Starting phenix.real_space_refine on Thu May 22 20:59:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opb_17047/05_2025/8opb_17047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opb_17047/05_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_17047/05_2025/8opb_17047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opb_17047/05_2025/8opb_17047.map" model { file = "/net/cci-nas-00/data/ceres_data/8opb_17047/05_2025/8opb_17047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opb_17047/05_2025/8opb_17047.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, Ak, Aj, Am, Al, Ao, An, Ap Time building chain proxies: 5.56, per 1000 atoms: 0.24 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: 5.00 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 1.96 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: 5.73 Time building geometry restraints manager: 5.89 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: 0.19 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' selection = chain 'Ae' selection = chain 'Ad' selection = chain 'Ag' selection = chain 'Af' selection = chain 'Ai' selection = chain 'Ah' selection = chain 'Ak' selection = chain 'Aj' selection = chain 'Am' selection = chain 'Al' selection = chain 'Ao' selection = chain 'An' 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: 1.690 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: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 37.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- 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 : 9.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRPAj 132 HIS 0.011 0.003 HISAc 69 PHE 0.007 0.002 PHEAp 200 TYR 0.027 0.002 TYRAm 184 ARG 0.007 0.001 ARGAd 183 Details of bonding type rmsd hydrogen bonds : bond 0.27659 ( 800) hydrogen bonds : angle 8.15013 ( 2304) covalent geometry : bond 0.00444 (23856) covalent geometry : angle 0.88748 (32336) *********************** 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 : 2.600 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: 0.4126 time to fit residues: 540.8251 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 : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 151 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN Af 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 151 ASN Ai 151 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN An 151 ASN ** Ao 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098510 restraints weight = 38604.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101453 restraints weight = 25359.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103430 restraints weight = 19420.680| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23856 Z= 0.138 Angle : 0.669 9.037 32336 Z= 0.331 Chirality : 0.041 0.117 3520 Planarity : 0.006 0.050 4192 Dihedral : 4.300 15.557 3216 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.45 % Allowed : 18.55 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2864 helix: -0.38 (0.14), residues: 1424 sheet: 0.11 (0.44), residues: 160 loop : -1.47 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 93 HIS 0.007 0.001 HISAj 69 PHE 0.008 0.001 PHEAp 200 TYR 0.024 0.002 TYRAl 198 ARG 0.005 0.001 ARGAa 157 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 800) hydrogen bonds : angle 5.19021 ( 2304) covalent geometry : bond 0.00311 (23856) covalent geometry : angle 0.66877 (32336) *********************** 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 918 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 856 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 136 ASP cc_start: 0.7545 (m-30) cc_final: 0.7120 (m-30) REVERT: Aa 181 MET cc_start: 0.8707 (tpp) cc_final: 0.8504 (tpp) REVERT: Aa 183 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7425 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8492 (t0) cc_final: 0.8187 (t0) REVERT: Ab 54 MET cc_start: 0.7578 (ttp) cc_final: 0.6859 (ttp) REVERT: Ab 136 ASP cc_start: 0.7674 (m-30) cc_final: 0.7238 (m-30) REVERT: Ac 157 ARG cc_start: 0.8542 (ttp80) cc_final: 0.8288 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7676 (t0) cc_final: 0.7308 (t0) REVERT: Ac 201 ASP cc_start: 0.8438 (t0) cc_final: 0.8149 (t0) REVERT: Ad 76 GLN cc_start: 0.8372 (mp10) cc_final: 0.8155 (mp10) REVERT: Ad 102 ASP cc_start: 0.8615 (t0) cc_final: 0.8304 (t0) REVERT: Ad 157 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8251 (ttt-90) REVERT: Ad 174 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: Ae 102 ASP cc_start: 0.8508 (t0) cc_final: 0.8197 (t0) REVERT: Ae 165 ASP cc_start: 0.7832 (t0) cc_final: 0.7594 (t0) REVERT: Ae 174 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: Ae 181 MET cc_start: 0.8631 (tpp) cc_final: 0.8327 (tpp) REVERT: Ag 102 ASP cc_start: 0.8498 (t0) cc_final: 0.8232 (t0) REVERT: Ag 157 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8541 (ttt-90) REVERT: Ah 54 MET cc_start: 0.7712 (ttp) cc_final: 0.7363 (ttp) REVERT: Ah 76 GLN cc_start: 0.8434 (mp10) cc_final: 0.8118 (mp10) REVERT: Ah 157 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8312 (ttt90) REVERT: Ai 56 MET cc_start: 0.8559 (mmp) cc_final: 0.8337 (mmp) REVERT: Ai 60 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8400 (mmtm) REVERT: Ai 73 TYR cc_start: 0.8769 (t80) cc_final: 0.8531 (t80) REVERT: Ai 136 ASP cc_start: 0.7596 (m-30) cc_final: 0.7240 (m-30) REVERT: Ai 157 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8449 (ttt90) REVERT: Ai 160 MET cc_start: 0.8898 (tpp) cc_final: 0.8460 (mmm) REVERT: Aj 56 MET cc_start: 0.8543 (mmp) cc_final: 0.8071 (mmp) REVERT: Aj 157 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8334 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.7997 (t0) cc_final: 0.7751 (t0) REVERT: Ak 73 TYR cc_start: 0.8770 (t80) cc_final: 0.8490 (t80) REVERT: Ak 77 GLN cc_start: 0.8372 (tp40) cc_final: 0.7862 (tp40) REVERT: Ak 136 ASP cc_start: 0.7933 (m-30) cc_final: 0.7509 (m-30) REVERT: Ak 157 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8293 (ttt-90) REVERT: Ak 165 ASP cc_start: 0.7754 (t0) cc_final: 0.7550 (t0) REVERT: Ak 174 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8392 (t0) cc_final: 0.8137 (t0) REVERT: Ak 204 GLU cc_start: 0.8110 (pp20) cc_final: 0.7788 (pp20) REVERT: Al 136 ASP cc_start: 0.8092 (m-30) cc_final: 0.7557 (m-30) REVERT: Al 157 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8362 (ttt90) REVERT: Al 204 GLU cc_start: 0.8018 (pp20) cc_final: 0.7808 (pp20) REVERT: Am 69 HIS cc_start: 0.8432 (t-170) cc_final: 0.8207 (t-170) REVERT: Am 157 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8420 (ttt-90) REVERT: Am 160 MET cc_start: 0.8862 (tpp) cc_final: 0.8342 (mmm) REVERT: Am 165 ASP cc_start: 0.7876 (t0) cc_final: 0.7621 (t0) REVERT: An 165 ASP cc_start: 0.7716 (t0) cc_final: 0.7507 (t0) REVERT: An 174 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7359 (mmm-85) REVERT: Ao 157 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8395 (ttt90) REVERT: Ao 174 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: Ap 165 ASP cc_start: 0.7732 (t0) cc_final: 0.7352 (t0) outliers start: 62 outliers final: 14 residues processed: 894 average time/residue: 0.4135 time to fit residues: 549.6312 Evaluate side-chains 833 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 818 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa 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 Aj residue 205 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 88 optimal weight: 9.9990 chunk 201 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ab 158 GLN Ac 140 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 140 GLN Ae 129 ASN Ae 140 GLN Af 140 GLN Af 151 ASN Af 158 GLN Ag 151 ASN Ah 151 ASN Ai 140 GLN Aj 140 GLN Al 151 ASN An 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095778 restraints weight = 38983.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098516 restraints weight = 26508.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100304 restraints weight = 20671.983| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23856 Z= 0.192 Angle : 0.678 8.927 32336 Z= 0.334 Chirality : 0.043 0.151 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.484 17.670 3216 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.49 % Allowed : 18.39 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2864 helix: -0.08 (0.15), residues: 1360 sheet: 0.68 (0.41), residues: 160 loop : -1.37 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAa 93 HIS 0.008 0.002 HISAe 69 PHE 0.011 0.002 PHEAa 200 TYR 0.024 0.002 TYRAl 198 ARG 0.006 0.001 ARGAb 157 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 800) hydrogen bonds : angle 5.03814 ( 2304) covalent geometry : bond 0.00450 (23856) covalent geometry : angle 0.67772 (32336) *********************** 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 943 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 880 time to evaluate : 2.760 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 77 GLN cc_start: 0.8345 (tp40) cc_final: 0.6602 (tp40) REVERT: Aa 136 ASP cc_start: 0.7914 (m-30) cc_final: 0.7547 (m-30) REVERT: Aa 157 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8398 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8771 (tpp) cc_final: 0.8469 (tpp) REVERT: Aa 183 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7290 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8601 (t0) cc_final: 0.8236 (t0) REVERT: Ab 54 MET cc_start: 0.7772 (ttp) cc_final: 0.6810 (ttp) REVERT: Ab 121 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7739 (mm-30) REVERT: Ab 136 ASP cc_start: 0.7846 (m-30) cc_final: 0.7309 (m-30) REVERT: Ab 157 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8503 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7982 (t0) cc_final: 0.7760 (t0) REVERT: Ab 183 ARG cc_start: 0.8519 (ttp80) cc_final: 0.8311 (ttp80) REVERT: Ab 184 TYR cc_start: 0.7976 (t80) cc_final: 0.7758 (t80) REVERT: Ac 91 ASP cc_start: 0.8213 (m-30) cc_final: 0.7963 (m-30) REVERT: Ac 157 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8409 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7975 (t0) cc_final: 0.7440 (t0) REVERT: Ac 184 TYR cc_start: 0.7960 (t80) cc_final: 0.7754 (t80) REVERT: Ac 201 ASP cc_start: 0.8587 (t0) cc_final: 0.8298 (t0) REVERT: Ad 73 TYR cc_start: 0.8747 (t80) cc_final: 0.8404 (t80) REVERT: Ad 102 ASP cc_start: 0.8672 (t0) cc_final: 0.8411 (t0) REVERT: Ad 157 ARG cc_start: 0.8677 (ttp80) cc_final: 0.8428 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.7991 (t0) cc_final: 0.7700 (t0) REVERT: Ad 188 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6975 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8366 (mp10) cc_final: 0.8107 (mp10) REVERT: Ae 80 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8661 (pt) REVERT: Ae 102 ASP cc_start: 0.8580 (t0) cc_final: 0.8249 (t0) REVERT: Ae 157 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8439 (ttt-90) REVERT: Ae 174 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7534 (mmm-85) REVERT: Ae 181 MET cc_start: 0.8661 (tpp) cc_final: 0.8394 (tpp) REVERT: Ae 188 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6884 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8159 (pp20) cc_final: 0.7618 (pp20) REVERT: Af 157 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8521 (ttt-90) REVERT: Af 174 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7600 (mmm-85) REVERT: Af 188 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6866 (tpt170) REVERT: Ag 77 GLN cc_start: 0.8222 (tp40) cc_final: 0.7378 (tp40) REVERT: Ag 80 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8595 (pt) REVERT: Ag 102 ASP cc_start: 0.8647 (t0) cc_final: 0.8380 (t0) REVERT: Ag 135 MET cc_start: 0.8742 (mmm) cc_final: 0.8535 (mmm) REVERT: Ag 136 ASP cc_start: 0.7765 (m-30) cc_final: 0.7245 (m-30) REVERT: Ag 157 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8603 (ttt-90) REVERT: Ag 165 ASP cc_start: 0.8019 (t0) cc_final: 0.7774 (t0) REVERT: Ah 54 MET cc_start: 0.7850 (ttp) cc_final: 0.7109 (ttp) REVERT: Ah 157 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8428 (ttt90) REVERT: Ai 91 ASP cc_start: 0.8031 (m-30) cc_final: 0.7827 (m-30) REVERT: Ai 129 ASN cc_start: 0.8210 (p0) cc_final: 0.7989 (p0) REVERT: Ai 136 ASP cc_start: 0.7771 (m-30) cc_final: 0.7294 (m-30) REVERT: Ai 157 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8522 (ttt90) REVERT: Ai 165 ASP cc_start: 0.8114 (t0) cc_final: 0.7570 (t0) REVERT: Ai 198 TYR cc_start: 0.8820 (m-80) cc_final: 0.8604 (m-10) REVERT: Aj 157 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8507 (ttt-90) REVERT: Aj 188 ARG cc_start: 0.7143 (tpt170) cc_final: 0.6876 (tpt170) REVERT: Ak 77 GLN cc_start: 0.8081 (tp40) cc_final: 0.7495 (tp40) REVERT: Ak 80 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8471 (pt) REVERT: Ak 136 ASP cc_start: 0.7847 (m-30) cc_final: 0.7488 (m-30) REVERT: Ak 157 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8495 (ttt90) REVERT: Ak 188 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6936 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8524 (t0) cc_final: 0.8130 (t0) REVERT: Ak 204 GLU cc_start: 0.8172 (pp20) cc_final: 0.7887 (pp20) REVERT: Al 77 GLN cc_start: 0.8428 (tp40) cc_final: 0.7976 (tp40) REVERT: Al 80 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8796 (pt) REVERT: Al 136 ASP cc_start: 0.8041 (m-30) cc_final: 0.7513 (m-30) REVERT: Al 157 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8533 (ttt90) REVERT: Al 174 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7442 (mmm-85) REVERT: Al 183 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8045 (ttp80) REVERT: Al 204 GLU cc_start: 0.8166 (pp20) cc_final: 0.7843 (pp20) REVERT: Am 69 HIS cc_start: 0.8544 (t-170) cc_final: 0.8325 (t-170) REVERT: Am 157 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8470 (ttt90) REVERT: Am 165 ASP cc_start: 0.7903 (t0) cc_final: 0.7683 (t0) REVERT: An 56 MET cc_start: 0.8636 (mmp) cc_final: 0.8229 (mmp) REVERT: An 73 TYR cc_start: 0.9046 (t80) cc_final: 0.8625 (t80) REVERT: Ao 157 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8540 (ttt90) REVERT: Ao 160 MET cc_start: 0.9073 (tpp) cc_final: 0.8626 (mmm) REVERT: Ao 165 ASP cc_start: 0.7950 (t0) cc_final: 0.7679 (t0) REVERT: Ao 174 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7299 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7184 (tpt170) cc_final: 0.6946 (tpt170) REVERT: Ap 140 GLN cc_start: 0.8071 (mt0) cc_final: 0.7313 (mt0) REVERT: Ap 165 ASP cc_start: 0.8096 (t0) cc_final: 0.7635 (t0) REVERT: Ap 188 ARG cc_start: 0.7197 (tpt170) cc_final: 0.6936 (tpt170) REVERT: Ap 204 GLU cc_start: 0.8206 (pp20) cc_final: 0.7874 (pp20) outliers start: 63 outliers final: 32 residues processed: 904 average time/residue: 0.3914 time to fit residues: 518.6115 Evaluate side-chains 880 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 844 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 78 ILE 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 133 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ad residue 149 VAL 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 133 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 78 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Aj residue 78 ILE Chi-restraints excluded: chain Aj residue 99 LEU 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 78 ILE Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 119 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.0060 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 158 GLN Af 129 ASN Af 151 ASN Ah 151 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Al 151 ASN Am 129 ASN Am 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 129 ASN Ap 158 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095963 restraints weight = 39331.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098827 restraints weight = 26156.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100753 restraints weight = 20153.180| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23856 Z= 0.164 Angle : 0.684 9.834 32336 Z= 0.331 Chirality : 0.042 0.153 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.376 16.328 3216 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.88 % Allowed : 19.62 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2864 helix: 0.12 (0.15), residues: 1360 sheet: 1.42 (0.44), residues: 160 loop : -1.31 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAb 93 HIS 0.012 0.001 HISAd 69 PHE 0.009 0.001 PHEAa 200 TYR 0.024 0.002 TYRAn 198 ARG 0.006 0.001 ARGAk 183 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 800) hydrogen bonds : angle 4.94047 ( 2304) covalent geometry : bond 0.00385 (23856) covalent geometry : angle 0.68361 (32336) *********************** 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 991 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 893 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8329 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8669 (tpp) cc_final: 0.8427 (tpp) REVERT: Aa 183 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7398 (mpt180) REVERT: Ab 54 MET cc_start: 0.7658 (ttp) cc_final: 0.6721 (ttp) REVERT: Ab 136 ASP cc_start: 0.7026 (m-30) cc_final: 0.6587 (m-30) REVERT: Ab 157 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8443 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8015 (t0) cc_final: 0.7716 (t0) REVERT: Ac 157 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8294 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7927 (t0) cc_final: 0.7383 (t0) REVERT: Ad 102 ASP cc_start: 0.8566 (t0) cc_final: 0.8304 (t0) REVERT: Ad 157 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8314 (ttt-90) REVERT: Ad 174 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7460 (mmm-85) REVERT: Ae 76 GLN cc_start: 0.8298 (mp10) cc_final: 0.8024 (mp10) REVERT: Ae 80 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8702 (pt) REVERT: Ae 102 ASP cc_start: 0.8466 (t0) cc_final: 0.8139 (t0) REVERT: Ae 136 ASP cc_start: 0.7401 (m-30) cc_final: 0.6754 (m-30) REVERT: Ae 157 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8360 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7897 (t0) cc_final: 0.7674 (t0) REVERT: Ae 174 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7441 (mmm-85) REVERT: Ae 204 GLU cc_start: 0.8130 (pp20) cc_final: 0.7668 (pp20) REVERT: Af 54 MET cc_start: 0.7572 (ttp) cc_final: 0.6520 (ttp) REVERT: Af 56 MET cc_start: 0.8675 (mmp) cc_final: 0.8440 (mmp) REVERT: Af 73 TYR cc_start: 0.8937 (t80) cc_final: 0.8469 (t80) REVERT: Af 158 GLN cc_start: 0.8555 (mt0) cc_final: 0.8340 (mt0) REVERT: Af 174 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7567 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8523 (t0) cc_final: 0.8275 (t0) REVERT: Ag 136 ASP cc_start: 0.7688 (m-30) cc_final: 0.7206 (m-30) REVERT: Ag 165 ASP cc_start: 0.7939 (t0) cc_final: 0.7519 (t0) REVERT: Ah 54 MET cc_start: 0.7721 (ttp) cc_final: 0.7043 (ttp) REVERT: Ah 76 GLN cc_start: 0.8520 (mp10) cc_final: 0.8275 (mp10) REVERT: Ah 157 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8354 (ttt90) REVERT: Ai 76 GLN cc_start: 0.8365 (mp10) cc_final: 0.7786 (mp10) REVERT: Ai 77 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7465 (m-30) cc_final: 0.7022 (m-30) REVERT: Ai 165 ASP cc_start: 0.8096 (t0) cc_final: 0.7612 (t0) REVERT: Aj 157 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8386 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8030 (t0) cc_final: 0.7809 (t0) REVERT: Aj 188 ARG cc_start: 0.7011 (tpt170) cc_final: 0.6789 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8027 (pp20) cc_final: 0.7454 (pp20) REVERT: Ak 80 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (pt) REVERT: Ak 91 ASP cc_start: 0.7981 (m-30) cc_final: 0.7619 (m-30) REVERT: Ak 136 ASP cc_start: 0.7909 (m-30) cc_final: 0.7660 (m-30) REVERT: Ak 174 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8464 (t0) cc_final: 0.8055 (t0) REVERT: Ak 204 GLU cc_start: 0.8085 (pp20) cc_final: 0.7844 (pp20) REVERT: Al 80 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (pt) REVERT: Al 116 MET cc_start: 0.8735 (ttp) cc_final: 0.8388 (ttt) REVERT: Al 136 ASP cc_start: 0.7907 (m-30) cc_final: 0.7443 (m-30) REVERT: Al 157 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8408 (ttt90) REVERT: Al 183 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8163 (ttp80) REVERT: Al 204 GLU cc_start: 0.8078 (pp20) cc_final: 0.7780 (pp20) REVERT: Am 56 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8058 (mmp) REVERT: Am 69 HIS cc_start: 0.8423 (t-170) cc_final: 0.8196 (t-170) REVERT: Am 157 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8401 (ttt90) REVERT: Am 165 ASP cc_start: 0.7948 (t0) cc_final: 0.7716 (t0) REVERT: Am 184 TYR cc_start: 0.7879 (t80) cc_final: 0.7414 (t80) REVERT: An 56 MET cc_start: 0.8546 (mmp) cc_final: 0.8152 (mmp) REVERT: Ao 160 MET cc_start: 0.8944 (tpp) cc_final: 0.8652 (mmm) REVERT: Ao 165 ASP cc_start: 0.7952 (t0) cc_final: 0.7720 (t0) REVERT: Ao 174 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6871 (tpt170) REVERT: Ap 150 GLU cc_start: 0.7915 (tt0) cc_final: 0.7710 (tt0) REVERT: Ap 165 ASP cc_start: 0.8028 (t0) cc_final: 0.7536 (t0) outliers start: 98 outliers final: 58 residues processed: 945 average time/residue: 0.3795 time to fit residues: 527.8861 Evaluate side-chains 917 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 854 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN 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 129 ASN 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 71 LEU Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 80 ILE 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 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 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 77 GLN 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 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 80 ILE 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 80 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 Am residue 56 MET 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 Am residue 155 THR 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 71 LEU 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 193 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 129 ASN Ac 129 ASN Ac 140 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 129 ASN Af 140 GLN Af 151 ASN Af 158 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN 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 129 ASN Am 158 GLN Ao 129 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090202 restraints weight = 39557.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092767 restraints weight = 27176.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094542 restraints weight = 21434.491| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23856 Z= 0.291 Angle : 0.756 9.217 32336 Z= 0.372 Chirality : 0.045 0.171 3520 Planarity : 0.006 0.066 4192 Dihedral : 4.655 17.985 3216 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.31 % Allowed : 21.16 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2864 helix: 0.01 (0.15), residues: 1360 sheet: 1.07 (0.41), residues: 160 loop : -1.39 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRPAb 93 HIS 0.009 0.001 HISAe 69 PHE 0.016 0.002 PHEAa 200 TYR 0.029 0.003 TYRAc 198 ARG 0.006 0.001 ARGAc 183 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 800) hydrogen bonds : angle 5.27409 ( 2304) covalent geometry : bond 0.00681 (23856) covalent geometry : angle 0.75583 (32336) *********************** 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 1002 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 893 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8437 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8731 (tpp) cc_final: 0.8461 (tpp) REVERT: Aa 183 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7441 (mpt180) REVERT: Aa 188 ARG cc_start: 0.6971 (tpt170) cc_final: 0.6766 (tpt170) REVERT: Aa 201 ASP cc_start: 0.8602 (t0) cc_final: 0.8249 (t0) REVERT: Ab 54 MET cc_start: 0.7812 (ttp) cc_final: 0.6798 (ttp) REVERT: Ab 121 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7911 (mm-30) REVERT: Ab 136 ASP cc_start: 0.7262 (m-30) cc_final: 0.6731 (m-30) REVERT: Ab 157 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8565 (ttt90) REVERT: Ab 174 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: Ac 140 GLN cc_start: 0.8199 (mt0) cc_final: 0.7506 (mt0) REVERT: Ac 157 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8506 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.8170 (t0) cc_final: 0.7460 (t0) REVERT: Ac 188 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6784 (tpt170) REVERT: Ac 197 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8250 (mtp-110) REVERT: Ad 102 ASP cc_start: 0.8702 (t0) cc_final: 0.8449 (t0) REVERT: Ad 157 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8448 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.8018 (t0) cc_final: 0.7786 (t0) REVERT: Ad 174 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: Ae 76 GLN cc_start: 0.8418 (mp10) cc_final: 0.8092 (mp10) REVERT: Ae 102 ASP cc_start: 0.8611 (t0) cc_final: 0.8284 (t0) REVERT: Ae 136 ASP cc_start: 0.7280 (m-30) cc_final: 0.6651 (m-30) REVERT: Ae 157 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8494 (ttt-90) REVERT: Ae 174 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7526 (mmm-85) REVERT: Ae 198 TYR cc_start: 0.8716 (m-10) cc_final: 0.8497 (m-10) REVERT: Ae 204 GLU cc_start: 0.8144 (pp20) cc_final: 0.7638 (pp20) REVERT: Af 54 MET cc_start: 0.7839 (ttp) cc_final: 0.7008 (ttp) REVERT: Af 73 TYR cc_start: 0.9186 (t80) cc_final: 0.8949 (t80) REVERT: Af 174 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8718 (t0) cc_final: 0.8467 (t0) REVERT: Ag 136 ASP cc_start: 0.7758 (m-30) cc_final: 0.7406 (m-30) REVERT: Ag 165 ASP cc_start: 0.8130 (t0) cc_final: 0.7706 (t0) REVERT: Ah 54 MET cc_start: 0.7945 (ttp) cc_final: 0.7296 (ttp) REVERT: Ah 69 HIS cc_start: 0.8559 (t-170) cc_final: 0.8328 (t-170) REVERT: Ah 157 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8482 (ttt90) REVERT: Ah 165 ASP cc_start: 0.8172 (t0) cc_final: 0.7923 (t0) REVERT: Ai 76 GLN cc_start: 0.8506 (mp10) cc_final: 0.7876 (mp10) REVERT: Ai 77 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7707 (m-30) cc_final: 0.7144 (m-30) REVERT: Ai 165 ASP cc_start: 0.8236 (t0) cc_final: 0.7647 (t0) REVERT: Ai 174 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: Ai 201 ASP cc_start: 0.8598 (t0) cc_final: 0.8389 (t0) REVERT: Aj 80 ILE cc_start: 0.9374 (pt) cc_final: 0.9170 (pt) REVERT: Aj 157 ARG cc_start: 0.8751 (ttp80) cc_final: 0.8523 (ttt-90) REVERT: Aj 174 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6903 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8134 (pp20) cc_final: 0.7610 (pp20) REVERT: Ak 136 ASP cc_start: 0.7982 (m-30) cc_final: 0.7684 (m-30) REVERT: Ak 174 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7438 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8696 (t0) cc_final: 0.8240 (t0) REVERT: Ak 204 GLU cc_start: 0.8200 (pp20) cc_final: 0.7860 (pp20) REVERT: Al 136 ASP cc_start: 0.8024 (m-30) cc_final: 0.7684 (m-30) REVERT: Al 157 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8510 (ttt90) REVERT: Al 165 ASP cc_start: 0.8033 (t0) cc_final: 0.7830 (t0) REVERT: Al 174 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7360 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7109 (tpt170) cc_final: 0.6881 (tpt170) REVERT: Al 204 GLU cc_start: 0.8190 (pp20) cc_final: 0.7817 (pp20) REVERT: Am 157 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8542 (ttt90) REVERT: Am 165 ASP cc_start: 0.8200 (t0) cc_final: 0.7879 (t0) REVERT: Am 184 TYR cc_start: 0.8042 (t80) cc_final: 0.7652 (t80) REVERT: An 54 MET cc_start: 0.7947 (ttp) cc_final: 0.7442 (ttp) REVERT: An 165 ASP cc_start: 0.7994 (t0) cc_final: 0.7774 (t0) REVERT: Ao 102 ASP cc_start: 0.8657 (t0) cc_final: 0.8350 (t0) REVERT: Ao 165 ASP cc_start: 0.8234 (t0) cc_final: 0.7984 (t0) REVERT: Ao 174 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7553 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7282 (tpt170) cc_final: 0.7047 (tpt170) REVERT: Ap 150 GLU cc_start: 0.8046 (tt0) cc_final: 0.7845 (tt0) REVERT: Ap 165 ASP cc_start: 0.8242 (t0) cc_final: 0.7640 (t0) outliers start: 109 outliers final: 73 residues processed: 950 average time/residue: 0.3943 time to fit residues: 545.5265 Evaluate side-chains 939 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 865 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 80 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 99 LEU Chi-restraints excluded: chain Ad residue 133 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 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 Ae residue 195 LEU Chi-restraints excluded: chain Af residue 78 ILE Chi-restraints excluded: chain Af residue 99 LEU 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 133 VAL 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 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 159 ILE 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 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 129 ASN Chi-restraints excluded: chain Ak residue 133 VAL 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 99 LEU 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 149 VAL Chi-restraints excluded: chain Am residue 159 ILE 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 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 85 optimal weight: 0.6980 chunk 286 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 225 optimal weight: 0.0370 chunk 202 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 Ad 129 ASN Ae 158 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 129 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN ** Aj 69 HIS ** 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 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 129 ASN Ao 129 ASN ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 129 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098005 restraints weight = 38948.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100937 restraints weight = 25852.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102885 restraints weight = 19920.311| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3192 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= 0.120 Angle : 0.688 10.851 32336 Z= 0.332 Chirality : 0.042 0.165 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.354 17.257 3216 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.40 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2864 helix: 0.02 (0.14), residues: 1424 sheet: 1.67 (0.43), residues: 192 loop : -1.14 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAl 93 HIS 0.009 0.002 HISAc 69 PHE 0.005 0.001 PHEAl 200 TYR 0.027 0.002 TYRAl 198 ARG 0.007 0.001 ARGAc 183 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 800) hydrogen bonds : angle 4.90479 ( 2304) covalent geometry : bond 0.00263 (23856) covalent geometry : angle 0.68766 (32336) *********************** 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 1055 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 969 time to evaluate : 2.457 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 70 LEU cc_start: 0.9280 (tp) cc_final: 0.9047 (tp) REVERT: Aa 136 ASP cc_start: 0.7509 (m-30) cc_final: 0.7274 (m-30) REVERT: Aa 157 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8450 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8701 (tpp) cc_final: 0.8431 (tpp) REVERT: Aa 188 ARG cc_start: 0.6954 (tpt170) cc_final: 0.6715 (tpt170) REVERT: Ab 54 MET cc_start: 0.7722 (ttp) cc_final: 0.6664 (ttp) REVERT: Ab 136 ASP cc_start: 0.7139 (m-30) cc_final: 0.6591 (m-30) REVERT: Ac 138 ASP cc_start: 0.7893 (t0) cc_final: 0.7653 (t0) REVERT: Ac 165 ASP cc_start: 0.7942 (t0) cc_final: 0.7157 (t0) REVERT: Ac 184 TYR cc_start: 0.7932 (t80) cc_final: 0.7652 (t80) REVERT: Ac 188 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6720 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8361 (t0) cc_final: 0.8063 (t0) REVERT: Ad 73 TYR cc_start: 0.8678 (t80) cc_final: 0.8424 (t80) REVERT: Ad 76 GLN cc_start: 0.8302 (mp10) cc_final: 0.8002 (mp10) REVERT: Ad 102 ASP cc_start: 0.8701 (t0) cc_final: 0.8367 (t0) REVERT: Ad 138 ASP cc_start: 0.7733 (t0) cc_final: 0.7493 (t0) REVERT: Ad 174 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7110 (tpt170) cc_final: 0.6723 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8290 (mp10) cc_final: 0.7947 (mp10) REVERT: Ae 102 ASP cc_start: 0.8593 (t0) cc_final: 0.8271 (t0) REVERT: Ae 157 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8487 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7891 (t0) cc_final: 0.7674 (t0) REVERT: Ae 188 ARG cc_start: 0.6949 (tpt170) cc_final: 0.6670 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8165 (pp20) cc_final: 0.7665 (pp20) REVERT: Af 54 MET cc_start: 0.7761 (ttp) cc_final: 0.6919 (ttp) REVERT: Af 73 TYR cc_start: 0.9095 (t80) cc_final: 0.8530 (t80) REVERT: Af 174 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7445 (mmm-85) REVERT: Ag 70 LEU cc_start: 0.9367 (tp) cc_final: 0.9133 (tp) REVERT: Ag 102 ASP cc_start: 0.8674 (t0) cc_final: 0.8436 (t0) REVERT: Ag 136 ASP cc_start: 0.7712 (m-30) cc_final: 0.7363 (m-30) REVERT: Ag 165 ASP cc_start: 0.7994 (t0) cc_final: 0.7499 (t0) REVERT: Ag 204 GLU cc_start: 0.7819 (pp20) cc_final: 0.7593 (pp20) REVERT: Ah 54 MET cc_start: 0.7906 (ttp) cc_final: 0.7136 (ttp) REVERT: Ah 69 HIS cc_start: 0.8527 (t-170) cc_final: 0.8302 (t-170) REVERT: Ah 76 GLN cc_start: 0.8585 (mp10) cc_final: 0.8332 (mp10) REVERT: Ah 136 ASP cc_start: 0.7273 (m-30) cc_final: 0.7033 (m-30) REVERT: Ah 157 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8432 (ttt90) REVERT: Ah 188 ARG cc_start: 0.7073 (tpt170) cc_final: 0.6774 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8330 (mp10) cc_final: 0.7713 (mp10) REVERT: Ai 77 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7544 (m-30) cc_final: 0.6978 (m-30) REVERT: Ai 160 MET cc_start: 0.8605 (mmm) cc_final: 0.8303 (mmm) REVERT: Ai 165 ASP cc_start: 0.8027 (t0) cc_final: 0.7407 (t0) REVERT: Ai 188 ARG cc_start: 0.7088 (tpt170) cc_final: 0.6813 (tpt170) REVERT: Aj 165 ASP cc_start: 0.7967 (t0) cc_final: 0.7764 (t0) REVERT: Aj 204 GLU cc_start: 0.8097 (pp20) cc_final: 0.7617 (pp20) REVERT: Ak 56 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7972 (mmp) REVERT: Ak 136 ASP cc_start: 0.7862 (m-30) cc_final: 0.7588 (m-30) REVERT: Ak 165 ASP cc_start: 0.7872 (t0) cc_final: 0.7617 (t0) REVERT: Ak 188 ARG cc_start: 0.7090 (tpt170) cc_final: 0.6803 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8725 (t0) cc_final: 0.8390 (t0) REVERT: Ak 204 GLU cc_start: 0.8182 (pp20) cc_final: 0.7850 (pp20) REVERT: Al 116 MET cc_start: 0.8739 (ttp) cc_final: 0.8292 (ttt) REVERT: Al 136 ASP cc_start: 0.7979 (m-30) cc_final: 0.7267 (t0) REVERT: Al 174 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7283 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7261 (tpt170) cc_final: 0.7021 (tpt170) REVERT: Al 204 GLU cc_start: 0.8148 (pp20) cc_final: 0.7791 (pp20) REVERT: Am 69 HIS cc_start: 0.8551 (t70) cc_final: 0.8280 (t-170) REVERT: Am 129 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7672 (p0) REVERT: Am 157 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8563 (ttt-90) REVERT: Am 165 ASP cc_start: 0.8025 (t0) cc_final: 0.7606 (t0) REVERT: Am 184 TYR cc_start: 0.8013 (t80) cc_final: 0.7696 (t80) REVERT: An 54 MET cc_start: 0.7929 (ttp) cc_final: 0.7340 (ttp) REVERT: An 76 GLN cc_start: 0.8365 (mp10) cc_final: 0.7878 (mp10) REVERT: An 188 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6810 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8536 (mp10) cc_final: 0.8312 (mp10) REVERT: Ao 102 ASP cc_start: 0.8716 (t0) cc_final: 0.8438 (t0) REVERT: Ao 188 ARG cc_start: 0.7310 (tpt170) cc_final: 0.7084 (tpt170) REVERT: Ao 191 ARG cc_start: 0.8541 (ptp90) cc_final: 0.8279 (ptp90) REVERT: Ap 150 GLU cc_start: 0.8050 (tt0) cc_final: 0.7753 (tt0) REVERT: Ap 165 ASP cc_start: 0.8099 (t0) cc_final: 0.7495 (t0) REVERT: Ap 188 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6831 (tpt170) outliers start: 86 outliers final: 50 residues processed: 1010 average time/residue: 0.3782 time to fit residues: 561.6035 Evaluate side-chains 979 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 926 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN 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 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 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 77 GLN 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 56 MET Chi-restraints excluded: chain Ak residue 71 LEU 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 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 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 71 LEU 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 184 optimal weight: 9.9990 chunk 75 optimal weight: 0.0770 chunk 199 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- 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 Af 129 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 129 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 158 GLN Ai 129 ASN Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN Ao 129 ASN Ap 129 ASN Ap 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095394 restraints weight = 39315.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098190 restraints weight = 26356.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100083 restraints weight = 20491.745| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23856 Z= 0.176 Angle : 0.718 10.112 32336 Z= 0.349 Chirality : 0.044 0.158 3520 Planarity : 0.006 0.061 4192 Dihedral : 4.403 20.484 3216 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.76 % Allowed : 23.54 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2864 helix: -0.01 (0.14), residues: 1424 sheet: 2.14 (0.45), residues: 160 loop : -1.21 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAa 93 HIS 0.011 0.002 HISAp 69 PHE 0.010 0.001 PHEAl 200 TYR 0.033 0.002 TYRAm 198 ARG 0.009 0.001 ARGAn 197 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 800) hydrogen bonds : angle 5.04970 ( 2304) covalent geometry : bond 0.00415 (23856) covalent geometry : angle 0.71832 (32336) *********************** 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 1015 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 920 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 181 MET cc_start: 0.8707 (tpp) cc_final: 0.8418 (tpp) REVERT: Aa 188 ARG cc_start: 0.6952 (tpt170) cc_final: 0.6720 (tpt170) REVERT: Ab 54 MET cc_start: 0.7730 (ttp) cc_final: 0.6625 (ttp) REVERT: Ab 116 MET cc_start: 0.8804 (tmm) cc_final: 0.8563 (ttt) REVERT: Ab 136 ASP cc_start: 0.7115 (m-30) cc_final: 0.6607 (m-30) REVERT: Ab 165 ASP cc_start: 0.8060 (t0) cc_final: 0.7690 (t0) REVERT: Ac 165 ASP cc_start: 0.8083 (t0) cc_final: 0.7233 (t0) REVERT: Ac 184 TYR cc_start: 0.8036 (t80) cc_final: 0.7707 (t80) REVERT: Ac 188 ARG cc_start: 0.7063 (tpt170) cc_final: 0.6811 (tpt170) REVERT: Ad 76 GLN cc_start: 0.8346 (mp10) cc_final: 0.8003 (mp10) REVERT: Ad 102 ASP cc_start: 0.8718 (t0) cc_final: 0.8434 (t0) REVERT: Ad 116 MET cc_start: 0.8891 (tmm) cc_final: 0.8229 (ttt) REVERT: Ad 134 MET cc_start: 0.8180 (ttt) cc_final: 0.7880 (ttt) REVERT: Ad 138 ASP cc_start: 0.7794 (t0) cc_final: 0.7541 (t0) REVERT: Ad 174 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6832 (tpt170) REVERT: Ae 56 MET cc_start: 0.8791 (mmp) cc_final: 0.8450 (mmp) REVERT: Ae 76 GLN cc_start: 0.8306 (mp10) cc_final: 0.8009 (mp10) REVERT: Ae 80 ILE cc_start: 0.8955 (pt) cc_final: 0.8730 (pt) REVERT: Ae 102 ASP cc_start: 0.8583 (t0) cc_final: 0.8275 (t0) REVERT: Ae 165 ASP cc_start: 0.7989 (t0) cc_final: 0.7765 (t0) REVERT: Ae 174 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6694 (tpt170) REVERT: Ae 198 TYR cc_start: 0.8706 (m-10) cc_final: 0.8400 (m-10) REVERT: Ae 204 GLU cc_start: 0.8117 (pp20) cc_final: 0.7653 (pp20) REVERT: Af 54 MET cc_start: 0.7710 (ttp) cc_final: 0.6913 (ttp) REVERT: Af 73 TYR cc_start: 0.9158 (t80) cc_final: 0.8705 (t80) REVERT: Ag 102 ASP cc_start: 0.8665 (t0) cc_final: 0.8440 (t0) REVERT: Ag 136 ASP cc_start: 0.7713 (m-30) cc_final: 0.7306 (m-30) REVERT: Ag 165 ASP cc_start: 0.8061 (t0) cc_final: 0.7584 (t0) REVERT: Ag 204 GLU cc_start: 0.7834 (pp20) cc_final: 0.7597 (pp20) REVERT: Ah 54 MET cc_start: 0.7978 (ttp) cc_final: 0.7241 (ttp) REVERT: Ah 157 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8464 (ttt90) REVERT: Ah 188 ARG cc_start: 0.7081 (tpt170) cc_final: 0.6803 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8326 (mp10) cc_final: 0.7685 (mp10) REVERT: Ai 77 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7636 (m-30) cc_final: 0.7056 (m-30) REVERT: Ai 165 ASP cc_start: 0.8103 (t0) cc_final: 0.7471 (t0) REVERT: Ai 174 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6859 (tpt170) REVERT: Aj 165 ASP cc_start: 0.8045 (t0) cc_final: 0.7818 (t0) REVERT: Aj 174 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6999 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8056 (pp20) cc_final: 0.7626 (pp20) REVERT: Ak 80 ILE cc_start: 0.8806 (pt) cc_final: 0.8564 (pt) REVERT: Ak 136 ASP cc_start: 0.7905 (m-30) cc_final: 0.7681 (m-30) REVERT: Ak 165 ASP cc_start: 0.8003 (t0) cc_final: 0.7718 (t0) REVERT: Ak 188 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6885 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8712 (t0) cc_final: 0.8396 (t0) REVERT: Ak 204 GLU cc_start: 0.8184 (pp20) cc_final: 0.7849 (pp20) REVERT: Al 136 ASP cc_start: 0.7948 (m-30) cc_final: 0.7280 (t0) REVERT: Al 174 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7335 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7277 (tpt170) cc_final: 0.7022 (tpt170) REVERT: Al 204 GLU cc_start: 0.8161 (pp20) cc_final: 0.7801 (pp20) REVERT: Am 69 HIS cc_start: 0.8628 (t70) cc_final: 0.8371 (t-170) REVERT: Am 129 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7690 (p0) REVERT: Am 157 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8588 (ttt-90) REVERT: Am 165 ASP cc_start: 0.8087 (t0) cc_final: 0.7689 (t0) REVERT: Am 184 TYR cc_start: 0.8018 (t80) cc_final: 0.7710 (t80) REVERT: Am 188 ARG cc_start: 0.7244 (tpt170) cc_final: 0.6911 (tpt170) REVERT: An 54 MET cc_start: 0.7804 (ttp) cc_final: 0.7374 (ttp) REVERT: An 76 GLN cc_start: 0.8376 (mp10) cc_final: 0.7875 (mp10) REVERT: An 79 ASP cc_start: 0.8467 (m-30) cc_final: 0.8195 (m-30) REVERT: An 188 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6838 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8559 (mp10) cc_final: 0.8302 (mp10) REVERT: Ao 102 ASP cc_start: 0.8743 (t0) cc_final: 0.8461 (t0) REVERT: Ao 158 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: Ao 165 ASP cc_start: 0.7928 (t0) cc_final: 0.7431 (t0) REVERT: Ao 174 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7393 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7220 (tpt170) cc_final: 0.7012 (tpt170) REVERT: Ap 136 ASP cc_start: 0.7676 (m-30) cc_final: 0.7332 (t0) REVERT: Ap 150 GLU cc_start: 0.8070 (tt0) cc_final: 0.7858 (tt0) REVERT: Ap 165 ASP cc_start: 0.8207 (t0) cc_final: 0.7590 (t0) REVERT: Ap 188 ARG cc_start: 0.7261 (tpt170) cc_final: 0.6890 (tpt170) outliers start: 95 outliers final: 65 residues processed: 970 average time/residue: 0.3788 time to fit residues: 543.7207 Evaluate side-chains 978 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 910 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN 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 97 VAL 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 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 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 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 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 129 ASN 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 71 LEU Chi-restraints excluded: chain Ao residue 116 MET Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ao residue 158 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 129 ASN Ab 158 GLN ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 129 ASN Ah 151 ASN Ai 129 ASN Ai 158 GLN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN Ak 151 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN ** 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** Ao 129 ASN Ap 129 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100063 restraints weight = 39046.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102988 restraints weight = 25879.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104947 restraints weight = 19935.788| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3526 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= 0.124 Angle : 0.705 10.258 32336 Z= 0.342 Chirality : 0.043 0.159 3520 Planarity : 0.006 0.059 4192 Dihedral : 4.319 18.460 3216 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.20 % Allowed : 24.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2864 helix: 0.13 (0.15), residues: 1360 sheet: 2.54 (0.47), residues: 160 loop : -1.16 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAp 93 HIS 0.012 0.002 HISAp 69 PHE 0.007 0.001 PHEAg 200 TYR 0.036 0.002 TYRAn 198 ARG 0.009 0.001 ARGAl 157 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 800) hydrogen bonds : angle 4.94034 ( 2304) covalent geometry : bond 0.00281 (23856) covalent geometry : angle 0.70462 (32336) *********************** 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 1029 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 948 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 78 ILE cc_start: 0.7971 (tp) cc_final: 0.7622 (pt) REVERT: Aa 181 MET cc_start: 0.8688 (tpp) cc_final: 0.8393 (tpp) REVERT: Aa 188 ARG cc_start: 0.6874 (tpt170) cc_final: 0.6656 (tpt170) REVERT: Aa 198 TYR cc_start: 0.8557 (m-10) cc_final: 0.8295 (m-10) REVERT: Ab 54 MET cc_start: 0.7643 (ttp) cc_final: 0.6561 (ttp) REVERT: Ab 116 MET cc_start: 0.8828 (tmm) cc_final: 0.8547 (ttt) REVERT: Ab 121 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7904 (tp30) REVERT: Ac 165 ASP cc_start: 0.7954 (t0) cc_final: 0.7085 (t0) REVERT: Ac 184 TYR cc_start: 0.8019 (t80) cc_final: 0.7652 (t80) REVERT: Ac 188 ARG cc_start: 0.7130 (tpt170) cc_final: 0.6854 (tpt170) REVERT: Ad 76 GLN cc_start: 0.8062 (mp10) cc_final: 0.7711 (mp10) REVERT: Ad 102 ASP cc_start: 0.8645 (t0) cc_final: 0.8395 (t0) REVERT: Ad 116 MET cc_start: 0.8835 (tmm) cc_final: 0.8144 (ttt) REVERT: Ad 138 ASP cc_start: 0.7802 (t0) cc_final: 0.7565 (t0) REVERT: Ad 174 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7198 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7143 (tpt170) cc_final: 0.6817 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8201 (mp10) cc_final: 0.7914 (mp10) REVERT: Ae 102 ASP cc_start: 0.8569 (t0) cc_final: 0.8315 (t0) REVERT: Ae 157 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8498 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7894 (t0) cc_final: 0.7692 (t0) REVERT: Ae 188 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6673 (tpt170) REVERT: Ae 198 TYR cc_start: 0.8732 (m-10) cc_final: 0.8431 (m-10) REVERT: Ae 204 GLU cc_start: 0.8156 (pp20) cc_final: 0.7715 (pp20) REVERT: Af 54 MET cc_start: 0.7655 (ttp) cc_final: 0.6871 (ttp) REVERT: Af 73 TYR cc_start: 0.9094 (t80) cc_final: 0.8592 (t80) REVERT: Af 160 MET cc_start: 0.9056 (tpp) cc_final: 0.8835 (mmm) REVERT: Ag 77 GLN cc_start: 0.7665 (tp40) cc_final: 0.7249 (tp40) REVERT: Ag 80 ILE cc_start: 0.8444 (pt) cc_final: 0.8238 (pt) REVERT: Ag 102 ASP cc_start: 0.8633 (t0) cc_final: 0.8421 (t0) REVERT: Ag 136 ASP cc_start: 0.7648 (m-30) cc_final: 0.7229 (m-30) REVERT: Ag 165 ASP cc_start: 0.7963 (t0) cc_final: 0.7476 (t0) REVERT: Ag 204 GLU cc_start: 0.7840 (pp20) cc_final: 0.7558 (pp20) REVERT: Ah 54 MET cc_start: 0.7968 (ttp) cc_final: 0.7251 (ttp) REVERT: Ah 116 MET cc_start: 0.8976 (tmm) cc_final: 0.8478 (ttt) REVERT: Ah 121 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7832 (mm-30) REVERT: Ah 188 ARG cc_start: 0.7093 (tpt170) cc_final: 0.6846 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8218 (mp10) cc_final: 0.7596 (mp10) REVERT: Ai 77 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7617 (m-30) cc_final: 0.7049 (m-30) REVERT: Ai 138 ASP cc_start: 0.7648 (t0) cc_final: 0.7403 (t0) REVERT: Ai 165 ASP cc_start: 0.8011 (t0) cc_final: 0.7357 (t0) REVERT: Ai 188 ARG cc_start: 0.7012 (tpt170) cc_final: 0.6763 (tpt170) REVERT: Ai 201 ASP cc_start: 0.8438 (t0) cc_final: 0.7982 (t0) REVERT: Aj 174 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7522 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7268 (tpt170) cc_final: 0.7025 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8019 (pp20) cc_final: 0.7600 (pp20) REVERT: Ak 80 ILE cc_start: 0.8331 (pt) cc_final: 0.8049 (pt) REVERT: Ak 136 ASP cc_start: 0.7750 (m-30) cc_final: 0.7495 (m-30) REVERT: Ak 165 ASP cc_start: 0.7869 (t0) cc_final: 0.7571 (t0) REVERT: Ak 188 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6909 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8671 (t0) cc_final: 0.8331 (t0) REVERT: Ak 204 GLU cc_start: 0.8165 (pp20) cc_final: 0.7836 (pp20) REVERT: Al 116 MET cc_start: 0.8734 (ttp) cc_final: 0.8281 (ttt) REVERT: Al 136 ASP cc_start: 0.7844 (m-30) cc_final: 0.7229 (t0) REVERT: Al 188 ARG cc_start: 0.7202 (tpt170) cc_final: 0.6968 (tpt170) REVERT: Al 204 GLU cc_start: 0.8110 (pp20) cc_final: 0.7743 (pp20) REVERT: Am 69 HIS cc_start: 0.8601 (t70) cc_final: 0.8348 (t-170) REVERT: Am 129 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7714 (p0) REVERT: Am 157 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8526 (ttt-90) REVERT: Am 165 ASP cc_start: 0.7981 (t0) cc_final: 0.7545 (t0) REVERT: Am 184 TYR cc_start: 0.7966 (t80) cc_final: 0.7702 (t80) REVERT: Am 188 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6861 (tpt170) REVERT: An 54 MET cc_start: 0.7816 (ttp) cc_final: 0.7254 (ttp) REVERT: An 76 GLN cc_start: 0.8121 (mp10) cc_final: 0.7683 (mp10) REVERT: An 188 ARG cc_start: 0.7103 (tpt170) cc_final: 0.6827 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8325 (mp10) cc_final: 0.8099 (mp10) REVERT: Ao 102 ASP cc_start: 0.8700 (t0) cc_final: 0.8420 (t0) REVERT: Ao 174 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7196 (tpt170) cc_final: 0.6866 (tpt170) REVERT: Ao 191 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8285 (ptp90) REVERT: Ap 134 MET cc_start: 0.8311 (ttt) cc_final: 0.7933 (ttt) REVERT: Ap 158 GLN cc_start: 0.8736 (mt0) cc_final: 0.8261 (mm-40) REVERT: Ap 165 ASP cc_start: 0.8079 (t0) cc_final: 0.7510 (t0) REVERT: Ap 188 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6875 (tpt170) outliers start: 81 outliers final: 56 residues processed: 989 average time/residue: 0.3754 time to fit residues: 544.7075 Evaluate side-chains 984 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 926 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN 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 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 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 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 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 97 VAL 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 Aj residue 220 MET Chi-restraints excluded: chain Ak residue 47 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 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 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 47 ILE 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 195 optimal weight: 10.0000 chunk 4 optimal weight: 0.1980 chunk 269 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 142 optimal weight: 0.0270 chunk 222 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 129 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 129 ASN Ab 158 GLN Ac 129 ASN ** Af 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 129 ASN Ah 158 GLN Ai 129 ASN ** 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 158 GLN Ap 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099256 restraints weight = 39050.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102106 restraints weight = 26056.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104012 restraints weight = 20197.836| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23856 Z= 0.138 Angle : 0.719 10.132 32336 Z= 0.350 Chirality : 0.043 0.155 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.314 19.442 3216 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.36 % Allowed : 25.12 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2864 helix: -0.03 (0.14), residues: 1440 sheet: 2.62 (0.47), residues: 160 loop : -1.12 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAa 93 HIS 0.016 0.002 HISAd 69 PHE 0.009 0.001 PHEAl 200 TYR 0.033 0.002 TYRAm 198 ARG 0.009 0.001 ARGAl 157 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 800) hydrogen bonds : angle 4.97776 ( 2304) covalent geometry : bond 0.00321 (23856) covalent geometry : angle 0.71889 (32336) *********************** 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 1023 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 938 time to evaluate : 2.459 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 78 ILE cc_start: 0.7928 (tp) cc_final: 0.7619 (pt) REVERT: Aa 113 ASN cc_start: 0.8323 (t0) cc_final: 0.8074 (t0) REVERT: Aa 181 MET cc_start: 0.8698 (tpp) cc_final: 0.8415 (tpp) REVERT: Aa 188 ARG cc_start: 0.6905 (tpt170) cc_final: 0.6674 (tpt170) REVERT: Ab 54 MET cc_start: 0.7665 (ttp) cc_final: 0.6560 (ttp) REVERT: Ab 116 MET cc_start: 0.8879 (tmm) cc_final: 0.8585 (ttt) REVERT: Ab 121 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8047 (tp30) REVERT: Ab 188 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6626 (tpt170) REVERT: Ac 54 MET cc_start: 0.7767 (ttp) cc_final: 0.7346 (ttm) REVERT: Ac 165 ASP cc_start: 0.8014 (t0) cc_final: 0.7142 (t0) REVERT: Ac 184 TYR cc_start: 0.8048 (t80) cc_final: 0.7655 (t80) REVERT: Ac 188 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6917 (tpt170) REVERT: Ad 73 TYR cc_start: 0.8693 (t80) cc_final: 0.8236 (t80) REVERT: Ad 76 GLN cc_start: 0.7969 (mp10) cc_final: 0.7627 (mp10) REVERT: Ad 102 ASP cc_start: 0.8608 (t0) cc_final: 0.8360 (t0) REVERT: Ad 116 MET cc_start: 0.8837 (tmm) cc_final: 0.8183 (ttt) REVERT: Ad 138 ASP cc_start: 0.7938 (t0) cc_final: 0.7686 (t0) REVERT: Ad 174 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7129 (tpt170) cc_final: 0.6826 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8176 (mp10) cc_final: 0.7901 (mp10) REVERT: Ae 80 ILE cc_start: 0.8605 (pt) cc_final: 0.8341 (pt) REVERT: Ae 102 ASP cc_start: 0.8574 (t0) cc_final: 0.8327 (t0) REVERT: Ae 157 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8485 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7909 (t0) cc_final: 0.7693 (t0) REVERT: Ae 188 ARG cc_start: 0.6968 (tpt170) cc_final: 0.6768 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8161 (pp20) cc_final: 0.7701 (pp20) REVERT: Af 54 MET cc_start: 0.7642 (ttp) cc_final: 0.6882 (ttp) REVERT: Af 73 TYR cc_start: 0.9126 (t80) cc_final: 0.8664 (t80) REVERT: Af 188 ARG cc_start: 0.7255 (tpt170) cc_final: 0.6925 (tpt170) REVERT: Ag 80 ILE cc_start: 0.8431 (pt) cc_final: 0.8214 (pt) REVERT: Ag 102 ASP cc_start: 0.8624 (t0) cc_final: 0.8418 (t0) REVERT: Ag 136 ASP cc_start: 0.7698 (m-30) cc_final: 0.7247 (m-30) REVERT: Ag 165 ASP cc_start: 0.7995 (t0) cc_final: 0.7520 (t0) REVERT: Ag 184 TYR cc_start: 0.7797 (t80) cc_final: 0.7296 (t80) REVERT: Ag 204 GLU cc_start: 0.7833 (pp20) cc_final: 0.7573 (pp20) REVERT: Ah 54 MET cc_start: 0.7947 (ttp) cc_final: 0.7235 (ttp) REVERT: Ah 116 MET cc_start: 0.8971 (tmm) cc_final: 0.8535 (ttt) REVERT: Ah 135 MET cc_start: 0.8654 (mmm) cc_final: 0.8431 (mmm) REVERT: Ah 188 ARG cc_start: 0.7092 (tpt170) cc_final: 0.6811 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8236 (mp10) cc_final: 0.7618 (mp10) REVERT: Ai 77 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7610 (m-30) cc_final: 0.7265 (m-30) REVERT: Ai 138 ASP cc_start: 0.7651 (t0) cc_final: 0.7446 (t0) REVERT: Ai 165 ASP cc_start: 0.8034 (t0) cc_final: 0.7302 (t0) REVERT: Ai 188 ARG cc_start: 0.7146 (tpt170) cc_final: 0.6868 (tpt170) REVERT: Aj 188 ARG cc_start: 0.7334 (tpt170) cc_final: 0.7091 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8027 (pp20) cc_final: 0.7587 (pp20) REVERT: Ak 80 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (pt) REVERT: Ak 124 THR cc_start: 0.8929 (p) cc_final: 0.8116 (p) REVERT: Ak 136 ASP cc_start: 0.7754 (m-30) cc_final: 0.7487 (m-30) REVERT: Ak 174 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7349 (mmm-85) REVERT: Ak 188 ARG cc_start: 0.7204 (tpt170) cc_final: 0.6885 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8685 (t0) cc_final: 0.8370 (t0) REVERT: Ak 204 GLU cc_start: 0.8112 (pp20) cc_final: 0.7790 (pp20) REVERT: Al 136 ASP cc_start: 0.7705 (m-30) cc_final: 0.7180 (t0) REVERT: Al 188 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6979 (tpt170) REVERT: Al 204 GLU cc_start: 0.8095 (pp20) cc_final: 0.7705 (pp20) REVERT: Am 129 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7691 (p0) REVERT: Am 157 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8529 (ttt-90) REVERT: Am 165 ASP cc_start: 0.7986 (t0) cc_final: 0.7524 (t0) REVERT: Am 184 TYR cc_start: 0.7981 (t80) cc_final: 0.7775 (t80) REVERT: Am 188 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6850 (tpt170) REVERT: An 54 MET cc_start: 0.7857 (ttp) cc_final: 0.7268 (ttp) REVERT: An 73 TYR cc_start: 0.9023 (t80) cc_final: 0.8815 (t80) REVERT: An 76 GLN cc_start: 0.8091 (mp10) cc_final: 0.7567 (mp10) REVERT: An 183 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7685 (ttm-80) REVERT: An 188 ARG cc_start: 0.7113 (tpt170) cc_final: 0.6796 (tpt170) REVERT: An 197 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8239 (ptm-80) REVERT: Ao 76 GLN cc_start: 0.8160 (mp10) cc_final: 0.7945 (mp10) REVERT: Ao 102 ASP cc_start: 0.8700 (t0) cc_final: 0.8414 (t0) REVERT: Ao 158 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: Ao 174 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7341 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6931 (tpt170) REVERT: Ao 191 ARG cc_start: 0.8555 (ptp90) cc_final: 0.8327 (ptp90) REVERT: Ap 134 MET cc_start: 0.8163 (ttt) cc_final: 0.7863 (ttt) REVERT: Ap 165 ASP cc_start: 0.8116 (t0) cc_final: 0.7526 (t0) REVERT: Ap 188 ARG cc_start: 0.7269 (tpt170) cc_final: 0.6859 (tpt170) outliers start: 85 outliers final: 63 residues processed: 982 average time/residue: 0.3887 time to fit residues: 559.0376 Evaluate side-chains 990 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 923 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE 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 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 Ad residue 197 ARG 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 50 ILE Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 176 LYS 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 77 GLN Chi-restraints excluded: chain Ai residue 97 VAL 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 71 LEU Chi-restraints excluded: chain Ak residue 80 ILE 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 Am residue 119 CYS 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 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 54 MET Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ao residue 158 GLN Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 257 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 143 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 129 ASN Ab 158 GLN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 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 129 ASN Ai 129 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 69 HIS ** 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 = 0.3626 r_free = 0.3626 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101409 restraints weight = 38936.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104453 restraints weight = 25446.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106531 restraints weight = 19483.961| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23856 Z= 0.128 Angle : 0.723 10.951 32336 Z= 0.354 Chirality : 0.043 0.249 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.320 23.107 3216 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.65 % Allowed : 25.40 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2864 helix: 0.28 (0.15), residues: 1344 sheet: 2.55 (0.47), residues: 160 loop : -0.74 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAb 93 HIS 0.017 0.002 HISAd 69 PHE 0.007 0.001 PHEAl 200 TYR 0.031 0.002 TYRAm 198 ARG 0.009 0.001 ARGAl 157 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 800) hydrogen bonds : angle 5.05513 ( 2304) covalent geometry : bond 0.00288 (23856) covalent geometry : angle 0.72314 (32336) ********************** 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 1028 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 961 time to evaluate : 2.459 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: 0.7833 (tp) cc_final: 0.7520 (pt) REVERT: Aa 113 ASN cc_start: 0.8211 (t0) cc_final: 0.8004 (t0) REVERT: Aa 116 MET cc_start: 0.8886 (tmm) cc_final: 0.8328 (ttt) REVERT: Aa 124 THR cc_start: 0.8677 (p) cc_final: 0.7764 (p) REVERT: Aa 181 MET cc_start: 0.8671 (tpp) cc_final: 0.8396 (tpp) REVERT: Aa 201 ASP cc_start: 0.8409 (t0) cc_final: 0.8037 (t0) REVERT: Ab 54 MET cc_start: 0.7565 (ttp) cc_final: 0.6535 (ttp) REVERT: Ab 116 MET cc_start: 0.8857 (tmm) cc_final: 0.8512 (ttt) REVERT: Ab 135 MET cc_start: 0.8428 (mmm) cc_final: 0.8142 (mmm) REVERT: Ab 188 ARG cc_start: 0.6997 (tpt170) cc_final: 0.6735 (tpt170) REVERT: Ab 197 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8181 (mtp85) REVERT: Ac 54 MET cc_start: 0.7691 (ttp) cc_final: 0.7254 (ttm) REVERT: Ac 165 ASP cc_start: 0.7860 (t0) cc_final: 0.7013 (t0) REVERT: Ac 184 TYR cc_start: 0.7977 (t80) cc_final: 0.7577 (t80) REVERT: Ad 73 TYR cc_start: 0.8607 (t80) cc_final: 0.8025 (t80) REVERT: Ad 76 GLN cc_start: 0.7793 (mp10) cc_final: 0.7505 (mp10) REVERT: Ad 102 ASP cc_start: 0.8598 (t0) cc_final: 0.8375 (t0) REVERT: Ad 174 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7453 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7089 (tpt170) cc_final: 0.6725 (tpt170) REVERT: Ae 102 ASP cc_start: 0.8455 (t0) cc_final: 0.8232 (t0) REVERT: Ae 157 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8413 (ttt-90) REVERT: Ae 204 GLU cc_start: 0.8091 (pp20) cc_final: 0.7710 (pp20) REVERT: Af 54 MET cc_start: 0.7619 (ttp) cc_final: 0.6931 (ttp) REVERT: Af 73 TYR cc_start: 0.9140 (t80) cc_final: 0.8651 (t80) REVERT: Af 188 ARG cc_start: 0.7212 (tpt170) cc_final: 0.6732 (tpt170) REVERT: Ag 102 ASP cc_start: 0.8532 (t0) cc_final: 0.8226 (t0) REVERT: Ag 136 ASP cc_start: 0.7644 (m-30) cc_final: 0.7197 (m-30) REVERT: Ag 165 ASP cc_start: 0.7893 (t0) cc_final: 0.7493 (t0) REVERT: Ag 184 TYR cc_start: 0.7780 (t80) cc_final: 0.7254 (t80) REVERT: Ag 204 GLU cc_start: 0.7794 (pp20) cc_final: 0.7512 (pp20) REVERT: Ah 54 MET cc_start: 0.7876 (ttp) cc_final: 0.7191 (ttp) REVERT: Ah 116 MET cc_start: 0.8915 (tmm) cc_final: 0.8473 (ttt) REVERT: Ah 121 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8050 (mm-30) REVERT: Ah 158 GLN cc_start: 0.8411 (mt0) cc_final: 0.8021 (mm-40) REVERT: Ah 188 ARG cc_start: 0.7029 (tpt170) cc_final: 0.6796 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8169 (mp10) cc_final: 0.7557 (mp10) REVERT: Ai 77 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: Ai 116 MET cc_start: 0.9026 (tmm) cc_final: 0.8351 (ttt) REVERT: Ai 138 ASP cc_start: 0.7682 (t0) cc_final: 0.7480 (t0) REVERT: Ai 165 ASP cc_start: 0.7853 (t0) cc_final: 0.7172 (t0) REVERT: Ai 188 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6796 (tpt170) REVERT: Aj 188 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6956 (tpt170) REVERT: Aj 204 GLU cc_start: 0.7944 (pp20) cc_final: 0.7555 (pp20) REVERT: Ak 80 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7867 (pt) REVERT: Ak 124 THR cc_start: 0.8803 (p) cc_final: 0.8241 (p) REVERT: Ak 136 ASP cc_start: 0.7745 (m-30) cc_final: 0.7511 (m-30) REVERT: Ak 174 ARG cc_start: 0.7917 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: Ak 188 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6857 (tpt170) REVERT: Ak 204 GLU cc_start: 0.8086 (pp20) cc_final: 0.7831 (pp20) REVERT: Al 136 ASP cc_start: 0.7746 (m-30) cc_final: 0.7069 (t0) REVERT: Al 188 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6979 (tpt170) REVERT: Al 204 GLU cc_start: 0.8043 (pp20) cc_final: 0.7598 (pp20) REVERT: Am 129 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7601 (p0) REVERT: Am 157 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8440 (ttt-90) REVERT: Am 165 ASP cc_start: 0.7822 (t0) cc_final: 0.7434 (t0) REVERT: Am 188 ARG cc_start: 0.7201 (tpt170) cc_final: 0.6829 (tpt170) REVERT: An 46 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.6646 (mmt180) REVERT: An 54 MET cc_start: 0.7738 (ttp) cc_final: 0.7139 (ttp) REVERT: An 76 GLN cc_start: 0.7863 (mp10) cc_final: 0.7480 (mp10) REVERT: An 183 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7815 (ttm-80) REVERT: An 188 ARG cc_start: 0.7136 (tpt170) cc_final: 0.6839 (tpt170) REVERT: An 197 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8239 (ptm-80) REVERT: Ao 76 GLN cc_start: 0.7879 (mp10) cc_final: 0.7523 (mp10) REVERT: Ao 102 ASP cc_start: 0.8651 (t0) cc_final: 0.8409 (t0) REVERT: Ao 136 ASP cc_start: 0.7729 (m-30) cc_final: 0.7407 (t0) REVERT: Ao 188 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6926 (tpt170) REVERT: Ao 191 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8321 (ptp90) REVERT: Ap 134 MET cc_start: 0.8079 (ttt) cc_final: 0.7674 (ttt) REVERT: Ap 165 ASP cc_start: 0.7983 (t0) cc_final: 0.7439 (t0) REVERT: Ap 188 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6906 (tpt170) outliers start: 67 outliers final: 50 residues processed: 991 average time/residue: 0.3768 time to fit residues: 548.9906 Evaluate side-chains 989 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 936 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 129 ASN Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR 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 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 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 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 77 GLN Chi-restraints excluded: chain Ai residue 97 VAL 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 80 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 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 149 VAL 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 149 VAL 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 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 7.9990 chunk 109 optimal weight: 0.0020 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 129 ASN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 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** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 129 ASN Ai 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN ** Al 69 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100430 restraints weight = 39008.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103383 restraints weight = 25671.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105398 restraints weight = 19705.326| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 23856 Z= 0.218 Angle : 0.860 59.191 32336 Z= 0.456 Chirality : 0.048 0.861 3520 Planarity : 0.006 0.084 4192 Dihedral : 4.343 36.438 3216 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 2.57 % Allowed : 26.82 % Favored : 70.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2864 helix: 0.24 (0.15), residues: 1344 sheet: 2.54 (0.47), residues: 160 loop : -0.75 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAb 93 HIS 0.014 0.002 HISAd 69 PHE 0.009 0.002 PHEAf 163 TYR 0.024 0.002 TYRAa 198 ARG 0.008 0.001 ARGAb 157 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 800) hydrogen bonds : angle 5.06373 ( 2304) covalent geometry : bond 0.00475 (23856) covalent geometry : angle 0.86026 (32336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10001.37 seconds wall clock time: 174 minutes 14.28 seconds (10454.28 seconds total)