Starting phenix.real_space_refine on Sun Aug 24 22:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.map" model { file = "/net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opb_17047/08_2025/8opb_17047.cif" } resolution = 3.58 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= 0.010 sd= 0.083 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 192 5.16 5 C 14736 2.51 5 N 4064 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap Time building chain proxies: 2.41, per 1000 atoms: 0.10 Number of scatterers: 23328 At special positions: 0 Unit cell: (129.2, 129.2, 173.85, 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 192 16.00 O 4336 8.00 N 4064 7.00 C 14736 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: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5536 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 50.8% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAa 117 " --> pdb=" O ASNAa 113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAa 168 " --> pdb=" O SERAa 164 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 187 Processing helix chain 'Aa' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAa 199 " --> pdb=" O ALAAa 196 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAa 217 " --> pdb=" O ALAAa 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAa 218 " --> pdb=" O ARGAa 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAa 219 " --> pdb=" O GLUAa 215 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAb 117 " --> pdb=" O ASNAb 113 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAb 168 " --> pdb=" O SERAb 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 187 Processing helix chain 'Ab' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAb 199 " --> pdb=" O ALAAb 196 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAb 217 " --> pdb=" O ALAAb 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAb 218 " --> pdb=" O ARGAb 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAb 219 " --> pdb=" O GLUAb 215 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 66 through 71 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAc 117 " --> pdb=" O ASNAc 113 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAc 168 " --> pdb=" O SERAc 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 187 Processing helix chain 'Ac' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAc 199 " --> pdb=" O ALAAc 196 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAc 217 " --> pdb=" O ALAAc 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAc 218 " --> pdb=" O ARGAc 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAc 219 " --> pdb=" O GLUAc 215 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAd 117 " --> pdb=" O ASNAd 113 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAd 168 " --> pdb=" O SERAd 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 187 Processing helix chain 'Ad' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAd 199 " --> pdb=" O ALAAd 196 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAd 217 " --> pdb=" O ALAAd 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAd 218 " --> pdb=" O ARGAd 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAd 219 " --> pdb=" O GLUAd 215 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 66 through 71 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAe 117 " --> pdb=" O ASNAe 113 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAe 168 " --> pdb=" O SERAe 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 187 Processing helix chain 'Ae' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAe 199 " --> pdb=" O ALAAe 196 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAe 217 " --> pdb=" O ALAAe 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAe 219 " --> pdb=" O GLUAe 215 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAf 117 " --> pdb=" O ASNAf 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAf 168 " --> pdb=" O SERAf 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 187 Processing helix chain 'Af' and resid 193 through 199 removed outlier: 3.873A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAf 199 " --> pdb=" O ALAAf 196 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAf 217 " --> pdb=" O ALAAf 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAf 218 " --> pdb=" O ARGAf 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAf 219 " --> pdb=" O GLUAf 215 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 71 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAg 117 " --> pdb=" O ASNAg 113 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAg 168 " --> pdb=" O SERAg 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 187 Processing helix chain 'Ag' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAg 199 " --> pdb=" O ALAAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 3.724A pdb=" N HISAg 217 " --> pdb=" O ALAAg 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAg 219 " --> pdb=" O GLUAg 215 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAh 117 " --> pdb=" O ASNAh 113 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAh 168 " --> pdb=" O SERAh 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 187 Processing helix chain 'Ah' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAh 199 " --> pdb=" O ALAAh 196 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAh 217 " --> pdb=" O ALAAh 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAh 218 " --> pdb=" O ARGAh 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAh 219 " --> pdb=" O GLUAh 215 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.701A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAi 117 " --> pdb=" O ASNAi 113 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAi 168 " --> pdb=" O SERAi 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 187 Processing helix chain 'Ai' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAi 199 " --> pdb=" O ALAAi 196 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAi 217 " --> pdb=" O ALAAi 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAi 218 " --> pdb=" O ARGAi 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAi 219 " --> pdb=" O GLUAi 215 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 86 through 102 Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAj 117 " --> pdb=" O ASNAj 113 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAj 168 " --> pdb=" O SERAj 164 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 187 Processing helix chain 'Aj' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAj 199 " --> pdb=" O ALAAj 196 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAj 217 " --> pdb=" O ALAAj 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAj 218 " --> pdb=" O ARGAj 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAj 219 " --> pdb=" O GLUAj 215 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 66 through 71 Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAk 117 " --> pdb=" O ASNAk 113 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAk 168 " --> pdb=" O SERAk 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 187 Processing helix chain 'Ak' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAk 199 " --> pdb=" O ALAAk 196 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAk 217 " --> pdb=" O ALAAk 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAk 218 " --> pdb=" O ARGAk 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAk 219 " --> pdb=" O GLUAk 215 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 86 through 102 Processing helix chain 'Al' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAl 117 " --> pdb=" O ASNAl 113 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAl 168 " --> pdb=" O SERAl 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 187 Processing helix chain 'Al' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAl 199 " --> pdb=" O ALAAl 196 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAl 217 " --> pdb=" O ALAAl 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAl 218 " --> pdb=" O ARGAl 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAl 219 " --> pdb=" O GLUAl 215 " (cutoff:3.500A) Processing helix chain 'Am' and resid 66 through 71 Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAm 117 " --> pdb=" O ASNAm 113 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAm 168 " --> pdb=" O SERAm 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 187 Processing helix chain 'Am' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAm 199 " --> pdb=" O ALAAm 196 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAm 217 " --> pdb=" O ALAAm 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAm 219 " --> pdb=" O GLUAm 215 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 Processing helix chain 'An' and resid 86 through 102 Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.701A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAn 117 " --> pdb=" O ASNAn 113 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAn 168 " --> pdb=" O SERAn 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 187 Processing helix chain 'An' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAn 199 " --> pdb=" O ALAAn 196 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAn 217 " --> pdb=" O ALAAn 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAn 218 " --> pdb=" O ARGAn 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAn 219 " --> pdb=" O GLUAn 215 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 71 Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAo 117 " --> pdb=" O ASNAo 113 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAo 168 " --> pdb=" O SERAo 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 187 Processing helix chain 'Ao' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAo 199 " --> pdb=" O ALAAo 196 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAo 217 " --> pdb=" O ALAAo 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAo 219 " --> pdb=" O GLUAo 215 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 Processing helix chain 'Ap' and resid 86 through 102 Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAp 117 " --> pdb=" O ASNAp 113 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAp 168 " --> pdb=" O SERAp 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 187 Processing helix chain 'Ap' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAp 199 " --> pdb=" O ALAAp 196 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAp 217 " --> pdb=" O ALAAp 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAp 218 " --> pdb=" O ARGAp 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAp 219 " --> pdb=" O GLUAp 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 133 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 133 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 133 Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 133 Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 133 Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 133 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 133 Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 133 800 hydrogen bonds defined for protein. 2304 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: 3.57 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4705 1.33 - 1.45: 5443 1.45 - 1.57: 13340 1.57 - 1.69: 0 1.69 - 1.81: 368 Bond restraints: 23856 Sorted by residual: bond pdb=" CA ASNAf 129 " pdb=" C ASNAf 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.06e+01 bond pdb=" CA ASNAk 129 " pdb=" C ASNAk 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAg 129 " pdb=" C ASNAg 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAb 129 " pdb=" C ASNAb 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAi 129 " pdb=" C ASNAi 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 30785 1.71 - 3.41: 1136 3.41 - 5.12: 258 5.12 - 6.83: 125 6.83 - 8.54: 32 Bond angle restraints: 32336 Sorted by residual: angle pdb=" O VALAd 133 " pdb=" C VALAd 133 " pdb=" N METAd 134 " ideal model delta sigma weight residual 123.14 117.78 5.36 1.02e+00 9.61e-01 2.76e+01 angle pdb=" O VALAa 133 " pdb=" C VALAa 133 " pdb=" N METAa 134 " ideal model delta sigma weight residual 123.14 117.80 5.34 1.02e+00 9.61e-01 2.74e+01 angle pdb=" O VALAi 133 " pdb=" C VALAi 133 " pdb=" N METAi 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 angle pdb=" O VALAn 133 " pdb=" C VALAn 133 " pdb=" N METAn 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 angle pdb=" O VALAj 133 " pdb=" C VALAj 133 " pdb=" N METAj 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 ... (remaining 32331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 12565 16.93 - 33.86: 1691 33.86 - 50.79: 304 50.79 - 67.72: 48 67.72 - 84.65: 32 Dihedral angle restraints: 14640 sinusoidal: 6080 harmonic: 8560 Sorted by residual: dihedral pdb=" CA TRPAb 132 " pdb=" C TRPAb 132 " pdb=" N VALAb 133 " pdb=" CA VALAb 133 " ideal model delta harmonic sigma weight residual -180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TRPAl 132 " pdb=" C TRPAl 132 " pdb=" N VALAl 133 " pdb=" CA VALAl 133 " ideal model delta harmonic sigma weight residual -180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TRPAj 132 " pdb=" C TRPAj 132 " pdb=" N VALAj 133 " pdb=" CA VALAj 133 " ideal model delta harmonic sigma weight residual -180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1758 0.026 - 0.052: 987 0.052 - 0.077: 483 0.077 - 0.103: 228 0.103 - 0.129: 64 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CA VALAf 187 " pdb=" N VALAf 187 " pdb=" C VALAf 187 " pdb=" CB VALAf 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VALAe 187 " pdb=" N VALAe 187 " pdb=" C VALAe 187 " pdb=" CB VALAe 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VALAk 187 " pdb=" N VALAk 187 " pdb=" C VALAk 187 " pdb=" CB VALAk 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 3517 not shown) Planarity restraints: 4192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALAb 44 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PROAb 45 " 0.138 5.00e-02 4.00e+02 pdb=" CA PROAb 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PROAb 45 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAf 44 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PROAf 45 " -0.138 5.00e-02 4.00e+02 pdb=" CA PROAf 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PROAf 45 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAh 44 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PROAh 45 " -0.138 5.00e-02 4.00e+02 pdb=" CA PROAh 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PROAh 45 " 0.042 5.00e-02 4.00e+02 ... (remaining 4189 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8185 2.84 - 3.36: 22103 3.36 - 3.87: 35946 3.87 - 4.39: 40877 4.39 - 4.90: 67134 Nonbonded interactions: 174245 Sorted by model distance: nonbonded pdb=" O SERAo 125 " pdb=" OG SERAo 125 " model vdw 2.325 3.040 nonbonded pdb=" O SERAb 125 " pdb=" OG SERAb 125 " model vdw 2.325 3.040 nonbonded pdb=" O SERAk 125 " pdb=" OG SERAk 125 " model vdw 2.325 3.040 nonbonded pdb=" O SERAl 125 " pdb=" OG SERAl 125 " model vdw 2.325 3.040 nonbonded pdb=" O SERAj 125 " pdb=" OG SERAj 125 " model vdw 2.326 3.040 ... (remaining 174240 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: 0.10 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.070 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.056 23856 Z= 0.272 Angle : 0.887 8.535 32336 Z= 0.525 Chirality : 0.042 0.129 3520 Planarity : 0.007 0.080 4192 Dihedral : 15.409 84.650 9104 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.03 % Favored : 94.41 % Rotamer: Outliers : 0.63 % Allowed : 18.91 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.15), residues: 2864 helix: -1.08 (0.15), residues: 1184 sheet: -0.25 (0.44), residues: 160 loop : -1.14 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAd 183 TYR 0.027 0.002 TYRAm 184 PHE 0.007 0.002 PHEAp 200 TRP 0.010 0.001 TRPAj 132 HIS 0.011 0.003 HISAc 69 Details of bonding type rmsd covalent geometry : bond 0.00444 (23856) covalent geometry : angle 0.88748 (32336) hydrogen bonds : bond 0.27659 ( 800) hydrogen bonds : angle 8.15013 ( 2304) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 911 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: Aa 69 HIS cc_start: 0.8679 (t-170) cc_final: 0.8428 (t-170) REVERT: Aa 127 ASN cc_start: 0.8607 (p0) cc_final: 0.8326 (p0) REVERT: Aa 183 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7028 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8531 (t0) cc_final: 0.8303 (t0) REVERT: Ab 60 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8801 (mmtm) REVERT: Ab 73 TYR cc_start: 0.8610 (t80) cc_final: 0.7738 (t80) REVERT: Ab 78 ILE cc_start: 0.8890 (tp) cc_final: 0.8616 (tp) REVERT: Ab 127 ASN cc_start: 0.8648 (p0) cc_final: 0.8350 (p0) REVERT: Ab 129 ASN cc_start: 0.8481 (p0) cc_final: 0.8196 (p0) REVERT: Ab 165 ASP cc_start: 0.8025 (t0) cc_final: 0.7551 (t0) REVERT: Ac 69 HIS cc_start: 0.8632 (t-170) cc_final: 0.8345 (t-170) REVERT: Ac 127 ASN cc_start: 0.8541 (p0) cc_final: 0.8256 (p0) REVERT: Ad 55 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8370 (mtp85) REVERT: Ad 69 HIS cc_start: 0.8723 (t-170) cc_final: 0.8378 (t-170) REVERT: Ad 73 TYR cc_start: 0.8632 (t80) cc_final: 0.8339 (t80) REVERT: Ad 76 GLN cc_start: 0.8423 (mp10) cc_final: 0.8178 (mp10) REVERT: Ad 127 ASN cc_start: 0.8529 (p0) cc_final: 0.8282 (p0) REVERT: Ad 158 GLN cc_start: 0.8743 (mt0) cc_final: 0.8456 (mt0) REVERT: Ad 165 ASP cc_start: 0.8061 (t0) cc_final: 0.7508 (t0) REVERT: Ae 76 GLN cc_start: 0.8560 (mp10) cc_final: 0.8320 (mp10) REVERT: Ae 102 ASP cc_start: 0.8793 (t0) cc_final: 0.8548 (t0) REVERT: Ae 158 GLN cc_start: 0.8858 (mt0) cc_final: 0.8511 (mt0) REVERT: Ae 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7523 (t0) REVERT: Af 121 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8281 (mm-30) REVERT: Af 143 TYR cc_start: 0.9370 (m-80) cc_final: 0.8951 (m-80) REVERT: Af 165 ASP cc_start: 0.8029 (t0) cc_final: 0.7606 (t0) REVERT: Af 208 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7619 (mtm180) REVERT: Ag 165 ASP cc_start: 0.7934 (t0) cc_final: 0.7411 (t0) REVERT: Ah 69 HIS cc_start: 0.8724 (t-170) cc_final: 0.8263 (t-170) REVERT: Ah 76 GLN cc_start: 0.8438 (mp10) cc_final: 0.8225 (mp10) REVERT: Ah 127 ASN cc_start: 0.8598 (p0) cc_final: 0.8336 (p0) REVERT: Ah 165 ASP cc_start: 0.7982 (t0) cc_final: 0.7415 (t0) REVERT: Ai 73 TYR cc_start: 0.8605 (t80) cc_final: 0.8187 (t80) REVERT: Ai 127 ASN cc_start: 0.8553 (p0) cc_final: 0.8316 (p0) REVERT: Ai 165 ASP cc_start: 0.8095 (t0) cc_final: 0.7472 (t0) REVERT: Aj 76 GLN cc_start: 0.8569 (mp10) cc_final: 0.8358 (mp10) REVERT: Aj 134 MET cc_start: 0.8684 (ttt) cc_final: 0.8473 (ttt) REVERT: Aj 165 ASP cc_start: 0.7998 (t0) cc_final: 0.7462 (t0) REVERT: Ak 69 HIS cc_start: 0.8801 (t-170) cc_final: 0.8497 (t-170) REVERT: Ak 73 TYR cc_start: 0.8751 (t80) cc_final: 0.8303 (t80) REVERT: Ak 76 GLN cc_start: 0.8501 (mp10) cc_final: 0.8251 (mp10) REVERT: Ak 91 ASP cc_start: 0.7688 (m-30) cc_final: 0.7445 (m-30) REVERT: Ak 165 ASP cc_start: 0.7904 (t0) cc_final: 0.7350 (t0) REVERT: Al 121 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8222 (mm-30) REVERT: Al 134 MET cc_start: 0.8774 (ttt) cc_final: 0.8545 (ttt) REVERT: Al 165 ASP cc_start: 0.7986 (t0) cc_final: 0.7697 (t0) REVERT: Al 181 MET cc_start: 0.9055 (tpp) cc_final: 0.8684 (tpp) REVERT: Am 69 HIS cc_start: 0.8759 (t-170) cc_final: 0.8481 (t-170) REVERT: Am 127 ASN cc_start: 0.8505 (p0) cc_final: 0.8269 (p0) REVERT: Am 157 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8676 (ttt-90) REVERT: Am 165 ASP cc_start: 0.8088 (t0) cc_final: 0.7514 (t0) REVERT: An 69 HIS cc_start: 0.8713 (t-170) cc_final: 0.8488 (t-170) REVERT: An 73 TYR cc_start: 0.8688 (t80) cc_final: 0.8211 (t80) REVERT: An 127 ASN cc_start: 0.8556 (p0) cc_final: 0.8295 (p0) REVERT: Ao 76 GLN cc_start: 0.8488 (mp10) cc_final: 0.8256 (mp10) REVERT: Ao 127 ASN cc_start: 0.8565 (p0) cc_final: 0.8330 (p0) REVERT: Ao 134 MET cc_start: 0.8784 (ttt) cc_final: 0.8563 (ttt) REVERT: Ao 165 ASP cc_start: 0.7959 (t0) cc_final: 0.7430 (t0) REVERT: Ap 158 GLN cc_start: 0.8744 (mt0) cc_final: 0.8534 (mt0) REVERT: Ap 165 ASP cc_start: 0.7981 (t0) cc_final: 0.7439 (t0) outliers start: 16 outliers final: 0 residues processed: 911 average time/residue: 0.1903 time to fit residues: 251.3238 Evaluate side-chains 846 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 846 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 151 ASN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN Af 158 GLN Ag 151 ASN Ai 151 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN An 151 ASN Ao 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095738 restraints weight = 38886.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098465 restraints weight = 25935.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100403 restraints weight = 20157.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101595 restraints weight = 17025.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102456 restraints weight = 15299.823| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23856 Z= 0.178 Angle : 0.690 8.843 32336 Z= 0.344 Chirality : 0.042 0.124 3520 Planarity : 0.006 0.052 4192 Dihedral : 4.375 15.232 3216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.41 % Allowed : 18.55 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.15), residues: 2864 helix: -0.41 (0.14), residues: 1360 sheet: -0.11 (0.41), residues: 160 loop : -1.57 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAk 55 TYR 0.023 0.002 TYRAl 198 PHE 0.010 0.002 PHEAd 200 TRP 0.013 0.002 TRPAk 93 HIS 0.007 0.001 HISAj 69 Details of bonding type rmsd covalent geometry : bond 0.00410 (23856) covalent geometry : angle 0.68999 (32336) hydrogen bonds : bond 0.04436 ( 800) hydrogen bonds : angle 5.21532 ( 2304) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 854 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 136 ASP cc_start: 0.7569 (m-30) cc_final: 0.7117 (m-30) REVERT: Aa 183 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7434 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8489 (t0) cc_final: 0.8207 (t0) REVERT: Aa 208 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7195 (mtm180) REVERT: Ab 54 MET cc_start: 0.7581 (ttp) cc_final: 0.6917 (ttp) REVERT: Ab 136 ASP cc_start: 0.7651 (m-30) cc_final: 0.7212 (m-30) REVERT: Ab 157 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8382 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7923 (t0) cc_final: 0.7717 (t0) REVERT: Ac 80 ILE cc_start: 0.8607 (pt) cc_final: 0.8406 (pt) REVERT: Ac 157 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8263 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7796 (t0) cc_final: 0.7397 (t0) REVERT: Ad 102 ASP cc_start: 0.8555 (t0) cc_final: 0.8308 (t0) REVERT: Ad 157 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8217 (ttt-90) REVERT: Ad 174 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: Ae 77 GLN cc_start: 0.8489 (tp40) cc_final: 0.7518 (tp40) REVERT: Ae 102 ASP cc_start: 0.8464 (t0) cc_final: 0.8153 (t0) REVERT: Ae 165 ASP cc_start: 0.7960 (t0) cc_final: 0.7716 (t0) REVERT: Ae 174 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: Ae 181 MET cc_start: 0.8587 (tpp) cc_final: 0.8301 (tpp) REVERT: Af 121 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7791 (mm-30) REVERT: Af 165 ASP cc_start: 0.7916 (t0) cc_final: 0.7698 (t0) REVERT: Ag 102 ASP cc_start: 0.8492 (t0) cc_final: 0.8237 (t0) REVERT: Ag 136 ASP cc_start: 0.7755 (m-30) cc_final: 0.7314 (m-30) REVERT: Ag 165 ASP cc_start: 0.7941 (t0) cc_final: 0.7736 (t0) REVERT: Ag 208 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7422 (mtm180) REVERT: Ah 54 MET cc_start: 0.7676 (ttp) cc_final: 0.6977 (ttp) REVERT: Ah 77 GLN cc_start: 0.8252 (tm-30) cc_final: 0.8015 (tp40) REVERT: Ah 80 ILE cc_start: 0.8712 (pt) cc_final: 0.8491 (pt) REVERT: Ah 157 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8313 (ttt-90) REVERT: Ai 60 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8399 (mmtm) REVERT: Ai 136 ASP cc_start: 0.7558 (m-30) cc_final: 0.7176 (m-30) REVERT: Ai 157 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8410 (ttt90) REVERT: Ai 165 ASP cc_start: 0.7953 (t0) cc_final: 0.7523 (t0) REVERT: Aj 56 MET cc_start: 0.8522 (mmp) cc_final: 0.8038 (mmp) REVERT: Aj 129 ASN cc_start: 0.7997 (p0) cc_final: 0.7765 (p0) REVERT: Aj 157 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8307 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8020 (t0) cc_final: 0.7762 (t0) REVERT: Ak 77 GLN cc_start: 0.8432 (tp40) cc_final: 0.6772 (tp40) REVERT: Ak 129 ASN cc_start: 0.8081 (p0) cc_final: 0.7821 (p0) REVERT: Ak 136 ASP cc_start: 0.7917 (m-30) cc_final: 0.7513 (m-30) REVERT: Ak 157 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8266 (ttt-90) REVERT: Ak 174 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7687 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8399 (t0) cc_final: 0.8135 (t0) REVERT: Ak 204 GLU cc_start: 0.8160 (pp20) cc_final: 0.7803 (pp20) REVERT: Al 80 ILE cc_start: 0.8641 (pt) cc_final: 0.8402 (pt) REVERT: Al 136 ASP cc_start: 0.8070 (m-30) cc_final: 0.7569 (m-30) REVERT: Al 157 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8362 (ttt90) REVERT: Al 160 MET cc_start: 0.8914 (tpp) cc_final: 0.8410 (mmm) REVERT: Al 204 GLU cc_start: 0.8060 (pp20) cc_final: 0.7834 (pp20) REVERT: Am 69 HIS cc_start: 0.8423 (t-170) cc_final: 0.8222 (t-170) REVERT: Am 78 ILE cc_start: 0.8777 (tp) cc_final: 0.8570 (tp) REVERT: Am 157 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8470 (ttt90) REVERT: Am 165 ASP cc_start: 0.7951 (t0) cc_final: 0.7695 (t0) REVERT: An 73 TYR cc_start: 0.8928 (t80) cc_final: 0.8640 (t80) REVERT: An 165 ASP cc_start: 0.7767 (t0) cc_final: 0.7545 (t0) REVERT: An 174 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7387 (mmm-85) REVERT: Ao 157 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8382 (ttt90) REVERT: Ao 165 ASP cc_start: 0.7857 (t0) cc_final: 0.7636 (t0) REVERT: Ao 174 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7409 (mmm-85) REVERT: Ap 165 ASP cc_start: 0.7884 (t0) cc_final: 0.7484 (t0) outliers start: 61 outliers final: 16 residues processed: 891 average time/residue: 0.1770 time to fit residues: 234.3584 Evaluate side-chains 839 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 822 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 60 LYS Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 0.0370 chunk 270 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ab 140 GLN Ab 158 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 140 GLN Ae 129 ASN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 140 GLN Af 151 ASN Af 158 GLN Ag 151 ASN Ah 151 ASN Ai 140 GLN Al 151 ASN Am 158 GLN An 151 ASN Ao 140 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095850 restraints weight = 39092.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098837 restraints weight = 25614.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100852 restraints weight = 19610.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102177 restraints weight = 16456.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102939 restraints weight = 14674.761| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23856 Z= 0.159 Angle : 0.665 9.244 32336 Z= 0.325 Chirality : 0.042 0.152 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.444 18.581 3216 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.53 % Allowed : 18.24 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.16), residues: 2864 helix: -0.08 (0.14), residues: 1424 sheet: 0.78 (0.42), residues: 160 loop : -1.35 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAe 157 TYR 0.024 0.002 TYRAl 198 PHE 0.009 0.001 PHEAe 200 TRP 0.011 0.002 TRPAa 93 HIS 0.008 0.002 HISAe 69 Details of bonding type rmsd covalent geometry : bond 0.00368 (23856) covalent geometry : angle 0.66494 (32336) hydrogen bonds : bond 0.03537 ( 800) hydrogen bonds : angle 4.94650 ( 2304) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 896 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 77 GLN cc_start: 0.8229 (tp40) cc_final: 0.6584 (tp40) REVERT: Aa 136 ASP cc_start: 0.7873 (m-30) cc_final: 0.7480 (m-30) REVERT: Aa 157 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8334 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8671 (tpp) cc_final: 0.8455 (tpp) REVERT: Aa 183 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7325 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8497 (t0) cc_final: 0.8108 (t0) REVERT: Aa 208 ARG cc_start: 0.7534 (mtm180) cc_final: 0.7329 (mtm180) REVERT: Ab 54 MET cc_start: 0.7668 (ttp) cc_final: 0.6760 (ttp) REVERT: Ab 121 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7826 (mm-30) REVERT: Ab 136 ASP cc_start: 0.7801 (m-30) cc_final: 0.7336 (m-30) REVERT: Ab 157 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8439 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7680 (t0) REVERT: Ab 184 TYR cc_start: 0.7930 (t80) cc_final: 0.7679 (t80) REVERT: Ac 80 ILE cc_start: 0.8754 (pt) cc_final: 0.8551 (pt) REVERT: Ac 91 ASP cc_start: 0.8177 (m-30) cc_final: 0.7879 (m-30) REVERT: Ac 157 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8372 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7863 (t0) cc_final: 0.7383 (t0) REVERT: Ac 201 ASP cc_start: 0.8440 (t0) cc_final: 0.8174 (t0) REVERT: Ad 73 TYR cc_start: 0.8769 (t80) cc_final: 0.8469 (t80) REVERT: Ad 76 GLN cc_start: 0.8383 (mp10) cc_final: 0.8152 (mp10) REVERT: Ad 102 ASP cc_start: 0.8612 (t0) cc_final: 0.8354 (t0) REVERT: Ad 136 ASP cc_start: 0.7860 (m-30) cc_final: 0.7503 (m-30) REVERT: Ad 157 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8348 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.7915 (t0) cc_final: 0.7631 (t0) REVERT: Ad 188 ARG cc_start: 0.7081 (tpt170) cc_final: 0.6878 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8422 (mp10) cc_final: 0.8114 (mp10) REVERT: Ae 77 GLN cc_start: 0.8430 (tp40) cc_final: 0.7869 (tp40) REVERT: Ae 80 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8535 (pt) REVERT: Ae 102 ASP cc_start: 0.8513 (t0) cc_final: 0.8181 (t0) REVERT: Ae 136 ASP cc_start: 0.7363 (m-30) cc_final: 0.6868 (m-30) REVERT: Ae 157 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8374 (ttt-90) REVERT: Ae 174 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7527 (mmm-85) REVERT: Ae 204 GLU cc_start: 0.8139 (pp20) cc_final: 0.7623 (pp20) REVERT: Af 54 MET cc_start: 0.7721 (ttp) cc_final: 0.7061 (ttp) REVERT: Af 157 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8463 (ttt-90) REVERT: Ag 77 GLN cc_start: 0.8141 (tp40) cc_final: 0.7754 (tp40) REVERT: Ag 80 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8414 (pt) REVERT: Ag 102 ASP cc_start: 0.8579 (t0) cc_final: 0.8314 (t0) REVERT: Ag 135 MET cc_start: 0.8676 (mmm) cc_final: 0.8470 (mmm) REVERT: Ag 136 ASP cc_start: 0.7724 (m-30) cc_final: 0.7213 (m-30) REVERT: Ag 157 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8469 (ttt-90) REVERT: Ag 165 ASP cc_start: 0.7997 (t0) cc_final: 0.7650 (t0) REVERT: Ah 54 MET cc_start: 0.7753 (ttp) cc_final: 0.7079 (ttp) REVERT: Ah 69 HIS cc_start: 0.8489 (t-170) cc_final: 0.8222 (t-170) REVERT: Ah 76 GLN cc_start: 0.8537 (mp10) cc_final: 0.8329 (mp10) REVERT: Ah 108 MET cc_start: 0.8585 (tpp) cc_final: 0.8360 (tpp) REVERT: Ah 157 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8336 (ttt90) REVERT: Ai 73 TYR cc_start: 0.8828 (t80) cc_final: 0.8590 (t80) REVERT: Ai 76 GLN cc_start: 0.8304 (mp10) cc_final: 0.7811 (mp10) REVERT: Ai 80 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8487 (pt) REVERT: Ai 136 ASP cc_start: 0.7720 (m-30) cc_final: 0.7249 (m-30) REVERT: Ai 157 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8463 (ttt90) REVERT: Ai 160 MET cc_start: 0.8872 (tpp) cc_final: 0.8410 (mmm) REVERT: Ai 165 ASP cc_start: 0.8015 (t0) cc_final: 0.7532 (t0) REVERT: Ai 198 TYR cc_start: 0.8830 (m-10) cc_final: 0.8630 (m-10) REVERT: Aj 157 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8420 (ttt-90) REVERT: Ak 73 TYR cc_start: 0.8905 (t80) cc_final: 0.8704 (t80) REVERT: Ak 80 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8367 (pt) REVERT: Ak 136 ASP cc_start: 0.7830 (m-30) cc_final: 0.7476 (m-30) REVERT: Ak 157 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8429 (ttt90) REVERT: Ak 165 ASP cc_start: 0.7816 (t0) cc_final: 0.7572 (t0) REVERT: Ak 174 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7650 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8441 (t0) cc_final: 0.8063 (t0) REVERT: Ak 204 GLU cc_start: 0.8130 (pp20) cc_final: 0.7854 (pp20) REVERT: Al 77 GLN cc_start: 0.8422 (tp40) cc_final: 0.8007 (tp40) REVERT: Al 80 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8636 (pt) REVERT: Al 136 ASP cc_start: 0.7966 (m-30) cc_final: 0.7474 (m-30) REVERT: Al 157 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8446 (ttt90) REVERT: Al 183 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8077 (ttp80) REVERT: Al 204 GLU cc_start: 0.8099 (pp20) cc_final: 0.7802 (pp20) REVERT: Am 69 HIS cc_start: 0.8471 (t-170) cc_final: 0.8216 (t-170) REVERT: Am 165 ASP cc_start: 0.7870 (t0) cc_final: 0.7658 (t0) REVERT: An 73 TYR cc_start: 0.9051 (t80) cc_final: 0.8686 (t80) REVERT: An 165 ASP cc_start: 0.7908 (t0) cc_final: 0.7653 (t0) REVERT: Ao 157 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8474 (ttt90) REVERT: Ao 160 MET cc_start: 0.8987 (tpp) cc_final: 0.8577 (mmm) REVERT: Ao 174 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7308 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7065 (tpt170) cc_final: 0.6847 (tpt170) REVERT: Ap 165 ASP cc_start: 0.7976 (t0) cc_final: 0.7559 (t0) REVERT: Ap 188 ARG cc_start: 0.7061 (tpt170) cc_final: 0.6841 (tpt170) REVERT: Ap 204 GLU cc_start: 0.8160 (pp20) cc_final: 0.7843 (pp20) REVERT: Ap 205 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (p) outliers start: 64 outliers final: 28 residues processed: 921 average time/residue: 0.1702 time to fit residues: 232.4587 Evaluate side-chains 873 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 839 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Aj residue 78 ILE Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 28 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 81 optimal weight: 0.0070 chunk 95 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ac 129 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 129 ASN Ae 140 GLN Ae 158 GLN Af 129 ASN Af 151 ASN Ah 151 ASN Ai 129 ASN Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Al 151 ASN Am 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 129 ASN ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096075 restraints weight = 39184.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098914 restraints weight = 26173.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100817 restraints weight = 20247.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102108 restraints weight = 17124.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102950 restraints weight = 15266.285| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23856 Z= 0.162 Angle : 0.675 9.858 32336 Z= 0.327 Chirality : 0.042 0.154 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.355 17.084 3216 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.92 % Allowed : 19.22 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.16), residues: 2864 helix: 0.06 (0.14), residues: 1424 sheet: 1.35 (0.44), residues: 160 loop : -1.23 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAm 157 TYR 0.025 0.002 TYRAn 198 PHE 0.010 0.001 PHEAa 200 TRP 0.010 0.002 TRPAa 93 HIS 0.011 0.001 HISAd 69 Details of bonding type rmsd covalent geometry : bond 0.00380 (23856) covalent geometry : angle 0.67489 (32336) hydrogen bonds : bond 0.03222 ( 800) hydrogen bonds : angle 4.90190 ( 2304) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 891 time to evaluate : 0.710 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: Aa 136 ASP cc_start: 0.7664 (m-30) cc_final: 0.7398 (m-30) REVERT: Aa 157 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8306 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8596 (tpp) cc_final: 0.8368 (tpp) REVERT: Aa 183 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7422 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8490 (t0) cc_final: 0.8093 (t0) REVERT: Ab 54 MET cc_start: 0.7634 (ttp) cc_final: 0.6708 (ttp) REVERT: Ab 73 TYR cc_start: 0.9116 (t80) cc_final: 0.8868 (t80) REVERT: Ab 80 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8603 (pt) REVERT: Ab 136 ASP cc_start: 0.7368 (m-30) cc_final: 0.6949 (m-30) REVERT: Ab 157 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8396 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8025 (t0) cc_final: 0.7792 (t0) REVERT: Ab 183 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8216 (ttp80) REVERT: Ac 91 ASP cc_start: 0.8201 (m-30) cc_final: 0.7922 (m-30) REVERT: Ac 157 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8361 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7915 (t0) cc_final: 0.7454 (t0) REVERT: Ac 201 ASP cc_start: 0.8436 (t0) cc_final: 0.8159 (t0) REVERT: Ad 76 GLN cc_start: 0.8525 (mp10) cc_final: 0.8295 (mp10) REVERT: Ad 102 ASP cc_start: 0.8527 (t0) cc_final: 0.8260 (t0) REVERT: Ad 174 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: Ae 54 MET cc_start: 0.7632 (ttp) cc_final: 0.7352 (ttp) REVERT: Ae 76 GLN cc_start: 0.8392 (mp10) cc_final: 0.8033 (mp10) REVERT: Ae 102 ASP cc_start: 0.8451 (t0) cc_final: 0.8127 (t0) REVERT: Ae 136 ASP cc_start: 0.7142 (m-30) cc_final: 0.6656 (m-30) REVERT: Ae 157 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8372 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7885 (t0) cc_final: 0.7673 (t0) REVERT: Ae 174 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: Ae 204 GLU cc_start: 0.8105 (pp20) cc_final: 0.7657 (pp20) REVERT: Af 54 MET cc_start: 0.7705 (ttp) cc_final: 0.7133 (ttp) REVERT: Af 165 ASP cc_start: 0.7854 (t0) cc_final: 0.7589 (t0) REVERT: Af 174 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: Ag 70 LEU cc_start: 0.9302 (tp) cc_final: 0.9064 (tp) REVERT: Ag 102 ASP cc_start: 0.8493 (t0) cc_final: 0.8243 (t0) REVERT: Ag 136 ASP cc_start: 0.7659 (m-30) cc_final: 0.7286 (m-30) REVERT: Ag 165 ASP cc_start: 0.8016 (t0) cc_final: 0.7677 (t0) REVERT: Ah 54 MET cc_start: 0.7715 (ttp) cc_final: 0.7075 (ttp) REVERT: Ah 157 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8355 (ttt90) REVERT: Ai 73 TYR cc_start: 0.9005 (t80) cc_final: 0.8731 (t80) REVERT: Ai 77 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: Ai 80 ILE cc_start: 0.8877 (pt) cc_final: 0.8631 (pt) REVERT: Ai 136 ASP cc_start: 0.7403 (m-30) cc_final: 0.6886 (m-30) REVERT: Ai 165 ASP cc_start: 0.8082 (t0) cc_final: 0.7597 (t0) REVERT: Ai 201 ASP cc_start: 0.8368 (t0) cc_final: 0.8161 (t0) REVERT: Aj 80 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8723 (pt) REVERT: Aj 157 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8386 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8073 (t0) cc_final: 0.7859 (t0) REVERT: Aj 204 GLU cc_start: 0.8024 (pp20) cc_final: 0.7504 (pp20) REVERT: Ak 136 ASP cc_start: 0.7851 (m-30) cc_final: 0.7610 (m-30) REVERT: Ak 157 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8445 (ttt90) REVERT: Ak 160 MET cc_start: 0.8960 (tpp) cc_final: 0.8521 (tpt) REVERT: Ak 201 ASP cc_start: 0.8449 (t0) cc_final: 0.8032 (t0) REVERT: Ak 204 GLU cc_start: 0.8037 (pp20) cc_final: 0.7801 (pp20) REVERT: Al 80 ILE cc_start: 0.8944 (pt) cc_final: 0.8725 (pt) REVERT: Al 116 MET cc_start: 0.8776 (ttp) cc_final: 0.8383 (ttt) REVERT: Al 136 ASP cc_start: 0.7855 (m-30) cc_final: 0.7358 (m-30) REVERT: Al 157 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8402 (ttt90) REVERT: Al 183 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8140 (ttp80) REVERT: Al 204 GLU cc_start: 0.8061 (pp20) cc_final: 0.7799 (pp20) REVERT: Am 54 MET cc_start: 0.7687 (ttp) cc_final: 0.7064 (ttp) REVERT: Am 69 HIS cc_start: 0.8385 (t-170) cc_final: 0.8162 (t-170) REVERT: Am 70 LEU cc_start: 0.9300 (tp) cc_final: 0.9018 (tp) REVERT: Am 76 GLN cc_start: 0.8432 (mp10) cc_final: 0.8223 (mp10) REVERT: Am 165 ASP cc_start: 0.7932 (t0) cc_final: 0.7702 (t0) REVERT: Am 184 TYR cc_start: 0.7877 (t80) cc_final: 0.7420 (t80) REVERT: An 77 GLN cc_start: 0.8283 (tp40) cc_final: 0.7750 (tp40) REVERT: An 165 ASP cc_start: 0.7947 (t0) cc_final: 0.7527 (t0) REVERT: Ao 80 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8567 (pt) REVERT: Ao 157 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8440 (ttt90) REVERT: Ao 174 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7376 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6815 (tpt170) REVERT: Ap 150 GLU cc_start: 0.7903 (tt0) cc_final: 0.7607 (tt0) REVERT: Ap 165 ASP cc_start: 0.8021 (t0) cc_final: 0.7513 (t0) outliers start: 99 outliers final: 59 residues processed: 943 average time/residue: 0.1744 time to fit residues: 244.4086 Evaluate side-chains 922 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 859 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 129 ASN Chi-restraints excluded: chain Ab residue 155 THR Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 129 ASN Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ab 129 ASN Ab 140 GLN Ab 158 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 129 ASN Ae 129 ASN Af 140 GLN Af 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN Am 129 ASN Am 158 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093754 restraints weight = 39237.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096541 restraints weight = 26577.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098407 restraints weight = 20693.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099662 restraints weight = 17555.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100480 restraints weight = 15717.920| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23856 Z= 0.217 Angle : 0.708 9.595 32336 Z= 0.346 Chirality : 0.044 0.154 3520 Planarity : 0.006 0.065 4192 Dihedral : 4.492 18.905 3216 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.00 % Allowed : 21.40 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.16), residues: 2864 helix: 0.03 (0.14), residues: 1424 sheet: 1.38 (0.43), residues: 160 loop : -1.22 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAm 157 TYR 0.026 0.002 TYRAb 198 PHE 0.012 0.002 PHEAe 200 TRP 0.011 0.002 TRPAa 93 HIS 0.009 0.001 HISAe 69 Details of bonding type rmsd covalent geometry : bond 0.00511 (23856) covalent geometry : angle 0.70839 (32336) hydrogen bonds : bond 0.03403 ( 800) hydrogen bonds : angle 5.05613 ( 2304) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 886 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8495 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8635 (tpp) cc_final: 0.8361 (tpp) REVERT: Aa 183 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7438 (mpt180) REVERT: Ab 73 TYR cc_start: 0.9210 (t80) cc_final: 0.8925 (t80) REVERT: Ab 136 ASP cc_start: 0.7447 (m-30) cc_final: 0.6918 (m-30) REVERT: Ab 157 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8538 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8140 (t0) cc_final: 0.7843 (t0) REVERT: Ab 188 ARG cc_start: 0.7027 (tpt170) cc_final: 0.6827 (tpt170) REVERT: Ac 91 ASP cc_start: 0.8272 (m-30) cc_final: 0.7966 (m-30) REVERT: Ac 135 MET cc_start: 0.8659 (mmm) cc_final: 0.8430 (mmm) REVERT: Ac 157 ARG cc_start: 0.8784 (ttp80) cc_final: 0.8540 (ttt-90) REVERT: Ac 160 MET cc_start: 0.8996 (tpp) cc_final: 0.8589 (mmm) REVERT: Ac 165 ASP cc_start: 0.8100 (t0) cc_final: 0.7500 (t0) REVERT: Ac 188 ARG cc_start: 0.6990 (tpt170) cc_final: 0.6756 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8650 (t0) cc_final: 0.8315 (t0) REVERT: Ad 76 GLN cc_start: 0.8549 (mp10) cc_final: 0.8316 (mp10) REVERT: Ad 102 ASP cc_start: 0.8711 (t0) cc_final: 0.8417 (t0) REVERT: Ad 165 ASP cc_start: 0.7975 (t0) cc_final: 0.7763 (t0) REVERT: Ad 174 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: Ae 76 GLN cc_start: 0.8493 (mp10) cc_final: 0.8146 (mp10) REVERT: Ae 102 ASP cc_start: 0.8575 (t0) cc_final: 0.8242 (t0) REVERT: Ae 136 ASP cc_start: 0.7025 (m-30) cc_final: 0.6624 (m-30) REVERT: Ae 157 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8511 (ttt-90) REVERT: Ae 174 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: Ae 204 GLU cc_start: 0.8143 (pp20) cc_final: 0.7668 (pp20) REVERT: Af 54 MET cc_start: 0.7837 (ttp) cc_final: 0.7325 (ttp) REVERT: Af 73 TYR cc_start: 0.9109 (t80) cc_final: 0.8764 (t80) REVERT: Af 165 ASP cc_start: 0.8066 (t0) cc_final: 0.7854 (t0) REVERT: Af 174 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8692 (t0) cc_final: 0.8427 (t0) REVERT: Ag 136 ASP cc_start: 0.7724 (m-30) cc_final: 0.7379 (m-30) REVERT: Ag 165 ASP cc_start: 0.8089 (t0) cc_final: 0.7703 (t0) REVERT: Ah 54 MET cc_start: 0.7805 (ttp) cc_final: 0.7244 (ttp) REVERT: Ah 69 HIS cc_start: 0.8579 (t-170) cc_final: 0.8340 (t-170) REVERT: Ah 157 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8470 (ttt90) REVERT: Ah 165 ASP cc_start: 0.8054 (t0) cc_final: 0.7608 (t0) REVERT: Ai 73 TYR cc_start: 0.9122 (t80) cc_final: 0.8898 (t80) REVERT: Ai 80 ILE cc_start: 0.9065 (pt) cc_final: 0.8859 (pt) REVERT: Ai 129 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7623 (p0) REVERT: Ai 136 ASP cc_start: 0.7636 (m-30) cc_final: 0.7114 (m-30) REVERT: Ai 165 ASP cc_start: 0.8207 (t0) cc_final: 0.7594 (t0) REVERT: Ai 201 ASP cc_start: 0.8595 (t0) cc_final: 0.8336 (t0) REVERT: Aj 157 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8536 (ttt-90) REVERT: Aj 204 GLU cc_start: 0.8084 (pp20) cc_final: 0.7597 (pp20) REVERT: Ak 77 GLN cc_start: 0.8101 (tp40) cc_final: 0.7742 (tp40) REVERT: Ak 136 ASP cc_start: 0.7956 (m-30) cc_final: 0.7698 (m-30) REVERT: Ak 160 MET cc_start: 0.9033 (tpp) cc_final: 0.8730 (mmm) REVERT: Ak 201 ASP cc_start: 0.8639 (t0) cc_final: 0.8149 (t0) REVERT: Ak 204 GLU cc_start: 0.8126 (pp20) cc_final: 0.7841 (pp20) REVERT: Al 136 ASP cc_start: 0.7986 (m-30) cc_final: 0.7658 (m-30) REVERT: Al 157 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8502 (ttt90) REVERT: Al 188 ARG cc_start: 0.7003 (tpt170) cc_final: 0.6788 (tpt170) REVERT: Al 204 GLU cc_start: 0.8148 (pp20) cc_final: 0.7795 (pp20) REVERT: Am 54 MET cc_start: 0.7753 (ttp) cc_final: 0.7027 (ttp) REVERT: Am 76 GLN cc_start: 0.8563 (mp10) cc_final: 0.8329 (mp10) REVERT: Am 165 ASP cc_start: 0.8121 (t0) cc_final: 0.7799 (t0) REVERT: Am 184 TYR cc_start: 0.7974 (t80) cc_final: 0.7560 (t80) REVERT: An 73 TYR cc_start: 0.9112 (t80) cc_final: 0.8899 (t80) REVERT: An 165 ASP cc_start: 0.8074 (t0) cc_final: 0.7600 (t0) REVERT: An 188 ARG cc_start: 0.7060 (tpt170) cc_final: 0.6672 (tpt170) REVERT: Ao 102 ASP cc_start: 0.8626 (t0) cc_final: 0.8322 (t0) REVERT: Ao 157 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8562 (ttt90) REVERT: Ao 188 ARG cc_start: 0.7228 (tpt170) cc_final: 0.6995 (tpt170) REVERT: Ap 134 MET cc_start: 0.8371 (ttt) cc_final: 0.8136 (ttt) REVERT: Ap 165 ASP cc_start: 0.8206 (t0) cc_final: 0.7617 (t0) outliers start: 101 outliers final: 68 residues processed: 938 average time/residue: 0.1864 time to fit residues: 259.1092 Evaluate side-chains 937 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 868 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 78 ILE Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 80 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 47 ILE Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 214 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 chunk 70 optimal weight: 8.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ab 158 GLN Ac 129 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 129 ASN Ad 140 GLN Af 129 ASN Af 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Ai 158 GLN Aj 129 ASN ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 129 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN Ao 129 ASN ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095147 restraints weight = 39339.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098019 restraints weight = 26366.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099925 restraints weight = 20338.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101187 restraints weight = 17210.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101851 restraints weight = 15394.317| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23856 Z= 0.172 Angle : 0.702 9.928 32336 Z= 0.341 Chirality : 0.043 0.156 3520 Planarity : 0.006 0.065 4192 Dihedral : 4.452 19.695 3216 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.11 % Allowed : 22.27 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.16), residues: 2864 helix: 0.03 (0.14), residues: 1424 sheet: 1.72 (0.45), residues: 160 loop : -1.21 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAm 157 TYR 0.030 0.002 TYRAb 198 PHE 0.010 0.001 PHEAa 200 TRP 0.012 0.002 TRPAl 93 HIS 0.009 0.002 HISAe 69 Details of bonding type rmsd covalent geometry : bond 0.00405 (23856) covalent geometry : angle 0.70234 (32336) hydrogen bonds : bond 0.03138 ( 800) hydrogen bonds : angle 5.00358 ( 2304) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 922 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 78 ILE cc_start: 0.8583 (tp) cc_final: 0.8166 (pt) REVERT: Aa 181 MET cc_start: 0.8635 (tpp) cc_final: 0.8348 (tpp) REVERT: Aa 183 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7462 (mpt180) REVERT: Aa 188 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6744 (tpt170) REVERT: Ab 54 MET cc_start: 0.7667 (ttp) cc_final: 0.7365 (ttp) REVERT: Ab 73 TYR cc_start: 0.9202 (t80) cc_final: 0.8824 (t80) REVERT: Ab 108 MET cc_start: 0.8569 (tpp) cc_final: 0.8310 (tpp) REVERT: Ab 136 ASP cc_start: 0.7333 (m-30) cc_final: 0.6726 (m-30) REVERT: Ab 157 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8543 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8115 (t0) cc_final: 0.7778 (t0) REVERT: Ab 188 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6815 (tpt170) REVERT: Ac 91 ASP cc_start: 0.8246 (m-30) cc_final: 0.8020 (m-30) REVERT: Ac 157 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8563 (ttt90) REVERT: Ac 165 ASP cc_start: 0.7978 (t0) cc_final: 0.7582 (t0) REVERT: Ac 188 ARG cc_start: 0.6987 (tpt170) cc_final: 0.6750 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8675 (t0) cc_final: 0.8333 (t0) REVERT: Ad 76 GLN cc_start: 0.8474 (mp10) cc_final: 0.8038 (mp10) REVERT: Ad 102 ASP cc_start: 0.8712 (t0) cc_final: 0.8431 (t0) REVERT: Ad 136 ASP cc_start: 0.7241 (m-30) cc_final: 0.7041 (m-30) REVERT: Ad 174 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7492 (mmm-85) REVERT: Ae 76 GLN cc_start: 0.8457 (mp10) cc_final: 0.8092 (mp10) REVERT: Ae 102 ASP cc_start: 0.8604 (t0) cc_final: 0.8271 (t0) REVERT: Ae 136 ASP cc_start: 0.6989 (m-30) cc_final: 0.6630 (m-30) REVERT: Ae 165 ASP cc_start: 0.8007 (t0) cc_final: 0.7762 (t0) REVERT: Ae 174 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7440 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6935 (tpt170) cc_final: 0.6663 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8105 (pp20) cc_final: 0.7623 (pp20) REVERT: Af 73 TYR cc_start: 0.9115 (t80) cc_final: 0.8757 (t80) REVERT: Af 158 GLN cc_start: 0.8639 (mt0) cc_final: 0.8438 (mt0) REVERT: Af 165 ASP cc_start: 0.8118 (t0) cc_final: 0.7900 (t0) REVERT: Af 174 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7524 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8672 (t0) cc_final: 0.8420 (t0) REVERT: Ag 136 ASP cc_start: 0.7660 (m-30) cc_final: 0.7173 (m-30) REVERT: Ag 165 ASP cc_start: 0.8099 (t0) cc_final: 0.7700 (t0) REVERT: Ag 184 TYR cc_start: 0.7813 (t80) cc_final: 0.7493 (t80) REVERT: Ah 54 MET cc_start: 0.7933 (ttp) cc_final: 0.7161 (ttp) REVERT: Ah 69 HIS cc_start: 0.8590 (t-170) cc_final: 0.8323 (t-170) REVERT: Ah 157 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8453 (ttt90) REVERT: Ah 174 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7534 (mmm-85) REVERT: Ah 188 ARG cc_start: 0.6974 (tpt170) cc_final: 0.6751 (tpt170) REVERT: Ai 80 ILE cc_start: 0.8961 (pt) cc_final: 0.8758 (pt) REVERT: Ai 136 ASP cc_start: 0.7549 (m-30) cc_final: 0.6987 (m-30) REVERT: Ai 165 ASP cc_start: 0.8132 (t0) cc_final: 0.7528 (t0) REVERT: Ai 188 ARG cc_start: 0.7064 (tpt170) cc_final: 0.6821 (tpt170) REVERT: Ai 201 ASP cc_start: 0.8609 (t0) cc_final: 0.8320 (t0) REVERT: Aj 157 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8551 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8097 (t0) cc_final: 0.7878 (t0) REVERT: Aj 174 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7342 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7039 (tpt170) cc_final: 0.6767 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8050 (pp20) cc_final: 0.7607 (pp20) REVERT: Ak 56 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8005 (mmp) REVERT: Ak 77 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: Ak 80 ILE cc_start: 0.8820 (pt) cc_final: 0.8578 (pt) REVERT: Ak 136 ASP cc_start: 0.7788 (m-30) cc_final: 0.7543 (m-30) REVERT: Ak 160 MET cc_start: 0.9000 (tpp) cc_final: 0.8798 (mmm) REVERT: Ak 188 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6844 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8708 (t0) cc_final: 0.8219 (t0) REVERT: Ak 204 GLU cc_start: 0.8142 (pp20) cc_final: 0.7816 (pp20) REVERT: Al 136 ASP cc_start: 0.7952 (m-30) cc_final: 0.7656 (m-30) REVERT: Al 157 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8503 (ttt90) REVERT: Al 188 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6842 (tpt170) REVERT: Al 204 GLU cc_start: 0.8142 (pp20) cc_final: 0.7815 (pp20) REVERT: Am 54 MET cc_start: 0.7670 (ttp) cc_final: 0.6250 (ttp) REVERT: Am 76 GLN cc_start: 0.8552 (mp10) cc_final: 0.8329 (mp10) REVERT: Am 160 MET cc_start: 0.8854 (tpp) cc_final: 0.8450 (mmm) REVERT: Am 165 ASP cc_start: 0.8110 (t0) cc_final: 0.7744 (t0) REVERT: Am 184 TYR cc_start: 0.8015 (t80) cc_final: 0.7606 (t80) REVERT: An 165 ASP cc_start: 0.8036 (t0) cc_final: 0.7171 (t0) REVERT: An 188 ARG cc_start: 0.7075 (tpt170) cc_final: 0.6653 (tpt170) REVERT: Ao 102 ASP cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: Ao 188 ARG cc_start: 0.7218 (tpt170) cc_final: 0.7000 (tpt170) REVERT: Ap 134 MET cc_start: 0.8246 (ttt) cc_final: 0.7893 (ttt) REVERT: Ap 165 ASP cc_start: 0.8190 (t0) cc_final: 0.7590 (t0) REVERT: Ap 188 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6802 (tpt170) outliers start: 104 outliers final: 68 residues processed: 977 average time/residue: 0.1956 time to fit residues: 282.5754 Evaluate side-chains 967 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 897 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 56 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 166 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 24 optimal weight: 0.0030 chunk 256 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 170 optimal weight: 0.0020 chunk 12 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 234 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 129 ASN Ab 158 GLN Ac 129 ASN Ac 151 ASN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 129 ASN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Af 140 GLN Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 151 ASN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098601 restraints weight = 39052.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101427 restraints weight = 25718.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103415 restraints weight = 19864.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104710 restraints weight = 16737.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105596 restraints weight = 14920.044| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23856 Z= 0.126 Angle : 0.696 9.663 32336 Z= 0.338 Chirality : 0.042 0.170 3520 Planarity : 0.006 0.061 4192 Dihedral : 4.333 18.610 3216 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.60 % Allowed : 23.30 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2864 helix: 0.05 (0.14), residues: 1424 sheet: 2.17 (0.46), residues: 160 loop : -1.17 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAm 157 TYR 0.039 0.002 TYRAk 198 PHE 0.006 0.001 PHEAk 200 TRP 0.011 0.001 TRPAa 93 HIS 0.010 0.002 HISAo 69 Details of bonding type rmsd covalent geometry : bond 0.00287 (23856) covalent geometry : angle 0.69639 (32336) hydrogen bonds : bond 0.02832 ( 800) hydrogen bonds : angle 4.92183 ( 2304) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 953 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 67 LEU cc_start: 0.8929 (mm) cc_final: 0.8728 (mm) REVERT: Aa 70 LEU cc_start: 0.9275 (tp) cc_final: 0.9068 (tp) REVERT: Aa 78 ILE cc_start: 0.8374 (tp) cc_final: 0.8022 (pt) REVERT: Aa 181 MET cc_start: 0.8661 (tpp) cc_final: 0.8381 (tpp) REVERT: Aa 183 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7451 (mpt180) REVERT: Aa 188 ARG cc_start: 0.6808 (tpt170) cc_final: 0.6598 (tpt170) REVERT: Ab 73 TYR cc_start: 0.9129 (t80) cc_final: 0.8708 (t80) REVERT: Ab 136 ASP cc_start: 0.7217 (m-30) cc_final: 0.6557 (m-30) REVERT: Ab 165 ASP cc_start: 0.8046 (t0) cc_final: 0.7662 (t0) REVERT: Ab 188 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6900 (tpt170) REVERT: Ac 157 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8506 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7891 (t0) cc_final: 0.7244 (t0) REVERT: Ac 188 ARG cc_start: 0.7076 (tpt170) cc_final: 0.6842 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8641 (t0) cc_final: 0.8255 (t0) REVERT: Ad 73 TYR cc_start: 0.8734 (t80) cc_final: 0.8414 (t80) REVERT: Ad 76 GLN cc_start: 0.8266 (mp10) cc_final: 0.7889 (mp10) REVERT: Ad 102 ASP cc_start: 0.8656 (t0) cc_final: 0.8323 (t0) REVERT: Ad 174 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7057 (tpt170) cc_final: 0.6779 (tpt170) REVERT: Ad 191 ARG cc_start: 0.8626 (ptp90) cc_final: 0.8423 (ptp90) REVERT: Ae 76 GLN cc_start: 0.8296 (mp10) cc_final: 0.7967 (mp10) REVERT: Ae 102 ASP cc_start: 0.8604 (t0) cc_final: 0.8285 (t0) REVERT: Ae 136 ASP cc_start: 0.7007 (m-30) cc_final: 0.6616 (m-30) REVERT: Ae 157 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8514 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7904 (t0) cc_final: 0.7627 (t0) REVERT: Ae 174 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7405 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6915 (tpt170) cc_final: 0.6634 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8067 (pp20) cc_final: 0.7608 (pp20) REVERT: Af 73 TYR cc_start: 0.9093 (t80) cc_final: 0.8619 (t80) REVERT: Af 165 ASP cc_start: 0.7975 (t0) cc_final: 0.7739 (t0) REVERT: Ag 70 LEU cc_start: 0.9363 (tp) cc_final: 0.9098 (tp) REVERT: Ag 80 ILE cc_start: 0.8633 (pt) cc_final: 0.8417 (pt) REVERT: Ag 102 ASP cc_start: 0.8640 (t0) cc_final: 0.8410 (t0) REVERT: Ag 136 ASP cc_start: 0.7209 (m-30) cc_final: 0.6632 (m-30) REVERT: Ag 165 ASP cc_start: 0.7995 (t0) cc_final: 0.7748 (t0) REVERT: Ag 184 TYR cc_start: 0.7773 (t80) cc_final: 0.7375 (t80) REVERT: Ah 54 MET cc_start: 0.7923 (ttp) cc_final: 0.7236 (ttp) REVERT: Ah 69 HIS cc_start: 0.8505 (t-170) cc_final: 0.8247 (t-170) REVERT: Ah 157 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8423 (ttt90) REVERT: Ah 174 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7415 (mmm-85) REVERT: Ai 76 GLN cc_start: 0.8350 (mp10) cc_final: 0.7809 (mp10) REVERT: Ai 80 ILE cc_start: 0.8651 (pt) cc_final: 0.8399 (pt) REVERT: Ai 136 ASP cc_start: 0.7619 (m-30) cc_final: 0.7083 (m-30) REVERT: Ai 165 ASP cc_start: 0.8024 (t0) cc_final: 0.7377 (t0) REVERT: Ai 188 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6765 (tpt170) REVERT: Aj 188 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6863 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8044 (pp20) cc_final: 0.7624 (pp20) REVERT: Ak 56 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8276 (mmp) REVERT: Ak 80 ILE cc_start: 0.8506 (pt) cc_final: 0.8223 (pt) REVERT: Ak 136 ASP cc_start: 0.7715 (m-30) cc_final: 0.7477 (m-30) REVERT: Ak 188 ARG cc_start: 0.7034 (tpt170) cc_final: 0.6830 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8703 (t0) cc_final: 0.8364 (t0) REVERT: Ak 204 GLU cc_start: 0.8153 (pp20) cc_final: 0.7832 (pp20) REVERT: Al 116 MET cc_start: 0.8801 (ttp) cc_final: 0.8371 (ttt) REVERT: Al 136 ASP cc_start: 0.7846 (m-30) cc_final: 0.7581 (m-30) REVERT: Al 188 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6933 (tpt170) REVERT: Al 204 GLU cc_start: 0.8142 (pp20) cc_final: 0.7816 (pp20) REVERT: Am 54 MET cc_start: 0.7616 (ttp) cc_final: 0.6067 (ttp) REVERT: Am 69 HIS cc_start: 0.8533 (t70) cc_final: 0.8280 (t-170) REVERT: Am 129 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (p0) REVERT: Am 165 ASP cc_start: 0.8017 (t0) cc_final: 0.7597 (t0) REVERT: Am 184 TYR cc_start: 0.7959 (t80) cc_final: 0.7615 (t80) REVERT: Am 188 ARG cc_start: 0.7102 (tpt170) cc_final: 0.6813 (tpt170) REVERT: An 69 HIS cc_start: 0.8556 (t-170) cc_final: 0.8351 (t-170) REVERT: An 73 TYR cc_start: 0.9037 (t80) cc_final: 0.8794 (t80) REVERT: An 76 GLN cc_start: 0.8366 (mp10) cc_final: 0.7872 (mp10) REVERT: An 79 ASP cc_start: 0.8399 (m-30) cc_final: 0.8164 (m-30) REVERT: An 165 ASP cc_start: 0.8014 (t0) cc_final: 0.7127 (t0) REVERT: An 188 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6788 (tpt170) REVERT: An 197 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7943 (mtp-110) REVERT: An 201 ASP cc_start: 0.8286 (t0) cc_final: 0.8010 (t0) REVERT: Ao 102 ASP cc_start: 0.8693 (t0) cc_final: 0.8417 (t0) REVERT: Ao 204 GLU cc_start: 0.7961 (pp20) cc_final: 0.7370 (pp20) REVERT: Ap 165 ASP cc_start: 0.8100 (t0) cc_final: 0.7491 (t0) REVERT: Ap 188 ARG cc_start: 0.7125 (tpt170) cc_final: 0.6773 (tpt170) outliers start: 91 outliers final: 63 residues processed: 997 average time/residue: 0.1957 time to fit residues: 290.5474 Evaluate side-chains 995 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 930 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 97 VAL Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 56 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 9 optimal weight: 5.9990 chunk 278 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 283 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 overall best weight: 2.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ab 158 GLN Ac 129 ASN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN Ah 158 GLN Ai 129 ASN Aj 129 ASN Aj 158 GLN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097496 restraints weight = 39031.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100350 restraints weight = 26072.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102269 restraints weight = 20186.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103538 restraints weight = 17071.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104391 restraints weight = 15271.288| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23856 Z= 0.158 Angle : 0.717 9.975 32336 Z= 0.350 Chirality : 0.043 0.166 3520 Planarity : 0.006 0.061 4192 Dihedral : 4.342 21.327 3216 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.72 % Allowed : 24.05 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.16), residues: 2864 helix: 0.02 (0.14), residues: 1424 sheet: 2.42 (0.47), residues: 160 loop : -1.18 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAm 157 TYR 0.035 0.002 TYRAm 198 PHE 0.010 0.001 PHEAa 200 TRP 0.012 0.002 TRPAg 93 HIS 0.010 0.002 HISAo 69 Details of bonding type rmsd covalent geometry : bond 0.00370 (23856) covalent geometry : angle 0.71733 (32336) hydrogen bonds : bond 0.03017 ( 800) hydrogen bonds : angle 5.01463 ( 2304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 942 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 78 ILE cc_start: 0.8262 (tp) cc_final: 0.7910 (pt) REVERT: Aa 181 MET cc_start: 0.8592 (tpp) cc_final: 0.8361 (tpp) REVERT: Aa 183 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7510 (mpt180) REVERT: Ab 54 MET cc_start: 0.7616 (ttp) cc_final: 0.7284 (ttp) REVERT: Ab 73 TYR cc_start: 0.9134 (t80) cc_final: 0.8796 (t80) REVERT: Ab 116 MET cc_start: 0.8769 (tmm) cc_final: 0.8525 (ttt) REVERT: Ab 165 ASP cc_start: 0.7998 (t0) cc_final: 0.7647 (t0) REVERT: Ac 157 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8370 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7876 (t0) cc_final: 0.7505 (t0) REVERT: Ac 197 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8269 (mtp-110) REVERT: Ac 201 ASP cc_start: 0.8502 (t0) cc_final: 0.8055 (t0) REVERT: Ad 76 GLN cc_start: 0.8272 (mp10) cc_final: 0.7933 (mp10) REVERT: Ad 102 ASP cc_start: 0.8504 (t0) cc_final: 0.8264 (t0) REVERT: Ad 174 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6721 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8256 (mp10) cc_final: 0.7968 (mp10) REVERT: Ae 102 ASP cc_start: 0.8449 (t0) cc_final: 0.8211 (t0) REVERT: Ae 136 ASP cc_start: 0.7056 (m-30) cc_final: 0.6726 (m-30) REVERT: Ae 157 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8383 (ttt-90) REVERT: Ae 188 ARG cc_start: 0.6800 (tpt170) cc_final: 0.6572 (tpt170) REVERT: Ae 198 TYR cc_start: 0.8791 (m-10) cc_final: 0.8502 (m-10) REVERT: Ae 204 GLU cc_start: 0.8025 (pp20) cc_final: 0.7617 (pp20) REVERT: Af 54 MET cc_start: 0.7608 (ttp) cc_final: 0.6920 (ttp) REVERT: Af 73 TYR cc_start: 0.9107 (t80) cc_final: 0.8783 (t80) REVERT: Ag 165 ASP cc_start: 0.7915 (t0) cc_final: 0.7529 (t0) REVERT: Ag 184 TYR cc_start: 0.7846 (t80) cc_final: 0.7506 (t80) REVERT: Ah 54 MET cc_start: 0.7910 (ttp) cc_final: 0.7264 (ttp) REVERT: Ah 69 HIS cc_start: 0.8367 (t-170) cc_final: 0.8160 (t-170) REVERT: Ah 79 ASP cc_start: 0.8399 (m-30) cc_final: 0.8055 (m-30) REVERT: Ah 116 MET cc_start: 0.8947 (tmm) cc_final: 0.8514 (ttt) REVERT: Ah 174 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7426 (mmm-85) REVERT: Ah 188 ARG cc_start: 0.6861 (tpt170) cc_final: 0.6608 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8345 (mp10) cc_final: 0.7741 (mp10) REVERT: Ai 80 ILE cc_start: 0.8769 (pt) cc_final: 0.8560 (pt) REVERT: Ai 136 ASP cc_start: 0.7676 (m-30) cc_final: 0.7275 (m-30) REVERT: Ai 165 ASP cc_start: 0.8000 (t0) cc_final: 0.7382 (t0) REVERT: Aj 165 ASP cc_start: 0.7896 (t0) cc_final: 0.7672 (t0) REVERT: Aj 188 ARG cc_start: 0.7027 (tpt170) cc_final: 0.6782 (tpt170) REVERT: Aj 204 GLU cc_start: 0.7961 (pp20) cc_final: 0.7603 (pp20) REVERT: Ak 174 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7418 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8571 (t0) cc_final: 0.8277 (t0) REVERT: Ak 204 GLU cc_start: 0.8107 (pp20) cc_final: 0.7817 (pp20) REVERT: Al 136 ASP cc_start: 0.7842 (m-30) cc_final: 0.7585 (m-30) REVERT: Al 174 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7300 (mmm-85) REVERT: Al 204 GLU cc_start: 0.8074 (pp20) cc_final: 0.7764 (pp20) REVERT: Am 54 MET cc_start: 0.7532 (ttp) cc_final: 0.6847 (ttp) REVERT: Am 69 HIS cc_start: 0.8396 (t70) cc_final: 0.8187 (t-170) REVERT: Am 129 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7542 (p0) REVERT: Am 165 ASP cc_start: 0.7968 (t0) cc_final: 0.7607 (t0) REVERT: Am 184 TYR cc_start: 0.7955 (t80) cc_final: 0.7723 (t80) REVERT: Am 188 ARG cc_start: 0.6977 (tpt170) cc_final: 0.6751 (tpt170) REVERT: An 73 TYR cc_start: 0.9033 (t80) cc_final: 0.8771 (t80) REVERT: An 76 GLN cc_start: 0.8280 (mp10) cc_final: 0.7843 (mp10) REVERT: An 165 ASP cc_start: 0.7934 (t0) cc_final: 0.7487 (t0) REVERT: An 188 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6699 (tpt170) REVERT: Ao 102 ASP cc_start: 0.8581 (t0) cc_final: 0.8335 (t0) REVERT: Ao 188 ARG cc_start: 0.6950 (tpt170) cc_final: 0.6704 (tpt170) REVERT: Ao 204 GLU cc_start: 0.7945 (pp20) cc_final: 0.7380 (pp20) REVERT: Ap 136 ASP cc_start: 0.7694 (m-30) cc_final: 0.7383 (t0) REVERT: Ap 165 ASP cc_start: 0.8082 (t0) cc_final: 0.7558 (t0) REVERT: Ap 188 ARG cc_start: 0.6965 (tpt170) cc_final: 0.6710 (tpt170) outliers start: 94 outliers final: 73 residues processed: 990 average time/residue: 0.1891 time to fit residues: 275.7087 Evaluate side-chains 1002 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 928 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 97 VAL Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 197 ARG Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 47 ILE Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 149 VAL Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 47 ILE Chi-restraints excluded: chain An residue 129 ASN Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 264 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 129 ASN Ab 158 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 129 ASN ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Af 140 GLN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 140 GLN Ak 129 ASN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 129 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 129 ASN ** Ao 151 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.124348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094028 restraints weight = 39310.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096742 restraints weight = 26668.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098584 restraints weight = 20860.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099804 restraints weight = 17736.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100624 restraints weight = 15924.471| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23856 Z= 0.248 Angle : 0.775 9.807 32336 Z= 0.383 Chirality : 0.046 0.177 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.588 23.809 3216 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.72 % Allowed : 24.05 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.16), residues: 2864 helix: -0.14 (0.14), residues: 1424 sheet: 1.56 (0.41), residues: 192 loop : -1.16 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAm 157 TYR 0.034 0.003 TYRAm 198 PHE 0.015 0.002 PHEAa 200 TRP 0.012 0.002 TRPAp 93 HIS 0.012 0.002 HISAc 69 Details of bonding type rmsd covalent geometry : bond 0.00582 (23856) covalent geometry : angle 0.77456 (32336) hydrogen bonds : bond 0.03534 ( 800) hydrogen bonds : angle 5.32572 ( 2304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 930 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 181 MET cc_start: 0.8613 (tpp) cc_final: 0.8320 (tpp) REVERT: Aa 183 ARG cc_start: 0.8299 (ttp80) cc_final: 0.7480 (mpt180) REVERT: Ab 73 TYR cc_start: 0.9212 (t80) cc_final: 0.8899 (t80) REVERT: Ab 116 MET cc_start: 0.8952 (tmm) cc_final: 0.8620 (ttt) REVERT: Ab 157 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8579 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8141 (t0) cc_final: 0.7759 (t0) REVERT: Ab 188 ARG cc_start: 0.7182 (tpt170) cc_final: 0.6814 (tpt170) REVERT: Ac 138 ASP cc_start: 0.7641 (t0) cc_final: 0.7407 (t0) REVERT: Ac 157 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8492 (ttt90) REVERT: Ac 165 ASP cc_start: 0.8091 (t0) cc_final: 0.7455 (t0) REVERT: Ac 188 ARG cc_start: 0.7061 (tpt170) cc_final: 0.6589 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8701 (t0) cc_final: 0.8469 (t0) REVERT: Ad 76 GLN cc_start: 0.8503 (mp10) cc_final: 0.8111 (mp10) REVERT: Ad 102 ASP cc_start: 0.8707 (t0) cc_final: 0.8412 (t0) REVERT: Ad 116 MET cc_start: 0.8939 (tmm) cc_final: 0.8640 (ttt) REVERT: Ad 165 ASP cc_start: 0.8046 (t0) cc_final: 0.7834 (t0) REVERT: Ad 174 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7411 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7119 (tpt170) cc_final: 0.6825 (tpt170) REVERT: Ae 102 ASP cc_start: 0.8618 (t0) cc_final: 0.8306 (t0) REVERT: Ae 157 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8492 (ttt-90) REVERT: Ae 188 ARG cc_start: 0.6927 (tpt170) cc_final: 0.6703 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8150 (pp20) cc_final: 0.7625 (pp20) REVERT: Af 54 MET cc_start: 0.7671 (ttp) cc_final: 0.7046 (ttp) REVERT: Af 73 TYR cc_start: 0.9185 (t80) cc_final: 0.8938 (t80) REVERT: Af 188 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6838 (tpt170) REVERT: Ag 116 MET cc_start: 0.9062 (tmm) cc_final: 0.8490 (ttt) REVERT: Ag 165 ASP cc_start: 0.8135 (t0) cc_final: 0.7748 (t0) REVERT: Ag 184 TYR cc_start: 0.7995 (t80) cc_final: 0.7560 (t80) REVERT: Ah 69 HIS cc_start: 0.8577 (t-170) cc_final: 0.8343 (t-170) REVERT: Ah 116 MET cc_start: 0.9005 (tmm) cc_final: 0.8599 (ttt) REVERT: Ah 165 ASP cc_start: 0.8039 (t0) cc_final: 0.7639 (t0) REVERT: Ah 174 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7480 (mmm-85) REVERT: Ah 188 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6848 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8460 (mp10) cc_final: 0.7895 (mp10) REVERT: Ai 129 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7715 (p0) REVERT: Ai 165 ASP cc_start: 0.8079 (t0) cc_final: 0.7827 (t0) REVERT: Ai 174 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7441 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6563 (tpt170) REVERT: Aj 80 ILE cc_start: 0.9324 (pt) cc_final: 0.9092 (pt) REVERT: Aj 165 ASP cc_start: 0.8113 (t0) cc_final: 0.7826 (t0) REVERT: Aj 188 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6936 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8095 (pp20) cc_final: 0.7672 (pp20) REVERT: Ak 56 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7889 (mmp) REVERT: Ak 77 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: Ak 174 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7330 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8717 (t0) cc_final: 0.8308 (t0) REVERT: Ak 204 GLU cc_start: 0.8175 (pp20) cc_final: 0.7815 (pp20) REVERT: Al 136 ASP cc_start: 0.7979 (m-30) cc_final: 0.7644 (m-30) REVERT: Al 174 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: Al 204 GLU cc_start: 0.8174 (pp20) cc_final: 0.7838 (pp20) REVERT: Am 54 MET cc_start: 0.7524 (ttp) cc_final: 0.6777 (ttp) REVERT: Am 69 HIS cc_start: 0.8598 (t70) cc_final: 0.8358 (t-170) REVERT: Am 129 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7555 (p0) REVERT: Am 165 ASP cc_start: 0.8155 (t0) cc_final: 0.7768 (t0) REVERT: Am 188 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6906 (tpt170) REVERT: An 108 MET cc_start: 0.8616 (ttt) cc_final: 0.8398 (tpp) REVERT: An 165 ASP cc_start: 0.8131 (t0) cc_final: 0.7596 (t0) REVERT: An 188 ARG cc_start: 0.7350 (tpt170) cc_final: 0.7025 (tpt170) REVERT: Ao 102 ASP cc_start: 0.8701 (t0) cc_final: 0.8431 (t0) REVERT: Ao 165 ASP cc_start: 0.8019 (t0) cc_final: 0.7679 (t0) REVERT: Ao 188 ARG cc_start: 0.7092 (tpt170) cc_final: 0.6813 (tpt170) REVERT: Ap 136 ASP cc_start: 0.7798 (m-30) cc_final: 0.7392 (t0) REVERT: Ap 165 ASP cc_start: 0.8307 (t0) cc_final: 0.7756 (t0) REVERT: Ap 188 ARG cc_start: 0.7177 (tpt170) cc_final: 0.6847 (tpt170) outliers start: 94 outliers final: 68 residues processed: 988 average time/residue: 0.2082 time to fit residues: 301.5665 Evaluate side-chains 998 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 926 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 97 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 97 VAL Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 97 VAL Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 80 ILE Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 197 ARG Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 97 VAL Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 56 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 47 ILE Chi-restraints excluded: chain An residue 129 ASN Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 36 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 279 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ab 158 GLN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 151 ASN Ad 129 ASN Ae 158 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 158 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 77 GLN Al 158 GLN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 ASN ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098323 restraints weight = 38868.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101353 restraints weight = 25487.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103385 restraints weight = 19510.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104742 restraints weight = 16386.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105631 restraints weight = 14594.147| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23856 Z= 0.138 Angle : 0.742 10.065 32336 Z= 0.367 Chirality : 0.043 0.176 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.458 22.650 3216 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.89 % Allowed : 25.00 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.16), residues: 2864 helix: -0.19 (0.14), residues: 1440 sheet: 2.39 (0.46), residues: 160 loop : -1.00 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAn 197 TYR 0.044 0.002 TYRAa 198 PHE 0.007 0.001 PHEAa 200 TRP 0.014 0.002 TRPAp 93 HIS 0.014 0.002 HISAl 69 Details of bonding type rmsd covalent geometry : bond 0.00311 (23856) covalent geometry : angle 0.74229 (32336) hydrogen bonds : bond 0.02908 ( 800) hydrogen bonds : angle 5.16049 ( 2304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 959 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 181 MET cc_start: 0.8658 (tpp) cc_final: 0.8360 (tpp) REVERT: Aa 183 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7432 (mpt180) REVERT: Aa 188 ARG cc_start: 0.6683 (tpt170) cc_final: 0.6368 (tpt170) REVERT: Ab 54 MET cc_start: 0.7439 (ttp) cc_final: 0.7148 (ttp) REVERT: Ab 116 MET cc_start: 0.8864 (tmm) cc_final: 0.8533 (ttt) REVERT: Ab 157 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8540 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7961 (t0) cc_final: 0.7578 (t0) REVERT: Ab 188 ARG cc_start: 0.7114 (tpt170) cc_final: 0.6797 (tpt170) REVERT: Ac 54 MET cc_start: 0.7767 (ttp) cc_final: 0.7495 (ttp) REVERT: Ac 124 THR cc_start: 0.8909 (p) cc_final: 0.8595 (t) REVERT: Ac 157 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8339 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7837 (t0) cc_final: 0.7429 (t0) REVERT: Ac 188 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6684 (tpt170) REVERT: Ad 54 MET cc_start: 0.7568 (ttp) cc_final: 0.7367 (ttm) REVERT: Ad 76 GLN cc_start: 0.8301 (mp10) cc_final: 0.7968 (mp10) REVERT: Ad 102 ASP cc_start: 0.8608 (t0) cc_final: 0.8280 (t0) REVERT: Ad 116 MET cc_start: 0.8851 (tmm) cc_final: 0.8099 (ttt) REVERT: Ad 188 ARG cc_start: 0.6988 (tpt170) cc_final: 0.6655 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8153 (mp10) cc_final: 0.7950 (mp10) REVERT: Ae 102 ASP cc_start: 0.8495 (t0) cc_final: 0.8268 (t0) REVERT: Ae 174 ARG cc_start: 0.7837 (mmm-85) cc_final: 0.7357 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6857 (tpt170) cc_final: 0.6589 (tpt170) REVERT: Ae 190 LEU cc_start: 0.7906 (tt) cc_final: 0.7253 (mm) REVERT: Ae 204 GLU cc_start: 0.8133 (pp20) cc_final: 0.7604 (pp20) REVERT: Af 54 MET cc_start: 0.7528 (ttp) cc_final: 0.6799 (ttp) REVERT: Af 73 TYR cc_start: 0.9122 (t80) cc_final: 0.8704 (t80) REVERT: Af 174 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7480 (mmm-85) REVERT: Af 188 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6794 (tpt170) REVERT: Ag 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7579 (t0) REVERT: Ag 184 TYR cc_start: 0.7937 (t80) cc_final: 0.7511 (t80) REVERT: Ah 69 HIS cc_start: 0.8505 (t-170) cc_final: 0.8268 (t-170) REVERT: Ah 116 MET cc_start: 0.8944 (tmm) cc_final: 0.8560 (ttt) REVERT: Ah 188 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6806 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8260 (mp10) cc_final: 0.7716 (mp10) REVERT: Ai 77 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: Ai 80 ILE cc_start: 0.8622 (pt) cc_final: 0.8380 (pt) REVERT: Ai 129 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7637 (p0) REVERT: Ai 165 ASP cc_start: 0.7950 (t0) cc_final: 0.7470 (t0) REVERT: Ai 188 ARG cc_start: 0.6850 (tpt170) cc_final: 0.6557 (tpt170) REVERT: Aj 204 GLU cc_start: 0.7976 (pp20) cc_final: 0.7614 (pp20) REVERT: Ak 80 ILE cc_start: 0.8635 (pt) cc_final: 0.8388 (pt) REVERT: Ak 136 ASP cc_start: 0.7762 (m-30) cc_final: 0.7371 (t0) REVERT: Ak 188 ARG cc_start: 0.6835 (tpt170) cc_final: 0.6504 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8618 (t0) cc_final: 0.8314 (t0) REVERT: Ak 204 GLU cc_start: 0.8116 (pp20) cc_final: 0.7841 (pp20) REVERT: Al 136 ASP cc_start: 0.7861 (m-30) cc_final: 0.7548 (m-30) REVERT: Al 174 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7336 (mmm-85) REVERT: Al 204 GLU cc_start: 0.8120 (pp20) cc_final: 0.7754 (pp20) REVERT: Am 54 MET cc_start: 0.7446 (ttp) cc_final: 0.6661 (ttp) REVERT: Am 69 HIS cc_start: 0.8525 (t70) cc_final: 0.8270 (t-170) REVERT: Am 165 ASP cc_start: 0.7950 (t0) cc_final: 0.7534 (t0) REVERT: Am 188 ARG cc_start: 0.7229 (tpt170) cc_final: 0.6856 (tpt170) REVERT: Am 197 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8131 (mtp85) REVERT: An 76 GLN cc_start: 0.8203 (mp10) cc_final: 0.7714 (mp10) REVERT: An 165 ASP cc_start: 0.7940 (t0) cc_final: 0.7455 (t0) REVERT: An 183 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7737 (ttm-80) REVERT: An 188 ARG cc_start: 0.7208 (tpt170) cc_final: 0.6986 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8462 (mp10) cc_final: 0.8208 (mp10) REVERT: Ao 102 ASP cc_start: 0.8644 (t0) cc_final: 0.8393 (t0) REVERT: Ao 157 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8469 (ttt-90) REVERT: Ap 136 ASP cc_start: 0.7548 (m-30) cc_final: 0.7088 (t0) REVERT: Ap 165 ASP cc_start: 0.8091 (t0) cc_final: 0.7550 (t0) REVERT: Ap 188 ARG cc_start: 0.7055 (tpt170) cc_final: 0.6801 (tpt170) outliers start: 73 outliers final: 57 residues processed: 995 average time/residue: 0.1981 time to fit residues: 289.4649 Evaluate side-chains 997 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 938 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 129 ASN Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 197 ARG Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 47 ILE Chi-restraints excluded: chain An residue 129 ASN Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.0070 chunk 237 optimal weight: 1.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 158 GLN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 77 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ap 151 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.129144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.098050 restraints weight = 38789.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100949 restraints weight = 25578.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102925 restraints weight = 19750.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104237 restraints weight = 16665.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.105002 restraints weight = 14923.505| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23856 Z= 0.151 Angle : 0.756 10.546 32336 Z= 0.374 Chirality : 0.044 0.166 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.456 25.954 3216 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.85 % Allowed : 25.83 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2864 helix: -0.15 (0.14), residues: 1440 sheet: 2.40 (0.46), residues: 160 loop : -0.99 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAm 157 TYR 0.041 0.002 TYRAl 198 PHE 0.009 0.001 PHEAa 200 TRP 0.013 0.001 TRPAg 93 HIS 0.015 0.002 HISAn 69 Details of bonding type rmsd covalent geometry : bond 0.00349 (23856) covalent geometry : angle 0.75639 (32336) hydrogen bonds : bond 0.03025 ( 800) hydrogen bonds : angle 5.15691 ( 2304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5315.35 seconds wall clock time: 91 minutes 51.90 seconds (5511.90 seconds total)