Starting phenix.real_space_refine on Thu Oct 22 18:59:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h7u_51914/10_2026/9h7u_51914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h7u_51914/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9h7u_51914/10_2026/9h7u_51914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h7u_51914/10_2026/9h7u_51914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h7u_51914/10_2026/9h7u_51914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h7u_51914/10_2026/9h7u_51914.map" } 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-2.3rc1-6221/lib/python3.11/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: 1.50, per 1000 atoms: 0.39 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: 0.35 Conformation dependent library (CDL) restraints added in 139.0 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: 0.10 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: 0.56 Time building geometry restraints manager: 0.49 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: 3.260 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: 0.020 Process input model: 6.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3413 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 : 0.122 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: 0.5680 time to fit residues: 139.9790 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 : 0.118 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 114 GLN Ah 134 ASN Ai 141 GLN Ai 143 ASN Ao 152 ASN Co 233 ASN Cr 260 ASN Cw 258 GLN Ex 26 ASN Ey 35 ASN Ez 44 ASN Fa 53 ASN Fb 60 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.246579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.221254 restraints weight = 4888.091| |-----------------------------------------------------------------------------| r_work (start): 0.5118 rms_B_bonded: 3.47 r_work: 0.4996 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.9014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3834 Z= 0.231 Angle : 0.784 5.779 5022 Z= 0.424 Chirality : 0.061 0.151 648 Planarity : 0.004 0.016 594 Dihedral : 17.771 87.923 488 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 10.49 % Allowed : 29.42 % Favored : 60.08 % 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: -0.51 (0.45), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 ( 3834) covalent geometry : angle 0.78421 / 0.42 ( 5022) hydrogen bonds : bond 0.02947 / 1.88 ( 102) hydrogen bonds : angle 8.60736 / 5.46 ( 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 232 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ag 122 SER cc_start: 0.8450 (m) cc_final: 0.8236 (p) REVERT: Ag 126 MET cc_start: 0.5181 (mmm) cc_final: 0.4916 (tpp) REVERT: Ah 127 LYS cc_start: 0.7904 (tttp) cc_final: 0.7491 (mptt) REVERT: Ah 129 LYS cc_start: 0.7717 (tptm) cc_final: 0.7309 (tptp) REVERT: Ai 138 LYS cc_start: 0.7152 (tptm) cc_final: 0.6940 (ptmm) REVERT: Aj 147 LYS cc_start: 0.7637 (tptm) cc_final: 0.6857 (ptmm) REVERT: Ak 157 VAL cc_start: 0.8295 (t) cc_final: 0.7919 (p) REVERT: Ak 158 SER cc_start: 0.7794 (m) cc_final: 0.7352 (t) REVERT: Al 165 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7670 (ptmm) REVERT: Al 167 SER cc_start: 0.8182 (m) cc_final: 0.7824 (p) REVERT: Cm 253 LYS cc_start: 0.7164 (mttt) cc_final: 0.5516 (ttpp) REVERT: Cn 270 MET cc_start: 0.5463 (mtt) cc_final: 0.5093 (mtp) REVERT: Co 232 ILE cc_start: 0.6261 (mp) cc_final: 0.5621 (mp) REVERT: Cp 237 LYS cc_start: 0.7263 (tptm) cc_final: 0.6460 (pptt) REVERT: Cp 243 MET cc_start: 0.4794 (OUTLIER) cc_final: 0.4177 (ptp) REVERT: Cr 253 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7071 (tmtp) REVERT: Cs 262 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7179 (mtpt) REVERT: Ct 279 MET cc_start: 0.5178 (pmm) cc_final: 0.4921 (pmm) REVERT: Ev 52 ILE cc_start: 0.6367 (mp) cc_final: 0.6108 (mm) REVERT: Ew 10 LYS cc_start: 0.8098 (tptp) cc_final: 0.7684 (mptt) REVERT: Ew 12 LYS cc_start: 0.8022 (tptm) cc_final: 0.7329 (ptmm) REVERT: Ew 15 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5639 (tp40) REVERT: Ex 21 LYS cc_start: 0.7928 (tptm) cc_final: 0.7462 (mmpt) REVERT: Ey 28 LYS cc_start: 0.7898 (tptp) cc_final: 0.7483 (mtmm) REVERT: Fa 46 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7553 (mtmm) REVERT: Fa 50 SER cc_start: 0.7707 (m) cc_final: 0.7148 (t) REVERT: Fb 57 LYS cc_start: 0.7962 (tppt) cc_final: 0.7384 (ptmm) outliers start: 51 outliers final: 11 residues processed: 220 average time/residue: 0.5238 time to fit residues: 118.6181 Evaluate side-chains 140 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Al residue 164 VAL Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain An residue 141 GLN Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Cp residue 243 MET Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Cu residue 240 GLN Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 15 GLN Chi-restraints excluded: chain Fa residue 46 LYS Chi-restraints excluded: chain Fa residue 47 VAL Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fg residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Aa 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 152 ASN ** Ai 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 168 GLN ** Ap 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 260 ASN Cq 251 ASN Cu 240 GLN ** Cv 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ey 35 ASN Fe 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.209220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.185224 restraints weight = 5163.784| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 3.04 r_work: 0.4729 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 1.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.089 3834 Z= 0.658 Angle : 1.446 11.405 5022 Z= 0.747 Chirality : 0.080 0.267 648 Planarity : 0.007 0.026 594 Dihedral : 14.961 88.610 486 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 36.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 20.58 % Allowed : 36.63 % Favored : 42.80 % 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: -1.34 (0.39), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.30), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01393 / 0.66 ( 3834) covalent geometry : angle 1.44636 / 0.75 ( 5022) hydrogen bonds : bond 0.05553 / 3.65 ( 102) hydrogen bonds : angle 10.93196 / 7.14 ( 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 270 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 170 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 152 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.6384 (t0) REVERT: Ae 153 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.5069 (mtp) REVERT: Ah 127 LYS cc_start: 0.7657 (tptp) cc_final: 0.7137 (mptt) REVERT: Ah 129 LYS cc_start: 0.8369 (tptm) cc_final: 0.7943 (tptp) REVERT: Aj 149 SER cc_start: 0.8189 (m) cc_final: 0.7514 (t) REVERT: Aj 153 MET cc_start: 0.5989 (tmm) cc_final: 0.5269 (tpp) REVERT: Ak 154 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: Al 165 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7438 (ptmm) REVERT: Co 230 SER cc_start: 0.8592 (m) cc_final: 0.8221 (t) REVERT: Co 232 ILE cc_start: 0.6676 (mp) cc_final: 0.6443 (mp) REVERT: Cp 237 LYS cc_start: 0.7889 (tptm) cc_final: 0.7409 (tptp) REVERT: Cr 253 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6981 (tmtp) REVERT: Cr 261 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6214 (ptp) REVERT: Cs 262 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7382 (tmtp) REVERT: Cs 266 SER cc_start: 0.8635 (m) cc_final: 0.8065 (t) REVERT: Ct 279 MET cc_start: 0.6631 (pmm) cc_final: 0.5726 (pmm) REVERT: Cx 268 ILE cc_start: 0.6066 (mt) cc_final: 0.5632 (pp) REVERT: Es 25 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.5679 (mp) REVERT: Ew 10 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: Ew 12 LYS cc_start: 0.8236 (tptm) cc_final: 0.7595 (ptmt) REVERT: Ew 15 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: Ex 21 LYS cc_start: 0.8242 (tptm) cc_final: 0.7633 (tptp) REVERT: Ex 22 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7694 (t) REVERT: Ey 29 VAL cc_start: 0.8217 (t) cc_final: 0.7998 (p) REVERT: Ey 30 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7410 (ttpp) REVERT: Ez 38 VAL cc_start: 0.8173 (t) cc_final: 0.7784 (p) REVERT: Ez 39 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6799 (ptmt) REVERT: Fc 25 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6958 (tt) REVERT: Ff 54 MET cc_start: 0.3886 (mtt) cc_final: 0.3593 (mtt) outliers start: 100 outliers final: 52 residues processed: 231 average time/residue: 0.5031 time to fit residues: 120.7494 Evaluate side-chains 211 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 145 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 115 ILE Chi-restraints excluded: chain Ab residue 121 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 152 ASN Chi-restraints excluded: chain Ae residue 153 MET Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ah residue 133 ILE Chi-restraints excluded: chain Ai residue 137 VAL Chi-restraints excluded: chain Aj residue 146 VAL Chi-restraints excluded: chain Ak residue 154 LYS Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 164 VAL Chi-restraints excluded: chain Al residue 165 LYS Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Am residue 133 ILE Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ar residue 178 ILE Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Cl residue 245 VAL 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 Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 256 VAL Chi-restraints excluded: chain Co residue 227 VAL Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 234 MET Chi-restraints excluded: chain Cp residue 236 VAL Chi-restraints excluded: chain Cp residue 243 MET Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 252 MET 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 261 MET Chi-restraints excluded: chain Cs residue 262 LYS Chi-restraints excluded: chain Cs residue 263 VAL 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 Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 251 ASN Chi-restraints excluded: chain Eq residue 7 ILE Chi-restraints excluded: chain Er residue 10 LYS Chi-restraints excluded: chain Er residue 16 ILE Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ew residue 10 LYS Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 15 GLN Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ez residue 39 LYS Chi-restraints excluded: chain Fa residue 47 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fg residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ai 143 ASN Aj 150 GLN Aj 152 ASN Ak 159 GLN Ak 161 ASN An 143 ASN Ap 159 GLN ** Cm 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 269 ASN Cv 251 ASN ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ez 44 ASN Fa 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.221308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.196349 restraints weight = 4807.602| |-----------------------------------------------------------------------------| r_work (start): 0.4960 rms_B_bonded: 3.15 r_work: 0.4844 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 1.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3834 Z= 0.196 Angle : 0.748 7.035 5022 Z= 0.404 Chirality : 0.058 0.256 648 Planarity : 0.003 0.018 594 Dihedral : 11.976 83.605 486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 16.67 % Allowed : 44.24 % Favored : 39.09 % 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: -0.52 (0.41), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.31), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 ( 3834) covalent geometry : angle 0.74790 / 0.40 ( 5022) hydrogen bonds : bond 0.03782 / 2.40 ( 102) hydrogen bonds : angle 8.87353 / 5.72 ( 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 249 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 168 time to evaluate : 0.192 Fit side-chains REVERT: Ac 135 MET cc_start: 0.6714 (ttm) cc_final: 0.6437 (ttm) REVERT: Af 162 MET cc_start: 0.5792 (mtt) cc_final: 0.5584 (mtp) REVERT: Ah 127 LYS cc_start: 0.7455 (tptp) cc_final: 0.7247 (tptp) REVERT: Ah 129 LYS cc_start: 0.8376 (tptm) cc_final: 0.8042 (tptp) REVERT: Ai 138 LYS cc_start: 0.7894 (tptm) cc_final: 0.7545 (ptmm) REVERT: Ai 140 SER cc_start: 0.8370 (m) cc_final: 0.8144 (p) REVERT: Ci 217 LYS cc_start: 0.7524 (mmtp) cc_final: 0.5634 (ttpp) REVERT: Cm 253 LYS cc_start: 0.7349 (mptm) cc_final: 0.5321 (ttpt) REVERT: Cp 237 LYS cc_start: 0.7882 (tptm) cc_final: 0.7399 (tptp) REVERT: Cr 253 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6905 (tmtp) REVERT: Cx 268 ILE cc_start: 0.5708 (mt) cc_final: 0.5462 (pp) REVERT: Cx 270 MET cc_start: 0.5348 (mtt) cc_final: 0.4828 (pmt) REVERT: Cz 287 ASN cc_start: 0.6303 (p0) cc_final: 0.5713 (m-40) REVERT: Cz 288 MET cc_start: 0.6413 (mtm) cc_final: 0.6136 (ttp) REVERT: Et 36 MET cc_start: 0.6542 (mtt) cc_final: 0.6285 (ttm) REVERT: Ew 10 LYS cc_start: 0.8083 (tptp) cc_final: 0.7777 (mptt) REVERT: Ew 12 LYS cc_start: 0.8160 (tptm) cc_final: 0.7498 (ptmm) REVERT: Ex 21 LYS cc_start: 0.8137 (tptm) cc_final: 0.7681 (tptp) REVERT: Ey 28 LYS cc_start: 0.7638 (tptp) cc_final: 0.7281 (tptm) REVERT: Ez 39 LYS cc_start: 0.7793 (tppt) cc_final: 0.7274 (ptmt) REVERT: Fb 57 LYS cc_start: 0.8011 (tppt) cc_final: 0.7424 (ptmt) REVERT: Fc 25 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6848 (tt) outliers start: 81 outliers final: 35 residues processed: 214 average time/residue: 0.4801 time to fit residues: 106.1533 Evaluate side-chains 180 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Am residue 133 ILE Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain An residue 143 ASN Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 178 ILE Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Cl residue 245 VAL Chi-restraints excluded: chain Cl residue 246 LYS 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 Cn residue 268 ILE Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Cz residue 286 ILE Chi-restraints excluded: chain Eq residue 7 ILE Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 16 ILE Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 141 GLN Aj 150 GLN Al 168 GLN ** Am 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cv 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ez 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 53 ASN Fb 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.204561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.179340 restraints weight = 5166.242| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 3.18 r_work: 0.4661 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 1.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.076 3834 Z= 0.625 Angle : 1.351 13.497 5022 Z= 0.696 Chirality : 0.078 0.512 648 Planarity : 0.005 0.019 594 Dihedral : 12.543 87.793 486 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 37.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 21.60 % Allowed : 39.92 % Favored : 38.48 % 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: -1.69 (0.38), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01283 / 0.62 ( 3834) covalent geometry : angle 1.35055 / 0.70 ( 5022) hydrogen bonds : bond 0.05365 / 3.39 ( 102) hydrogen bonds : angle 10.24761 / 6.62 ( 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 234 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 129 time to evaluate : 0.128 Fit side-chains REVERT: Ae 149 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7168 (p) REVERT: Ae 153 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5976 (mtt) REVERT: Ah 127 LYS cc_start: 0.7674 (tptp) cc_final: 0.7468 (tppp) REVERT: Ai 138 LYS cc_start: 0.8303 (tptm) cc_final: 0.7580 (pptt) REVERT: Aj 149 SER cc_start: 0.7704 (m) cc_final: 0.6972 (p) REVERT: Al 163 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7771 (mptt) REVERT: Cm 253 LYS cc_start: 0.8022 (mptm) cc_final: 0.7801 (mppt) REVERT: Cp 237 LYS cc_start: 0.8063 (tptm) cc_final: 0.7677 (tptp) REVERT: Cr 253 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7009 (tmtp) REVERT: Cx 268 ILE cc_start: 0.6125 (mt) cc_final: 0.5867 (pp) REVERT: Cy 277 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.5908 (pp) REVERT: Et 36 MET cc_start: 0.6719 (mtt) cc_final: 0.6412 (ttp) REVERT: Ev 54 MET cc_start: 0.6392 (mtp) cc_final: 0.4755 (ttp) REVERT: Ew 10 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: Ex 21 LYS cc_start: 0.8162 (tptm) cc_final: 0.7739 (mmpt) REVERT: Ex 22 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7538 (t) REVERT: Ey 28 LYS cc_start: 0.8049 (tptp) cc_final: 0.7518 (tptm) REVERT: Ez 39 LYS cc_start: 0.8002 (tppt) cc_final: 0.7455 (ptmm) REVERT: Fc 25 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6967 (tt) outliers start: 105 outliers final: 63 residues processed: 199 average time/residue: 0.4030 time to fit residues: 83.2780 Evaluate side-chains 195 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 149 SER Chi-restraints excluded: chain Ae residue 153 MET Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE 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 Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 164 VAL Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain An residue 143 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Aq residue 169 ILE Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Cl residue 246 LYS 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 259 ILE Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Co residue 227 VAL Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Cp residue 236 VAL 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 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 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 251 ASN Chi-restraints excluded: chain Cy residue 277 ILE Chi-restraints excluded: chain Er residue 16 ILE Chi-restraints excluded: chain Es residue 25 ILE Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Ew residue 10 LYS Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 16 ILE Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ez residue 45 MET Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 58 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 150 GLN Aj 152 ASN An 143 ASN Ap 159 GLN Aq 168 GLN Cn 269 ASN Cr 258 GLN ** Cu 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cv 251 ASN ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ey 33 GLN ** Fc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.219096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.192067 restraints weight = 4993.220| |-----------------------------------------------------------------------------| r_work (start): 0.4922 rms_B_bonded: 3.36 r_work: 0.4801 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 1.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3834 Z= 0.195 Angle : 0.756 6.277 5022 Z= 0.406 Chirality : 0.060 0.387 648 Planarity : 0.003 0.017 594 Dihedral : 10.751 88.532 486 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 15.84 % Allowed : 46.50 % Favored : 37.65 % 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: -1.03 (0.40), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 ( 3834) covalent geometry : angle 0.75630 / 0.41 ( 5022) hydrogen bonds : bond 0.03549 / 2.20 ( 102) hydrogen bonds : angle 8.66002 / 5.55 ( 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 218 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 141 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 114 GLN cc_start: 0.7438 (pt0) cc_final: 0.6537 (tp40) REVERT: Ai 138 LYS cc_start: 0.8349 (tptm) cc_final: 0.7673 (pptt) REVERT: Ao 152 ASN cc_start: 0.6419 (OUTLIER) cc_final: 0.6111 (p0) REVERT: Cl 248 SER cc_start: 0.7213 (OUTLIER) cc_final: 0.6738 (p) REVERT: Cp 237 LYS cc_start: 0.7956 (tptm) cc_final: 0.7471 (tptp) REVERT: Cr 253 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7199 (tmtp) REVERT: Er 18 MET cc_start: 0.6326 (mtm) cc_final: 0.5873 (ttp) REVERT: Et 36 MET cc_start: 0.6654 (mtt) cc_final: 0.6246 (ttp) REVERT: Ev 54 MET cc_start: 0.5782 (mtp) cc_final: 0.5169 (ttp) REVERT: Ew 10 LYS cc_start: 0.8243 (tptp) cc_final: 0.7873 (mptt) REVERT: Ex 21 LYS cc_start: 0.8085 (tptm) cc_final: 0.7699 (tptp) REVERT: Ey 28 LYS cc_start: 0.7773 (tptp) cc_final: 0.7412 (ttmm) REVERT: Ey 30 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7413 (tmtt) REVERT: Ey 31 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8100 (m) REVERT: Ez 39 LYS cc_start: 0.7837 (tppt) cc_final: 0.7272 (ptmt) REVERT: Fb 57 LYS cc_start: 0.8032 (tppt) cc_final: 0.7434 (ptmm) REVERT: Fc 25 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6864 (tt) outliers start: 77 outliers final: 47 residues processed: 190 average time/residue: 0.4331 time to fit residues: 85.2223 Evaluate side-chains 181 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 155 VAL Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Am residue 128 VAL Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 137 VAL Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 248 SER Chi-restraints excluded: chain Cl residue 250 ILE 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 259 ILE Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Co residue 229 VAL Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Ct residue 274 VAL Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ew residue 16 ILE Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fe residue 43 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aj 150 GLN Aj 152 ASN Ak 161 ASN Al 170 ASN ** Am 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 269 ASN Cv 251 ASN ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Fa 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.203302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.178534 restraints weight = 5321.431| |-----------------------------------------------------------------------------| r_work (start): 0.4775 rms_B_bonded: 3.18 r_work: 0.4651 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 1.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.075 3834 Z= 0.630 Angle : 1.357 13.673 5022 Z= 0.695 Chirality : 0.079 0.575 648 Planarity : 0.005 0.020 594 Dihedral : 12.269 79.902 486 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 38.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 19.55 % Allowed : 43.83 % Favored : 36.63 % 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: -1.92 (0.38), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.29), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01296 / 0.63 ( 3834) covalent geometry : angle 1.35729 / 0.69 ( 5022) hydrogen bonds : bond 0.05230 / 3.35 ( 102) hydrogen bonds : angle 10.13671 / 6.48 ( 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 215 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 120 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: Ac 131 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.6762 (p) REVERT: Ae 149 SER cc_start: 0.7365 (OUTLIER) cc_final: 0.6983 (p) REVERT: Ah 127 LYS cc_start: 0.7577 (tptp) cc_final: 0.7052 (ttmm) REVERT: Ai 138 LYS cc_start: 0.8636 (tptm) cc_final: 0.7920 (pptt) REVERT: Ak 158 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.7712 (p) REVERT: Al 163 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7733 (mptt) REVERT: Ao 152 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6282 (p0) REVERT: Cl 248 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7057 (p) REVERT: Cn 266 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7450 (p) REVERT: Cp 237 LYS cc_start: 0.8057 (tptm) cc_final: 0.7356 (pptt) REVERT: Cr 253 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7161 (tmtp) REVERT: Cw 261 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.4485 (mpp) REVERT: Et 36 MET cc_start: 0.6794 (mtt) cc_final: 0.6553 (ttp) REVERT: Ev 54 MET cc_start: 0.6451 (mtp) cc_final: 0.5294 (ttp) REVERT: Ew 10 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8073 (mptt) REVERT: Ex 21 LYS cc_start: 0.8166 (tptm) cc_final: 0.7693 (tmtt) REVERT: Ey 28 LYS cc_start: 0.7894 (tptp) cc_final: 0.7368 (tptm) REVERT: Ez 44 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7639 (m-40) REVERT: Fa 48 LYS cc_start: 0.8103 (tppt) cc_final: 0.7729 (mmmt) REVERT: Fc 25 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6831 (tt) REVERT: Ff 53 ASN cc_start: 0.6220 (p0) cc_final: 0.5971 (p0) REVERT: Ff 54 MET cc_start: 0.6113 (ptp) cc_final: 0.5826 (ptt) outliers start: 95 outliers final: 58 residues processed: 183 average time/residue: 0.3616 time to fit residues: 68.9715 Evaluate side-chains 188 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 119 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 113 SER Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ac residue 131 SER Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 149 SER Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 148 VAL Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 158 SER Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 137 VAL Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 178 ILE Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Ck residue 241 ILE Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 248 SER 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 259 ILE Chi-restraints excluded: chain Cn residue 266 SER Chi-restraints excluded: chain Co residue 227 VAL Chi-restraints excluded: chain Co residue 228 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 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 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Cs residue 266 SER Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Cv residue 252 MET Chi-restraints excluded: chain Cw residue 261 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Eu residue 43 ILE Chi-restraints excluded: chain Ev residue 46 LYS Chi-restraints excluded: chain Ew residue 10 LYS Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 16 ILE Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Ez residue 44 ASN Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fe residue 43 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 150 GLN Aj 152 ASN Ap 161 ASN Cn 269 ASN Cv 251 ASN ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fc 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.219645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.193550 restraints weight = 4903.175| |-----------------------------------------------------------------------------| r_work (start): 0.4954 rms_B_bonded: 3.16 r_work: 0.4837 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 1.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3834 Z= 0.196 Angle : 0.788 8.449 5022 Z= 0.418 Chirality : 0.061 0.436 648 Planarity : 0.003 0.018 594 Dihedral : 10.449 83.158 486 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 14.20 % Allowed : 49.18 % Favored : 36.63 % 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: -1.15 (0.41), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.32), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 ( 3834) covalent geometry : angle 0.78811 / 0.42 ( 5022) hydrogen bonds : bond 0.03334 / 2.09 ( 102) hydrogen bonds : angle 8.55418 / 5.46 ( 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 209 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 0.204 Fit side-chains REVERT: Aa 113 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.6914 (p) REVERT: Aa 114 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6537 (tp40) REVERT: Ai 138 LYS cc_start: 0.8475 (tptm) cc_final: 0.7781 (pptt) REVERT: Cl 248 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6692 (p) REVERT: Cp 237 LYS cc_start: 0.7874 (tptm) cc_final: 0.7449 (tptp) REVERT: Cr 253 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7238 (tmtp) REVERT: Cu 243 MET cc_start: 0.6054 (ttp) cc_final: 0.5829 (ttp) REVERT: Cz 288 MET cc_start: 0.6388 (mtm) cc_final: 0.6151 (ttp) REVERT: Et 36 MET cc_start: 0.6676 (mtt) cc_final: 0.6356 (ttp) REVERT: Ev 54 MET cc_start: 0.5921 (mtp) cc_final: 0.5324 (ttp) REVERT: Ew 10 LYS cc_start: 0.8347 (tptp) cc_final: 0.7956 (mptt) REVERT: Ew 12 LYS cc_start: 0.8332 (tppt) cc_final: 0.7433 (ptmm) REVERT: Ew 18 MET cc_start: 0.4788 (ttm) cc_final: 0.4587 (ttm) REVERT: Ex 21 LYS cc_start: 0.8140 (tptm) cc_final: 0.7775 (tmtt) REVERT: Ey 28 LYS cc_start: 0.7876 (tptp) cc_final: 0.7371 (tptm) REVERT: Ey 31 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (m) REVERT: Fb 57 LYS cc_start: 0.8003 (tppt) cc_final: 0.7403 (ptmm) REVERT: Fc 25 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6989 (tt) REVERT: Ff 54 MET cc_start: 0.5827 (ptp) cc_final: 0.5577 (ptt) outliers start: 69 outliers final: 44 residues processed: 184 average time/residue: 0.4467 time to fit residues: 85.1591 Evaluate side-chains 178 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 113 SER Chi-restraints excluded: chain Aa residue 114 GLN Chi-restraints excluded: chain Ac residue 130 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ai residue 140 SER Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 155 VAL Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 137 VAL Chi-restraints excluded: chain An residue 142 ILE Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 248 SER Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Cn residue 269 ASN Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 247 VAL Chi-restraints excluded: chain Cr residue 253 LYS Chi-restraints excluded: chain Cr residue 254 VAL Chi-restraints excluded: chain Cs residue 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ex residue 25 ILE Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fe residue 43 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 150 GLN Aj 152 ASN ** Am 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 269 ASN Cv 251 ASN Cx 267 GLN ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 17 ASN ** 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** ** Fa 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Fd 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.208377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.179267 restraints weight = 5469.020| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 3.22 r_work: 0.4644 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 1.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.076 3834 Z= 0.622 Angle : 1.362 14.112 5022 Z= 0.692 Chirality : 0.080 0.604 648 Planarity : 0.005 0.017 594 Dihedral : 11.324 76.260 486 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 37.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 17.08 % Allowed : 47.74 % Favored : 35.19 % 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: -1.94 (0.38), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.29), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01285 / 0.62 ( 3834) covalent geometry : angle 1.36187 / 0.69 ( 5022) hydrogen bonds : bond 0.05140 / 3.20 ( 102) hydrogen bonds : angle 10.01678 / 6.40 ( 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 209 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 126 time to evaluate : 0.141 Fit side-chains REVERT: Ab 122 SER cc_start: 0.7462 (OUTLIER) cc_final: 0.7053 (p) REVERT: Ac 127 LYS cc_start: 0.8048 (mttt) cc_final: 0.7687 (mtmm) REVERT: Ad 136 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7638 (mtmm) REVERT: Ae 149 SER cc_start: 0.7209 (OUTLIER) cc_final: 0.6935 (p) REVERT: Ah 127 LYS cc_start: 0.7664 (tptp) cc_final: 0.7061 (ttmm) REVERT: Ai 138 LYS cc_start: 0.8532 (tptm) cc_final: 0.7832 (pptt) REVERT: Ai 144 MET cc_start: 0.5854 (tpp) cc_final: 0.5595 (mtt) REVERT: Al 163 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7731 (mptt) REVERT: Cl 248 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.7011 (p) REVERT: Cn 266 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7463 (p) REVERT: Cp 237 LYS cc_start: 0.8073 (tptm) cc_final: 0.7705 (tptp) REVERT: Cr 253 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7166 (tmtp) REVERT: Cr 255 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6550 (pptt) REVERT: Et 36 MET cc_start: 0.6863 (mtt) cc_final: 0.6643 (ttp) REVERT: Ev 54 MET cc_start: 0.6311 (mtp) cc_final: 0.5892 (ttp) REVERT: Ew 10 LYS cc_start: 0.8619 (tptp) cc_final: 0.8126 (mptt) REVERT: Ex 21 LYS cc_start: 0.8150 (tptm) cc_final: 0.7590 (tmtt) REVERT: Ey 28 LYS cc_start: 0.7775 (tptp) cc_final: 0.7281 (tptm) REVERT: Fb 57 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7483 (tppt) REVERT: Fc 25 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6798 (tt) REVERT: Ff 54 MET cc_start: 0.6135 (ptp) cc_final: 0.5808 (ptt) outliers start: 83 outliers final: 55 residues processed: 180 average time/residue: 0.3924 time to fit residues: 73.3435 Evaluate side-chains 186 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 113 SER Chi-restraints excluded: chain Ab residue 122 SER Chi-restraints excluded: chain Ad residue 136 LYS Chi-restraints excluded: chain Ad residue 137 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 149 SER Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ah residue 128 VAL Chi-restraints excluded: chain Ah residue 130 VAL Chi-restraints excluded: chain Ai residue 140 SER Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Aj residue 151 ILE Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Al residue 171 MET Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 137 VAL Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ar residue 178 ILE Chi-restraints excluded: chain Ci residue 221 SER Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 248 SER Chi-restraints excluded: chain Cl residue 252 MET Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cn residue 266 SER Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Co residue 227 VAL Chi-restraints excluded: chain Co residue 228 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 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 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Cv residue 252 MET Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Eu residue 38 VAL Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ew residue 13 VAL Chi-restraints excluded: chain Ew residue 16 ILE Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 57 LYS Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fb residue 63 MET Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 134 ASN Aj 150 GLN Aj 152 ASN Ao 152 ASN Cn 269 ASN Cv 251 ASN ** Ex 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ey 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ez 42 GLN ** Fa 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5117 r_free = 0.5117 target = 0.218588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.192091 restraints weight = 5010.291| |-----------------------------------------------------------------------------| r_work (start): 0.4935 rms_B_bonded: 3.26 r_work: 0.4819 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 1.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3834 Z= 0.199 Angle : 0.818 8.118 5022 Z= 0.432 Chirality : 0.061 0.410 648 Planarity : 0.003 0.017 594 Dihedral : 9.625 71.950 486 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 13.17 % Allowed : 52.26 % Favored : 34.57 % 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: -1.17 (0.43), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.32), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 3834) covalent geometry : angle 0.81819 / 0.43 ( 5022) hydrogen bonds : bond 0.03518 / 2.26 ( 102) hydrogen bonds : angle 8.65247 / 5.55 ( 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 197 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: Aa 114 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6567 (tp40) REVERT: Ae 149 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6767 (p) REVERT: Ai 138 LYS cc_start: 0.8437 (tptm) cc_final: 0.7779 (pptt) REVERT: Aj 149 SER cc_start: 0.7595 (m) cc_final: 0.7195 (p) REVERT: Cl 248 SER cc_start: 0.7214 (OUTLIER) cc_final: 0.6625 (p) REVERT: Cp 237 LYS cc_start: 0.7813 (tptm) cc_final: 0.7295 (tptp) REVERT: Cr 253 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7146 (tmtp) REVERT: Cr 255 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6314 (pptt) REVERT: Cz 288 MET cc_start: 0.6471 (mtm) cc_final: 0.6233 (ttp) REVERT: Et 36 MET cc_start: 0.6860 (mtt) cc_final: 0.6585 (ttp) REVERT: Ev 54 MET cc_start: 0.6031 (mtp) cc_final: 0.5388 (ttp) REVERT: Ew 10 LYS cc_start: 0.8340 (tptp) cc_final: 0.7953 (mptt) REVERT: Ew 12 LYS cc_start: 0.8393 (tppt) cc_final: 0.7541 (ptmt) REVERT: Ew 18 MET cc_start: 0.4363 (ttm) cc_final: 0.3824 (mmp) REVERT: Ex 21 LYS cc_start: 0.8121 (tptm) cc_final: 0.7713 (tmtt) REVERT: Ex 23 SER cc_start: 0.8455 (m) cc_final: 0.7819 (p) REVERT: Ey 28 LYS cc_start: 0.7791 (tptp) cc_final: 0.7329 (tptm) REVERT: Fb 57 LYS cc_start: 0.8048 (tppt) cc_final: 0.7421 (ptmm) REVERT: Fc 25 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6963 (tt) REVERT: Ff 54 MET cc_start: 0.5875 (ptp) cc_final: 0.5602 (ptt) outliers start: 64 outliers final: 45 residues processed: 177 average time/residue: 0.4028 time to fit residues: 74.0438 Evaluate side-chains 178 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 113 SER Chi-restraints excluded: chain Aa residue 114 GLN Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 149 SER Chi-restraints excluded: chain Af residue 159 GLN Chi-restraints excluded: chain Ag residue 124 ILE Chi-restraints excluded: chain Ai residue 140 SER Chi-restraints excluded: chain Ai residue 142 ILE Chi-restraints excluded: chain Ak residue 155 VAL Chi-restraints excluded: chain Ak residue 160 ILE Chi-restraints excluded: chain Am residue 134 ASN Chi-restraints excluded: chain An residue 137 VAL Chi-restraints excluded: chain Ao residue 152 ASN Chi-restraints excluded: chain Aq residue 164 VAL Chi-restraints excluded: chain Ar residue 176 SER Chi-restraints excluded: chain Ci residue 223 ILE Chi-restraints excluded: chain Cj residue 232 ILE Chi-restraints excluded: chain Cl residue 246 LYS Chi-restraints excluded: chain Cl residue 248 SER Chi-restraints excluded: chain Cm residue 254 VAL Chi-restraints excluded: chain Cm residue 255 LYS Chi-restraints excluded: chain Cm residue 259 ILE Chi-restraints excluded: chain Cn residue 268 ILE Chi-restraints excluded: chain Co residue 228 LYS Chi-restraints excluded: chain Cp residue 238 VAL Chi-restraints excluded: chain Cq residue 245 VAL Chi-restraints excluded: chain Cq residue 247 VAL 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 263 VAL Chi-restraints excluded: chain Cs residue 265 VAL Chi-restraints excluded: chain Ct residue 272 VAL Chi-restraints excluded: chain Ct residue 273 LYS Chi-restraints excluded: chain Cv residue 249 GLN Chi-restraints excluded: chain Et residue 29 VAL Chi-restraints excluded: chain Et residue 34 ILE Chi-restraints excluded: chain Ev residue 52 ILE Chi-restraints excluded: chain Ew residue 11 VAL Chi-restraints excluded: chain Ex residue 22 VAL Chi-restraints excluded: chain Ey residue 30 LYS Chi-restraints excluded: chain Ey residue 31 VAL Chi-restraints excluded: chain Fa residue 49 VAL Chi-restraints excluded: chain Fb residue 61 ILE Chi-restraints excluded: chain Fc residue 23 SER Chi-restraints excluded: chain Fc residue 25 ILE Chi-restraints excluded: chain Fd residue 34 ILE Chi-restraints excluded: chain Fg residue 61 ILE Chi-restraints excluded: chain Fh residue 68 SER Chi-restraints excluded: chain Fh residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ac 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 150 GLN Aj 152 ASN ** Am 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 269 ASN Cv 251 ASN ** Ew 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ew 17 ASN ** 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 ** Fa 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Fd 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.204185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.178731 restraints weight = 5254.495| |-----------------------------------------------------------------------------| r_work (start): 0.4773 rms_B_bonded: 3.19 r_work: 0.4650 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 1.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.078 3834 Z= 0.620 Angle : 1.372 17.260 5022 Z= 0.696 Chirality : 0.080 0.662 648 Planarity : 0.005 0.019 594 Dihedral : 11.159 63.982 486 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 37.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 16.46 % Allowed : 48.97 % Favored : 34.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.93 (0.39), residues: 378 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 378 Details of bonding type rmsd/Z covalent geometry : bond 0.01285 / 0.62 ( 3834) covalent geometry : angle 1.37201 / 0.70 ( 5022) hydrogen bonds : bond 0.05105 / 3.19 ( 102) hydrogen bonds : angle 10.05263 / 6.41 ( 306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.81 seconds wall clock time: 29 minutes 38.24 seconds (1778.24 seconds total)