Starting phenix.real_space_refine on Fri Jun 20 05:05:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opb_17047/06_2025/8opb_17047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opb_17047/06_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_17047/06_2025/8opb_17047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opb_17047/06_2025/8opb_17047.map" model { file = "/net/cci-nas-00/data/ceres_data/8opb_17047/06_2025/8opb_17047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opb_17047/06_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-5710/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: 6.13, per 1000 atoms: 0.26 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: 5.49 Conformation dependent library (CDL) restraints added in 3.0 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: 2.26 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: 5.90 Time building geometry restraints manager: 6.41 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: 0.22 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: 1.840 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: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 40.640 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- 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 : 2.623 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: 0.4270 time to fit residues: 561.1485 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 : 2.444 ------------------------------------------------------------------------------- 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 = 0.129375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098491 restraints weight = 38604.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101430 restraints weight = 25390.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103397 restraints weight = 19491.522| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 136 ASP cc_start: 0.7544 (m-30) cc_final: 0.7117 (m-30) REVERT: Aa 181 MET cc_start: 0.8709 (tpp) cc_final: 0.8505 (tpp) REVERT: Aa 183 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7424 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8493 (t0) cc_final: 0.8189 (t0) REVERT: Ab 54 MET cc_start: 0.7577 (ttp) cc_final: 0.6859 (ttp) REVERT: Ab 136 ASP cc_start: 0.7674 (m-30) cc_final: 0.7241 (m-30) REVERT: Ab 165 ASP cc_start: 0.7856 (t0) cc_final: 0.7655 (t0) REVERT: Ac 157 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8291 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7676 (t0) cc_final: 0.7308 (t0) REVERT: Ac 201 ASP cc_start: 0.8439 (t0) cc_final: 0.8151 (t0) REVERT: Ad 76 GLN cc_start: 0.8374 (mp10) cc_final: 0.8156 (mp10) REVERT: Ad 102 ASP cc_start: 0.8614 (t0) cc_final: 0.8302 (t0) REVERT: Ad 157 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8252 (ttt-90) REVERT: Ad 174 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: Ae 102 ASP cc_start: 0.8506 (t0) cc_final: 0.8197 (t0) REVERT: Ae 165 ASP cc_start: 0.7830 (t0) cc_final: 0.7592 (t0) REVERT: Ae 174 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7420 (mmm-85) REVERT: Ae 181 MET cc_start: 0.8632 (tpp) cc_final: 0.8326 (tpp) REVERT: Ag 102 ASP cc_start: 0.8497 (t0) cc_final: 0.8233 (t0) REVERT: Ag 157 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8544 (ttt-90) REVERT: Ah 54 MET cc_start: 0.7710 (ttp) cc_final: 0.7360 (ttp) REVERT: Ah 76 GLN cc_start: 0.8437 (mp10) cc_final: 0.8119 (mp10) REVERT: Ah 157 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8313 (ttt90) REVERT: Ai 56 MET cc_start: 0.8559 (mmp) cc_final: 0.8336 (mmp) REVERT: Ai 60 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8399 (mmtm) REVERT: Ai 73 TYR cc_start: 0.8771 (t80) cc_final: 0.8532 (t80) REVERT: Ai 136 ASP cc_start: 0.7593 (m-30) cc_final: 0.7239 (m-30) REVERT: Ai 157 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8450 (ttt90) REVERT: Ai 160 MET cc_start: 0.8900 (tpp) cc_final: 0.8459 (mmm) REVERT: Aj 56 MET cc_start: 0.8542 (mmp) cc_final: 0.8071 (mmp) REVERT: Aj 157 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8335 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8000 (t0) cc_final: 0.7753 (t0) REVERT: Ak 73 TYR cc_start: 0.8770 (t80) cc_final: 0.8491 (t80) REVERT: Ak 77 GLN cc_start: 0.8372 (tp40) cc_final: 0.7862 (tp40) REVERT: Ak 136 ASP cc_start: 0.7931 (m-30) cc_final: 0.7509 (m-30) REVERT: Ak 157 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8294 (ttt-90) REVERT: Ak 165 ASP cc_start: 0.7753 (t0) cc_final: 0.7549 (t0) REVERT: Ak 174 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8393 (t0) cc_final: 0.8137 (t0) REVERT: Ak 204 GLU cc_start: 0.8109 (pp20) cc_final: 0.7787 (pp20) REVERT: Al 136 ASP cc_start: 0.8089 (m-30) cc_final: 0.7556 (m-30) REVERT: Al 157 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8362 (ttt90) REVERT: Al 204 GLU cc_start: 0.8020 (pp20) cc_final: 0.7808 (pp20) REVERT: Am 69 HIS cc_start: 0.8433 (t-170) cc_final: 0.8207 (t-170) REVERT: Am 157 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8421 (ttt-90) REVERT: Am 160 MET cc_start: 0.8863 (tpp) cc_final: 0.8341 (mmm) REVERT: Am 165 ASP cc_start: 0.7877 (t0) cc_final: 0.7620 (t0) REVERT: An 165 ASP cc_start: 0.7717 (t0) cc_final: 0.7508 (t0) REVERT: An 174 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7359 (mmm-85) REVERT: Ao 157 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8397 (ttt90) REVERT: Ao 165 ASP cc_start: 0.7859 (t0) cc_final: 0.7658 (t0) REVERT: Ao 174 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: Ap 165 ASP cc_start: 0.7733 (t0) cc_final: 0.7353 (t0) outliers start: 62 outliers final: 14 residues processed: 894 average time/residue: 0.4316 time to fit residues: 576.1109 Evaluate side-chains 834 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 819 time to evaluate : 2.469 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 266 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ac 140 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 140 GLN Ae 129 ASN Ae 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094583 restraints weight = 38870.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097362 restraints weight = 26090.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099230 restraints weight = 20272.226| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23856 Z= 0.219 Angle : 0.695 8.821 32336 Z= 0.343 Chirality : 0.043 0.152 3520 Planarity : 0.006 0.065 4192 Dihedral : 4.573 18.241 3216 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.73 % Allowed : 18.55 % Favored : 78.72 % 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: -1.02 (0.16), residues: 2864 helix: -0.12 (0.15), residues: 1360 sheet: 0.53 (0.39), residues: 160 loop : -1.38 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAa 93 HIS 0.009 0.002 HISAe 69 PHE 0.013 0.002 PHEAa 200 TYR 0.023 0.002 TYRAl 198 ARG 0.006 0.001 ARGAb 157 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 800) hydrogen bonds : angle 5.11535 ( 2304) covalent geometry : bond 0.00512 (23856) covalent geometry : angle 0.69537 (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 944 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 875 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 136 ASP cc_start: 0.7935 (m-30) cc_final: 0.7586 (m-30) REVERT: Aa 157 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8302 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8706 (tpp) cc_final: 0.8426 (tpp) REVERT: Aa 183 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7378 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8501 (t0) cc_final: 0.8186 (t0) REVERT: Ab 54 MET cc_start: 0.7666 (ttp) cc_final: 0.6783 (ttp) REVERT: Ab 121 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7982 (mm-30) REVERT: Ab 136 ASP cc_start: 0.7894 (m-30) cc_final: 0.7360 (m-30) REVERT: Ab 157 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8413 (ttt90) REVERT: Ab 183 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8368 (ttp80) REVERT: Ac 91 ASP cc_start: 0.8145 (m-30) cc_final: 0.7895 (m-30) REVERT: Ac 157 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8270 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7958 (t0) cc_final: 0.7498 (t0) REVERT: Ad 102 ASP cc_start: 0.8544 (t0) cc_final: 0.8298 (t0) REVERT: Ad 157 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8321 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.7967 (t0) cc_final: 0.7687 (t0) REVERT: Ae 76 GLN cc_start: 0.8344 (mp10) cc_final: 0.8117 (mp10) REVERT: Ae 80 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8869 (pt) REVERT: Ae 102 ASP cc_start: 0.8477 (t0) cc_final: 0.8173 (t0) REVERT: Ae 136 ASP cc_start: 0.7410 (m-30) cc_final: 0.6905 (m-30) REVERT: Ae 157 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8292 (ttt-90) REVERT: Ae 160 MET cc_start: 0.8832 (tpp) cc_final: 0.8624 (tpt) REVERT: Ae 174 ARG cc_start: 0.7904 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: Ae 181 MET cc_start: 0.8608 (tpp) cc_final: 0.8367 (tpp) REVERT: Ae 204 GLU cc_start: 0.8129 (pp20) cc_final: 0.7625 (pp20) REVERT: Af 157 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8403 (ttt-90) REVERT: Af 174 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: Ag 77 GLN cc_start: 0.8215 (tp40) cc_final: 0.7397 (tp40) REVERT: Ag 80 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8765 (pt) REVERT: Ag 102 ASP cc_start: 0.8539 (t0) cc_final: 0.8305 (t0) REVERT: Ag 135 MET cc_start: 0.8730 (mmm) cc_final: 0.8518 (mmm) REVERT: Ag 157 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8453 (ttt-90) REVERT: Ag 165 ASP cc_start: 0.7938 (t0) cc_final: 0.7714 (t0) REVERT: Ah 54 MET cc_start: 0.7824 (ttp) cc_final: 0.7132 (ttp) REVERT: Ah 157 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8352 (ttt90) REVERT: Ai 91 ASP cc_start: 0.7936 (m-30) cc_final: 0.7716 (m-30) REVERT: Ai 129 ASN cc_start: 0.8110 (p0) cc_final: 0.7892 (p0) REVERT: Ai 136 ASP cc_start: 0.7798 (m-30) cc_final: 0.7311 (m-30) REVERT: Ai 157 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8417 (ttt90) REVERT: Ai 165 ASP cc_start: 0.8092 (t0) cc_final: 0.7597 (t0) REVERT: Aj 157 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8398 (ttt-90) REVERT: Aj 188 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6768 (tpt170) REVERT: Ak 77 GLN cc_start: 0.8050 (tp40) cc_final: 0.7480 (tp40) REVERT: Ak 80 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8659 (pt) REVERT: Ak 91 ASP cc_start: 0.7853 (m-30) cc_final: 0.7211 (m-30) REVERT: Ak 136 ASP cc_start: 0.7860 (m-30) cc_final: 0.7544 (m-30) REVERT: Ak 165 ASP cc_start: 0.7928 (t0) cc_final: 0.7714 (t0) REVERT: Ak 174 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8416 (t0) cc_final: 0.8068 (t0) REVERT: Ak 204 GLU cc_start: 0.8135 (pp20) cc_final: 0.7864 (pp20) REVERT: Al 77 GLN cc_start: 0.8408 (tp40) cc_final: 0.7997 (tp40) REVERT: Al 136 ASP cc_start: 0.8049 (m-30) cc_final: 0.7537 (m-30) REVERT: Al 157 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8426 (ttt90) REVERT: Al 174 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: Al 183 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8060 (ttp80) REVERT: Al 204 GLU cc_start: 0.8142 (pp20) cc_final: 0.7811 (pp20) REVERT: Am 69 HIS cc_start: 0.8422 (t-170) cc_final: 0.8218 (t-170) REVERT: Am 157 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8416 (ttt90) REVERT: An 73 TYR cc_start: 0.9043 (t80) cc_final: 0.8762 (t80) REVERT: An 91 ASP cc_start: 0.8123 (m-30) cc_final: 0.7896 (m-30) REVERT: An 165 ASP cc_start: 0.7989 (t0) cc_final: 0.7780 (t0) REVERT: Ao 54 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7617 (ttp) REVERT: Ao 157 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8418 (ttt90) REVERT: Ao 160 MET cc_start: 0.9013 (tpp) cc_final: 0.8626 (mmm) REVERT: Ao 165 ASP cc_start: 0.8094 (t0) cc_final: 0.7875 (t0) REVERT: Ao 174 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7031 (tpt170) cc_final: 0.6820 (tpt170) REVERT: Ap 165 ASP cc_start: 0.8079 (t0) cc_final: 0.7638 (t0) REVERT: Ap 204 GLU cc_start: 0.8189 (pp20) cc_final: 0.7869 (pp20) outliers start: 69 outliers final: 40 residues processed: 908 average time/residue: 0.3941 time to fit residues: 524.7642 Evaluate side-chains 886 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 842 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 155 THR 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 Ad residue 155 THR Chi-restraints excluded: chain Ae residue 50 ILE Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 129 ASN 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 155 THR 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 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 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 155 THR 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 Ao residue 54 MET Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 119 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ab 158 GLN Ac 129 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 129 ASN Ae 158 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Ah 151 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN 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** ** An 151 ASN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095621 restraints weight = 39369.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098489 restraints weight = 26235.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100401 restraints weight = 20268.964| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23856 Z= 0.165 Angle : 0.682 9.743 32336 Z= 0.331 Chirality : 0.042 0.155 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.388 16.533 3216 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.52 % Allowed : 20.13 % Favored : 76.34 % 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: -0.75 (0.16), residues: 2864 helix: 0.10 (0.15), residues: 1360 sheet: 1.32 (0.43), residues: 160 loop : -1.32 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAb 93 HIS 0.008 0.001 HISAc 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 0.03233 ( 800) hydrogen bonds : angle 4.96759 ( 2304) covalent geometry : bond 0.00386 (23856) covalent geometry : angle 0.68173 (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 987 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 898 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8481 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8749 (tpp) cc_final: 0.8458 (tpp) REVERT: Aa 183 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7337 (mpt180) REVERT: Ab 54 MET cc_start: 0.7827 (ttp) cc_final: 0.6859 (ttp) REVERT: Ab 73 TYR cc_start: 0.9179 (t80) cc_final: 0.8775 (t80) REVERT: Ab 136 ASP cc_start: 0.7431 (m-30) cc_final: 0.6883 (m-30) REVERT: Ab 157 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8558 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8033 (t0) cc_final: 0.7720 (t0) REVERT: Ac 157 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8458 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.8016 (t0) cc_final: 0.7408 (t0) REVERT: Ac 201 ASP cc_start: 0.8482 (t0) cc_final: 0.8161 (t0) REVERT: Ad 69 HIS cc_start: 0.8641 (t-170) cc_final: 0.8379 (t-170) REVERT: Ad 102 ASP cc_start: 0.8724 (t0) cc_final: 0.8449 (t0) REVERT: Ad 157 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8444 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.8000 (t0) cc_final: 0.7779 (t0) REVERT: Ad 174 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: Ae 76 GLN cc_start: 0.8394 (mp10) cc_final: 0.8089 (mp10) REVERT: Ae 80 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8728 (pt) REVERT: Ae 102 ASP cc_start: 0.8632 (t0) cc_final: 0.8287 (t0) REVERT: Ae 136 ASP cc_start: 0.7083 (m-30) cc_final: 0.6615 (m-30) REVERT: Ae 157 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8495 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.8004 (t0) cc_final: 0.7733 (t0) REVERT: Ae 174 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7453 (mmm-85) REVERT: Ae 204 GLU cc_start: 0.8190 (pp20) cc_final: 0.7672 (pp20) REVERT: Af 54 MET cc_start: 0.7800 (ttp) cc_final: 0.7164 (ttp) REVERT: Af 73 TYR cc_start: 0.8986 (t80) cc_final: 0.8399 (t80) REVERT: Af 158 GLN cc_start: 0.8692 (mt0) cc_final: 0.8437 (mt0) REVERT: Af 174 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: Ag 77 GLN cc_start: 0.7948 (tp40) cc_final: 0.7540 (tp40) REVERT: Ag 102 ASP cc_start: 0.8677 (t0) cc_final: 0.8411 (t0) REVERT: Ag 157 ARG cc_start: 0.8791 (ttp80) cc_final: 0.8580 (ttt-90) REVERT: Ag 165 ASP cc_start: 0.8058 (t0) cc_final: 0.7682 (t0) REVERT: Ah 54 MET cc_start: 0.7801 (ttp) cc_final: 0.7072 (ttp) REVERT: Ah 69 HIS cc_start: 0.8571 (t-170) cc_final: 0.8307 (t-170) REVERT: Ah 157 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8471 (ttt90) REVERT: Ai 76 GLN cc_start: 0.8445 (mp10) cc_final: 0.7829 (mp10) REVERT: Ai 77 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7508 (m-30) cc_final: 0.6964 (m-30) REVERT: Ai 165 ASP cc_start: 0.8186 (t0) cc_final: 0.7622 (t0) REVERT: Aj 157 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8536 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8119 (t0) cc_final: 0.7855 (t0) REVERT: Aj 188 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6915 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8115 (pp20) cc_final: 0.7534 (pp20) REVERT: Ak 80 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8543 (pt) REVERT: Ak 91 ASP cc_start: 0.8139 (m-30) cc_final: 0.7824 (m-30) REVERT: Ak 136 ASP cc_start: 0.7910 (m-30) cc_final: 0.7663 (m-30) REVERT: Ak 160 MET cc_start: 0.9044 (tpp) cc_final: 0.8540 (tpt) REVERT: Ak 165 ASP cc_start: 0.7902 (t0) cc_final: 0.7631 (t0) REVERT: Ak 174 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7514 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8641 (t0) cc_final: 0.8154 (t0) REVERT: Ak 204 GLU cc_start: 0.8145 (pp20) cc_final: 0.7872 (pp20) REVERT: Al 70 LEU cc_start: 0.9283 (tp) cc_final: 0.9045 (tp) REVERT: Al 135 MET cc_start: 0.8979 (mmm) cc_final: 0.8770 (mmm) REVERT: Al 136 ASP cc_start: 0.7963 (m-30) cc_final: 0.7439 (m-30) REVERT: Al 157 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8543 (ttt90) REVERT: Al 183 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8184 (ttp80) REVERT: Al 204 GLU cc_start: 0.8159 (pp20) cc_final: 0.7825 (pp20) REVERT: Am 56 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8197 (mmp) REVERT: Am 69 HIS cc_start: 0.8581 (t-170) cc_final: 0.8306 (t-170) REVERT: Am 157 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8499 (ttt90) REVERT: Am 165 ASP cc_start: 0.7919 (t0) cc_final: 0.7658 (t0) REVERT: Am 184 TYR cc_start: 0.7950 (t80) cc_final: 0.7437 (t80) REVERT: An 56 MET cc_start: 0.8669 (mmp) cc_final: 0.8229 (mmp) REVERT: An 91 ASP cc_start: 0.8247 (m-30) cc_final: 0.8047 (m-30) REVERT: An 165 ASP cc_start: 0.8145 (t0) cc_final: 0.7770 (t0) REVERT: Ao 157 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8564 (ttt90) REVERT: Ao 165 ASP cc_start: 0.8146 (t0) cc_final: 0.7913 (t0) REVERT: Ao 174 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7312 (tpt170) cc_final: 0.7052 (tpt170) REVERT: Ap 150 GLU cc_start: 0.8070 (tt0) cc_final: 0.7861 (tt0) REVERT: Ap 165 ASP cc_start: 0.8105 (t0) cc_final: 0.7546 (t0) outliers start: 89 outliers final: 47 residues processed: 942 average time/residue: 0.3862 time to fit residues: 536.4913 Evaluate side-chains 911 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 860 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 78 ILE Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 149 VAL 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 149 VAL Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 149 VAL 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 187 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 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 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 129 ASN Chi-restraints excluded: chain Al residue 149 VAL 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 An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 193 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 129 ASN Ab 158 GLN Ac 151 ASN Ae 129 ASN Af 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 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Am 129 ASN Am 158 GLN Ao 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094760 restraints weight = 39123.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097710 restraints weight = 25654.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099688 restraints weight = 19676.385| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23856 Z= 0.141 Angle : 0.678 9.871 32336 Z= 0.328 Chirality : 0.042 0.157 3520 Planarity : 0.006 0.064 4192 Dihedral : 4.306 15.916 3216 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.60 % Allowed : 22.19 % Favored : 74.21 % 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: 0.21 (0.15), residues: 1360 sheet: 1.74 (0.46), residues: 160 loop : -1.24 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAb 93 HIS 0.009 0.001 HISAe 69 PHE 0.008 0.001 PHEAa 200 TYR 0.031 0.002 TYRAg 73 ARG 0.006 0.001 ARGAi 157 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 800) hydrogen bonds : angle 4.87775 ( 2304) covalent geometry : bond 0.00327 (23856) covalent geometry : angle 0.67841 (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 1016 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 925 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8379 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8705 (tpp) cc_final: 0.8405 (tpp) REVERT: Aa 183 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7420 (mpt180) REVERT: Aa 188 ARG cc_start: 0.6897 (tpt170) cc_final: 0.6669 (tpt170) REVERT: Ab 54 MET cc_start: 0.7752 (ttp) cc_final: 0.6697 (ttp) REVERT: Ab 70 LEU cc_start: 0.9267 (tp) cc_final: 0.9029 (tp) REVERT: Ab 73 TYR cc_start: 0.9159 (t80) cc_final: 0.8769 (t80) REVERT: Ab 136 ASP cc_start: 0.7104 (m-30) cc_final: 0.6580 (m-30) REVERT: Ab 157 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8528 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8050 (t0) cc_final: 0.7706 (t0) REVERT: Ab 188 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6829 (tpt170) REVERT: Ac 165 ASP cc_start: 0.7961 (t0) cc_final: 0.7258 (t0) REVERT: Ac 184 TYR cc_start: 0.7842 (t80) cc_final: 0.7547 (t80) REVERT: Ac 188 ARG cc_start: 0.6894 (tpt170) cc_final: 0.6671 (tpt170) REVERT: Ac 201 ASP cc_start: 0.8440 (t0) cc_final: 0.8128 (t0) REVERT: Ad 69 HIS cc_start: 0.8489 (t-170) cc_final: 0.8277 (t-170) REVERT: Ad 102 ASP cc_start: 0.8661 (t0) cc_final: 0.8378 (t0) REVERT: Ad 174 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7454 (mmm-85) REVERT: Ae 56 MET cc_start: 0.8714 (mmp) cc_final: 0.8496 (mmp) REVERT: Ae 76 GLN cc_start: 0.8299 (mp10) cc_final: 0.7971 (mp10) REVERT: Ae 102 ASP cc_start: 0.8531 (t0) cc_final: 0.8199 (t0) REVERT: Ae 136 ASP cc_start: 0.6774 (m-30) cc_final: 0.6354 (m-30) REVERT: Ae 157 ARG cc_start: 0.8652 (ttp80) cc_final: 0.8436 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.7994 (t0) cc_final: 0.7727 (t0) REVERT: Ae 174 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7427 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6897 (tpt170) cc_final: 0.6571 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8109 (pp20) cc_final: 0.7639 (pp20) REVERT: Af 54 MET cc_start: 0.7840 (ttp) cc_final: 0.7243 (ttp) REVERT: Af 73 TYR cc_start: 0.9020 (t80) cc_final: 0.8496 (t80) REVERT: Af 174 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7520 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8588 (t0) cc_final: 0.8323 (t0) REVERT: Ag 165 ASP cc_start: 0.8028 (t0) cc_final: 0.7635 (t0) REVERT: Ah 54 MET cc_start: 0.7839 (ttp) cc_final: 0.7263 (ttp) REVERT: Ah 121 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7621 (mm-30) REVERT: Ah 157 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8430 (ttt-90) REVERT: Ai 76 GLN cc_start: 0.8370 (mp10) cc_final: 0.7760 (mp10) REVERT: Ai 77 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7609 (m-30) cc_final: 0.7093 (m-30) REVERT: Ai 160 MET cc_start: 0.8720 (mmm) cc_final: 0.8426 (mmm) REVERT: Ai 165 ASP cc_start: 0.8119 (t0) cc_final: 0.7563 (t0) REVERT: Ai 174 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7455 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.7105 (tpt170) cc_final: 0.6773 (tpt170) REVERT: Aj 157 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8467 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8047 (t0) cc_final: 0.7825 (t0) REVERT: Aj 174 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7030 (tpt170) cc_final: 0.6817 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8077 (pp20) cc_final: 0.7559 (pp20) REVERT: Ak 136 ASP cc_start: 0.7905 (m-30) cc_final: 0.7646 (m-30) REVERT: Ak 160 MET cc_start: 0.8960 (tpp) cc_final: 0.8516 (tpt) REVERT: Ak 165 ASP cc_start: 0.7905 (t0) cc_final: 0.7668 (t0) REVERT: Ak 174 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7430 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8616 (t0) cc_final: 0.8156 (t0) REVERT: Ak 204 GLU cc_start: 0.8051 (pp20) cc_final: 0.7797 (pp20) REVERT: Al 116 MET cc_start: 0.8749 (ttp) cc_final: 0.8361 (ttt) REVERT: Al 136 ASP cc_start: 0.7831 (m-30) cc_final: 0.7368 (m-30) REVERT: Al 183 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8054 (ttp80) REVERT: Al 188 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6744 (tpt170) REVERT: Al 204 GLU cc_start: 0.8092 (pp20) cc_final: 0.7773 (pp20) REVERT: Am 56 MET cc_start: 0.8373 (mmp) cc_final: 0.8126 (mmp) REVERT: Am 70 LEU cc_start: 0.9295 (tp) cc_final: 0.9029 (tp) REVERT: Am 157 ARG cc_start: 0.8728 (ttp80) cc_final: 0.8420 (ttt90) REVERT: Am 165 ASP cc_start: 0.7832 (t0) cc_final: 0.7529 (t0) REVERT: Am 184 TYR cc_start: 0.7937 (t80) cc_final: 0.7551 (t80) REVERT: An 56 MET cc_start: 0.8624 (mmp) cc_final: 0.8182 (mmp) REVERT: An 76 GLN cc_start: 0.8492 (mp10) cc_final: 0.7976 (mp10) REVERT: An 165 ASP cc_start: 0.8047 (t0) cc_final: 0.7712 (t0) REVERT: An 188 ARG cc_start: 0.7013 (tpt170) cc_final: 0.6624 (tpt170) REVERT: Ao 157 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8485 (ttt-90) REVERT: Ao 165 ASP cc_start: 0.7983 (t0) cc_final: 0.7748 (t0) REVERT: Ao 174 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7331 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7248 (tpt170) cc_final: 0.7012 (tpt170) REVERT: Ap 150 GLU cc_start: 0.7992 (tt0) cc_final: 0.7676 (tt0) REVERT: Ap 158 GLN cc_start: 0.8742 (mt0) cc_final: 0.8163 (mm-40) REVERT: Ap 165 ASP cc_start: 0.8084 (t0) cc_final: 0.7456 (t0) outliers start: 91 outliers final: 59 residues processed: 967 average time/residue: 0.3857 time to fit residues: 555.6704 Evaluate side-chains 954 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 894 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 176 LYS 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 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 187 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 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 149 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 129 ASN Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Chi-restraints excluded: chain Ap residue 198 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 85 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Aa 158 GLN Ab 129 ASN Ab 158 GLN Ad 140 GLN Ae 129 ASN Af 129 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 158 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 129 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 129 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092658 restraints weight = 39218.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095336 restraints weight = 26453.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097185 restraints weight = 20656.380| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23856 Z= 0.262 Angle : 0.741 9.188 32336 Z= 0.363 Chirality : 0.045 0.164 3520 Planarity : 0.006 0.066 4192 Dihedral : 4.540 21.327 3216 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.15 % Allowed : 22.51 % Favored : 73.34 % 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: -0.79 (0.16), residues: 2864 helix: -0.05 (0.14), residues: 1424 sheet: 1.36 (0.42), residues: 160 loop : -1.25 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAb 93 HIS 0.009 0.002 HISAc 69 PHE 0.014 0.002 PHEAk 200 TYR 0.030 0.002 TYRAb 198 ARG 0.006 0.001 ARGAc 183 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 800) hydrogen bonds : angle 5.22529 ( 2304) covalent geometry : bond 0.00616 (23856) covalent geometry : angle 0.74090 (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 1024 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 919 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 181 MET cc_start: 0.8685 (tpp) cc_final: 0.8438 (tpp) REVERT: Aa 188 ARG cc_start: 0.6955 (tpt170) cc_final: 0.6726 (tpt170) REVERT: Ab 54 MET cc_start: 0.7825 (ttp) cc_final: 0.6729 (ttp) REVERT: Ab 73 TYR cc_start: 0.9272 (t80) cc_final: 0.8982 (t80) REVERT: Ab 136 ASP cc_start: 0.7272 (m-30) cc_final: 0.6701 (m-30) REVERT: Ab 157 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8628 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8176 (t0) cc_final: 0.7923 (t0) REVERT: Ab 188 ARG cc_start: 0.7120 (tpt170) cc_final: 0.6872 (tpt170) REVERT: Ac 160 MET cc_start: 0.9020 (tpp) cc_final: 0.8583 (mmm) REVERT: Ac 165 ASP cc_start: 0.8162 (t0) cc_final: 0.7404 (t0) REVERT: Ac 184 TYR cc_start: 0.8077 (t80) cc_final: 0.7794 (t80) REVERT: Ac 188 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6769 (tpt170) REVERT: Ad 69 HIS cc_start: 0.8616 (t-170) cc_final: 0.8365 (t-170) REVERT: Ad 102 ASP cc_start: 0.8708 (t0) cc_final: 0.8503 (t0) REVERT: Ad 138 ASP cc_start: 0.7902 (t0) cc_final: 0.7618 (t0) REVERT: Ad 165 ASP cc_start: 0.8070 (t0) cc_final: 0.7851 (t0) REVERT: Ad 174 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7470 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6811 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8405 (mp10) cc_final: 0.8121 (mp10) REVERT: Ae 102 ASP cc_start: 0.8632 (t0) cc_final: 0.8302 (t0) REVERT: Ae 157 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8524 (ttt-90) REVERT: Ae 174 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7467 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6961 (tpt170) cc_final: 0.6635 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8128 (pp20) cc_final: 0.7652 (pp20) REVERT: Af 54 MET cc_start: 0.7760 (ttp) cc_final: 0.7195 (ttp) REVERT: Af 73 TYR cc_start: 0.9175 (t80) cc_final: 0.8818 (t80) REVERT: Af 165 ASP cc_start: 0.8109 (t0) cc_final: 0.7842 (t0) REVERT: Af 174 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7507 (mmm-85) REVERT: Ag 77 GLN cc_start: 0.8032 (tp40) cc_final: 0.7810 (tp40) REVERT: Ag 102 ASP cc_start: 0.8715 (t0) cc_final: 0.8457 (t0) REVERT: Ag 165 ASP cc_start: 0.8075 (t0) cc_final: 0.7707 (t0) REVERT: Ag 184 TYR cc_start: 0.7870 (t80) cc_final: 0.7595 (t80) REVERT: Ag 188 ARG cc_start: 0.7207 (tpt170) cc_final: 0.6983 (tpt170) REVERT: Ah 54 MET cc_start: 0.8005 (ttp) cc_final: 0.7227 (ttp) REVERT: Ah 136 ASP cc_start: 0.7527 (m-30) cc_final: 0.7003 (m-30) REVERT: Ah 157 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8496 (ttt90) REVERT: Ai 76 GLN cc_start: 0.8481 (mp10) cc_final: 0.7939 (mp10) REVERT: Ai 77 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7628 (m-30) cc_final: 0.7066 (m-30) REVERT: Ai 165 ASP cc_start: 0.8223 (t0) cc_final: 0.7654 (t0) REVERT: Ai 174 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6832 (tpt170) REVERT: Aj 80 ILE cc_start: 0.9327 (pt) cc_final: 0.9085 (pt) REVERT: Aj 165 ASP cc_start: 0.8140 (t0) cc_final: 0.7934 (t0) REVERT: Aj 174 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: Aj 204 GLU cc_start: 0.8093 (pp20) cc_final: 0.7652 (pp20) REVERT: Ak 136 ASP cc_start: 0.7912 (m-30) cc_final: 0.7633 (m-30) REVERT: Ak 160 MET cc_start: 0.9036 (tpp) cc_final: 0.8664 (mmm) REVERT: Ak 165 ASP cc_start: 0.8034 (t0) cc_final: 0.7759 (t0) REVERT: Ak 174 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: Ak 188 ARG cc_start: 0.7102 (tpt170) cc_final: 0.6882 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8760 (t0) cc_final: 0.8377 (t0) REVERT: Ak 204 GLU cc_start: 0.8178 (pp20) cc_final: 0.7852 (pp20) REVERT: Al 174 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7294 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6906 (tpt170) REVERT: Al 204 GLU cc_start: 0.8169 (pp20) cc_final: 0.7828 (pp20) REVERT: Am 54 MET cc_start: 0.8236 (ttm) cc_final: 0.8009 (ptp) REVERT: Am 69 HIS cc_start: 0.8638 (t70) cc_final: 0.8369 (t-170) REVERT: Am 129 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7614 (p0) REVERT: Am 157 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8564 (ttt90) REVERT: Am 165 ASP cc_start: 0.8051 (t0) cc_final: 0.7718 (t0) REVERT: Am 184 TYR cc_start: 0.8057 (t80) cc_final: 0.7753 (t80) REVERT: An 165 ASP cc_start: 0.8243 (t0) cc_final: 0.7917 (t0) REVERT: Ao 102 ASP cc_start: 0.8661 (t0) cc_final: 0.8369 (t0) REVERT: Ao 157 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8613 (ttt-90) REVERT: Ao 165 ASP cc_start: 0.8105 (t0) cc_final: 0.7780 (t0) REVERT: Ao 174 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7305 (tpt170) cc_final: 0.7083 (tpt170) REVERT: Ap 165 ASP cc_start: 0.8281 (t0) cc_final: 0.7675 (t0) REVERT: Ap 188 ARG cc_start: 0.7165 (tpt170) cc_final: 0.6832 (tpt170) outliers start: 105 outliers final: 70 residues processed: 978 average time/residue: 0.4763 time to fit residues: 683.3042 Evaluate side-chains 960 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 888 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 97 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 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 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 71 LEU Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 133 VAL 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 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 99 LEU Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 187 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 71 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 129 ASN Ab 158 GLN Ac 151 ASN Ad 129 ASN Ae 129 ASN Ae 158 GLN Af 129 ASN Af 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Aj 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Al 158 GLN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 129 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 129 ASN Ao 129 ASN Ap 129 ASN Ap 158 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095056 restraints weight = 39258.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097871 restraints weight = 26390.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099763 restraints weight = 20504.133| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23856 Z= 0.163 Angle : 0.714 10.381 32336 Z= 0.347 Chirality : 0.043 0.160 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.424 20.586 3216 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.72 % Allowed : 23.66 % Favored : 72.63 % 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: -0.06 (0.14), residues: 1424 sheet: 1.65 (0.42), residues: 192 loop : -1.16 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAb 93 HIS 0.011 0.002 HISAc 69 PHE 0.009 0.001 PHEAk 200 TYR 0.043 0.002 TYRAl 198 ARG 0.009 0.001 ARGAl 157 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 800) hydrogen bonds : angle 5.04711 ( 2304) covalent geometry : bond 0.00381 (23856) covalent geometry : angle 0.71390 (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 1030 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 936 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 78 ILE cc_start: 0.8425 (tp) cc_final: 0.8028 (pt) REVERT: Aa 181 MET cc_start: 0.8718 (tpp) cc_final: 0.8453 (tpp) REVERT: Aa 188 ARG cc_start: 0.6971 (tpt170) cc_final: 0.6747 (tpt170) REVERT: Ab 73 TYR cc_start: 0.9196 (t80) cc_final: 0.8834 (t80) REVERT: Ab 136 ASP cc_start: 0.7193 (m-30) cc_final: 0.6693 (m-30) REVERT: Ab 157 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8619 (ttt90) REVERT: Ab 165 ASP cc_start: 0.8130 (t0) cc_final: 0.7817 (t0) REVERT: Ab 188 ARG cc_start: 0.7193 (tpt170) cc_final: 0.6926 (tpt170) REVERT: Ac 165 ASP cc_start: 0.8075 (t0) cc_final: 0.7260 (t0) REVERT: Ac 184 TYR cc_start: 0.8106 (t80) cc_final: 0.7776 (t80) REVERT: Ac 188 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6810 (tpt170) REVERT: Ad 102 ASP cc_start: 0.8726 (t0) cc_final: 0.8445 (t0) REVERT: Ad 138 ASP cc_start: 0.7832 (t0) cc_final: 0.7616 (t0) REVERT: Ad 165 ASP cc_start: 0.8058 (t0) cc_final: 0.7844 (t0) REVERT: Ad 174 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7411 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7173 (tpt170) cc_final: 0.6809 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8374 (mp10) cc_final: 0.8037 (mp10) REVERT: Ae 102 ASP cc_start: 0.8615 (t0) cc_final: 0.8299 (t0) REVERT: Ae 165 ASP cc_start: 0.8039 (t0) cc_final: 0.7821 (t0) REVERT: Ae 174 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7366 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6929 (tpt170) cc_final: 0.6675 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8136 (pp20) cc_final: 0.7674 (pp20) REVERT: Af 54 MET cc_start: 0.7724 (ttp) cc_final: 0.7189 (ttp) REVERT: Af 73 TYR cc_start: 0.9149 (t80) cc_final: 0.8808 (t80) REVERT: Af 174 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7468 (mmm-85) REVERT: Ag 102 ASP cc_start: 0.8678 (t0) cc_final: 0.8441 (t0) REVERT: Ag 165 ASP cc_start: 0.8002 (t0) cc_final: 0.7613 (t0) REVERT: Ag 184 TYR cc_start: 0.7854 (t80) cc_final: 0.7517 (t80) REVERT: Ag 188 ARG cc_start: 0.7212 (tpt170) cc_final: 0.6979 (tpt170) REVERT: Ag 204 GLU cc_start: 0.7943 (pp20) cc_final: 0.7681 (pp20) REVERT: Ah 54 MET cc_start: 0.7956 (ttp) cc_final: 0.7255 (ttp) REVERT: Ah 136 ASP cc_start: 0.7048 (m-30) cc_final: 0.6471 (m-30) REVERT: Ah 157 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8465 (ttt90) REVERT: Ah 165 ASP cc_start: 0.8062 (t0) cc_final: 0.7827 (t0) REVERT: Ah 188 ARG cc_start: 0.6987 (tpt170) cc_final: 0.6761 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8412 (mp10) cc_final: 0.7760 (mp10) REVERT: Ai 77 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: Ai 136 ASP cc_start: 0.7696 (m-30) cc_final: 0.7256 (m-30) REVERT: Ai 165 ASP cc_start: 0.8151 (t0) cc_final: 0.7473 (t0) REVERT: Ai 174 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7401 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6901 (tpt170) REVERT: Ai 201 ASP cc_start: 0.8487 (t0) cc_final: 0.8255 (t0) REVERT: Aj 80 ILE cc_start: 0.9120 (pt) cc_final: 0.8901 (pt) REVERT: Aj 136 ASP cc_start: 0.8366 (m-30) cc_final: 0.8166 (m-30) REVERT: Aj 157 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8542 (ttt-90) REVERT: Aj 174 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7280 (tpt170) cc_final: 0.7004 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8082 (pp20) cc_final: 0.7630 (pp20) REVERT: Ak 80 ILE cc_start: 0.8837 (pt) cc_final: 0.8603 (pt) REVERT: Ak 136 ASP cc_start: 0.7906 (m-30) cc_final: 0.7650 (m-30) REVERT: Ak 165 ASP cc_start: 0.7947 (t0) cc_final: 0.7673 (t0) REVERT: Ak 188 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6914 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8738 (t0) cc_final: 0.8301 (t0) REVERT: Ak 204 GLU cc_start: 0.8172 (pp20) cc_final: 0.7843 (pp20) REVERT: Al 188 ARG cc_start: 0.7245 (tpt170) cc_final: 0.6966 (tpt170) REVERT: Al 204 GLU cc_start: 0.8175 (pp20) cc_final: 0.7864 (pp20) REVERT: Am 69 HIS cc_start: 0.8618 (t70) cc_final: 0.8361 (t-170) REVERT: Am 157 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8531 (ttt90) REVERT: Am 165 ASP cc_start: 0.8030 (t0) cc_final: 0.7668 (t0) REVERT: Am 184 TYR cc_start: 0.8077 (t80) cc_final: 0.7792 (t80) REVERT: Am 188 ARG cc_start: 0.7095 (tpt170) cc_final: 0.6797 (tpt170) REVERT: An 54 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7306 (ttp) REVERT: An 76 GLN cc_start: 0.8445 (mp10) cc_final: 0.7911 (mp10) REVERT: An 165 ASP cc_start: 0.8151 (t0) cc_final: 0.7911 (t0) REVERT: An 188 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6878 (tpt170) REVERT: An 197 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.7976 (mtp-110) REVERT: Ao 76 GLN cc_start: 0.8554 (mp10) cc_final: 0.8315 (mp10) REVERT: Ao 102 ASP cc_start: 0.8685 (t0) cc_final: 0.8376 (t0) REVERT: Ao 165 ASP cc_start: 0.7979 (t0) cc_final: 0.7670 (t0) REVERT: Ao 174 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7197 (tpt170) cc_final: 0.6996 (tpt170) REVERT: Ap 165 ASP cc_start: 0.8256 (t0) cc_final: 0.7602 (t0) REVERT: Ap 188 ARG cc_start: 0.7087 (tpt170) cc_final: 0.6746 (tpt170) outliers start: 94 outliers final: 69 residues processed: 990 average time/residue: 0.4490 time to fit residues: 661.9977 Evaluate side-chains 992 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 921 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 97 VAL Chi-restraints excluded: chain Ac residue 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 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 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 97 VAL Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain 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 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 129 ASN Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 54 MET Chi-restraints excluded: chain An residue 129 ASN Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 78 ILE Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 129 ASN Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Aj 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 ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096007 restraints weight = 39054.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098949 restraints weight = 25786.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100920 restraints weight = 19904.166| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23856 Z= 0.144 Angle : 0.717 10.775 32336 Z= 0.349 Chirality : 0.043 0.158 3520 Planarity : 0.006 0.060 4192 Dihedral : 4.354 21.177 3216 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.52 % Allowed : 23.85 % Favored : 72.63 % 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: -0.46 (0.16), residues: 2864 helix: 0.12 (0.15), residues: 1344 sheet: 1.92 (0.43), residues: 192 loop : -1.06 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAl 93 HIS 0.013 0.002 HISAp 69 PHE 0.008 0.001 PHEAl 200 TYR 0.035 0.002 TYRAb 198 ARG 0.009 0.001 ARGAl 157 Details of bonding type rmsd hydrogen bonds : bond 0.02965 ( 800) hydrogen bonds : angle 5.02721 ( 2304) covalent geometry : bond 0.00335 (23856) covalent geometry : angle 0.71693 (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 1030 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 941 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 76 GLN cc_start: 0.8278 (mp10) cc_final: 0.8045 (mp10) REVERT: Aa 78 ILE cc_start: 0.8357 (tp) cc_final: 0.7969 (pt) REVERT: Aa 116 MET cc_start: 0.8852 (tmm) cc_final: 0.8260 (ttt) REVERT: Aa 181 MET cc_start: 0.8713 (tpp) cc_final: 0.8422 (tpp) REVERT: Aa 188 ARG cc_start: 0.6928 (tpt170) cc_final: 0.6708 (tpt170) REVERT: Ab 54 MET cc_start: 0.7498 (ttp) cc_final: 0.7260 (ttp) REVERT: Ab 73 TYR cc_start: 0.9155 (t80) cc_final: 0.8843 (t80) REVERT: Ab 136 ASP cc_start: 0.7156 (m-30) cc_final: 0.6651 (m-30) REVERT: Ab 165 ASP cc_start: 0.8086 (t0) cc_final: 0.7757 (t0) REVERT: Ab 188 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6974 (tpt170) REVERT: Ac 138 ASP cc_start: 0.7604 (t0) cc_final: 0.7402 (t0) REVERT: Ac 165 ASP cc_start: 0.7915 (t0) cc_final: 0.7540 (t0) REVERT: Ac 184 TYR cc_start: 0.8050 (t80) cc_final: 0.7739 (t80) REVERT: Ac 188 ARG cc_start: 0.7086 (tpt170) cc_final: 0.6849 (tpt170) REVERT: Ad 73 TYR cc_start: 0.8665 (t80) cc_final: 0.8314 (t80) REVERT: Ad 102 ASP cc_start: 0.8647 (t0) cc_final: 0.8377 (t0) REVERT: Ad 116 MET cc_start: 0.8765 (tmm) cc_final: 0.8161 (ttt) REVERT: Ad 165 ASP cc_start: 0.8002 (t0) cc_final: 0.7797 (t0) REVERT: Ad 174 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7353 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7092 (tpt170) cc_final: 0.6753 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8327 (mp10) cc_final: 0.8042 (mp10) REVERT: Ae 102 ASP cc_start: 0.8504 (t0) cc_final: 0.8212 (t0) REVERT: Ae 174 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.6959 (tpt170) cc_final: 0.6725 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8098 (pp20) cc_final: 0.7653 (pp20) REVERT: Af 54 MET cc_start: 0.7768 (ttp) cc_final: 0.7247 (ttp) REVERT: Af 73 TYR cc_start: 0.9150 (t80) cc_final: 0.8754 (t80) REVERT: Ag 102 ASP cc_start: 0.8583 (t0) cc_final: 0.8359 (t0) REVERT: Ag 165 ASP cc_start: 0.7903 (t0) cc_final: 0.7498 (t0) REVERT: Ag 184 TYR cc_start: 0.7907 (t80) cc_final: 0.7483 (t80) REVERT: Ag 204 GLU cc_start: 0.7941 (pp20) cc_final: 0.7700 (pp20) REVERT: Ah 54 MET cc_start: 0.7875 (ttp) cc_final: 0.7178 (ttp) REVERT: Ah 116 MET cc_start: 0.8959 (tmm) cc_final: 0.8501 (ttt) REVERT: Ah 136 ASP cc_start: 0.7121 (m-30) cc_final: 0.6533 (m-30) REVERT: Ah 138 ASP cc_start: 0.7770 (t0) cc_final: 0.7565 (t0) REVERT: Ah 188 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6763 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8273 (mp10) cc_final: 0.7634 (mp10) REVERT: Ai 77 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: Ai 116 MET cc_start: 0.9113 (tmm) cc_final: 0.8315 (ttt) REVERT: Ai 136 ASP cc_start: 0.7663 (m-30) cc_final: 0.7217 (m-30) REVERT: Ai 165 ASP cc_start: 0.8034 (t0) cc_final: 0.7437 (t0) REVERT: Ai 188 ARG cc_start: 0.7121 (tpt170) cc_final: 0.6902 (tpt170) REVERT: Aj 80 ILE cc_start: 0.9008 (pt) cc_final: 0.8779 (pt) REVERT: Aj 174 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7560 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6941 (tpt170) REVERT: Aj 197 ARG cc_start: 0.8726 (mtp85) cc_final: 0.8310 (mtp-110) REVERT: Aj 204 GLU cc_start: 0.8051 (pp20) cc_final: 0.7601 (pp20) REVERT: Ak 80 ILE cc_start: 0.8681 (pt) cc_final: 0.8422 (pt) REVERT: Ak 136 ASP cc_start: 0.7841 (m-30) cc_final: 0.7583 (m-30) REVERT: Ak 165 ASP cc_start: 0.7858 (t0) cc_final: 0.7611 (t0) REVERT: Ak 201 ASP cc_start: 0.8675 (t0) cc_final: 0.8334 (t0) REVERT: Ak 204 GLU cc_start: 0.8108 (pp20) cc_final: 0.7803 (pp20) REVERT: Al 174 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7378 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7154 (tpt170) cc_final: 0.6883 (tpt170) REVERT: Al 204 GLU cc_start: 0.8103 (pp20) cc_final: 0.7752 (pp20) REVERT: Am 69 HIS cc_start: 0.8556 (t70) cc_final: 0.8297 (t-170) REVERT: Am 129 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7591 (p0) REVERT: Am 157 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8470 (ttt90) REVERT: Am 165 ASP cc_start: 0.7926 (t0) cc_final: 0.7583 (t0) REVERT: Am 184 TYR cc_start: 0.8002 (t80) cc_final: 0.7778 (t80) REVERT: Am 188 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6860 (tpt170) REVERT: An 76 GLN cc_start: 0.8333 (mp10) cc_final: 0.7834 (mp10) REVERT: An 188 ARG cc_start: 0.7033 (tpt170) cc_final: 0.6641 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8534 (mp10) cc_final: 0.8307 (mp10) REVERT: Ao 102 ASP cc_start: 0.8658 (t0) cc_final: 0.8408 (t0) REVERT: Ao 165 ASP cc_start: 0.7913 (t0) cc_final: 0.7614 (t0) REVERT: Ao 174 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7343 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7158 (tpt170) cc_final: 0.6850 (tpt170) REVERT: Ap 158 GLN cc_start: 0.8716 (mt0) cc_final: 0.8211 (mm-40) REVERT: Ap 165 ASP cc_start: 0.8137 (t0) cc_final: 0.7582 (t0) REVERT: Ap 188 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6681 (tpt170) outliers start: 89 outliers final: 66 residues processed: 993 average time/residue: 0.4047 time to fit residues: 591.1802 Evaluate side-chains 989 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 921 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 97 VAL Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 47 ILE 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 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 176 LYS Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 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 54 MET 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 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 129 ASN Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 129 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 129 ASN Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 269 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 148 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN Ab 129 ASN Ab 158 GLN Ac 129 ASN Ad 129 ASN Ae 129 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN Al 129 ASN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 ASN Ap 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094412 restraints weight = 39353.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097102 restraints weight = 26712.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098970 restraints weight = 20927.168| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23856 Z= 0.228 Angle : 0.773 10.630 32336 Z= 0.381 Chirality : 0.045 0.179 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.522 23.861 3216 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.52 % Allowed : 24.49 % Favored : 71.99 % 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: -0.65 (0.16), residues: 2864 helix: 0.01 (0.15), residues: 1344 sheet: 2.29 (0.44), residues: 160 loop : -1.19 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAa 93 HIS 0.012 0.002 HISAc 69 PHE 0.013 0.002 PHEAl 200 TYR 0.035 0.002 TYRAb 198 ARG 0.009 0.001 ARGAl 197 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 800) hydrogen bonds : angle 5.29255 ( 2304) covalent geometry : bond 0.00537 (23856) covalent geometry : angle 0.77345 (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 1017 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 928 time to evaluate : 2.502 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 116 MET cc_start: 0.8916 (tmm) cc_final: 0.8431 (ttt) REVERT: Aa 188 ARG cc_start: 0.6970 (tpt170) cc_final: 0.6726 (tpt170) REVERT: Ab 54 MET cc_start: 0.7485 (ttp) cc_final: 0.7243 (ttp) REVERT: Ab 73 TYR cc_start: 0.9205 (t80) cc_final: 0.8907 (t80) REVERT: Ab 165 ASP cc_start: 0.8139 (t0) cc_final: 0.7817 (t0) REVERT: Ab 188 ARG cc_start: 0.7292 (tpt170) cc_final: 0.7025 (tpt170) REVERT: Ac 165 ASP cc_start: 0.8035 (t0) cc_final: 0.7615 (t0) REVERT: Ac 184 TYR cc_start: 0.8152 (t80) cc_final: 0.7783 (t80) REVERT: Ac 188 ARG cc_start: 0.7180 (tpt170) cc_final: 0.6915 (tpt170) REVERT: Ac 197 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8158 (mtp-110) REVERT: Ad 102 ASP cc_start: 0.8717 (t0) cc_final: 0.8418 (t0) REVERT: Ad 116 MET cc_start: 0.8830 (tmm) cc_final: 0.8298 (ttt) REVERT: Ad 138 ASP cc_start: 0.7776 (t0) cc_final: 0.7562 (t0) REVERT: Ad 165 ASP cc_start: 0.8079 (t0) cc_final: 0.7806 (t0) REVERT: Ad 174 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7364 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6803 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8429 (mp10) cc_final: 0.8149 (mp10) REVERT: Ae 102 ASP cc_start: 0.8626 (t0) cc_final: 0.8314 (t0) REVERT: Ae 165 ASP cc_start: 0.7927 (t0) cc_final: 0.7690 (t0) REVERT: Ae 174 ARG cc_start: 0.7957 (mmm-85) cc_final: 0.7458 (mmm-85) REVERT: Ae 188 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6881 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8154 (pp20) cc_final: 0.7667 (pp20) REVERT: Af 54 MET cc_start: 0.7769 (ttp) cc_final: 0.7201 (ttp) REVERT: Af 73 TYR cc_start: 0.9163 (t80) cc_final: 0.8828 (t80) REVERT: Af 188 ARG cc_start: 0.7239 (tpt170) cc_final: 0.6893 (tpt170) REVERT: Ag 77 GLN cc_start: 0.8035 (tp40) cc_final: 0.7736 (tp-100) REVERT: Ag 102 ASP cc_start: 0.8690 (t0) cc_final: 0.8450 (t0) REVERT: Ag 165 ASP cc_start: 0.8072 (t0) cc_final: 0.7648 (t0) REVERT: Ag 184 TYR cc_start: 0.7982 (t80) cc_final: 0.7606 (t80) REVERT: Ag 204 GLU cc_start: 0.8024 (pp20) cc_final: 0.7745 (pp20) REVERT: Ah 54 MET cc_start: 0.7878 (ttp) cc_final: 0.7184 (ttp) REVERT: Ah 116 MET cc_start: 0.9022 (tmm) cc_final: 0.8582 (ttt) REVERT: Ah 121 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8068 (mm-30) REVERT: Ah 138 ASP cc_start: 0.7909 (t0) cc_final: 0.7706 (t0) REVERT: Ah 165 ASP cc_start: 0.8192 (t0) cc_final: 0.7910 (t0) REVERT: Ah 174 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: Ah 188 ARG cc_start: 0.7050 (tpt170) cc_final: 0.6840 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8359 (mp10) cc_final: 0.7707 (mp10) REVERT: Ai 77 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: Ai 116 MET cc_start: 0.9106 (tmm) cc_final: 0.8410 (ttt) REVERT: Ai 165 ASP cc_start: 0.8116 (t0) cc_final: 0.7391 (t0) REVERT: Ai 174 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: Ai 188 ARG cc_start: 0.7162 (tpt170) cc_final: 0.6925 (tpt170) REVERT: Aj 174 ARG cc_start: 0.7918 (mmm-85) cc_final: 0.7426 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7270 (tpt170) cc_final: 0.7060 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8093 (pp20) cc_final: 0.7637 (pp20) REVERT: Ak 56 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8212 (mmp) REVERT: Ak 80 ILE cc_start: 0.9021 (pt) cc_final: 0.8819 (pt) REVERT: Ak 136 ASP cc_start: 0.7881 (m-30) cc_final: 0.7638 (m-30) REVERT: Ak 165 ASP cc_start: 0.7999 (t0) cc_final: 0.7713 (t0) REVERT: Ak 204 GLU cc_start: 0.8154 (pp20) cc_final: 0.7819 (pp20) REVERT: Al 136 ASP cc_start: 0.7912 (m-30) cc_final: 0.7523 (m-30) REVERT: Al 174 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: Al 188 ARG cc_start: 0.7247 (tpt170) cc_final: 0.6980 (tpt170) REVERT: Al 204 GLU cc_start: 0.8150 (pp20) cc_final: 0.7795 (pp20) REVERT: Am 69 HIS cc_start: 0.8640 (t70) cc_final: 0.8406 (t-170) REVERT: Am 129 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7619 (p0) REVERT: Am 157 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8555 (ttt90) REVERT: Am 165 ASP cc_start: 0.8081 (t0) cc_final: 0.7733 (t0) REVERT: Am 184 TYR cc_start: 0.8110 (t80) cc_final: 0.7908 (t80) REVERT: Am 188 ARG cc_start: 0.7205 (tpt170) cc_final: 0.6902 (tpt170) REVERT: An 76 GLN cc_start: 0.8404 (mp10) cc_final: 0.7868 (mp10) REVERT: An 165 ASP cc_start: 0.8235 (t0) cc_final: 0.7873 (t0) REVERT: An 188 ARG cc_start: 0.7372 (tpt170) cc_final: 0.6843 (tpt170) REVERT: Ao 76 GLN cc_start: 0.8532 (mp10) cc_final: 0.8318 (mp10) REVERT: Ao 102 ASP cc_start: 0.8700 (t0) cc_final: 0.8434 (t0) REVERT: Ao 158 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: Ao 165 ASP cc_start: 0.8044 (t0) cc_final: 0.7730 (t0) REVERT: Ao 174 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7291 (tpt170) cc_final: 0.6961 (tpt170) REVERT: Ap 158 GLN cc_start: 0.8801 (mt0) cc_final: 0.8248 (mm-40) REVERT: Ap 165 ASP cc_start: 0.8286 (t0) cc_final: 0.7684 (t0) REVERT: Ap 188 ARG cc_start: 0.7204 (tpt170) cc_final: 0.6851 (tpt170) outliers start: 89 outliers final: 65 residues processed: 982 average time/residue: 0.3863 time to fit residues: 556.5011 Evaluate side-chains 984 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 915 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN 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 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 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 71 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 56 MET Chi-restraints excluded: chain Ak residue 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 47 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 Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 97 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 257 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 262 optimal weight: 0.8980 chunk 178 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 129 ASN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 158 GLN Ad 129 ASN ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 129 ASN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN Ah 151 ASN Ai 129 ASN Ai 158 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 129 ASN ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Al 158 GLN ** 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** Ao 129 ASN Ap 129 ASN ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098980 restraints weight = 38905.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101977 restraints weight = 25694.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103974 restraints weight = 19754.853| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23856 Z= 0.131 Angle : 0.747 10.328 32336 Z= 0.366 Chirality : 0.043 0.243 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.414 22.657 3216 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.41 % Allowed : 25.55 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.16), residues: 2864 helix: -0.15 (0.14), residues: 1440 sheet: 2.50 (0.45), residues: 160 loop : -1.02 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAl 93 HIS 0.013 0.002 HISAc 69 PHE 0.005 0.001 PHEAl 200 TYR 0.030 0.002 TYRAb 198 ARG 0.008 0.001 ARGAb 157 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 800) hydrogen bonds : angle 5.11456 ( 2304) covalent geometry : bond 0.00289 (23856) covalent geometry : angle 0.74695 (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 1023 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 962 time to evaluate : 2.507 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: 0.8336 (tp) cc_final: 0.7973 (pt) REVERT: Aa 116 MET cc_start: 0.8795 (tmm) cc_final: 0.8203 (ttt) REVERT: Aa 188 ARG cc_start: 0.6889 (tpt170) cc_final: 0.6637 (tpt170) REVERT: Ab 54 MET cc_start: 0.7407 (ttp) cc_final: 0.7138 (ttp) REVERT: Ab 165 ASP cc_start: 0.8031 (t0) cc_final: 0.7665 (t0) REVERT: Ab 188 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6953 (tpt170) REVERT: Ac 54 MET cc_start: 0.7783 (ttp) cc_final: 0.7448 (ttp) REVERT: Ac 165 ASP cc_start: 0.7803 (t0) cc_final: 0.7431 (t0) REVERT: Ac 184 TYR cc_start: 0.8015 (t80) cc_final: 0.7729 (t80) REVERT: Ac 188 ARG cc_start: 0.7073 (tpt170) cc_final: 0.6857 (tpt170) REVERT: Ad 102 ASP cc_start: 0.8588 (t0) cc_final: 0.8327 (t0) REVERT: Ad 116 MET cc_start: 0.8750 (tmm) cc_final: 0.8125 (ttt) REVERT: Ad 174 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: Ad 188 ARG cc_start: 0.7065 (tpt170) cc_final: 0.6787 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8206 (mp10) cc_final: 0.7964 (mp10) REVERT: Ae 102 ASP cc_start: 0.8485 (t0) cc_final: 0.8247 (t0) REVERT: Ae 188 ARG cc_start: 0.6845 (tpt170) cc_final: 0.6623 (tpt170) REVERT: Ae 190 LEU cc_start: 0.7875 (tt) cc_final: 0.7146 (mm) REVERT: Ae 204 GLU cc_start: 0.8102 (pp20) cc_final: 0.7659 (pp20) REVERT: Af 54 MET cc_start: 0.7702 (ttp) cc_final: 0.7058 (ttp) REVERT: Af 73 TYR cc_start: 0.9141 (t80) cc_final: 0.8651 (t80) REVERT: Af 121 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7890 (mm-30) REVERT: Af 188 ARG cc_start: 0.7168 (tpt170) cc_final: 0.6874 (tpt170) REVERT: Ag 80 ILE cc_start: 0.8444 (pt) cc_final: 0.8237 (pt) REVERT: Ag 102 ASP cc_start: 0.8547 (t0) cc_final: 0.8335 (t0) REVERT: Ag 165 ASP cc_start: 0.7865 (t0) cc_final: 0.7471 (t0) REVERT: Ag 184 TYR cc_start: 0.7906 (t80) cc_final: 0.7557 (t80) REVERT: Ag 204 GLU cc_start: 0.7955 (pp20) cc_final: 0.7697 (pp20) REVERT: Ah 116 MET cc_start: 0.8935 (tmm) cc_final: 0.8507 (ttt) REVERT: Ai 76 GLN cc_start: 0.8210 (mp10) cc_final: 0.7597 (mp10) REVERT: Ai 77 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: Ai 116 MET cc_start: 0.9021 (tmm) cc_final: 0.8296 (ttt) REVERT: Ai 136 ASP cc_start: 0.7285 (m-30) cc_final: 0.6961 (m-30) REVERT: Ai 160 MET cc_start: 0.8841 (mmm) cc_final: 0.8593 (mmp) REVERT: Ai 165 ASP cc_start: 0.7876 (t0) cc_final: 0.7536 (t0) REVERT: Ai 174 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7245 (mmm-85) REVERT: Aj 174 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7501 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7134 (tpt170) cc_final: 0.6883 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8045 (pp20) cc_final: 0.7624 (pp20) REVERT: Ak 80 ILE cc_start: 0.8316 (pt) cc_final: 0.8042 (pt) REVERT: Ak 136 ASP cc_start: 0.7875 (m-30) cc_final: 0.7609 (m-30) REVERT: Ak 165 ASP cc_start: 0.7743 (t0) cc_final: 0.7506 (t0) REVERT: Ak 188 ARG cc_start: 0.6973 (tpt170) cc_final: 0.6710 (tpt170) REVERT: Ak 204 GLU cc_start: 0.8055 (pp20) cc_final: 0.7776 (pp20) REVERT: Al 136 ASP cc_start: 0.7773 (m-30) cc_final: 0.7379 (m-30) REVERT: Al 188 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6861 (tpt170) REVERT: Al 204 GLU cc_start: 0.8076 (pp20) cc_final: 0.7726 (pp20) REVERT: Am 69 HIS cc_start: 0.8553 (t70) cc_final: 0.8283 (t-170) REVERT: Am 129 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7520 (p0) REVERT: Am 157 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8443 (ttt-90) REVERT: Am 165 ASP cc_start: 0.7850 (t0) cc_final: 0.7478 (t0) REVERT: Am 188 ARG cc_start: 0.7184 (tpt170) cc_final: 0.6948 (tpt170) REVERT: An 76 GLN cc_start: 0.8004 (mp10) cc_final: 0.7553 (mp10) REVERT: An 135 MET cc_start: 0.8762 (mmm) cc_final: 0.8524 (mmm) REVERT: An 183 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7779 (ttm-80) REVERT: An 188 ARG cc_start: 0.7317 (tpt170) cc_final: 0.7041 (tpt170) REVERT: Ao 102 ASP cc_start: 0.8619 (t0) cc_final: 0.8387 (t0) REVERT: Ao 157 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8388 (ttt-90) REVERT: Ao 165 ASP cc_start: 0.7833 (t0) cc_final: 0.7468 (t0) REVERT: Ao 174 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7340 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7159 (tpt170) cc_final: 0.6934 (tpt170) REVERT: Ap 136 ASP cc_start: 0.7766 (m-30) cc_final: 0.7276 (t0) REVERT: Ap 158 GLN cc_start: 0.8688 (mt0) cc_final: 0.8256 (mm-40) REVERT: Ap 165 ASP cc_start: 0.8063 (t0) cc_final: 0.7492 (t0) outliers start: 61 outliers final: 39 residues processed: 989 average time/residue: 0.3913 time to fit residues: 565.7483 Evaluate side-chains 979 residues out of total 2528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 938 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 129 ASN 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 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 Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 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 149 VAL Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 158 GLN 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** Al 77 GLN ** Am 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101198 restraints weight = 39086.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104093 restraints weight = 26013.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106022 restraints weight = 20083.041| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23856 Z= 0.131 Angle : 0.748 10.567 32336 Z= 0.366 Chirality : 0.043 0.229 3520 Planarity : 0.006 0.066 4192 Dihedral : 4.336 20.653 3216 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.18 % Allowed : 26.90 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.16), residues: 2864 helix: -0.04 (0.14), residues: 1440 sheet: 2.63 (0.46), residues: 160 loop : -0.96 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAa 93 HIS 0.016 0.002 HISAe 69 PHE 0.007 0.001 PHEAl 200 TYR 0.031 0.002 TYRAb 198 ARG 0.009 0.001 ARGAb 157 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 800) hydrogen bonds : angle 5.05925 ( 2304) covalent geometry : bond 0.00295 (23856) covalent geometry : angle 0.74780 (32336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10819.52 seconds wall clock time: 188 minutes 13.60 seconds (11293.60 seconds total)