection = chain 'Fh' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3166 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 : 0.016 0.048 3834 Z= 1.005 Angle : 2.340 7.581 5022 Z= 1.512 Chirality : 0.128 0.262 648 Planarity : 0.029 0.094 594 Dihedral : 21.800 81.762 1620 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.46), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01562 / 1.00 ( 3834) covalent geometry : angle 2.34023 / 1.51 ( 5022) hydrogen bonds : bond 0.16572 / 10.24 ( 102) hydrogen bonds : angle 10.56579 / 6.90 ( 306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.137 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: Ak 160 ILE cc_start: 0.4159 (mp) cc_final: 0.3608 (tt) REVERT: Al 169 ILE cc_start: 0.4258 (mp) cc_final: 0.3936 (tt) REVERT: Cs 268 ILE cc_start: 0.4276 (mp) cc_final: 0.3417 (pp) REVERT: Ct 277 ILE cc_start: 0.4341 (mp) cc_final: 0.3830 (tt) REVERT: Fa 52 ILE cc_start: 0.4499 (mp) cc_final: 0.4073 (mm) outliers start: 0 outliers final: 1 residues processed: 240 average time/residue: 0.6077 time to fit residues: 149.6687 Evaluate side-chains 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Fd residue 35 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 134 ASN ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 179 ASN ** Cl 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 233 ASN Cr 260 ASN ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cw 258 GLN Cz 287 ASN ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ez 44 ASN ** Fa 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 53 ASN ** Fb 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fc 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Fe 42 GLN Fg 62 ASN ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.166513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.146749 restraints weight = 9083.847| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 3.17 r_work: 0.4266 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 1.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.655 3834 Z= 7.078 Angle : 8.942 61.131 5022 Z= 4.352 Chirality : 0.498 3.396 648 Planarity : 0.043 0.108 594 Dihedral : 26.290 89.897 488 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 186.80 Ramachandran Plot: Outliers : 19.84 % Allowed : 33.33 % Favored : 46.83 % Rotamer: Outliers : 45.68 % Allowed : 23.46 % Favored : 30.86 % Cbeta Deviations : 47.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 21.30 % 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: -7.85 (0.22), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.98 (0.17), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15105 / 7.08 ( 3834) covalent geometry : angle 8.94222 / 4.35 ( 5022) hydrogen bonds : bond 0.45428 / 29.41 ( 102) hydrogen bonds : angle 19.45442 / 12.59 ( 306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 87 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ad 141 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7801 (tp40) REVERT: Af 156 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8320 (ptpp) REVERT: Aj 145 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7920 (mptt) REVERT: Aj 147 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7699 (ptmm) REVERT: Ak 162 MET cc_start: 0.7410 (mmm) cc_final: 0.6997 (tmm) REVERT: Aq 168 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: Aq 169 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6690 (pt) REVERT: Aq 171 MET cc_start: 0.8103 (mtt) cc_final: 0.7865 (mtt) REVERT: Ci 219 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7338 (pptt) REVERT: Cj 228 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7557 (pptt) REVERT: Cj 232 ILE cc_start: 0.6537 (OUTLIER) cc_final: 0.5670 (pp) REVERT: Cl 252 MET cc_start: 0.8327 (mtt) cc_final: 0.7780 (mtp) REVERT: Cn 262 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6187 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7619 (pttp) REVERT: Cn 267 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: Co 226 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: Cp 235 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8037 (mmtm) REVERT: Cp 237 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.6997 (pttp) REVERT: Cr 253 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8110 (mppt) REVERT: Cs 262 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7620 (mptt) REVERT: Cs 264 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7247 (pttt) REVERT: Cu 243 MET cc_start: 0.8059 (mtt) cc_final: 0.7606 (mtp) REVERT: Cx 269 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7525 (t0) REVERT: Eq 7 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7917 (mt) REVERT: Ev 46 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7578 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8251 (tptp) cc_final: 0.7458 (mttt) REVERT: Ex 19 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7457 (mppt) REVERT: Ey 36 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7049 (tmm) REVERT: Ez 41 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.7896 (p) REVERT: Fc 27 MET cc_start: 0.8289 (mtt) cc_final: 0.8006 (mtp) REVERT: Fe 39 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6867 (ttpp) REVERT: Ff 53 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7491 (p0) REVERT: Fg 57 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7156 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: Fh 72 MET cc_start: 0.8454 (mtt) cc_final: 0.8179 (mtp) outliers start: 222 outliers final: 124 residues processed: 265 average time/residue: 0.5450 time to fit residues: 148.6137 Evaluate side-chains 232 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Ae residue 153 MET Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 147 LYS Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 267 GLN Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 235 LYS Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 255 LYS Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 268 ILE Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 7 ILE Chi-restraints excluded: chain Er residue 12 LYS Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 53 ASN Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 29 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 41 SER Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Ff residue 46 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 60 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 242 ASN ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Er 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fb 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fe 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.161936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145356 restraints weight = 8550.374| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.79 r_work: 0.4208 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 1.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.152 0.658 3834 Z= 7.109 Angle : 8.803 60.417 5022 Z= 4.274 Chirality : 0.482 1.619 648 Planarity : 0.041 0.105 594 Dihedral : 27.112 86.668 486 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 197.06 Ramachandran Plot: Outliers : 14.81 % Allowed : 46.83 % Favored : 38.36 % Rotamer: Outliers : 49.18 % Allowed : 25.31 % Favored : 25.51 % Cbeta Deviations : 43.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 21.99 % 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: -8.34 (0.20), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.36 (0.15), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15184 / 7.11 ( 3834) covalent geometry : angle 8.80346 / 4.27 ( 5022) hydrogen bonds : bond 0.46674 / 30.18 ( 102) hydrogen bonds : angle 19.89602 / 12.84 ( 306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7613 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7360 (tp-100) REVERT: Ad 141 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7796 (tp40) REVERT: Af 156 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8373 (ptpp) REVERT: Af 162 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: Aj 145 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7801 (mptt) REVERT: Aj 147 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7723 (ptmm) REVERT: Ap 162 MET cc_start: 0.7016 (mtm) cc_final: 0.6729 (mtm) REVERT: Aq 169 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6739 (pt) REVERT: Ci 219 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7417 (pptt) REVERT: Cj 228 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7452 (pptt) REVERT: Cj 232 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6041 (pp) REVERT: Ck 237 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7626 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: Cn 262 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6212 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7277 (pptt) REVERT: Cp 237 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7088 (pttp) REVERT: Cr 253 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8022 (mppt) REVERT: Cs 262 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7655 (mptt) REVERT: Cs 264 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7256 (pttp) REVERT: Cu 243 MET cc_start: 0.8184 (mtt) cc_final: 0.7962 (mtp) REVERT: Cw 260 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7792 (t0) REVERT: Cx 269 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7839 (t0) REVERT: Et 32 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8072 (p) REVERT: Et 33 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: Ev 46 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7476 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8302 (tptp) cc_final: 0.7664 (mtpt) REVERT: Ex 19 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7436 (mtpt) REVERT: Ey 36 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.6854 (tmm) REVERT: Fa 54 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7468 (tmm) REVERT: Fb 55 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8119 (mptt) REVERT: Fe 39 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7179 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7531 (p0) REVERT: Fg 57 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7224 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.6977 (tp40) outliers start: 239 outliers final: 160 residues processed: 272 average time/residue: 0.5370 time to fit residues: 150.3952 Evaluate side-chains 262 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 70 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Af residue 162 MET Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 141 GLN Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 147 LYS Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 275 SER Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 53 ASN Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Ff residue 49 VAL Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 267 GLN ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Es 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.160773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.144371 restraints weight = 8592.521| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.75 r_work: 0.4200 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 1.8766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.152 0.762 3834 Z= 7.111 Angle : 8.716 59.608 5022 Z= 4.232 Chirality : 0.485 1.639 648 Planarity : 0.041 0.104 594 Dihedral : 27.205 89.649 486 Min Nonbonded Distance : 1.531 Molprobity Statistics. All-atom Clashscore : 192.52 Ramachandran Plot: Outliers : 13.23 % Allowed : 50.26 % Favored : 36.51 % Rotamer: Outliers : 52.88 % Allowed : 23.05 % Favored : 24.07 % Cbeta Deviations : 40.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 22.92 % 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: -8.36 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.37 (0.15), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15156 / 7.11 ( 3834) covalent geometry : angle 8.71648 / 4.23 ( 5022) hydrogen bonds : bond 0.46814 / 30.39 ( 102) hydrogen bonds : angle 19.96645 / 12.91 ( 306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 69 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7589 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: Ad 141 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: Ad 144 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7856 (ttp) REVERT: Af 156 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8394 (ptpp) REVERT: Aj 145 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7863 (mptt) REVERT: Ao 153 MET cc_start: 0.7961 (mtp) cc_final: 0.7569 (mtm) REVERT: Ap 161 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: Ap 162 MET cc_start: 0.7009 (mtt) cc_final: 0.6681 (mtm) REVERT: Aq 169 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6744 (pt) REVERT: Ci 219 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7425 (pptt) REVERT: Cj 228 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7475 (pptt) REVERT: Cj 232 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.5915 (pp) REVERT: Ck 237 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7581 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7591 (tp40) REVERT: Cl 246 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7964 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7183 (pttp) REVERT: Cn 262 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6216 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7285 (pptt) REVERT: Co 226 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (mptt) REVERT: Cp 237 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7123 (pttp) REVERT: Cr 253 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8082 (mppt) REVERT: Cr 260 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: Cs 262 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7703 (mptt) REVERT: Cs 264 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7130 (pttp) REVERT: Cw 260 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7756 (t0) REVERT: Es 26 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6673 (t0) REVERT: Et 32 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8175 (p) REVERT: Et 33 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: Ev 46 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7802 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8250 (tptp) cc_final: 0.7598 (mttt) REVERT: Ew 12 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7584 (tptm) REVERT: Ex 19 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7457 (mtpt) REVERT: Ey 36 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.6846 (tmm) REVERT: Ez 39 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7447 (ptmm) REVERT: Fa 53 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8543 (m-40) REVERT: Fa 54 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: Fb 55 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8111 (mptt) REVERT: Fe 39 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7078 (ttpp) REVERT: Ff 53 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7433 (p0) REVERT: Fg 57 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7292 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7000 (tp40) outliers start: 257 outliers final: 180 residues processed: 286 average time/residue: 0.5259 time to fit residues: 154.9961 Evaluate side-chains 288 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 69 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 141 GLN Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 53 ASN Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 22 VAL Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.160566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.143834 restraints weight = 8700.695| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.83 r_work: 0.4234 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 1.8807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.755 3834 Z= 7.104 Angle : 8.685 59.915 5022 Z= 4.215 Chirality : 0.485 1.745 648 Planarity : 0.041 0.104 594 Dihedral : 27.347 88.716 486 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 195.68 Ramachandran Plot: Outliers : 13.23 % Allowed : 52.12 % Favored : 34.66 % Rotamer: Outliers : 53.50 % Allowed : 23.05 % Favored : 23.46 % Cbeta Deviations : 41.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 23.84 % 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: -8.45 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.15), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15115 / 7.10 ( 3834) covalent geometry : angle 8.68502 / 4.21 ( 5022) hydrogen bonds : bond 0.46735 / 30.30 ( 102) hydrogen bonds : angle 19.99625 / 12.92 ( 306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 69 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7528 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7403 (tp-100) REVERT: Ad 141 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7829 (tp40) REVERT: Ad 144 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7863 (ttp) REVERT: Af 156 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8401 (ptpp) REVERT: Aj 145 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7911 (mptt) REVERT: Am 135 MET cc_start: 0.8447 (mtt) cc_final: 0.8074 (mtp) REVERT: Ap 161 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7540 (m-40) REVERT: Ap 162 MET cc_start: 0.7049 (mtt) cc_final: 0.6709 (mtm) REVERT: Aq 169 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6744 (pt) REVERT: Ci 219 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7433 (pptt) REVERT: Cj 228 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7461 (pptt) REVERT: Cj 232 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.5952 (pp) REVERT: Ck 237 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7589 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.7640 (tp40) REVERT: Cl 246 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7924 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7213 (pttp) REVERT: Cn 262 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6218 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7284 (pptt) REVERT: Co 226 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8126 (mptt) REVERT: Cp 237 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7141 (pttp) REVERT: Cr 253 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8022 (mppt) REVERT: Cr 260 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: Cs 262 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7706 (mptt) REVERT: Cs 264 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7308 (pttm) REVERT: Cs 266 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8666 (m) REVERT: Cw 260 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7788 (t0) REVERT: Cx 269 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7908 (t0) REVERT: Er 15 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7686 (tp40) REVERT: Es 24 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7441 (tp40) REVERT: Es 26 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6680 (t0) REVERT: Et 32 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8164 (p) REVERT: Et 33 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: Ev 46 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7811 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8260 (tptp) cc_final: 0.7655 (mtpt) REVERT: Ew 12 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7778 (tptm) REVERT: Ex 19 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7472 (mtpt) REVERT: Ey 36 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6855 (tmm) REVERT: Ez 39 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7469 (ptmt) REVERT: Fa 53 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8547 (m-40) REVERT: Fa 54 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: Fe 39 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7326 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7367 (p0) REVERT: Fg 57 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7267 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.6993 (tp40) outliers start: 260 outliers final: 187 residues processed: 287 average time/residue: 0.5161 time to fit residues: 152.6927 Evaluate side-chains 297 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 68 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 22 VAL Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.160052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.143371 restraints weight = 8860.332| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.89 r_work: 0.4188 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 1.8818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.784 3834 Z= 7.100 Angle : 8.673 60.649 5022 Z= 4.208 Chirality : 0.486 1.797 648 Planarity : 0.041 0.104 594 Dihedral : 27.600 89.873 486 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 195.39 Ramachandran Plot: Outliers : 12.96 % Allowed : 51.06 % Favored : 35.98 % Rotamer: Outliers : 53.70 % Allowed : 23.05 % Favored : 23.25 % Cbeta Deviations : 41.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 23.84 % 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: -8.44 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.43 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15107 / 7.10 ( 3834) covalent geometry : angle 8.67290 / 4.21 ( 5022) hydrogen bonds : bond 0.46752 / 30.31 ( 102) hydrogen bonds : angle 20.03094 / 12.96 ( 306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 68 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7529 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: Ad 141 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7832 (tp40) REVERT: Ad 144 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7839 (ttp) REVERT: Aj 145 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (mptt) REVERT: Am 135 MET cc_start: 0.8433 (mtt) cc_final: 0.8060 (mtp) REVERT: Ap 161 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7530 (m-40) REVERT: Ap 162 MET cc_start: 0.7034 (mtt) cc_final: 0.6681 (mtm) REVERT: Aq 169 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6796 (pt) REVERT: Ci 219 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7420 (pptt) REVERT: Cj 228 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7455 (pptt) REVERT: Cj 232 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.5958 (pp) REVERT: Ck 237 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7582 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: Cl 246 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7903 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7201 (pttp) REVERT: Cn 262 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6236 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7284 (pptt) REVERT: Co 226 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8141 (mptt) REVERT: Cp 237 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7144 (pttp) REVERT: Cr 253 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8033 (mppt) REVERT: Cr 260 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: Cs 262 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7659 (mptt) REVERT: Cs 264 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7015 (pptt) REVERT: Cw 260 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7793 (t0) REVERT: Cx 269 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7861 (t0) REVERT: Er 15 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7624 (tp40) REVERT: Es 24 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7531 (tp40) REVERT: Es 26 ASN cc_start: 0.7076 (OUTLIER) cc_final: 0.6847 (t0) REVERT: Et 32 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8164 (p) REVERT: Et 33 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: Ev 46 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7849 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8260 (tptp) cc_final: 0.7630 (mtpt) REVERT: Ex 19 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7472 (mtpt) REVERT: Ey 36 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.6861 (tmm) REVERT: Ez 39 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7493 (ptmt) REVERT: Ez 44 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: Fa 53 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: Fa 54 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7279 (tmm) REVERT: Fe 39 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7299 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7322 (p0) REVERT: Fg 57 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7251 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7011 (tp40) outliers start: 261 outliers final: 193 residues processed: 289 average time/residue: 0.5072 time to fit residues: 151.1447 Evaluate side-chains 301 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 68 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ar residue 179 ASN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 268 ILE Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.143264 restraints weight = 8969.349| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.90 r_work: 0.4170 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 1.8829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.777 3834 Z= 7.098 Angle : 8.645 59.788 5022 Z= 4.199 Chirality : 0.485 1.823 648 Planarity : 0.041 0.104 594 Dihedral : 27.692 89.496 486 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 197.91 Ramachandran Plot: Outliers : 13.23 % Allowed : 50.53 % Favored : 36.24 % Rotamer: Outliers : 52.88 % Allowed : 23.46 % Favored : 23.66 % Cbeta Deviations : 40.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 24.07 % 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: -8.46 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15102 / 7.10 ( 3834) covalent geometry : angle 8.64463 / 4.20 ( 5022) hydrogen bonds : bond 0.46788 / 30.33 ( 102) hydrogen bonds : angle 20.04980 / 12.96 ( 306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 68 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7535 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: Ad 141 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7828 (tp40) REVERT: Ad 144 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7845 (ttp) REVERT: Aj 145 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7909 (mptt) REVERT: Am 135 MET cc_start: 0.8461 (mtp) cc_final: 0.8101 (mtp) REVERT: Ap 161 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7508 (m-40) REVERT: Ap 162 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6680 (mtt) REVERT: Aq 169 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6812 (pt) REVERT: Ci 219 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7445 (pptt) REVERT: Cj 228 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7465 (pptt) REVERT: Cj 232 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5977 (pp) REVERT: Ck 237 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7599 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: Cl 246 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7926 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7224 (pttp) REVERT: Cn 262 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6216 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7302 (pptt) REVERT: Co 226 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8177 (mptt) REVERT: Cp 237 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7144 (pttp) REVERT: Cr 253 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8041 (mppt) REVERT: Cr 260 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7825 (m-40) REVERT: Cs 262 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: Cs 264 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.6965 (pptt) REVERT: Cw 260 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7787 (t0) REVERT: Cx 269 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7786 (t0) REVERT: Er 15 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7639 (tp40) REVERT: Es 24 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7568 (tp40) REVERT: Es 26 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6810 (t0) REVERT: Et 32 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8173 (p) REVERT: Et 33 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: Ev 46 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7829 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8275 (tptp) cc_final: 0.7674 (mtpt) REVERT: Ex 19 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7457 (mtpt) REVERT: Ey 36 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.6885 (tmm) REVERT: Ez 39 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7509 (ptmt) REVERT: Ez 44 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: Fa 53 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (m-40) REVERT: Fa 54 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7344 (tmm) REVERT: Fe 39 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7336 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7321 (p0) REVERT: Fg 57 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7248 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7037 (tp40) outliers start: 257 outliers final: 192 residues processed: 286 average time/residue: 0.5168 time to fit residues: 152.3290 Evaluate side-chains 301 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 68 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Ap residue 162 MET Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ar residue 179 ASN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 255 LYS Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.159810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.143295 restraints weight = 8735.892| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.85 r_work: 0.4188 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 1.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.773 3834 Z= 7.096 Angle : 8.647 59.917 5022 Z= 4.200 Chirality : 0.486 1.848 648 Planarity : 0.041 0.104 594 Dihedral : 27.763 89.040 486 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 198.66 Ramachandran Plot: Outliers : 13.23 % Allowed : 50.79 % Favored : 35.98 % Rotamer: Outliers : 52.47 % Allowed : 23.66 % Favored : 23.87 % Cbeta Deviations : 40.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 24.31 % 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: -8.46 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15101 / 7.10 ( 3834) covalent geometry : angle 8.64737 / 4.20 ( 5022) hydrogen bonds : bond 0.46798 / 30.34 ( 102) hydrogen bonds : angle 20.06957 / 12.97 ( 306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 68 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7515 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: Ad 141 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7786 (tp40) REVERT: Ad 144 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7834 (ttp) REVERT: Aj 145 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7901 (mptt) REVERT: Am 135 MET cc_start: 0.8466 (mtp) cc_final: 0.8104 (mtp) REVERT: Ap 161 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: Ap 162 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6682 (mtt) REVERT: Aq 169 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6791 (pt) REVERT: Ci 219 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7409 (pptt) REVERT: Cj 228 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7446 (pptt) REVERT: Cj 232 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.5958 (pp) REVERT: Ck 237 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7604 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7608 (tp40) REVERT: Cl 246 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7891 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7193 (pttp) REVERT: Cn 262 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6237 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7274 (pptt) REVERT: Co 226 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8146 (mptt) REVERT: Cp 237 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7128 (pttp) REVERT: Cr 253 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8033 (mppt) REVERT: Cr 260 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: Cs 262 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7657 (mptt) REVERT: Cs 264 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.6987 (pptt) REVERT: Cs 266 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8664 (m) REVERT: Cw 260 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7792 (t0) REVERT: Cx 269 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7784 (t0) REVERT: Er 15 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: Es 24 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7545 (tp40) REVERT: Et 32 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8156 (p) REVERT: Et 33 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: Ev 46 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7842 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8258 (tptp) cc_final: 0.7639 (mtpt) REVERT: Ex 19 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: Ey 36 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.6862 (tmm) REVERT: Ez 39 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7500 (ptmt) REVERT: Ez 44 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8192 (m-40) REVERT: Fa 53 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: Fa 54 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7297 (tmm) REVERT: Fe 39 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7303 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7328 (p0) REVERT: Fg 57 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7232 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7015 (tp40) outliers start: 255 outliers final: 192 residues processed: 284 average time/residue: 0.4937 time to fit residues: 144.6324 Evaluate side-chains 301 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 68 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Ap residue 162 MET Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ar residue 179 ASN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 255 LYS Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Cz residue 287 ASN Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 12 LYS Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.159592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.142965 restraints weight = 8822.297| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.84 r_work: 0.4195 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 1.8839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.778 3834 Z= 7.094 Angle : 8.640 59.817 5022 Z= 4.195 Chirality : 0.486 1.864 648 Planarity : 0.041 0.104 594 Dihedral : 27.792 89.542 486 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 198.78 Ramachandran Plot: Outliers : 13.23 % Allowed : 51.32 % Favored : 35.45 % Rotamer: Outliers : 50.62 % Allowed : 25.93 % Favored : 23.46 % Cbeta Deviations : 40.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 24.31 % 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: -8.48 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.46 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15093 / 7.09 ( 3834) covalent geometry : angle 8.64008 / 4.19 ( 5022) hydrogen bonds : bond 0.46840 / 30.37 ( 102) hydrogen bonds : angle 20.05204 / 12.96 ( 306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 67 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7535 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: Ad 141 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7873 (tp40) REVERT: Ad 144 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7834 (ttp) REVERT: Aj 145 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: Am 135 MET cc_start: 0.8473 (mtp) cc_final: 0.8153 (mtp) REVERT: Ap 161 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7509 (m-40) REVERT: Ap 162 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6689 (mtt) REVERT: Aq 169 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6801 (pt) REVERT: Ci 219 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7433 (pptt) REVERT: Cj 228 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7471 (pptt) REVERT: Cj 232 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.5980 (pp) REVERT: Ck 237 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7631 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7598 (tp40) REVERT: Cl 246 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7908 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7219 (pttp) REVERT: Cn 262 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6239 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7301 (pptt) REVERT: Co 226 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8161 (mptt) REVERT: Cp 237 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7156 (pttp) REVERT: Cr 253 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8053 (mppt) REVERT: Cr 260 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7832 (m-40) REVERT: Cs 262 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7666 (mptt) REVERT: Cs 264 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7359 (pttm) REVERT: Cs 266 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8726 (m) REVERT: Cw 260 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7801 (t0) REVERT: Cx 269 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7782 (t0) REVERT: Er 15 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: Es 24 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7545 (tp40) REVERT: Es 26 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6739 (t0) REVERT: Et 32 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8161 (p) REVERT: Et 33 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: Ev 46 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7855 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8268 (tptp) cc_final: 0.7637 (mtpt) REVERT: Ex 19 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7524 (mtpt) REVERT: Ey 36 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.6859 (tmm) REVERT: Ez 39 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7492 (ptmm) REVERT: Ez 44 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: Fa 53 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8559 (m-40) REVERT: Fa 54 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7303 (tmm) REVERT: Fe 39 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7340 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7330 (p0) REVERT: Fg 57 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7266 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7017 (tp40) outliers start: 246 outliers final: 193 residues processed: 275 average time/residue: 0.4913 time to fit residues: 139.2868 Evaluate side-chains 302 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ac residue 135 MET Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Ap residue 162 MET Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ar residue 179 ASN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 249 GLN Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 255 LYS Chi-restraints excluded: chain Cw residue 257 SER Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 12 LYS Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.159688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.143154 restraints weight = 8868.478| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.86 r_work: 0.4172 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 1.8844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.775 3834 Z= 7.097 Angle : 8.630 59.826 5022 Z= 4.192 Chirality : 0.485 1.870 648 Planarity : 0.041 0.104 594 Dihedral : 27.828 88.795 486 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 197.21 Ramachandran Plot: Outliers : 13.23 % Allowed : 52.12 % Favored : 34.66 % Rotamer: Outliers : 50.21 % Allowed : 26.34 % Favored : 23.46 % Cbeta Deviations : 40.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 24.07 % 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: -8.48 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.46 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15099 / 7.10 ( 3834) covalent geometry : angle 8.62997 / 4.19 ( 5022) hydrogen bonds : bond 0.46884 / 30.38 ( 102) hydrogen bonds : angle 20.03098 / 12.95 ( 306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 66 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 123 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7523 (tp-100) REVERT: Ac 132 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: Ad 141 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: Ad 144 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7836 (ttp) REVERT: Aj 145 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: Am 135 MET cc_start: 0.8470 (mtp) cc_final: 0.8160 (mtp) REVERT: Ao 153 MET cc_start: 0.7933 (mtp) cc_final: 0.7607 (mtp) REVERT: Ap 161 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7501 (m-40) REVERT: Ap 162 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6682 (mtt) REVERT: Aq 169 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6790 (pt) REVERT: Ci 219 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7429 (pptt) REVERT: Cj 228 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7456 (pptt) REVERT: Cj 232 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.5967 (pp) REVERT: Ck 237 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7625 (pmtt) REVERT: Ck 240 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7629 (tp40) REVERT: Cl 246 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7912 (mtmt) REVERT: Cm 255 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7217 (pttp) REVERT: Cn 262 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6254 (tmmt) REVERT: Cn 264 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7292 (pptt) REVERT: Co 226 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8175 (mptt) REVERT: Cp 237 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7131 (pttp) REVERT: Cr 253 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8032 (mppt) REVERT: Cr 260 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: Cs 262 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7696 (mptt) REVERT: Cs 264 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.6990 (pptt) REVERT: Cw 260 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7794 (t0) REVERT: Cx 269 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7789 (t0) REVERT: Er 15 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7636 (tp40) REVERT: Es 24 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7571 (tp40) REVERT: Es 26 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6758 (t0) REVERT: Et 32 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8163 (p) REVERT: Et 33 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: Ev 46 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7853 (mmtm) REVERT: Ew 10 LYS cc_start: 0.8277 (tptp) cc_final: 0.7633 (mtpt) REVERT: Ex 19 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7490 (mtpt) REVERT: Ey 36 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.6881 (tmm) REVERT: Ez 39 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7512 (ptmm) REVERT: Ez 44 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8196 (m-40) REVERT: Fa 53 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8561 (m-40) REVERT: Fa 54 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7298 (tmm) REVERT: Fe 39 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7316 (ttpt) REVERT: Ff 53 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7340 (p0) REVERT: Fg 57 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7227 (ttpt) REVERT: Fg 60 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7033 (tp40) outliers start: 244 outliers final: 196 residues processed: 273 average time/residue: 0.4211 time to fit residues: 118.4812 Evaluate side-chains 303 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 66 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 109 LYS Chi-restraints excluded: chain Aa residue 111 LYS Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Aa residue 116 ASN Chi-restraints excluded: chain Ab residue 120 LYS Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ab residue 123 GLN Chi-restraints excluded: chain Ab residue 124 ILE Chi-restraints excluded: chain Ac residue 129 LYS Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ac residue 132 GLN Chi-restraints excluded: chain Ac residue 133 ILE Chi-restraints excluded: chain Ac residue 134 ASN Chi-restraints excluded: chain Ac residue 135 MET Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ad residue 139 VAL Chi-restraints excluded: chain Ad residue 140 SER Chi-restraints excluded: chain Ad residue 141 GLN Chi-restraints excluded: chain Ad residue 142 ILE Chi-restraints excluded: chain Ad residue 143 ASN Chi-restraints excluded: chain Ad residue 144 MET Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 148 VAL Chi-restraints excluded: chain Ae residue 150 GLN Chi-restraints excluded: chain Ae residue 151 ILE Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Af residue 154 LYS Chi-restraints excluded: chain Af residue 156 LYS Chi-restraints excluded: chain Af residue 160 ILE Chi-restraints excluded: chain Ag residue 121 VAL Chi-restraints excluded: chain Ag residue 123 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ag residue 126 MET Chi-restraints excluded: chain Ah residue 127 LYS Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 129 LYS Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ah residue 131 SER Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ah residue 135 MET Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Ai residue 138 LYS Chi-restraints excluded: chain Ai residue 139 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ai residue 144 MET Chi-restraints excluded: chain Aj residue 145 LYS Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 150 GLN Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 156 LYS Chi-restraints excluded: chain Ak residue 157 VAL Chi-restraints excluded: chain Ak residue 159 GLN Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Al residue 167 SER Chi-restraints excluded: chain Al residue 168 GLN Chi-restraints excluded: chain Al residue 169 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 131 SER Chi-restraints excluded: chain An residue 138 LYS Chi-restraints excluded: chain An residue 140 SER Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 149 SER Chi-restraints excluded: chain Ao residue 151 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Ap residue 156 LYS Chi-restraints excluded: chain Ap residue 160 ILE Chi-restraints excluded: chain Ap residue 161 ASN Chi-restraints excluded: chain Ap residue 162 MET Chi-restraints excluded: chain Aq residue 163 LYS Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 167 SER Chi-restraints excluded: chain Aq residue 168 GLN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 172 LYS Chi-restraints excluded: chain Ar residue 174 LYS Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 177 GLN Chi-restraints excluded: chain Ar residue 179 ASN Chi-restraints excluded: chain Ci residue 219 LYS Chi-restraints excluded: chain Ci residue 222 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Ci residue 224 ASN Chi-restraints excluded: chain Ci residue 225 MET Chi-restraints excluded: chain Cj residue 228 LYS Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cj residue 233 ASN Chi-restraints excluded: chain Cj residue 234 MET Chi-restraints excluded: chain Ck residue 237 LYS Chi-restraints excluded: chain Ck residue 240 GLN Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Ck residue 242 ASN Chi-restraints excluded: chain Ck residue 243 MET Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 247 VAL Chi-restraints excluded: chain Cl residue 249 GLN Chi-restraints excluded: chain Cl residue 250 ILE Chi-restraints excluded: chain Cl residue 251 ASN Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Cm residue 257 SER Chi-restraints excluded: chain Cm residue 258 GLN Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cm residue 260 ASN Chi-restraints excluded: chain Cm residue 261 MET Chi-restraints excluded: chain Cn residue 262 LYS Chi-restraints excluded: chain Cn residue 264 LYS Chi-restraints excluded: chain Cn residue 265 VAL Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Cn residue 270 MET Chi-restraints excluded: chain Co residue 226 LYS Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 237 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 246 LYS Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cq residue 248 SER Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cr residue 255 LYS Chi-restraints excluded: chain Cr residue 256 VAL Chi-restraints excluded: chain Cr residue 260 ASN Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 264 LYS Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Ct residue 279 MET Chi-restraints excluded: chain Cu residue 235 LYS Chi-restraints excluded: chain Cu residue 237 LYS Chi-restraints excluded: chain Cu residue 239 SER Chi-restraints excluded: chain Cu residue 241 ILE Chi-restraints excluded: chain Cu residue 242 ASN Chi-restraints excluded: chain Cv residue 248 SER Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 250 ILE Chi-restraints excluded: chain Cw residue 255 LYS Chi-restraints excluded: chain Cw residue 257 SER Chi-restraints excluded: chain Cw residue 259 ILE Chi-restraints excluded: chain Cw residue 260 ASN Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Cx residue 266 SER Chi-restraints excluded: chain Cx residue 267 GLN Chi-restraints excluded: chain Cx residue 269 ASN Chi-restraints excluded: chain Cy residue 275 SER Chi-restraints excluded: chain Cz residue 282 LYS Chi-restraints excluded: chain Eq residue 1 LYS Chi-restraints excluded: chain Eq residue 3 LYS Chi-restraints excluded: chain Eq residue 9 MET Chi-restraints excluded: chain Er residue 12 LYS Chi-restraints excluded: chain Er residue 15 GLN Chi-restraints excluded: chain Er residue 18 MET Chi-restraints excluded: chain Es residue 24 GLN Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Es residue 26 ASN Chi-restraints excluded: chain Es residue 27 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 31 VAL Chi-restraints excluded: chain Et residue 32 SER Chi-restraints excluded: chain Et residue 33 GLN Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Et residue 35 ASN Chi-restraints excluded: chain Et residue 36 MET Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 40 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Eu residue 45 MET Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ev residue 48 LYS Chi-restraints excluded: chain Ev residue 49 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ev residue 54 MET Chi-restraints excluded: chain Ew residue 12 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 14 SER Chi-restraints excluded: chain Ew residue 18 MET Chi-restraints excluded: chain Ex residue 19 LYS Chi-restraints excluded: chain Ex residue 20 VAL Chi-restraints excluded: chain Ex residue 21 LYS Chi-restraints excluded: chain Ex residue 23 SER Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ex residue 27 MET Chi-restraints excluded: chain Ey residue 28 LYS Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ey residue 32 SER Chi-restraints excluded: chain Ey residue 36 MET Chi-restraints excluded: chain Ez residue 37 LYS Chi-restraints excluded: chain Ez residue 38 VAL Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Ez residue 40 VAL Chi-restraints excluded: chain Ez residue 42 GLN Chi-restraints excluded: chain Ez residue 43 ILE Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 48 LYS Chi-restraints excluded: chain Fa residue 50 SER Chi-restraints excluded: chain Fa residue 51 GLN Chi-restraints excluded: chain Fa residue 52 ILE Chi-restraints excluded: chain Fa residue 53 ASN Chi-restraints excluded: chain Fa residue 54 MET Chi-restraints excluded: chain Fb residue 55 LYS Chi-restraints excluded: chain Fb residue 56 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 59 SER Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 21 LYS Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fc residue 26 ASN Chi-restraints excluded: chain Fd residue 30 LYS Chi-restraints excluded: chain Fd residue 31 VAL Chi-restraints excluded: chain Fd residue 32 SER Chi-restraints excluded: chain Fd residue 33 GLN Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fd residue 35 ASN Chi-restraints excluded: chain Fe residue 37 LYS Chi-restraints excluded: chain Fe residue 39 LYS Chi-restraints excluded: chain Fe residue 45 MET Chi-restraints excluded: chain Ff residue 48 LYS Chi-restraints excluded: chain Ff residue 53 ASN Chi-restraints excluded: chain Fg residue 57 LYS Chi-restraints excluded: chain Fg residue 58 VAL Chi-restraints excluded: chain Fg residue 59 SER Chi-restraints excluded: chain Fg residue 60 GLN Chi-restraints excluded: chain Fh residue 71 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Et 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.159664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.143049 restraints weight = 8894.790| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.84 r_work: 0.4191 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 1.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.151 0.777 3834 Z= 7.095 Angle : 8.630 59.826 5022 Z= 4.192 Chirality : 0.485 1.875 648 Planarity : 0.041 0.104 594 Dihedral : 27.836 87.522 486 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 197.93 Ramachandran Plot: Outliers : 13.49 % Allowed : 51.85 % Favored : 34.66 % Rotamer: Outliers : 50.82 % Allowed : 25.51 % Favored : 23.66 % Cbeta Deviations : 40.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 24.31 % 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: -8.48 (0.19), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.46 (0.14), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.15096 / 7.09 ( 3834) covalent geometry : angle 8.62990 / 4.19 ( 5022) hydrogen bonds : bond 0.46912 / 30.40 ( 102) hydrogen bonds : angle 20.03641 / 12.95 ( 306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2166.93 seconds wall clock time: 38 minutes 59.97 seconds (2339.97 seconds total)