Starting phenix.real_space_refine on Tue Aug 26 09:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opd_17049/08_2025/8opd_17049.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 288 5.16 5 C 22128 2.51 5 N 6096 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35040 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax Time building chain proxies: 2.24, per 1000 atoms: 0.06 Number of scatterers: 35040 At special positions: 0 Unit cell: (137.127, 137.127, 164.765, 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 288 16.00 O 6528 8.00 N 6096 7.00 C 22128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 24 sheets defined 55.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 Processing helix chain 'Aa' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAa 80 " --> pdb=" O GLNAa 77 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAa 97 " --> pdb=" O TRPAa 93 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAa 117 " --> pdb=" O ASNAa 113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAa 151 " --> pdb=" O PROAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAa 162 " --> pdb=" O GLNAa 158 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAa 173 " --> pdb=" O ALAAa 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAa 177 " --> pdb=" O METAa 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAa 178 " --> pdb=" O ARGAa 174 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAa 188 " --> pdb=" O TYRAa 184 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAa 215 " --> pdb=" O VALAa 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAa 216 " --> pdb=" O ARGAa 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAa 217 " --> pdb=" O ALAAa 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAa 218 " --> pdb=" O ARGAa 214 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAb 80 " --> pdb=" O GLNAb 77 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAb 97 " --> pdb=" O TRPAb 93 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAb 117 " --> pdb=" O ASNAb 113 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAb 151 " --> pdb=" O PROAb 147 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAb 162 " --> pdb=" O GLNAb 158 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAb 173 " --> pdb=" O ALAAb 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAb 177 " --> pdb=" O METAb 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAb 178 " --> pdb=" O ARGAb 174 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAb 188 " --> pdb=" O TYRAb 184 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAb 215 " --> pdb=" O VALAb 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAb 216 " --> pdb=" O ARGAb 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAb 217 " --> pdb=" O ALAAb 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAb 218 " --> pdb=" O ARGAb 214 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 66 through 71 Processing helix chain 'Ac' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAc 80 " --> pdb=" O GLNAc 77 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAc 97 " --> pdb=" O TRPAc 93 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAc 117 " --> pdb=" O ASNAc 113 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAc 151 " --> pdb=" O PROAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAc 162 " --> pdb=" O GLNAc 158 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAc 173 " --> pdb=" O ALAAc 169 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYSAc 177 " --> pdb=" O METAc 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAc 178 " --> pdb=" O ARGAc 174 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAc 188 " --> pdb=" O TYRAc 184 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAc 215 " --> pdb=" O VALAc 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAc 216 " --> pdb=" O ARGAc 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAc 217 " --> pdb=" O ALAAc 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAc 218 " --> pdb=" O ARGAc 214 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAd 80 " --> pdb=" O GLNAd 77 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAd 97 " --> pdb=" O TRPAd 93 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAd 117 " --> pdb=" O ASNAd 113 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAd 151 " --> pdb=" O PROAd 147 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAd 162 " --> pdb=" O GLNAd 158 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAd 173 " --> pdb=" O ALAAd 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAd 177 " --> pdb=" O METAd 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAd 178 " --> pdb=" O ARGAd 174 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAd 188 " --> pdb=" O TYRAd 184 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAd 215 " --> pdb=" O VALAd 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAd 216 " --> pdb=" O ARGAd 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAd 217 " --> pdb=" O ALAAd 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAd 218 " --> pdb=" O ARGAd 214 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 66 through 71 Processing helix chain 'Ae' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAe 80 " --> pdb=" O GLNAe 77 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAe 97 " --> pdb=" O TRPAe 93 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAe 117 " --> pdb=" O ASNAe 113 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAe 151 " --> pdb=" O PROAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAe 162 " --> pdb=" O GLNAe 158 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAe 173 " --> pdb=" O ALAAe 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAe 177 " --> pdb=" O METAe 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAe 178 " --> pdb=" O ARGAe 174 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAe 188 " --> pdb=" O TYRAe 184 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAe 215 " --> pdb=" O VALAe 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAe 216 " --> pdb=" O ARGAe 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAe 217 " --> pdb=" O ALAAe 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 Processing helix chain 'Af' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAf 80 " --> pdb=" O GLNAf 77 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAf 97 " --> pdb=" O TRPAf 93 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAf 117 " --> pdb=" O ASNAf 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAf 151 " --> pdb=" O PROAf 147 " (cutoff:3.500A) Processing helix chain 'Af' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAf 162 " --> pdb=" O GLNAf 158 " (cutoff:3.500A) Processing helix chain 'Af' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAf 173 " --> pdb=" O ALAAf 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAf 177 " --> pdb=" O METAf 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAf 178 " --> pdb=" O ARGAf 174 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAf 188 " --> pdb=" O TYRAf 184 " (cutoff:3.500A) Processing helix chain 'Af' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAf 215 " --> pdb=" O VALAf 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAf 216 " --> pdb=" O ARGAf 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAf 217 " --> pdb=" O ALAAf 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAf 218 " --> pdb=" O ARGAf 214 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 71 Processing helix chain 'Ag' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAg 80 " --> pdb=" O GLNAg 77 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAg 97 " --> pdb=" O TRPAg 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAg 117 " --> pdb=" O ASNAg 113 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAg 151 " --> pdb=" O PROAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAg 162 " --> pdb=" O GLNAg 158 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAg 173 " --> pdb=" O ALAAg 169 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYSAg 177 " --> pdb=" O METAg 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAg 178 " --> pdb=" O ARGAg 174 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAg 188 " --> pdb=" O TYRAg 184 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAg 215 " --> pdb=" O VALAg 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAg 216 " --> pdb=" O ARGAg 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAg 217 " --> pdb=" O ALAAg 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 Processing helix chain 'Ah' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAh 80 " --> pdb=" O GLNAh 77 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAh 97 " --> pdb=" O TRPAh 93 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALAh 117 " --> pdb=" O ASNAh 113 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAh 151 " --> pdb=" O PROAh 147 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAh 162 " --> pdb=" O GLNAh 158 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAh 173 " --> pdb=" O ALAAh 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAh 177 " --> pdb=" O METAh 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAh 178 " --> pdb=" O ARGAh 174 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAh 188 " --> pdb=" O TYRAh 184 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAh 215 " --> pdb=" O VALAh 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAh 216 " --> pdb=" O ARGAh 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAh 217 " --> pdb=" O ALAAh 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAh 218 " --> pdb=" O ARGAh 214 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 Processing helix chain 'Ai' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAi 80 " --> pdb=" O GLNAi 77 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAi 97 " --> pdb=" O TRPAi 93 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALAi 117 " --> pdb=" O ASNAi 113 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAi 151 " --> pdb=" O PROAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAi 162 " --> pdb=" O GLNAi 158 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAi 173 " --> pdb=" O ALAAi 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAi 177 " --> pdb=" O METAi 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAi 178 " --> pdb=" O ARGAi 174 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAi 188 " --> pdb=" O TYRAi 184 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAi 215 " --> pdb=" O VALAi 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAi 216 " --> pdb=" O ARGAi 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAi 217 " --> pdb=" O ALAAi 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAi 218 " --> pdb=" O ARGAi 214 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAj 80 " --> pdb=" O GLNAj 77 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAj 97 " --> pdb=" O TRPAj 93 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAj 117 " --> pdb=" O ASNAj 113 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAj 151 " --> pdb=" O PROAj 147 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAj 162 " --> pdb=" O GLNAj 158 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAj 173 " --> pdb=" O ALAAj 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAj 177 " --> pdb=" O METAj 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAj 178 " --> pdb=" O ARGAj 174 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAj 188 " --> pdb=" O TYRAj 184 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAj 215 " --> pdb=" O VALAj 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAj 216 " --> pdb=" O ARGAj 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAj 217 " --> pdb=" O ALAAj 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAj 218 " --> pdb=" O ARGAj 214 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 66 through 71 Processing helix chain 'Ak' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 77 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAk 97 " --> pdb=" O TRPAk 93 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 123 removed outlier: 3.570A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAk 117 " --> pdb=" O ASNAk 113 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAk 151 " --> pdb=" O PROAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 155 through 162 removed outlier: 3.895A pdb=" N HISAk 162 " --> pdb=" O GLNAk 158 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAk 173 " --> pdb=" O ALAAk 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAk 177 " --> pdb=" O METAk 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAk 178 " --> pdb=" O ARGAk 174 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAk 188 " --> pdb=" O TYRAk 184 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 removed outlier: 3.692A pdb=" N GLUAk 215 " --> pdb=" O VALAk 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAk 216 " --> pdb=" O ARGAk 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAk 217 " --> pdb=" O ALAAk 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAk 218 " --> pdb=" O ARGAk 214 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAl 80 " --> pdb=" O GLNAl 77 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAl 97 " --> pdb=" O TRPAl 93 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAl 117 " --> pdb=" O ASNAl 113 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAl 151 " --> pdb=" O PROAl 147 " (cutoff:3.500A) Processing helix chain 'Al' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAl 162 " --> pdb=" O GLNAl 158 " (cutoff:3.500A) Processing helix chain 'Al' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAl 173 " --> pdb=" O ALAAl 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAl 177 " --> pdb=" O METAl 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAl 178 " --> pdb=" O ARGAl 174 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAl 188 " --> pdb=" O TYRAl 184 " (cutoff:3.500A) Processing helix chain 'Al' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAl 215 " --> pdb=" O VALAl 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAl 216 " --> pdb=" O ARGAl 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAl 217 " --> pdb=" O ALAAl 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAl 218 " --> pdb=" O ARGAl 214 " (cutoff:3.500A) Processing helix chain 'Am' and resid 66 through 71 Processing helix chain 'Am' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 77 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAm 97 " --> pdb=" O TRPAm 93 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAm 117 " --> pdb=" O ASNAm 113 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAm 151 " --> pdb=" O PROAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAm 162 " --> pdb=" O GLNAm 158 " (cutoff:3.500A) Processing helix chain 'Am' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAm 173 " --> pdb=" O ALAAm 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAm 177 " --> pdb=" O METAm 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAm 178 " --> pdb=" O ARGAm 174 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAm 188 " --> pdb=" O TYRAm 184 " (cutoff:3.500A) Processing helix chain 'Am' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAm 215 " --> pdb=" O VALAm 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAm 216 " --> pdb=" O ARGAm 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAm 217 " --> pdb=" O ALAAm 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 Processing helix chain 'An' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAn 80 " --> pdb=" O GLNAn 77 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAn 97 " --> pdb=" O TRPAn 93 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAn 117 " --> pdb=" O ASNAn 113 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAn 151 " --> pdb=" O PROAn 147 " (cutoff:3.500A) Processing helix chain 'An' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAn 162 " --> pdb=" O GLNAn 158 " (cutoff:3.500A) Processing helix chain 'An' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAn 173 " --> pdb=" O ALAAn 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAn 177 " --> pdb=" O METAn 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAn 178 " --> pdb=" O ARGAn 174 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAn 188 " --> pdb=" O TYRAn 184 " (cutoff:3.500A) Processing helix chain 'An' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAn 215 " --> pdb=" O VALAn 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAn 216 " --> pdb=" O ARGAn 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAn 217 " --> pdb=" O ALAAn 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAn 218 " --> pdb=" O ARGAn 214 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 71 Processing helix chain 'Ao' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 77 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAo 97 " --> pdb=" O TRPAo 93 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAo 117 " --> pdb=" O ASNAo 113 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAo 151 " --> pdb=" O PROAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAo 162 " --> pdb=" O GLNAo 158 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAo 173 " --> pdb=" O ALAAo 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAo 177 " --> pdb=" O METAo 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAo 178 " --> pdb=" O ARGAo 174 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAo 188 " --> pdb=" O TYRAo 184 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAo 215 " --> pdb=" O VALAo 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAo 216 " --> pdb=" O ARGAo 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAo 217 " --> pdb=" O ALAAo 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 Processing helix chain 'Ap' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAp 80 " --> pdb=" O GLNAp 77 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAp 97 " --> pdb=" O TRPAp 93 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAp 117 " --> pdb=" O ASNAp 113 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAp 151 " --> pdb=" O PROAp 147 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAp 162 " --> pdb=" O GLNAp 158 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAp 173 " --> pdb=" O ALAAp 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAp 177 " --> pdb=" O METAp 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAp 178 " --> pdb=" O ARGAp 174 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAp 188 " --> pdb=" O TYRAp 184 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAp 215 " --> pdb=" O VALAp 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAp 216 " --> pdb=" O ARGAp 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAp 217 " --> pdb=" O ALAAp 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAp 218 " --> pdb=" O ARGAp 214 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 66 through 71 Processing helix chain 'Aq' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAq 80 " --> pdb=" O GLNAq 77 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAq 97 " --> pdb=" O TRPAq 93 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAq 117 " --> pdb=" O ASNAq 113 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAq 151 " --> pdb=" O PROAq 147 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAq 162 " --> pdb=" O GLNAq 158 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAq 173 " --> pdb=" O ALAAq 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAq 177 " --> pdb=" O METAq 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAq 178 " --> pdb=" O ARGAq 174 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAq 188 " --> pdb=" O TYRAq 184 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAq 197 " --> pdb=" O SERAq 194 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAq 215 " --> pdb=" O VALAq 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAq 216 " --> pdb=" O ARGAq 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAq 217 " --> pdb=" O ALAAq 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAq 218 " --> pdb=" O ARGAq 214 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 66 through 71 Processing helix chain 'Ar' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAr 80 " --> pdb=" O GLNAr 77 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAr 97 " --> pdb=" O TRPAr 93 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAr 117 " --> pdb=" O ASNAr 113 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAr 151 " --> pdb=" O PROAr 147 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAr 162 " --> pdb=" O GLNAr 158 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAr 173 " --> pdb=" O ALAAr 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAr 177 " --> pdb=" O METAr 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAr 178 " --> pdb=" O ARGAr 174 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAr 188 " --> pdb=" O TYRAr 184 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAr 197 " --> pdb=" O SERAr 194 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAr 215 " --> pdb=" O VALAr 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAr 216 " --> pdb=" O ARGAr 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAr 217 " --> pdb=" O ALAAr 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAr 218 " --> pdb=" O ARGAr 214 " (cutoff:3.500A) Processing helix chain 'As' and resid 66 through 71 Processing helix chain 'As' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAs 80 " --> pdb=" O GLNAs 77 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAs 97 " --> pdb=" O TRPAs 93 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAs 117 " --> pdb=" O ASNAs 113 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAs 151 " --> pdb=" O PROAs 147 " (cutoff:3.500A) Processing helix chain 'As' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAs 162 " --> pdb=" O GLNAs 158 " (cutoff:3.500A) Processing helix chain 'As' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAs 173 " --> pdb=" O ALAAs 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAs 177 " --> pdb=" O METAs 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAs 178 " --> pdb=" O ARGAs 174 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAs 188 " --> pdb=" O TYRAs 184 " (cutoff:3.500A) Processing helix chain 'As' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAs 215 " --> pdb=" O VALAs 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAs 216 " --> pdb=" O ARGAs 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAs 217 " --> pdb=" O ALAAs 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAs 218 " --> pdb=" O ARGAs 214 " (cutoff:3.500A) Processing helix chain 'At' and resid 66 through 71 Processing helix chain 'At' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAt 80 " --> pdb=" O GLNAt 77 " (cutoff:3.500A) Processing helix chain 'At' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAt 97 " --> pdb=" O TRPAt 93 " (cutoff:3.500A) Processing helix chain 'At' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAt 111 " --> pdb=" O GLUAt 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAt 117 " --> pdb=" O ASNAt 113 " (cutoff:3.500A) Processing helix chain 'At' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAt 151 " --> pdb=" O PROAt 147 " (cutoff:3.500A) Processing helix chain 'At' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAt 162 " --> pdb=" O GLNAt 158 " (cutoff:3.500A) Processing helix chain 'At' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAt 173 " --> pdb=" O ALAAt 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAt 177 " --> pdb=" O METAt 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAt 178 " --> pdb=" O ARGAt 174 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAt 188 " --> pdb=" O TYRAt 184 " (cutoff:3.500A) Processing helix chain 'At' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAt 197 " --> pdb=" O SERAt 194 " (cutoff:3.500A) Processing helix chain 'At' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAt 215 " --> pdb=" O VALAt 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAt 216 " --> pdb=" O ARGAt 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAt 217 " --> pdb=" O ALAAt 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAt 218 " --> pdb=" O ARGAt 214 " (cutoff:3.500A) Processing helix chain 'Au' and resid 66 through 71 Processing helix chain 'Au' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAu 80 " --> pdb=" O GLNAu 77 " (cutoff:3.500A) Processing helix chain 'Au' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAu 97 " --> pdb=" O TRPAu 93 " (cutoff:3.500A) Processing helix chain 'Au' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAu 117 " --> pdb=" O ASNAu 113 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAu 151 " --> pdb=" O PROAu 147 " (cutoff:3.500A) Processing helix chain 'Au' and resid 155 through 162 removed outlier: 3.895A pdb=" N HISAu 162 " --> pdb=" O GLNAu 158 " (cutoff:3.500A) Processing helix chain 'Au' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAu 173 " --> pdb=" O ALAAu 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAu 177 " --> pdb=" O METAu 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAu 178 " --> pdb=" O ARGAu 174 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAu 188 " --> pdb=" O TYRAu 184 " (cutoff:3.500A) Processing helix chain 'Au' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAu 215 " --> pdb=" O VALAu 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAu 216 " --> pdb=" O ARGAu 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAu 217 " --> pdb=" O ALAAu 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAu 218 " --> pdb=" O ARGAu 214 " (cutoff:3.500A) Processing helix chain 'Av' and resid 66 through 71 Processing helix chain 'Av' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAv 80 " --> pdb=" O GLNAv 77 " (cutoff:3.500A) Processing helix chain 'Av' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAv 97 " --> pdb=" O TRPAv 93 " (cutoff:3.500A) Processing helix chain 'Av' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAv 111 " --> pdb=" O GLUAv 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAv 117 " --> pdb=" O ASNAv 113 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAv 151 " --> pdb=" O PROAv 147 " (cutoff:3.500A) Processing helix chain 'Av' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAv 162 " --> pdb=" O GLNAv 158 " (cutoff:3.500A) Processing helix chain 'Av' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAv 173 " --> pdb=" O ALAAv 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAv 177 " --> pdb=" O METAv 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAv 178 " --> pdb=" O ARGAv 174 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAv 188 " --> pdb=" O TYRAv 184 " (cutoff:3.500A) Processing helix chain 'Av' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAv 197 " --> pdb=" O SERAv 194 " (cutoff:3.500A) Processing helix chain 'Av' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAv 215 " --> pdb=" O VALAv 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAv 216 " --> pdb=" O ARGAv 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAv 217 " --> pdb=" O ALAAv 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAv 218 " --> pdb=" O ARGAv 214 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 66 through 71 Processing helix chain 'Aw' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAw 80 " --> pdb=" O GLNAw 77 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAw 97 " --> pdb=" O TRPAw 93 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAw 117 " --> pdb=" O ASNAw 113 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAw 151 " --> pdb=" O PROAw 147 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAw 162 " --> pdb=" O GLNAw 158 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 163 through 178 removed outlier: 3.945A pdb=" N METAw 173 " --> pdb=" O ALAAw 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAw 177 " --> pdb=" O METAw 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAw 178 " --> pdb=" O ARGAw 174 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAw 188 " --> pdb=" O TYRAw 184 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAw 215 " --> pdb=" O VALAw 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAw 216 " --> pdb=" O ARGAw 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAw 217 " --> pdb=" O ALAAw 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAw 218 " --> pdb=" O ARGAw 214 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 66 through 71 Processing helix chain 'Ax' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAx 80 " --> pdb=" O GLNAx 77 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAx 97 " --> pdb=" O TRPAx 93 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAx 111 " --> pdb=" O GLUAx 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAx 117 " --> pdb=" O ASNAx 113 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAx 151 " --> pdb=" O PROAx 147 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAx 162 " --> pdb=" O GLNAx 158 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAx 173 " --> pdb=" O ALAAx 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAx 177 " --> pdb=" O METAx 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAx 178 " --> pdb=" O ARGAx 174 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAx 188 " --> pdb=" O TYRAx 184 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAx 197 " --> pdb=" O SERAx 194 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAx 215 " --> pdb=" O VALAx 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAx 216 " --> pdb=" O ARGAx 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAx 217 " --> pdb=" O ALAAx 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAx 218 " --> pdb=" O ARGAx 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAa 136 " --> pdb=" O GLUAa 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAb 136 " --> pdb=" O GLUAb 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAc 136 " --> pdb=" O GLUAc 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAd 136 " --> pdb=" O GLUAd 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAe 136 " --> pdb=" O GLUAe 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAf 136 " --> pdb=" O GLUAf 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAg 136 " --> pdb=" O GLUAg 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 136 removed outlier: 4.179A pdb=" N ASPAh 136 " --> pdb=" O GLUAh 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAi 136 " --> pdb=" O GLUAi 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAj 136 " --> pdb=" O GLUAj 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAk 136 " --> pdb=" O GLUAk 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAl 136 " --> pdb=" O GLUAl 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAm 136 " --> pdb=" O GLUAm 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAn 136 " --> pdb=" O GLUAn 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAo 136 " --> pdb=" O GLUAo 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAp 136 " --> pdb=" O GLUAp 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Aq' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAq 136 " --> pdb=" O GLUAq 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ar' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAr 136 " --> pdb=" O GLUAr 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'As' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAs 136 " --> pdb=" O GLUAs 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'At' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAt 136 " --> pdb=" O GLUAt 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Au' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAu 136 " --> pdb=" O GLUAu 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Av' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAv 136 " --> pdb=" O GLUAv 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Aw' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAw 136 " --> pdb=" O GLUAw 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Ax' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAx 136 " --> pdb=" O GLUAx 139 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3528 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: 4.38 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7798 1.33 - 1.45: 7924 1.45 - 1.57: 19556 1.57 - 1.69: 2 1.69 - 1.81: 552 Bond restraints: 35832 Sorted by residual: bond pdb=" N GLNAo 158 " pdb=" CA GLNAo 158 " ideal model delta sigma weight residual 1.459 1.416 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N GLNAd 158 " pdb=" CA GLNAd 158 " ideal model delta sigma weight residual 1.459 1.416 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N GLNAu 158 " pdb=" CA GLNAu 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N GLNAv 158 " pdb=" CA GLNAv 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N GLNAx 158 " pdb=" CA GLNAx 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 35827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 45571 1.71 - 3.42: 2357 3.42 - 5.12: 384 5.12 - 6.83: 168 6.83 - 8.54: 96 Bond angle restraints: 48576 Sorted by residual: angle pdb=" N VALAd 205 " pdb=" CA VALAd 205 " pdb=" C VALAd 205 " ideal model delta sigma weight residual 108.12 99.78 8.34 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAf 205 " pdb=" CA VALAf 205 " pdb=" C VALAf 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAn 205 " pdb=" CA VALAn 205 " pdb=" C VALAn 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAt 205 " pdb=" CA VALAt 205 " pdb=" C VALAt 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAw 205 " pdb=" CA VALAw 205 " pdb=" C VALAw 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.86e+01 ... (remaining 48571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 19147 17.50 - 34.99: 2477 34.99 - 52.49: 310 52.49 - 69.98: 26 69.98 - 87.48: 24 Dihedral angle restraints: 21984 sinusoidal: 9144 harmonic: 12840 Sorted by residual: dihedral pdb=" CA METAh 135 " pdb=" C METAh 135 " pdb=" N ASPAh 136 " pdb=" CA ASPAh 136 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA METAl 135 " pdb=" C METAl 135 " pdb=" N ASPAl 136 " pdb=" CA ASPAl 136 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA METAt 135 " pdb=" C METAt 135 " pdb=" N ASPAt 136 " pdb=" CA ASPAt 136 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 21981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3448 0.037 - 0.075: 1357 0.075 - 0.112: 389 0.112 - 0.149: 86 0.149 - 0.187: 24 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA PROAf 210 " pdb=" N PROAf 210 " pdb=" C PROAf 210 " pdb=" CB PROAf 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA PROAj 210 " pdb=" N PROAj 210 " pdb=" C PROAj 210 " pdb=" CB PROAj 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA PROAs 210 " pdb=" N PROAs 210 " pdb=" C PROAs 210 " pdb=" CB PROAs 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 5301 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C METAf 181 " 0.052 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PROAf 182 " -0.130 5.00e-02 4.00e+02 pdb=" CA PROAf 182 " 0.037 5.00e-02 4.00e+02 pdb=" CD PROAf 182 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAl 181 " -0.051 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PROAl 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PROAl 182 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROAl 182 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAc 181 " -0.051 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PROAc 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PROAc 182 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROAc 182 " -0.042 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 15375 2.88 - 3.38: 33690 3.38 - 3.89: 53397 3.89 - 4.39: 64316 4.39 - 4.90: 101744 Nonbonded interactions: 268522 Sorted by model distance: nonbonded pdb=" O PROAh 45 " pdb=" OH TYRAj 143 " model vdw 2.372 3.040 nonbonded pdb=" OH TYRAa 143 " pdb=" O PROAx 45 " model vdw 2.374 3.040 nonbonded pdb=" O PROAd 45 " pdb=" OH TYRAn 143 " model vdw 2.376 3.040 nonbonded pdb=" OH TYRAe 143 " pdb=" O PROAt 45 " model vdw 2.376 3.040 nonbonded pdb=" O PROAb 45 " pdb=" OH TYRAl 143 " model vdw 2.382 3.040 ... (remaining 268517 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: 0.11 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } 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: 1.710 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: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.120 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.008 0.078 35832 Z= 0.492 Angle : 0.963 8.540 48576 Z= 0.610 Chirality : 0.044 0.187 5304 Planarity : 0.008 0.075 6288 Dihedral : 14.435 87.480 13680 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.11), residues: 4296 helix: -2.06 (0.10), residues: 1824 sheet: 0.80 (0.33), residues: 240 loop : -2.79 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAb 55 TYR 0.007 0.001 TYRAl 180 PHE 0.012 0.003 PHEAx 202 TRP 0.010 0.002 TRPAj 132 HIS 0.003 0.001 HISAm 69 Details of bonding type rmsd covalent geometry : bond 0.00815 (35832) covalent geometry : angle 0.96318 (48576) hydrogen bonds : bond 0.23942 ( 1272) hydrogen bonds : angle 9.94979 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 994 time to evaluate : 1.275 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8521 (tmm) cc_final: 0.8251 (tmm) REVERT: Ab 112 MET cc_start: 0.9289 (mmt) cc_final: 0.8949 (mmt) REVERT: Ab 150 GLU cc_start: 0.8250 (tt0) cc_final: 0.7987 (tt0) REVERT: Ac 129 ASN cc_start: 0.8684 (m-40) cc_final: 0.8394 (m110) REVERT: Ac 173 MET cc_start: 0.8469 (tmm) cc_final: 0.8203 (tmm) REVERT: Ad 112 MET cc_start: 0.9286 (mmt) cc_final: 0.8945 (mmt) REVERT: Ad 150 GLU cc_start: 0.8244 (tt0) cc_final: 0.7978 (tt0) REVERT: Ae 173 MET cc_start: 0.8495 (tmm) cc_final: 0.8237 (tmm) REVERT: Af 112 MET cc_start: 0.9304 (mmt) cc_final: 0.8966 (mmt) REVERT: Af 150 GLU cc_start: 0.8245 (tt0) cc_final: 0.7982 (tt0) REVERT: Ag 173 MET cc_start: 0.8491 (tmm) cc_final: 0.8232 (tmm) REVERT: Ah 112 MET cc_start: 0.9285 (mmt) cc_final: 0.8956 (mmt) REVERT: Ah 150 GLU cc_start: 0.8252 (tt0) cc_final: 0.7991 (tt0) REVERT: Ai 102 ASP cc_start: 0.8405 (t0) cc_final: 0.8189 (t0) REVERT: Ai 157 ARG cc_start: 0.8414 (ptm160) cc_final: 0.8083 (ptm160) REVERT: Ai 173 MET cc_start: 0.8571 (tmm) cc_final: 0.8121 (tmm) REVERT: Aj 102 ASP cc_start: 0.8432 (t0) cc_final: 0.8203 (t0) REVERT: Aj 173 MET cc_start: 0.8445 (tmm) cc_final: 0.7988 (tmm) REVERT: Ak 102 ASP cc_start: 0.8414 (t0) cc_final: 0.8210 (t0) REVERT: Ak 173 MET cc_start: 0.8526 (tmm) cc_final: 0.8016 (tmm) REVERT: Al 102 ASP cc_start: 0.8429 (t0) cc_final: 0.8200 (t0) REVERT: Al 173 MET cc_start: 0.8442 (tmm) cc_final: 0.7976 (tmm) REVERT: Am 102 ASP cc_start: 0.8409 (t0) cc_final: 0.8197 (t0) REVERT: Am 173 MET cc_start: 0.8582 (tmm) cc_final: 0.8093 (tmm) REVERT: An 102 ASP cc_start: 0.8432 (t0) cc_final: 0.8204 (t0) REVERT: An 173 MET cc_start: 0.8439 (tmm) cc_final: 0.7990 (tmm) REVERT: Ao 102 ASP cc_start: 0.8416 (t0) cc_final: 0.8213 (t0) REVERT: Ao 173 MET cc_start: 0.8549 (tmm) cc_final: 0.8039 (tmm) REVERT: Ap 102 ASP cc_start: 0.8433 (t0) cc_final: 0.8211 (t0) REVERT: Ap 173 MET cc_start: 0.8447 (tmm) cc_final: 0.7995 (tmm) REVERT: Aq 72 GLU cc_start: 0.8543 (tt0) cc_final: 0.8247 (tt0) REVERT: Aq 101 TYR cc_start: 0.8520 (m-10) cc_final: 0.8249 (m-10) REVERT: Aq 139 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6964 (pt0) REVERT: Aq 173 MET cc_start: 0.8360 (tmm) cc_final: 0.8074 (tmm) REVERT: Ar 72 GLU cc_start: 0.8628 (tt0) cc_final: 0.8344 (tt0) REVERT: Ar 112 MET cc_start: 0.9322 (mmt) cc_final: 0.8780 (mmt) REVERT: Ar 150 GLU cc_start: 0.8223 (tt0) cc_final: 0.7993 (tt0) REVERT: Ar 173 MET cc_start: 0.8490 (tmm) cc_final: 0.8153 (tmm) REVERT: Ar 201 ASP cc_start: 0.8568 (t0) cc_final: 0.8193 (t0) REVERT: As 72 GLU cc_start: 0.8587 (tt0) cc_final: 0.8288 (tt0) REVERT: As 101 TYR cc_start: 0.8529 (m-10) cc_final: 0.8253 (m-10) REVERT: As 139 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6899 (pt0) REVERT: At 72 GLU cc_start: 0.8628 (tt0) cc_final: 0.8343 (tt0) REVERT: At 112 MET cc_start: 0.9322 (mmt) cc_final: 0.8781 (mmt) REVERT: At 150 GLU cc_start: 0.8225 (tt0) cc_final: 0.7995 (tt0) REVERT: At 173 MET cc_start: 0.8486 (tmm) cc_final: 0.8148 (tmm) REVERT: At 201 ASP cc_start: 0.8572 (t0) cc_final: 0.8214 (t0) REVERT: Au 72 GLU cc_start: 0.8574 (tt0) cc_final: 0.8273 (tt0) REVERT: Au 101 TYR cc_start: 0.8557 (m-10) cc_final: 0.8213 (m-10) REVERT: Au 139 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6912 (pt0) REVERT: Av 72 GLU cc_start: 0.8615 (tt0) cc_final: 0.8331 (tt0) REVERT: Av 112 MET cc_start: 0.9324 (mmt) cc_final: 0.8784 (mmt) REVERT: Av 150 GLU cc_start: 0.8223 (tt0) cc_final: 0.7991 (tt0) REVERT: Av 173 MET cc_start: 0.8495 (tmm) cc_final: 0.8156 (tmm) REVERT: Av 201 ASP cc_start: 0.8568 (t0) cc_final: 0.8207 (t0) REVERT: Aw 72 GLU cc_start: 0.8589 (tt0) cc_final: 0.8283 (tt0) REVERT: Aw 101 TYR cc_start: 0.8527 (m-10) cc_final: 0.8246 (m-10) REVERT: Aw 139 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6898 (pt0) REVERT: Ax 72 GLU cc_start: 0.8613 (tt0) cc_final: 0.8324 (tt0) REVERT: Ax 112 MET cc_start: 0.9316 (mmt) cc_final: 0.8773 (mmt) REVERT: Ax 173 MET cc_start: 0.8497 (tmm) cc_final: 0.8163 (tmm) REVERT: Ax 201 ASP cc_start: 0.8564 (t0) cc_final: 0.8191 (t0) outliers start: 0 outliers final: 0 residues processed: 994 average time/residue: 0.2374 time to fit residues: 355.9440 Evaluate side-chains 940 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 940 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Aa 158 GLN Ab 158 GLN Ac 69 HIS Ac 127 ASN Ac 158 GLN Ad 158 GLN Ae 69 HIS Ae 158 GLN Af 158 GLN Ag 69 HIS Ag 158 GLN Ah 158 GLN Ai 69 HIS Ai 151 ASN Ai 158 GLN Aj 69 HIS Aj 158 GLN Ak 69 HIS Ak 151 ASN Ak 158 GLN Al 69 HIS Al 158 GLN Am 69 HIS Am 151 ASN Am 158 GLN An 69 HIS An 158 GLN Ao 69 HIS Ao 151 ASN Ao 158 GLN Ap 69 HIS Ap 158 GLN Aq 158 GLN Ar 127 ASN Ar 158 GLN As 158 GLN At 127 ASN At 158 GLN Au 158 GLN Av 127 ASN Av 158 GLN Aw 158 GLN Ax 127 ASN Ax 158 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.139300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.115711 restraints weight = 45420.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.120550 restraints weight = 22203.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123822 restraints weight = 13605.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.126105 restraints weight = 9544.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.127625 restraints weight = 7315.856| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35832 Z= 0.134 Angle : 0.584 4.874 48576 Z= 0.304 Chirality : 0.039 0.144 5304 Planarity : 0.006 0.056 6288 Dihedral : 4.480 21.231 4824 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.07 % Allowed : 17.14 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.13), residues: 4296 helix: -0.39 (0.12), residues: 1800 sheet: -0.33 (0.32), residues: 288 loop : -1.67 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAh 183 TYR 0.010 0.001 TYRAl 180 PHE 0.011 0.002 PHEAa 202 TRP 0.012 0.001 TRPAh 132 HIS 0.002 0.000 HISAb 217 Details of bonding type rmsd covalent geometry : bond 0.00331 (35832) covalent geometry : angle 0.58391 (48576) hydrogen bonds : bond 0.04328 ( 1272) hydrogen bonds : angle 5.76411 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 928 time to evaluate : 1.006 Fit side-chains REVERT: Aa 112 MET cc_start: 0.9237 (mmm) cc_final: 0.8614 (mmt) REVERT: Aa 181 MET cc_start: 0.8199 (tpp) cc_final: 0.7727 (tpp) REVERT: Aa 201 ASP cc_start: 0.8721 (t0) cc_final: 0.8353 (t0) REVERT: Ab 150 GLU cc_start: 0.8102 (tt0) cc_final: 0.7779 (tt0) REVERT: Ab 181 MET cc_start: 0.8087 (tpp) cc_final: 0.7664 (tpp) REVERT: Ab 201 ASP cc_start: 0.8705 (t0) cc_final: 0.8153 (t0) REVERT: Ac 112 MET cc_start: 0.9214 (mmm) cc_final: 0.8559 (mmt) REVERT: Ac 181 MET cc_start: 0.8210 (tpp) cc_final: 0.7749 (tpp) REVERT: Ac 194 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8405 (t) REVERT: Ac 201 ASP cc_start: 0.8697 (t0) cc_final: 0.8345 (t0) REVERT: Ad 77 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7425 (tm-30) REVERT: Ad 150 GLU cc_start: 0.8106 (tt0) cc_final: 0.7790 (tt0) REVERT: Ad 181 MET cc_start: 0.8080 (tpp) cc_final: 0.7559 (tpp) REVERT: Ad 201 ASP cc_start: 0.8706 (t0) cc_final: 0.8155 (t0) REVERT: Ae 112 MET cc_start: 0.9256 (mmm) cc_final: 0.8517 (mmt) REVERT: Ae 181 MET cc_start: 0.8209 (tpp) cc_final: 0.7903 (tpp) REVERT: Ae 201 ASP cc_start: 0.8714 (t0) cc_final: 0.8349 (t0) REVERT: Af 150 GLU cc_start: 0.8101 (tt0) cc_final: 0.7787 (tt0) REVERT: Af 181 MET cc_start: 0.8075 (tpp) cc_final: 0.7597 (tpp) REVERT: Af 201 ASP cc_start: 0.8706 (t0) cc_final: 0.8164 (t0) REVERT: Ag 112 MET cc_start: 0.9237 (mmm) cc_final: 0.8574 (mmt) REVERT: Ag 181 MET cc_start: 0.8222 (tpp) cc_final: 0.7760 (tpp) REVERT: Ag 201 ASP cc_start: 0.8704 (t0) cc_final: 0.8353 (t0) REVERT: Ah 150 GLU cc_start: 0.8109 (tt0) cc_final: 0.7785 (tt0) REVERT: Ah 181 MET cc_start: 0.8076 (tpp) cc_final: 0.7556 (tpp) REVERT: Ah 201 ASP cc_start: 0.8700 (t0) cc_final: 0.8173 (t0) REVERT: Ai 80 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (pt) REVERT: Ai 173 MET cc_start: 0.8198 (tmm) cc_final: 0.7649 (tmm) REVERT: Ai 201 ASP cc_start: 0.8869 (t0) cc_final: 0.8480 (t0) REVERT: Aj 77 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7898 (tm-30) REVERT: Aj 80 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8186 (pt) REVERT: Aj 102 ASP cc_start: 0.8418 (t0) cc_final: 0.8088 (t0) REVERT: Aj 151 ASN cc_start: 0.8857 (m-40) cc_final: 0.8191 (m-40) REVERT: Aj 173 MET cc_start: 0.8014 (tmm) cc_final: 0.7638 (tmm) REVERT: Aj 201 ASP cc_start: 0.8778 (t0) cc_final: 0.8473 (t0) REVERT: Ak 80 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8219 (pt) REVERT: Ak 173 MET cc_start: 0.8167 (tmm) cc_final: 0.7810 (tmm) REVERT: Ak 201 ASP cc_start: 0.8820 (t0) cc_final: 0.8409 (t0) REVERT: Al 77 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7918 (tm-30) REVERT: Al 102 ASP cc_start: 0.8421 (t0) cc_final: 0.8087 (t0) REVERT: Al 151 ASN cc_start: 0.8845 (m-40) cc_final: 0.8180 (m-40) REVERT: Al 173 MET cc_start: 0.8014 (tmm) cc_final: 0.7636 (tmm) REVERT: Al 201 ASP cc_start: 0.8778 (t0) cc_final: 0.8485 (t0) REVERT: Am 80 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8133 (pt) REVERT: Am 173 MET cc_start: 0.8170 (tmm) cc_final: 0.7821 (tmm) REVERT: Am 201 ASP cc_start: 0.8851 (t0) cc_final: 0.8423 (t0) REVERT: An 77 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7921 (tm-30) REVERT: An 102 ASP cc_start: 0.8419 (t0) cc_final: 0.8088 (t0) REVERT: An 173 MET cc_start: 0.8041 (tmm) cc_final: 0.7690 (tmm) REVERT: An 201 ASP cc_start: 0.8777 (t0) cc_final: 0.8497 (t0) REVERT: Ao 80 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8139 (pt) REVERT: Ao 173 MET cc_start: 0.8172 (tmm) cc_final: 0.7820 (tmm) REVERT: Ao 201 ASP cc_start: 0.8820 (t0) cc_final: 0.8409 (t0) REVERT: Ap 77 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7920 (tm-30) REVERT: Ap 102 ASP cc_start: 0.8414 (t0) cc_final: 0.8088 (t0) REVERT: Ap 151 ASN cc_start: 0.8829 (m-40) cc_final: 0.8172 (m-40) REVERT: Ap 173 MET cc_start: 0.8051 (tmm) cc_final: 0.7678 (tmm) REVERT: Ap 201 ASP cc_start: 0.8771 (t0) cc_final: 0.8479 (t0) REVERT: Aq 56 MET cc_start: 0.7777 (mmt) cc_final: 0.7365 (mmt) REVERT: Aq 72 GLU cc_start: 0.8514 (tt0) cc_final: 0.8169 (tt0) REVERT: Aq 73 TYR cc_start: 0.8574 (t80) cc_final: 0.8306 (t80) REVERT: Aq 101 TYR cc_start: 0.8122 (m-10) cc_final: 0.7794 (m-10) REVERT: Aq 112 MET cc_start: 0.9172 (mmt) cc_final: 0.8772 (mmt) REVERT: Aq 181 MET cc_start: 0.8194 (tpp) cc_final: 0.7822 (tpp) REVERT: Aq 201 ASP cc_start: 0.8620 (t0) cc_final: 0.8254 (t0) REVERT: Ar 72 GLU cc_start: 0.8614 (tt0) cc_final: 0.8299 (tt0) REVERT: Ar 112 MET cc_start: 0.9313 (mmt) cc_final: 0.8807 (mmt) REVERT: Ar 129 ASN cc_start: 0.8715 (m-40) cc_final: 0.8260 (m-40) REVERT: Ar 173 MET cc_start: 0.8079 (tmm) cc_final: 0.7818 (tmm) REVERT: Ar 181 MET cc_start: 0.8159 (tpp) cc_final: 0.7735 (tpp) REVERT: Ar 201 ASP cc_start: 0.8613 (t0) cc_final: 0.8233 (t0) REVERT: As 72 GLU cc_start: 0.8531 (tt0) cc_final: 0.8179 (tt0) REVERT: As 73 TYR cc_start: 0.8568 (t80) cc_final: 0.8298 (t80) REVERT: As 101 TYR cc_start: 0.8101 (m-10) cc_final: 0.7747 (m-10) REVERT: As 112 MET cc_start: 0.9194 (mmt) cc_final: 0.8814 (mmt) REVERT: As 201 ASP cc_start: 0.8601 (t0) cc_final: 0.8242 (t0) REVERT: At 56 MET cc_start: 0.7969 (mmt) cc_final: 0.7537 (mmt) REVERT: At 72 GLU cc_start: 0.8637 (tt0) cc_final: 0.8319 (tt0) REVERT: At 112 MET cc_start: 0.9313 (mmt) cc_final: 0.8811 (mmt) REVERT: At 129 ASN cc_start: 0.8714 (m-40) cc_final: 0.8262 (m-40) REVERT: At 173 MET cc_start: 0.8076 (tmm) cc_final: 0.7816 (tmm) REVERT: At 181 MET cc_start: 0.8151 (tpp) cc_final: 0.7725 (tpp) REVERT: At 201 ASP cc_start: 0.8618 (t0) cc_final: 0.8237 (t0) REVERT: Au 56 MET cc_start: 0.7853 (mmt) cc_final: 0.7440 (mmt) REVERT: Au 72 GLU cc_start: 0.8519 (tt0) cc_final: 0.8173 (tt0) REVERT: Au 73 TYR cc_start: 0.8562 (t80) cc_final: 0.8297 (t80) REVERT: Au 101 TYR cc_start: 0.8105 (m-10) cc_final: 0.7749 (m-10) REVERT: Au 112 MET cc_start: 0.9179 (mmt) cc_final: 0.8773 (mmt) REVERT: Au 181 MET cc_start: 0.8209 (tpp) cc_final: 0.7790 (tpp) REVERT: Au 201 ASP cc_start: 0.8630 (t0) cc_final: 0.8263 (t0) REVERT: Av 72 GLU cc_start: 0.8612 (tt0) cc_final: 0.8295 (tt0) REVERT: Av 112 MET cc_start: 0.9312 (mmt) cc_final: 0.8809 (mmt) REVERT: Av 129 ASN cc_start: 0.8714 (m-40) cc_final: 0.8261 (m-40) REVERT: Av 173 MET cc_start: 0.8079 (tmm) cc_final: 0.7816 (tmm) REVERT: Av 181 MET cc_start: 0.8161 (tpp) cc_final: 0.7732 (tpp) REVERT: Av 201 ASP cc_start: 0.8624 (t0) cc_final: 0.8241 (t0) REVERT: Aw 72 GLU cc_start: 0.8527 (tt0) cc_final: 0.8186 (tt0) REVERT: Aw 73 TYR cc_start: 0.8560 (t80) cc_final: 0.8348 (t80) REVERT: Aw 101 TYR cc_start: 0.8109 (m-10) cc_final: 0.7748 (m-10) REVERT: Aw 112 MET cc_start: 0.9164 (mmt) cc_final: 0.8792 (mmt) REVERT: Aw 201 ASP cc_start: 0.8598 (t0) cc_final: 0.8240 (t0) REVERT: Ax 72 GLU cc_start: 0.8630 (tt0) cc_final: 0.8311 (tt0) REVERT: Ax 112 MET cc_start: 0.9308 (mmt) cc_final: 0.8805 (mmt) REVERT: Ax 129 ASN cc_start: 0.8705 (m-40) cc_final: 0.8415 (m-40) REVERT: Ax 173 MET cc_start: 0.8086 (tmm) cc_final: 0.7828 (tmm) REVERT: Ax 181 MET cc_start: 0.8148 (tpp) cc_final: 0.7723 (tpp) REVERT: Ax 201 ASP cc_start: 0.8612 (t0) cc_final: 0.8231 (t0) outliers start: 117 outliers final: 36 residues processed: 982 average time/residue: 0.1958 time to fit residues: 310.2809 Evaluate side-chains 956 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 914 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 155 THR Chi-restraints excluded: chain Ab residue 194 SER Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 194 SER Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ad residue 194 SER Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 194 SER Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Aj residue 63 THR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Al residue 63 THR Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain An residue 63 THR Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ap residue 63 THR Chi-restraints excluded: chain Aq residue 63 THR Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 29 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS Ac 69 HIS Ad 69 HIS Ae 69 HIS Af 69 HIS Ag 69 HIS Ah 69 HIS Aj 69 HIS Ak 69 HIS Al 69 HIS Am 69 HIS An 69 HIS Ao 69 HIS Ap 69 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.106818 restraints weight = 46804.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.111181 restraints weight = 22788.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114229 restraints weight = 13967.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.116328 restraints weight = 9808.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117804 restraints weight = 7540.627| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35832 Z= 0.231 Angle : 0.614 7.069 48576 Z= 0.314 Chirality : 0.040 0.147 5304 Planarity : 0.006 0.056 6288 Dihedral : 4.503 24.090 4824 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.72 % Allowed : 17.06 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.13), residues: 4296 helix: -0.11 (0.12), residues: 1800 sheet: -0.50 (0.29), residues: 288 loop : -1.48 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAx 208 TYR 0.014 0.002 TYRAo 73 PHE 0.014 0.003 PHEAf 163 TRP 0.009 0.002 TRPAn 132 HIS 0.003 0.001 HISAj 217 Details of bonding type rmsd covalent geometry : bond 0.00536 (35832) covalent geometry : angle 0.61443 (48576) hydrogen bonds : bond 0.04134 ( 1272) hydrogen bonds : angle 5.53711 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1013 time to evaluate : 1.205 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 41 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6792 (m) REVERT: Aa 201 ASP cc_start: 0.8848 (t0) cc_final: 0.8448 (t0) REVERT: Ab 150 GLU cc_start: 0.8059 (tt0) cc_final: 0.7746 (tt0) REVERT: Ab 201 ASP cc_start: 0.8846 (t0) cc_final: 0.8273 (t0) REVERT: Ac 201 ASP cc_start: 0.8838 (t0) cc_final: 0.8432 (t0) REVERT: Ad 150 GLU cc_start: 0.8066 (tt0) cc_final: 0.7767 (tt0) REVERT: Ad 201 ASP cc_start: 0.8842 (t0) cc_final: 0.8269 (t0) REVERT: Ae 41 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6809 (m) REVERT: Ae 77 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8056 (tm-30) REVERT: Ae 112 MET cc_start: 0.9103 (mmm) cc_final: 0.8541 (mmt) REVERT: Ae 134 MET cc_start: 0.7957 (ttp) cc_final: 0.7591 (ttp) REVERT: Ae 135 MET cc_start: 0.8063 (mtp) cc_final: 0.7863 (mtp) REVERT: Ae 201 ASP cc_start: 0.8848 (t0) cc_final: 0.8448 (t0) REVERT: Af 150 GLU cc_start: 0.8071 (tt0) cc_final: 0.7771 (tt0) REVERT: Af 201 ASP cc_start: 0.8846 (t0) cc_final: 0.8271 (t0) REVERT: Ag 134 MET cc_start: 0.7961 (ttp) cc_final: 0.7472 (ttt) REVERT: Ag 201 ASP cc_start: 0.8848 (t0) cc_final: 0.8452 (t0) REVERT: Ah 54 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (ptt) REVERT: Ah 77 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7594 (tm-30) REVERT: Ah 150 GLU cc_start: 0.8065 (tt0) cc_final: 0.7754 (tt0) REVERT: Ah 201 ASP cc_start: 0.8856 (t0) cc_final: 0.8304 (t0) REVERT: Ai 77 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8052 (tp40) REVERT: Ai 151 ASN cc_start: 0.8528 (m110) cc_final: 0.8054 (m-40) REVERT: Ai 173 MET cc_start: 0.8434 (tmm) cc_final: 0.8025 (tmm) REVERT: Aj 77 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7629 (tm-30) REVERT: Aj 80 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (pt) REVERT: Aj 102 ASP cc_start: 0.8343 (t0) cc_final: 0.8056 (t0) REVERT: Aj 151 ASN cc_start: 0.8738 (m-40) cc_final: 0.8156 (m-40) REVERT: Aj 173 MET cc_start: 0.8315 (tmm) cc_final: 0.7832 (tmm) REVERT: Aj 201 ASP cc_start: 0.8843 (t0) cc_final: 0.8491 (t0) REVERT: Ak 77 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8240 (tp40) REVERT: Ak 151 ASN cc_start: 0.8534 (m110) cc_final: 0.7978 (m-40) REVERT: Ak 173 MET cc_start: 0.8422 (tmm) cc_final: 0.7986 (tmm) REVERT: Al 77 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7724 (tm-30) REVERT: Al 102 ASP cc_start: 0.8350 (t0) cc_final: 0.8063 (t0) REVERT: Al 151 ASN cc_start: 0.8720 (m-40) cc_final: 0.8133 (m-40) REVERT: Al 173 MET cc_start: 0.8322 (tmm) cc_final: 0.7837 (tmm) REVERT: Al 201 ASP cc_start: 0.8845 (t0) cc_final: 0.8496 (t0) REVERT: Am 77 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8146 (tp40) REVERT: Am 151 ASN cc_start: 0.8556 (m110) cc_final: 0.8066 (m-40) REVERT: Am 173 MET cc_start: 0.8444 (tmm) cc_final: 0.8013 (tmm) REVERT: An 77 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7673 (tm-30) REVERT: An 102 ASP cc_start: 0.8344 (t0) cc_final: 0.8056 (t0) REVERT: An 151 ASN cc_start: 0.8732 (m-40) cc_final: 0.8146 (m-40) REVERT: An 173 MET cc_start: 0.8323 (tmm) cc_final: 0.7832 (tmm) REVERT: An 201 ASP cc_start: 0.8844 (t0) cc_final: 0.8497 (t0) REVERT: Ao 77 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8020 (tp40) REVERT: Ao 151 ASN cc_start: 0.8532 (m110) cc_final: 0.7978 (m-40) REVERT: Ao 173 MET cc_start: 0.8425 (tmm) cc_final: 0.7991 (tmm) REVERT: Ap 77 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7717 (tm-30) REVERT: Ap 102 ASP cc_start: 0.8345 (t0) cc_final: 0.8066 (t0) REVERT: Ap 151 ASN cc_start: 0.8738 (m-40) cc_final: 0.8156 (m-40) REVERT: Ap 173 MET cc_start: 0.8316 (tmm) cc_final: 0.7830 (tmm) REVERT: Ap 201 ASP cc_start: 0.8842 (t0) cc_final: 0.8488 (t0) REVERT: Aq 72 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: Aq 77 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7672 (tm-30) REVERT: Aq 101 TYR cc_start: 0.8285 (m-10) cc_final: 0.7914 (m-10) REVERT: Aq 142 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: Aq 181 MET cc_start: 0.8212 (tpp) cc_final: 0.7640 (tpp) REVERT: Aq 201 ASP cc_start: 0.8857 (t0) cc_final: 0.8408 (t0) REVERT: Ar 72 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: Ar 129 ASN cc_start: 0.8869 (m-40) cc_final: 0.8620 (m-40) REVERT: Ar 201 ASP cc_start: 0.8809 (t0) cc_final: 0.8417 (t0) REVERT: As 72 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: As 77 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7690 (tm-30) REVERT: As 101 TYR cc_start: 0.8259 (m-10) cc_final: 0.7893 (m-10) REVERT: As 142 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: As 201 ASP cc_start: 0.8852 (t0) cc_final: 0.8407 (t0) REVERT: At 72 GLU cc_start: 0.8575 (tt0) cc_final: 0.8223 (tt0) REVERT: At 129 ASN cc_start: 0.8868 (m-40) cc_final: 0.8620 (m-40) REVERT: At 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8446 (t0) REVERT: Au 72 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: Au 77 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7664 (tm-30) REVERT: Au 101 TYR cc_start: 0.8277 (m-10) cc_final: 0.7912 (m-10) REVERT: Au 142 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: Au 181 MET cc_start: 0.8252 (tpp) cc_final: 0.7650 (tpp) REVERT: Au 201 ASP cc_start: 0.8861 (t0) cc_final: 0.8409 (t0) REVERT: Av 72 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: Av 129 ASN cc_start: 0.8870 (m-40) cc_final: 0.8628 (m-40) REVERT: Av 201 ASP cc_start: 0.8809 (t0) cc_final: 0.8418 (t0) REVERT: Aw 72 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: Aw 77 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7697 (tm-30) REVERT: Aw 101 TYR cc_start: 0.8278 (m-10) cc_final: 0.7913 (m-10) REVERT: Aw 201 ASP cc_start: 0.8855 (t0) cc_final: 0.8406 (t0) REVERT: Ax 72 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: Ax 129 ASN cc_start: 0.8868 (m-40) cc_final: 0.8616 (m-40) REVERT: Ax 201 ASP cc_start: 0.8827 (t0) cc_final: 0.8447 (t0) outliers start: 142 outliers final: 66 residues processed: 1081 average time/residue: 0.1968 time to fit residues: 343.2736 Evaluate side-chains 1075 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 995 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 41 THR Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ae residue 41 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 63 THR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 121 GLU Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 63 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 121 GLU Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 63 THR Chi-restraints excluded: chain An residue 121 GLU Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 63 THR Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 121 GLU Chi-restraints excluded: chain Aq residue 63 THR Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 80 ILE Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 80 ILE Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 416 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 379 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 69 HIS ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 69 HIS ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 69 HIS ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 69 HIS ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS Aq 151 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN ** At 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 151 ASN Av 151 ASN Aw 151 ASN ** Ax 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.112305 restraints weight = 46119.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.116825 restraints weight = 22470.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.119975 restraints weight = 13754.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122141 restraints weight = 9640.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123688 restraints weight = 7377.235| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35832 Z= 0.107 Angle : 0.553 6.726 48576 Z= 0.273 Chirality : 0.037 0.126 5304 Planarity : 0.006 0.061 6288 Dihedral : 4.300 21.595 4824 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.23 % Allowed : 19.52 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.13), residues: 4296 helix: 0.42 (0.12), residues: 1800 sheet: -0.06 (0.28), residues: 288 loop : -1.30 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAr 208 TYR 0.018 0.001 TYRAi 73 PHE 0.008 0.001 PHEAs 202 TRP 0.013 0.002 TRPAp 132 HIS 0.002 0.000 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00255 (35832) covalent geometry : angle 0.55273 (48576) hydrogen bonds : bond 0.03174 ( 1272) hydrogen bonds : angle 5.00332 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 998 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 151 ASN cc_start: 0.8427 (m110) cc_final: 0.8108 (m-40) REVERT: Aa 201 ASP cc_start: 0.8870 (t0) cc_final: 0.8512 (t0) REVERT: Ab 54 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6732 (ptt) REVERT: Ab 77 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7763 (tm-30) REVERT: Ab 181 MET cc_start: 0.7977 (tpp) cc_final: 0.7636 (tpp) REVERT: Ab 201 ASP cc_start: 0.8815 (t0) cc_final: 0.8286 (t0) REVERT: Ac 54 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6511 (ptt) REVERT: Ac 79 ASP cc_start: 0.7964 (m-30) cc_final: 0.7425 (t0) REVERT: Ac 134 MET cc_start: 0.7704 (ttp) cc_final: 0.7476 (ttp) REVERT: Ac 151 ASN cc_start: 0.8376 (m110) cc_final: 0.8059 (m-40) REVERT: Ac 201 ASP cc_start: 0.8867 (t0) cc_final: 0.8527 (t0) REVERT: Ad 77 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7774 (tm-30) REVERT: Ad 79 ASP cc_start: 0.8003 (m-30) cc_final: 0.7334 (t0) REVERT: Ad 108 MET cc_start: 0.8719 (tpp) cc_final: 0.8483 (tpp) REVERT: Ad 181 MET cc_start: 0.7952 (tpp) cc_final: 0.7523 (tpp) REVERT: Ad 201 ASP cc_start: 0.8852 (t0) cc_final: 0.8312 (t0) REVERT: Ae 151 ASN cc_start: 0.8519 (m110) cc_final: 0.8270 (m-40) REVERT: Ae 201 ASP cc_start: 0.8862 (t0) cc_final: 0.8507 (t0) REVERT: Af 54 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6710 (ptt) REVERT: Af 181 MET cc_start: 0.7941 (tpp) cc_final: 0.7513 (tpp) REVERT: Af 201 ASP cc_start: 0.8855 (t0) cc_final: 0.8314 (t0) REVERT: Ag 54 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6506 (ptt) REVERT: Ag 79 ASP cc_start: 0.7974 (m-30) cc_final: 0.7428 (t0) REVERT: Ag 134 MET cc_start: 0.7700 (ttp) cc_final: 0.7439 (ttp) REVERT: Ag 151 ASN cc_start: 0.8403 (m110) cc_final: 0.8160 (m-40) REVERT: Ag 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8551 (t0) REVERT: Ah 54 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6996 (ptt) REVERT: Ah 77 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7559 (tm-30) REVERT: Ah 108 MET cc_start: 0.8728 (tpp) cc_final: 0.8417 (tpp) REVERT: Ah 181 MET cc_start: 0.7944 (tpp) cc_final: 0.7515 (tpp) REVERT: Ah 201 ASP cc_start: 0.8844 (t0) cc_final: 0.8365 (t0) REVERT: Ai 56 MET cc_start: 0.8104 (mmt) cc_final: 0.7665 (mmt) REVERT: Ai 77 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8051 (tp40) REVERT: Ai 151 ASN cc_start: 0.8495 (m110) cc_final: 0.7945 (m110) REVERT: Ai 173 MET cc_start: 0.8310 (tmm) cc_final: 0.7884 (tmm) REVERT: Ai 201 ASP cc_start: 0.9000 (t0) cc_final: 0.8506 (t0) REVERT: Aj 80 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7787 (pt) REVERT: Aj 151 ASN cc_start: 0.8694 (m-40) cc_final: 0.8072 (m-40) REVERT: Aj 173 MET cc_start: 0.8225 (tmm) cc_final: 0.7802 (tmm) REVERT: Aj 201 ASP cc_start: 0.8928 (t0) cc_final: 0.8440 (t0) REVERT: Ak 56 MET cc_start: 0.8116 (mmt) cc_final: 0.7686 (mmt) REVERT: Ak 77 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7796 (tp-100) REVERT: Ak 151 ASN cc_start: 0.8463 (m110) cc_final: 0.7932 (m110) REVERT: Ak 173 MET cc_start: 0.8337 (tmm) cc_final: 0.7877 (tmm) REVERT: Ak 201 ASP cc_start: 0.9016 (t0) cc_final: 0.8571 (t0) REVERT: Al 77 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7754 (tm-30) REVERT: Al 151 ASN cc_start: 0.8683 (m-40) cc_final: 0.8059 (m-40) REVERT: Al 173 MET cc_start: 0.8231 (tmm) cc_final: 0.7799 (tmm) REVERT: Al 201 ASP cc_start: 0.8931 (t0) cc_final: 0.8495 (t0) REVERT: Am 56 MET cc_start: 0.8098 (mmt) cc_final: 0.7666 (mmt) REVERT: Am 77 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8050 (tp40) REVERT: Am 151 ASN cc_start: 0.8502 (m110) cc_final: 0.7964 (m110) REVERT: Am 173 MET cc_start: 0.8353 (tmm) cc_final: 0.7915 (tmm) REVERT: An 77 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7748 (tm-30) REVERT: An 151 ASN cc_start: 0.8693 (m-40) cc_final: 0.8071 (m-40) REVERT: An 173 MET cc_start: 0.8227 (tmm) cc_final: 0.7797 (tmm) REVERT: An 201 ASP cc_start: 0.8934 (t0) cc_final: 0.8445 (t0) REVERT: Ao 56 MET cc_start: 0.8108 (mmt) cc_final: 0.7682 (mmt) REVERT: Ao 77 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8042 (tp40) REVERT: Ao 151 ASN cc_start: 0.8463 (m110) cc_final: 0.7924 (m110) REVERT: Ao 173 MET cc_start: 0.8312 (tmm) cc_final: 0.7849 (tmm) REVERT: Ao 201 ASP cc_start: 0.9009 (t0) cc_final: 0.8568 (t0) REVERT: Ap 77 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7749 (tm-30) REVERT: Ap 151 ASN cc_start: 0.8697 (m-40) cc_final: 0.8080 (m-40) REVERT: Ap 173 MET cc_start: 0.8193 (tmm) cc_final: 0.7773 (tmm) REVERT: Ap 201 ASP cc_start: 0.8927 (t0) cc_final: 0.8493 (t0) REVERT: Aq 72 GLU cc_start: 0.8414 (tt0) cc_final: 0.8109 (tt0) REVERT: Aq 77 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7913 (tm-30) REVERT: Aq 99 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7460 (tp) REVERT: Aq 101 TYR cc_start: 0.8174 (m-10) cc_final: 0.7857 (m-10) REVERT: Aq 181 MET cc_start: 0.8031 (tpp) cc_final: 0.7468 (tpp) REVERT: Aq 201 ASP cc_start: 0.8836 (t0) cc_final: 0.8302 (t0) REVERT: Ar 72 GLU cc_start: 0.8581 (tt0) cc_final: 0.8219 (tt0) REVERT: Ar 129 ASN cc_start: 0.8849 (m-40) cc_final: 0.8514 (m-40) REVERT: Ar 142 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: Ar 201 ASP cc_start: 0.8833 (t0) cc_final: 0.8439 (t0) REVERT: As 72 GLU cc_start: 0.8408 (tt0) cc_final: 0.8100 (tt0) REVERT: As 77 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7905 (tm-30) REVERT: As 101 TYR cc_start: 0.8109 (m-10) cc_final: 0.7824 (m-10) REVERT: As 201 ASP cc_start: 0.8837 (t0) cc_final: 0.8310 (t0) REVERT: At 72 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: At 129 ASN cc_start: 0.8847 (m-40) cc_final: 0.8515 (m-40) REVERT: At 142 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: At 201 ASP cc_start: 0.8842 (t0) cc_final: 0.8449 (t0) REVERT: Au 72 GLU cc_start: 0.8380 (tt0) cc_final: 0.8088 (tt0) REVERT: Au 77 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7900 (tm-30) REVERT: Au 101 TYR cc_start: 0.8160 (m-10) cc_final: 0.7847 (m-10) REVERT: Au 181 MET cc_start: 0.8032 (tpp) cc_final: 0.7466 (tpp) REVERT: Au 201 ASP cc_start: 0.8839 (t0) cc_final: 0.8304 (t0) REVERT: Av 129 ASN cc_start: 0.8851 (m-40) cc_final: 0.8521 (m-40) REVERT: Av 142 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: Av 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8439 (t0) REVERT: Aw 72 GLU cc_start: 0.8414 (tt0) cc_final: 0.8114 (tt0) REVERT: Aw 77 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7869 (tm-30) REVERT: Aw 101 TYR cc_start: 0.8126 (m-10) cc_final: 0.7828 (m-10) REVERT: Aw 142 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: Aw 201 ASP cc_start: 0.8833 (t0) cc_final: 0.8306 (t0) REVERT: Ax 129 ASN cc_start: 0.8845 (m-40) cc_final: 0.8508 (m-40) REVERT: Ax 142 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: Ax 201 ASP cc_start: 0.8849 (t0) cc_final: 0.8463 (t0) outliers start: 85 outliers final: 47 residues processed: 1028 average time/residue: 0.2040 time to fit residues: 336.5227 Evaluate side-chains 1044 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 984 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 108 MET Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 125 SER Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 125 SER Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 125 SER Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 126 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 373 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 430 optimal weight: 0.9990 chunk 367 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 349 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS Ac 69 HIS ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS Ae 69 HIS ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 69 HIS Ag 69 HIS ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.109852 restraints weight = 46150.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.114300 restraints weight = 22372.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.117389 restraints weight = 13707.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.119480 restraints weight = 9624.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121010 restraints weight = 7425.069| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35832 Z= 0.147 Angle : 0.556 6.820 48576 Z= 0.276 Chirality : 0.038 0.131 5304 Planarity : 0.006 0.061 6288 Dihedral : 4.259 21.394 4824 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.33 % Allowed : 19.73 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 4296 helix: 0.50 (0.12), residues: 1800 sheet: 0.11 (0.28), residues: 288 loop : -1.17 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAr 208 TYR 0.019 0.001 TYRAj 73 PHE 0.012 0.002 PHEAg 163 TRP 0.010 0.002 TRPAg 93 HIS 0.002 0.000 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00346 (35832) covalent geometry : angle 0.55607 (48576) hydrogen bonds : bond 0.03423 ( 1272) hydrogen bonds : angle 4.93537 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1003 time to evaluate : 1.270 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: Aa 54 MET cc_start: 0.6408 (ptt) cc_final: 0.5818 (ptt) REVERT: Aa 135 MET cc_start: 0.7730 (mtp) cc_final: 0.7134 (mtp) REVERT: Aa 201 ASP cc_start: 0.8909 (t0) cc_final: 0.8530 (t0) REVERT: Ab 54 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6162 (ptt) REVERT: Ab 60 LYS cc_start: 0.8985 (mttp) cc_final: 0.8765 (mmtp) REVERT: Ab 77 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7883 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7305 (tp) REVERT: Ab 108 MET cc_start: 0.8726 (tpt) cc_final: 0.8503 (tpp) REVERT: Ab 201 ASP cc_start: 0.8835 (t0) cc_final: 0.8318 (t0) REVERT: Ac 54 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6304 (ptt) REVERT: Ac 201 ASP cc_start: 0.8879 (t0) cc_final: 0.8521 (t0) REVERT: Ad 77 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7899 (tm-30) REVERT: Ad 99 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7299 (tp) REVERT: Ad 112 MET cc_start: 0.9178 (mmp) cc_final: 0.8956 (mmm) REVERT: Ad 201 ASP cc_start: 0.8837 (t0) cc_final: 0.8315 (t0) REVERT: Ae 201 ASP cc_start: 0.8913 (t0) cc_final: 0.8562 (t0) REVERT: Af 54 MET cc_start: 0.6763 (ptt) cc_final: 0.6083 (ptt) REVERT: Af 55 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8256 (mtp85) REVERT: Af 60 LYS cc_start: 0.8985 (mttp) cc_final: 0.8767 (mmtp) REVERT: Af 99 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7302 (tp) REVERT: Af 201 ASP cc_start: 0.8845 (t0) cc_final: 0.8328 (t0) REVERT: Ag 54 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6315 (ptt) REVERT: Ag 134 MET cc_start: 0.7927 (ttp) cc_final: 0.7713 (ttp) REVERT: Ag 201 ASP cc_start: 0.8882 (t0) cc_final: 0.8533 (t0) REVERT: Ah 54 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6740 (ptt) REVERT: Ah 60 LYS cc_start: 0.8982 (mttp) cc_final: 0.8745 (mmtp) REVERT: Ah 79 ASP cc_start: 0.7967 (t0) cc_final: 0.7663 (t0) REVERT: Ah 99 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7298 (tp) REVERT: Ah 201 ASP cc_start: 0.8863 (t0) cc_final: 0.8385 (t0) REVERT: Ai 77 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8071 (tp40) REVERT: Ai 121 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: Ai 151 ASN cc_start: 0.8531 (m110) cc_final: 0.7996 (m-40) REVERT: Ai 173 MET cc_start: 0.8453 (tmm) cc_final: 0.8065 (tmm) REVERT: Aj 72 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: Aj 151 ASN cc_start: 0.8696 (m-40) cc_final: 0.8095 (m-40) REVERT: Aj 173 MET cc_start: 0.8295 (tmm) cc_final: 0.7894 (tmm) REVERT: Aj 201 ASP cc_start: 0.8938 (t0) cc_final: 0.8551 (t0) REVERT: Ak 77 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7775 (tp-100) REVERT: Ak 151 ASN cc_start: 0.8532 (m110) cc_final: 0.8008 (m-40) REVERT: Ak 173 MET cc_start: 0.8470 (tmm) cc_final: 0.8024 (tmm) REVERT: Al 77 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7964 (tm-30) REVERT: Al 134 MET cc_start: 0.7675 (tmm) cc_final: 0.7428 (ttp) REVERT: Al 151 ASN cc_start: 0.8681 (m-40) cc_final: 0.8088 (m-40) REVERT: Al 173 MET cc_start: 0.8307 (tmm) cc_final: 0.7893 (tmm) REVERT: Al 201 ASP cc_start: 0.8969 (t0) cc_final: 0.8534 (t0) REVERT: Am 77 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8073 (tp40) REVERT: Am 121 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: Am 151 ASN cc_start: 0.8529 (m110) cc_final: 0.7998 (m-40) REVERT: Am 173 MET cc_start: 0.8481 (tmm) cc_final: 0.8049 (tmm) REVERT: An 72 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: An 77 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7780 (tm-30) REVERT: An 151 ASN cc_start: 0.8643 (m-40) cc_final: 0.8052 (m-40) REVERT: An 173 MET cc_start: 0.8301 (tmm) cc_final: 0.7894 (tmm) REVERT: An 201 ASP cc_start: 0.8946 (t0) cc_final: 0.8540 (t0) REVERT: Ao 77 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8057 (tp40) REVERT: Ao 151 ASN cc_start: 0.8535 (m110) cc_final: 0.8011 (m-40) REVERT: Ao 173 MET cc_start: 0.8467 (tmm) cc_final: 0.8019 (tmm) REVERT: Ap 72 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: Ap 77 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7989 (tm-30) REVERT: Ap 151 ASN cc_start: 0.8703 (m-40) cc_final: 0.8103 (m-40) REVERT: Ap 173 MET cc_start: 0.8296 (tmm) cc_final: 0.7886 (tmm) REVERT: Ap 201 ASP cc_start: 0.8975 (t0) cc_final: 0.8538 (t0) REVERT: Aq 72 GLU cc_start: 0.8364 (tt0) cc_final: 0.8037 (tt0) REVERT: Aq 99 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7454 (tp) REVERT: Aq 101 TYR cc_start: 0.8324 (m-10) cc_final: 0.8014 (m-10) REVERT: Aq 112 MET cc_start: 0.9091 (mmt) cc_final: 0.8497 (mmt) REVERT: Aq 181 MET cc_start: 0.8129 (tpp) cc_final: 0.7497 (tpp) REVERT: Aq 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8314 (t0) REVERT: Ar 129 ASN cc_start: 0.8742 (m-40) cc_final: 0.8369 (m-40) REVERT: Ar 142 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: Ar 181 MET cc_start: 0.7877 (tpp) cc_final: 0.7531 (tpp) REVERT: Ar 201 ASP cc_start: 0.8796 (t0) cc_final: 0.8459 (t0) REVERT: As 72 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: As 101 TYR cc_start: 0.8244 (m-10) cc_final: 0.7914 (m-10) REVERT: As 150 GLU cc_start: 0.8138 (tt0) cc_final: 0.7903 (tt0) REVERT: As 201 ASP cc_start: 0.8875 (t0) cc_final: 0.8385 (t0) REVERT: At 72 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: At 129 ASN cc_start: 0.8744 (m-40) cc_final: 0.8369 (m-40) REVERT: At 142 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: At 181 MET cc_start: 0.7976 (tpp) cc_final: 0.7761 (tpp) REVERT: At 201 ASP cc_start: 0.8801 (t0) cc_final: 0.8466 (t0) REVERT: Au 72 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: Au 101 TYR cc_start: 0.8321 (m-10) cc_final: 0.8004 (m-10) REVERT: Au 181 MET cc_start: 0.8154 (tpp) cc_final: 0.7509 (tpp) REVERT: Au 201 ASP cc_start: 0.8853 (t0) cc_final: 0.8350 (t0) REVERT: Av 129 ASN cc_start: 0.8745 (m-40) cc_final: 0.8374 (m-40) REVERT: Av 142 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: Av 181 MET cc_start: 0.7986 (tpp) cc_final: 0.7768 (tpp) REVERT: Av 201 ASP cc_start: 0.8795 (t0) cc_final: 0.8456 (t0) REVERT: Aw 72 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: Aw 101 TYR cc_start: 0.8255 (m-10) cc_final: 0.7924 (m-10) REVERT: Aw 142 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: Aw 150 GLU cc_start: 0.8155 (tt0) cc_final: 0.7914 (tt0) REVERT: Aw 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8386 (t0) REVERT: Ax 129 ASN cc_start: 0.8739 (m-40) cc_final: 0.8363 (m-40) REVERT: Ax 142 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: Ax 181 MET cc_start: 0.7883 (tpp) cc_final: 0.7546 (tpp) REVERT: Ax 201 ASP cc_start: 0.8809 (t0) cc_final: 0.8501 (t0) outliers start: 127 outliers final: 78 residues processed: 1059 average time/residue: 0.2061 time to fit residues: 349.8572 Evaluate side-chains 1094 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 993 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 142 GLU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 142 GLU Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 142 GLU Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 121 GLU Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 142 GLU Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 142 GLU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 142 GLU Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Ai residue 121 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 121 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 121 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 121 GLU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 121 GLU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 127 ASN Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 127 ASN Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 127 ASN Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 127 ASN Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 350 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 49 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 357 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 232 optimal weight: 7.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS Ac 69 HIS Ad 69 HIS Ae 69 HIS Af 69 HIS Ag 69 HIS Ah 69 HIS Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 76 GLN ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 76 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.131390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108863 restraints weight = 46494.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113245 restraints weight = 22561.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.116304 restraints weight = 13816.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118415 restraints weight = 9714.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.119906 restraints weight = 7469.201| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35832 Z= 0.164 Angle : 0.563 8.339 48576 Z= 0.280 Chirality : 0.038 0.124 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.269 21.334 4824 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.51 % Allowed : 20.49 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.13), residues: 4296 helix: 0.49 (0.12), residues: 1800 sheet: 0.26 (0.29), residues: 288 loop : -1.11 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAo 157 TYR 0.018 0.001 TYRAk 73 PHE 0.011 0.002 PHEAh 163 TRP 0.009 0.002 TRPAe 93 HIS 0.002 0.000 HISAf 217 Details of bonding type rmsd covalent geometry : bond 0.00384 (35832) covalent geometry : angle 0.56333 (48576) hydrogen bonds : bond 0.03492 ( 1272) hydrogen bonds : angle 4.92131 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1015 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.6579 (ptt) cc_final: 0.5997 (ptt) REVERT: Aa 99 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7378 (tp) REVERT: Aa 108 MET cc_start: 0.9021 (tpt) cc_final: 0.8735 (tpp) REVERT: Aa 112 MET cc_start: 0.9052 (mmt) cc_final: 0.8836 (mmt) REVERT: Aa 201 ASP cc_start: 0.8915 (t0) cc_final: 0.8547 (t0) REVERT: Ab 54 MET cc_start: 0.6584 (ptt) cc_final: 0.5968 (ptt) REVERT: Ab 77 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7399 (tp) REVERT: Ab 181 MET cc_start: 0.8169 (tpp) cc_final: 0.7775 (tpp) REVERT: Ab 201 ASP cc_start: 0.8889 (t0) cc_final: 0.8371 (t0) REVERT: Ac 54 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6345 (ptt) REVERT: Ac 151 ASN cc_start: 0.7998 (m-40) cc_final: 0.7689 (m-40) REVERT: Ac 201 ASP cc_start: 0.8921 (t0) cc_final: 0.8536 (t0) REVERT: Ad 77 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Ad 99 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7398 (tp) REVERT: Ad 201 ASP cc_start: 0.8886 (t0) cc_final: 0.8370 (t0) REVERT: Ae 99 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7370 (tp) REVERT: Ae 108 MET cc_start: 0.9032 (tpt) cc_final: 0.8763 (tpp) REVERT: Ae 112 MET cc_start: 0.9260 (mmt) cc_final: 0.8839 (mmt) REVERT: Ae 201 ASP cc_start: 0.8922 (t0) cc_final: 0.8548 (t0) REVERT: Af 54 MET cc_start: 0.7001 (ptt) cc_final: 0.6373 (ptt) REVERT: Af 99 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7392 (tp) REVERT: Af 201 ASP cc_start: 0.8895 (t0) cc_final: 0.8382 (t0) REVERT: Ag 54 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6339 (ptt) REVERT: Ag 77 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8062 (tm-30) REVERT: Ag 99 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7362 (tp) REVERT: Ag 108 MET cc_start: 0.9033 (tpt) cc_final: 0.8749 (tpp) REVERT: Ag 112 MET cc_start: 0.9045 (mmt) cc_final: 0.8816 (mmt) REVERT: Ag 201 ASP cc_start: 0.8926 (t0) cc_final: 0.8555 (t0) REVERT: Ah 54 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6749 (ptt) REVERT: Ah 99 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7396 (tp) REVERT: Ah 181 MET cc_start: 0.8041 (tpp) cc_final: 0.7802 (tpp) REVERT: Ah 201 ASP cc_start: 0.8879 (t0) cc_final: 0.8395 (t0) REVERT: Ai 72 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: Ai 77 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7784 (tp-100) REVERT: Ai 121 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: Ai 151 ASN cc_start: 0.8605 (m110) cc_final: 0.8083 (m-40) REVERT: Ai 173 MET cc_start: 0.8536 (tmm) cc_final: 0.8191 (tmm) REVERT: Aj 72 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: Aj 77 GLN cc_start: 0.8591 (tm-30) cc_final: 0.7848 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8701 (m-40) cc_final: 0.8111 (m-40) REVERT: Aj 173 MET cc_start: 0.8339 (tmm) cc_final: 0.7964 (tmm) REVERT: Aj 201 ASP cc_start: 0.8937 (t0) cc_final: 0.8553 (t0) REVERT: Ak 72 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: Ak 151 ASN cc_start: 0.8573 (m110) cc_final: 0.8062 (m-40) REVERT: Ak 173 MET cc_start: 0.8532 (tmm) cc_final: 0.8130 (tmm) REVERT: Al 72 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: Al 77 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7775 (tm-30) REVERT: Al 151 ASN cc_start: 0.8685 (m-40) cc_final: 0.8102 (m-40) REVERT: Al 173 MET cc_start: 0.8351 (tmm) cc_final: 0.7973 (tmm) REVERT: Al 201 ASP cc_start: 0.8967 (t0) cc_final: 0.8586 (t0) REVERT: Am 72 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: Am 77 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7789 (tp-100) REVERT: Am 121 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: Am 151 ASN cc_start: 0.8608 (m110) cc_final: 0.8086 (m-40) REVERT: Am 173 MET cc_start: 0.8529 (tmm) cc_final: 0.8133 (tmm) REVERT: An 72 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: An 77 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7633 (tm-30) REVERT: An 151 ASN cc_start: 0.8687 (m-40) cc_final: 0.8101 (m-40) REVERT: An 173 MET cc_start: 0.8306 (tmm) cc_final: 0.7929 (tmm) REVERT: An 201 ASP cc_start: 0.8970 (t0) cc_final: 0.8583 (t0) REVERT: Ao 72 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: Ao 77 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7801 (tp-100) REVERT: Ao 151 ASN cc_start: 0.8580 (m110) cc_final: 0.8071 (m-40) REVERT: Ao 173 MET cc_start: 0.8479 (tmm) cc_final: 0.8070 (tmm) REVERT: Ap 72 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: Ap 77 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7772 (tm-30) REVERT: Ap 151 ASN cc_start: 0.8696 (m-40) cc_final: 0.8116 (m-40) REVERT: Ap 173 MET cc_start: 0.8333 (tmm) cc_final: 0.7957 (tmm) REVERT: Ap 201 ASP cc_start: 0.8966 (t0) cc_final: 0.8580 (t0) REVERT: Aq 72 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: Aq 77 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7934 (tm-30) REVERT: Aq 99 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7470 (tp) REVERT: Aq 142 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: Aq 151 ASN cc_start: 0.8410 (m110) cc_final: 0.7926 (m-40) REVERT: Aq 173 MET cc_start: 0.8725 (tmm) cc_final: 0.8445 (tmm) REVERT: Aq 181 MET cc_start: 0.8111 (tpp) cc_final: 0.7613 (tpp) REVERT: Aq 201 ASP cc_start: 0.8889 (t0) cc_final: 0.8473 (t0) REVERT: Ar 129 ASN cc_start: 0.8654 (m-40) cc_final: 0.8388 (m-40) REVERT: Ar 142 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: Ar 181 MET cc_start: 0.7931 (tpp) cc_final: 0.7681 (tpp) REVERT: Ar 201 ASP cc_start: 0.8830 (t0) cc_final: 0.8539 (t0) REVERT: As 72 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: As 77 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8243 (tm-30) REVERT: As 99 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7483 (tp) REVERT: As 101 TYR cc_start: 0.8250 (m-10) cc_final: 0.7928 (m-10) REVERT: As 150 GLU cc_start: 0.8125 (tt0) cc_final: 0.7791 (tt0) REVERT: As 151 ASN cc_start: 0.8518 (m110) cc_final: 0.7923 (m-40) REVERT: As 173 MET cc_start: 0.8657 (tmm) cc_final: 0.8370 (tmm) REVERT: As 201 ASP cc_start: 0.8912 (t0) cc_final: 0.8414 (t0) REVERT: At 72 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: At 129 ASN cc_start: 0.8659 (m-40) cc_final: 0.8393 (m-40) REVERT: At 142 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: At 201 ASP cc_start: 0.8816 (t0) cc_final: 0.8521 (t0) REVERT: Au 72 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: Au 99 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7472 (tp) REVERT: Au 142 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: Au 151 ASN cc_start: 0.8395 (m110) cc_final: 0.7913 (m-40) REVERT: Au 173 MET cc_start: 0.8673 (tmm) cc_final: 0.8379 (tmm) REVERT: Au 181 MET cc_start: 0.8126 (tpp) cc_final: 0.7621 (tpp) REVERT: Au 201 ASP cc_start: 0.8911 (t0) cc_final: 0.8502 (t0) REVERT: Av 129 ASN cc_start: 0.8642 (m-40) cc_final: 0.8388 (m-40) REVERT: Av 142 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: Av 201 ASP cc_start: 0.8812 (t0) cc_final: 0.8517 (t0) REVERT: Aw 72 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: Aw 77 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7931 (tm-30) REVERT: Aw 99 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7474 (tp) REVERT: Aw 142 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: Aw 150 GLU cc_start: 0.8140 (tt0) cc_final: 0.7815 (tt0) REVERT: Aw 151 ASN cc_start: 0.8533 (m110) cc_final: 0.7937 (m-40) REVERT: Aw 173 MET cc_start: 0.8650 (tmm) cc_final: 0.8364 (tmm) REVERT: Aw 201 ASP cc_start: 0.8916 (t0) cc_final: 0.8416 (t0) REVERT: Ax 72 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: Ax 129 ASN cc_start: 0.8653 (m-40) cc_final: 0.8388 (m-40) REVERT: Ax 142 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: Ax 181 MET cc_start: 0.7933 (tpp) cc_final: 0.7685 (tpp) REVERT: Ax 201 ASP cc_start: 0.8813 (t0) cc_final: 0.8523 (t0) outliers start: 134 outliers final: 78 residues processed: 1078 average time/residue: 0.1990 time to fit residues: 344.5141 Evaluate side-chains 1122 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1007 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 142 GLU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 142 GLU Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 142 GLU Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 121 GLU Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 142 GLU Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 142 GLU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 121 GLU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 142 GLU Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Ai residue 121 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 110 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 121 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 116 MET Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 116 MET Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 357 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 267 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 69 HIS Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112625 restraints weight = 46386.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117130 restraints weight = 22420.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.120234 restraints weight = 13686.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122373 restraints weight = 9575.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123868 restraints weight = 7329.137| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35832 Z= 0.108 Angle : 0.544 9.984 48576 Z= 0.267 Chirality : 0.037 0.128 5304 Planarity : 0.005 0.059 6288 Dihedral : 4.176 22.671 4824 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.12 % Allowed : 21.59 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.13), residues: 4296 helix: 0.59 (0.12), residues: 1800 sheet: 0.56 (0.28), residues: 288 loop : -1.04 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAw 55 TYR 0.020 0.001 TYRAl 73 PHE 0.007 0.001 PHEAs 202 TRP 0.013 0.002 TRPAx 93 HIS 0.002 0.000 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00261 (35832) covalent geometry : angle 0.54437 (48576) hydrogen bonds : bond 0.03041 ( 1272) hydrogen bonds : angle 4.71366 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1007 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.6643 (ptt) cc_final: 0.6120 (ptt) REVERT: Aa 55 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8179 (mmm-85) REVERT: Aa 112 MET cc_start: 0.8988 (mmt) cc_final: 0.8734 (mmt) REVERT: Aa 201 ASP cc_start: 0.8910 (t0) cc_final: 0.8536 (t0) REVERT: Ab 54 MET cc_start: 0.6743 (ptt) cc_final: 0.6102 (ptt) REVERT: Ab 77 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Ab 181 MET cc_start: 0.8093 (tpp) cc_final: 0.7675 (tpp) REVERT: Ab 201 ASP cc_start: 0.8899 (t0) cc_final: 0.8375 (t0) REVERT: Ac 54 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6263 (ptt) REVERT: Ac 99 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7361 (tp) REVERT: Ac 201 ASP cc_start: 0.8869 (t0) cc_final: 0.8476 (t0) REVERT: Ad 60 LYS cc_start: 0.8989 (mttp) cc_final: 0.8772 (mmtp) REVERT: Ad 77 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Ad 201 ASP cc_start: 0.8902 (t0) cc_final: 0.8377 (t0) REVERT: Ae 56 MET cc_start: 0.7383 (mmt) cc_final: 0.6835 (mmt) REVERT: Ae 112 MET cc_start: 0.9164 (mmt) cc_final: 0.8653 (mmt) REVERT: Ae 201 ASP cc_start: 0.8895 (t0) cc_final: 0.8515 (t0) REVERT: Af 54 MET cc_start: 0.7223 (ptt) cc_final: 0.6685 (ptt) REVERT: Af 60 LYS cc_start: 0.8948 (mttp) cc_final: 0.8747 (mmtp) REVERT: Af 201 ASP cc_start: 0.8903 (t0) cc_final: 0.8365 (t0) REVERT: Ag 54 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6250 (ptt) REVERT: Ag 112 MET cc_start: 0.8986 (mmt) cc_final: 0.8726 (mmt) REVERT: Ag 201 ASP cc_start: 0.8890 (t0) cc_final: 0.8551 (t0) REVERT: Ah 54 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6688 (ptt) REVERT: Ah 60 LYS cc_start: 0.8959 (mttp) cc_final: 0.8749 (mmtp) REVERT: Ah 201 ASP cc_start: 0.8908 (t0) cc_final: 0.8417 (t0) REVERT: Ai 56 MET cc_start: 0.7745 (mmt) cc_final: 0.7178 (mmt) REVERT: Ai 72 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: Ai 151 ASN cc_start: 0.8553 (m110) cc_final: 0.7993 (m110) REVERT: Ai 173 MET cc_start: 0.8426 (tmm) cc_final: 0.8066 (tmm) REVERT: Aj 72 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: Aj 77 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7959 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8681 (m-40) cc_final: 0.8021 (m-40) REVERT: Aj 173 MET cc_start: 0.8241 (tmm) cc_final: 0.7856 (tmm) REVERT: Aj 201 ASP cc_start: 0.8939 (t0) cc_final: 0.8536 (t0) REVERT: Ak 56 MET cc_start: 0.7761 (mmt) cc_final: 0.7195 (mmt) REVERT: Ak 72 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: Ak 151 ASN cc_start: 0.8509 (m110) cc_final: 0.7956 (m-40) REVERT: Ak 173 MET cc_start: 0.8519 (tmm) cc_final: 0.8082 (tmm) REVERT: Al 72 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: Al 77 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7576 (tm-30) REVERT: Al 151 ASN cc_start: 0.8671 (m-40) cc_final: 0.8013 (m-40) REVERT: Al 173 MET cc_start: 0.8245 (tmm) cc_final: 0.7859 (tmm) REVERT: Al 201 ASP cc_start: 0.8973 (t0) cc_final: 0.8571 (t0) REVERT: Am 72 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: Am 151 ASN cc_start: 0.8551 (m110) cc_final: 0.7991 (m110) REVERT: Am 173 MET cc_start: 0.8424 (tmm) cc_final: 0.8017 (tmm) REVERT: An 77 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7899 (tm-30) REVERT: An 151 ASN cc_start: 0.8671 (m-40) cc_final: 0.8004 (m-40) REVERT: An 173 MET cc_start: 0.8245 (tmm) cc_final: 0.7861 (tmm) REVERT: An 201 ASP cc_start: 0.8972 (t0) cc_final: 0.8569 (t0) REVERT: Ao 56 MET cc_start: 0.7768 (mmt) cc_final: 0.7205 (mmt) REVERT: Ao 72 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: Ao 151 ASN cc_start: 0.8506 (m110) cc_final: 0.7924 (m110) REVERT: Ao 173 MET cc_start: 0.8412 (tmm) cc_final: 0.7980 (tmm) REVERT: Ap 77 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7581 (tm-30) REVERT: Ap 151 ASN cc_start: 0.8677 (m-40) cc_final: 0.8021 (m-40) REVERT: Ap 173 MET cc_start: 0.8241 (tmm) cc_final: 0.7860 (tmm) REVERT: Ap 201 ASP cc_start: 0.8962 (t0) cc_final: 0.8553 (t0) REVERT: Aq 72 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: Aq 99 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7417 (tp) REVERT: Aq 112 MET cc_start: 0.9101 (mmt) cc_final: 0.8785 (mmt) REVERT: Aq 173 MET cc_start: 0.8590 (tmm) cc_final: 0.8380 (tmm) REVERT: Aq 181 MET cc_start: 0.8084 (tpp) cc_final: 0.7525 (tpp) REVERT: Aq 201 ASP cc_start: 0.8922 (t0) cc_final: 0.8436 (t0) REVERT: Ar 72 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: Ar 99 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7382 (tp) REVERT: Ar 129 ASN cc_start: 0.8626 (m-40) cc_final: 0.8364 (m-40) REVERT: Ar 134 MET cc_start: 0.6975 (ttp) cc_final: 0.6693 (ttp) REVERT: Ar 142 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: Ar 181 MET cc_start: 0.7853 (tpp) cc_final: 0.7629 (tpp) REVERT: Ar 201 ASP cc_start: 0.8843 (t0) cc_final: 0.8522 (t0) REVERT: As 72 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: As 99 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7426 (tp) REVERT: As 150 GLU cc_start: 0.8115 (tt0) cc_final: 0.7737 (tt0) REVERT: As 201 ASP cc_start: 0.8929 (t0) cc_final: 0.8412 (t0) REVERT: At 72 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: At 99 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7387 (tp) REVERT: At 129 ASN cc_start: 0.8631 (m-40) cc_final: 0.8371 (m-40) REVERT: At 134 MET cc_start: 0.6992 (ttp) cc_final: 0.6749 (ttp) REVERT: At 142 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: At 201 ASP cc_start: 0.8830 (t0) cc_final: 0.8512 (t0) REVERT: Au 72 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: Au 99 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7399 (tp) REVERT: Au 112 MET cc_start: 0.9099 (mmt) cc_final: 0.8729 (mmt) REVERT: Au 181 MET cc_start: 0.8129 (tpp) cc_final: 0.7575 (tpp) REVERT: Au 201 ASP cc_start: 0.8922 (t0) cc_final: 0.8432 (t0) REVERT: Av 72 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: Av 99 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7385 (tp) REVERT: Av 129 ASN cc_start: 0.8632 (m-40) cc_final: 0.8378 (m-40) REVERT: Av 134 MET cc_start: 0.6982 (ttp) cc_final: 0.6740 (ttp) REVERT: Av 142 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: Av 181 MET cc_start: 0.7923 (tpp) cc_final: 0.7590 (tpp) REVERT: Av 201 ASP cc_start: 0.8845 (t0) cc_final: 0.8519 (t0) REVERT: Aw 72 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: Aw 99 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7430 (tp) REVERT: Aw 142 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: Aw 150 GLU cc_start: 0.8117 (tt0) cc_final: 0.7759 (tt0) REVERT: Aw 201 ASP cc_start: 0.8926 (t0) cc_final: 0.8408 (t0) REVERT: Ax 72 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: Ax 99 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7399 (tp) REVERT: Ax 129 ASN cc_start: 0.8625 (m-40) cc_final: 0.8364 (m-40) REVERT: Ax 134 MET cc_start: 0.6992 (ttp) cc_final: 0.6749 (ttp) REVERT: Ax 142 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: Ax 181 MET cc_start: 0.7858 (tpp) cc_final: 0.7630 (tpp) REVERT: Ax 201 ASP cc_start: 0.8827 (t0) cc_final: 0.8508 (t0) outliers start: 119 outliers final: 61 residues processed: 1059 average time/residue: 0.1993 time to fit residues: 338.6694 Evaluate side-chains 1095 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1003 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 121 GLU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 110 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 415 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 425 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 346 optimal weight: 5.9990 chunk 335 optimal weight: 0.1980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 76 GLN Af 76 GLN Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS ** Au 77 GLN ** 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 = 0.3330 r_free = 0.3330 target = 0.128076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105265 restraints weight = 47100.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.109546 restraints weight = 23207.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.112505 restraints weight = 14400.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.114565 restraints weight = 10241.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116019 restraints weight = 7965.096| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 35832 Z= 0.248 Angle : 0.639 10.692 48576 Z= 0.318 Chirality : 0.039 0.120 5304 Planarity : 0.006 0.056 6288 Dihedral : 4.427 23.969 4824 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.88 % Allowed : 20.23 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.13), residues: 4296 helix: 0.32 (0.12), residues: 1800 sheet: 0.28 (0.29), residues: 288 loop : -1.06 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAe 157 TYR 0.019 0.002 TYRAf 73 PHE 0.018 0.003 PHEAh 163 TRP 0.007 0.002 TRPAh 93 HIS 0.002 0.001 HISAq 162 Details of bonding type rmsd covalent geometry : bond 0.00572 (35832) covalent geometry : angle 0.63864 (48576) hydrogen bonds : bond 0.03930 ( 1272) hydrogen bonds : angle 5.09987 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1045 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.7113 (ptt) cc_final: 0.6562 (ptt) REVERT: Aa 201 ASP cc_start: 0.8913 (t0) cc_final: 0.8533 (t0) REVERT: Ab 99 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7419 (tp) REVERT: Ab 201 ASP cc_start: 0.8907 (t0) cc_final: 0.8414 (t0) REVERT: Ac 54 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6481 (ptt) REVERT: Ac 99 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7435 (tp) REVERT: Ac 108 MET cc_start: 0.8999 (tpt) cc_final: 0.8742 (tpp) REVERT: Ac 112 MET cc_start: 0.9068 (mmt) cc_final: 0.8827 (mmt) REVERT: Ac 194 SER cc_start: 0.8766 (t) cc_final: 0.8505 (t) REVERT: Ac 201 ASP cc_start: 0.8903 (t0) cc_final: 0.8507 (t0) REVERT: Ad 77 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8286 (tm-30) REVERT: Ad 99 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7431 (tp) REVERT: Ad 201 ASP cc_start: 0.8906 (t0) cc_final: 0.8418 (t0) REVERT: Ae 201 ASP cc_start: 0.8912 (t0) cc_final: 0.8522 (t0) REVERT: Af 54 MET cc_start: 0.7284 (ptt) cc_final: 0.6710 (ptt) REVERT: Af 99 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7420 (tp) REVERT: Af 201 ASP cc_start: 0.8910 (t0) cc_final: 0.8433 (t0) REVERT: Ag 54 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6468 (ptt) REVERT: Ag 77 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8245 (tm-30) REVERT: Ag 201 ASP cc_start: 0.8907 (t0) cc_final: 0.8534 (t0) REVERT: Ah 54 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6666 (ptt) REVERT: Ah 99 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7421 (tp) REVERT: Ah 201 ASP cc_start: 0.8903 (t0) cc_final: 0.8433 (t0) REVERT: Ai 72 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: Ai 121 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: Ai 151 ASN cc_start: 0.8608 (m110) cc_final: 0.8402 (m110) REVERT: Ai 173 MET cc_start: 0.8532 (tmm) cc_final: 0.8246 (tmm) REVERT: Aj 56 MET cc_start: 0.7681 (mmt) cc_final: 0.7166 (mmp) REVERT: Aj 72 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: Aj 77 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8033 (tm-30) REVERT: Aj 99 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7615 (tp) REVERT: Aj 151 ASN cc_start: 0.8669 (m-40) cc_final: 0.8129 (m-40) REVERT: Aj 173 MET cc_start: 0.8372 (tmm) cc_final: 0.8055 (tmm) REVERT: Aj 201 ASP cc_start: 0.8987 (t0) cc_final: 0.8616 (t0) REVERT: Ak 72 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: Ak 151 ASN cc_start: 0.8584 (m110) cc_final: 0.8372 (m110) REVERT: Ak 173 MET cc_start: 0.8590 (tmm) cc_final: 0.8205 (tmm) REVERT: Al 72 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: Al 77 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8333 (tm-30) REVERT: Al 99 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7616 (tp) REVERT: Al 151 ASN cc_start: 0.8663 (m-40) cc_final: 0.8120 (m-40) REVERT: Al 173 MET cc_start: 0.8375 (tmm) cc_final: 0.8059 (tmm) REVERT: Al 201 ASP cc_start: 0.8942 (t0) cc_final: 0.8550 (t0) REVERT: Al 220 MET cc_start: 0.5049 (mmm) cc_final: 0.4628 (mmm) REVERT: Am 72 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: Am 121 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: Am 151 ASN cc_start: 0.8620 (m110) cc_final: 0.8417 (m110) REVERT: Am 173 MET cc_start: 0.8581 (tmm) cc_final: 0.8207 (tmm) REVERT: An 77 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7914 (tm-30) REVERT: An 99 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7617 (tp) REVERT: An 151 ASN cc_start: 0.8660 (m-40) cc_final: 0.8115 (m-40) REVERT: An 173 MET cc_start: 0.8374 (tmm) cc_final: 0.8059 (tmm) REVERT: An 201 ASP cc_start: 0.8980 (t0) cc_final: 0.8588 (t0) REVERT: An 220 MET cc_start: 0.5055 (mmm) cc_final: 0.4638 (mmm) REVERT: Ao 72 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: Ao 151 ASN cc_start: 0.8592 (m110) cc_final: 0.8381 (m110) REVERT: Ao 173 MET cc_start: 0.8558 (tmm) cc_final: 0.8186 (tmm) REVERT: Ap 72 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: Ap 77 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8324 (tm-30) REVERT: Ap 99 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7617 (tp) REVERT: Ap 151 ASN cc_start: 0.8669 (m-40) cc_final: 0.8129 (m-40) REVERT: Ap 173 MET cc_start: 0.8370 (tmm) cc_final: 0.8055 (tmm) REVERT: Ap 201 ASP cc_start: 0.8972 (t0) cc_final: 0.8566 (t0) REVERT: Aq 72 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: Aq 142 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: Aq 160 MET cc_start: 0.9162 (mmm) cc_final: 0.8880 (mmp) REVERT: Aq 173 MET cc_start: 0.8810 (tmm) cc_final: 0.8496 (tmm) REVERT: Aq 181 MET cc_start: 0.8314 (tpp) cc_final: 0.7619 (tpp) REVERT: Aq 201 ASP cc_start: 0.8909 (t0) cc_final: 0.8431 (t0) REVERT: Ar 72 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: Ar 99 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7339 (tp) REVERT: Ar 129 ASN cc_start: 0.8653 (m-40) cc_final: 0.8361 (m-40) REVERT: Ar 142 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: Ar 190 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7356 (tt) REVERT: Ar 201 ASP cc_start: 0.8774 (t0) cc_final: 0.8555 (t0) REVERT: As 72 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: As 99 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7448 (tp) REVERT: As 101 TYR cc_start: 0.8413 (m-10) cc_final: 0.8153 (m-10) REVERT: As 142 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: As 151 ASN cc_start: 0.8514 (m-40) cc_final: 0.8285 (m-40) REVERT: As 173 MET cc_start: 0.8413 (tmm) cc_final: 0.8077 (tmm) REVERT: As 201 ASP cc_start: 0.8910 (t0) cc_final: 0.8437 (t0) REVERT: At 72 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: At 99 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7343 (tp) REVERT: At 129 ASN cc_start: 0.8664 (m-40) cc_final: 0.8375 (m-40) REVERT: At 142 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: At 201 ASP cc_start: 0.8793 (t0) cc_final: 0.8589 (t0) REVERT: Au 72 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: Au 99 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7439 (tp) REVERT: Au 142 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: Au 160 MET cc_start: 0.9175 (mmm) cc_final: 0.8890 (mmp) REVERT: Au 173 MET cc_start: 0.8418 (tmm) cc_final: 0.8074 (tmm) REVERT: Au 181 MET cc_start: 0.8317 (tpp) cc_final: 0.7609 (tpp) REVERT: Au 201 ASP cc_start: 0.8918 (t0) cc_final: 0.8437 (t0) REVERT: Av 72 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: Av 99 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7341 (tp) REVERT: Av 129 ASN cc_start: 0.8661 (m-40) cc_final: 0.8371 (m-40) REVERT: Av 142 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: Av 201 ASP cc_start: 0.8766 (t0) cc_final: 0.8553 (t0) REVERT: Aw 55 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7975 (mtp85) REVERT: Aw 72 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: Aw 99 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7459 (tp) REVERT: Aw 142 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: Aw 151 ASN cc_start: 0.8524 (m-40) cc_final: 0.8273 (m-40) REVERT: Aw 173 MET cc_start: 0.8407 (tmm) cc_final: 0.8073 (tmm) REVERT: Aw 201 ASP cc_start: 0.8905 (t0) cc_final: 0.8433 (t0) REVERT: Ax 72 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: Ax 99 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7336 (tp) REVERT: Ax 129 ASN cc_start: 0.8651 (m-40) cc_final: 0.8361 (m-40) REVERT: Ax 142 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: Ax 190 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7370 (tt) REVERT: Ax 201 ASP cc_start: 0.8774 (t0) cc_final: 0.8554 (t0) outliers start: 148 outliers final: 71 residues processed: 1115 average time/residue: 0.1968 time to fit residues: 352.1108 Evaluate side-chains 1153 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1036 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 142 GLU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 142 GLU Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 121 GLU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 142 GLU Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 121 GLU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 121 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 110 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 121 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 116 MET Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 371 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 422 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ag 76 GLN Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107936 restraints weight = 46850.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.112293 restraints weight = 22985.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.115300 restraints weight = 14191.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117351 restraints weight = 10019.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118852 restraints weight = 7771.769| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35832 Z= 0.169 Angle : 0.611 11.997 48576 Z= 0.299 Chirality : 0.038 0.122 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.388 23.902 4824 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.56 % Allowed : 20.89 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.13), residues: 4296 helix: 0.37 (0.12), residues: 1800 sheet: 0.29 (0.29), residues: 288 loop : -1.03 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAg 157 TYR 0.020 0.001 TYRAj 73 PHE 0.011 0.002 PHEAb 163 TRP 0.010 0.002 TRPAe 93 HIS 0.001 0.000 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00399 (35832) covalent geometry : angle 0.61127 (48576) hydrogen bonds : bond 0.03550 ( 1272) hydrogen bonds : angle 4.97423 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1039 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.7056 (ptt) cc_final: 0.6517 (ptt) REVERT: Aa 99 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7431 (tp) REVERT: Aa 112 MET cc_start: 0.9030 (mmt) cc_final: 0.8778 (mmt) REVERT: Aa 201 ASP cc_start: 0.8904 (t0) cc_final: 0.8515 (t0) REVERT: Ab 54 MET cc_start: 0.6748 (ptt) cc_final: 0.6484 (ptt) REVERT: Ab 77 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8314 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7487 (tp) REVERT: Ab 201 ASP cc_start: 0.8866 (t0) cc_final: 0.8398 (t0) REVERT: Ac 54 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6244 (ptt) REVERT: Ac 99 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7401 (tp) REVERT: Ac 108 MET cc_start: 0.8966 (tpt) cc_final: 0.8714 (tpp) REVERT: Ac 112 MET cc_start: 0.9031 (mmt) cc_final: 0.8789 (mmt) REVERT: Ac 194 SER cc_start: 0.8790 (t) cc_final: 0.8534 (t) REVERT: Ac 201 ASP cc_start: 0.8890 (t0) cc_final: 0.8470 (t0) REVERT: Ad 77 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8290 (tm-30) REVERT: Ad 99 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7426 (tp) REVERT: Ad 201 ASP cc_start: 0.8864 (t0) cc_final: 0.8403 (t0) REVERT: Ae 99 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7378 (tp) REVERT: Ae 112 MET cc_start: 0.9230 (mmt) cc_final: 0.8923 (mmt) REVERT: Ae 201 ASP cc_start: 0.8900 (t0) cc_final: 0.8496 (t0) REVERT: Af 54 MET cc_start: 0.7220 (ptt) cc_final: 0.6701 (ptt) REVERT: Af 99 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7483 (tp) REVERT: Af 190 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7488 (tt) REVERT: Af 201 ASP cc_start: 0.8868 (t0) cc_final: 0.8419 (t0) REVERT: Ag 54 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6241 (ptt) REVERT: Ag 77 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8264 (tm-30) REVERT: Ag 99 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7431 (tp) REVERT: Ag 201 ASP cc_start: 0.8895 (t0) cc_final: 0.8499 (t0) REVERT: Ah 54 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6684 (ptt) REVERT: Ah 99 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7477 (tp) REVERT: Ah 201 ASP cc_start: 0.8910 (t0) cc_final: 0.8468 (t0) REVERT: Ai 56 MET cc_start: 0.7818 (mmt) cc_final: 0.7266 (mmt) REVERT: Ai 72 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: Ai 99 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7391 (tp) REVERT: Ai 121 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: Ai 151 ASN cc_start: 0.8622 (m110) cc_final: 0.8079 (m-40) REVERT: Ai 173 MET cc_start: 0.8488 (tmm) cc_final: 0.8224 (tmm) REVERT: Aj 56 MET cc_start: 0.7619 (mmt) cc_final: 0.7019 (mmp) REVERT: Aj 72 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: Aj 77 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8113 (tm-30) REVERT: Aj 99 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7594 (tp) REVERT: Aj 151 ASN cc_start: 0.8652 (m-40) cc_final: 0.8020 (m-40) REVERT: Aj 173 MET cc_start: 0.8359 (tmm) cc_final: 0.8071 (tmm) REVERT: Aj 201 ASP cc_start: 0.8988 (t0) cc_final: 0.8604 (t0) REVERT: Ak 56 MET cc_start: 0.7810 (mmt) cc_final: 0.7269 (mmt) REVERT: Ak 72 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: Ak 151 ASN cc_start: 0.8570 (m110) cc_final: 0.8044 (m-40) REVERT: Ak 173 MET cc_start: 0.8529 (tmm) cc_final: 0.8167 (tmm) REVERT: Al 72 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: Al 99 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7598 (tp) REVERT: Al 151 ASN cc_start: 0.8656 (m-40) cc_final: 0.8018 (m-40) REVERT: Al 173 MET cc_start: 0.8360 (tmm) cc_final: 0.8042 (tmm) REVERT: Al 201 ASP cc_start: 0.8957 (t0) cc_final: 0.8580 (t0) REVERT: Am 56 MET cc_start: 0.7679 (mmt) cc_final: 0.7266 (mmt) REVERT: Am 72 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: Am 99 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7390 (tp) REVERT: Am 121 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: Am 151 ASN cc_start: 0.8618 (m110) cc_final: 0.8077 (m-40) REVERT: Am 173 MET cc_start: 0.8537 (tmm) cc_final: 0.8173 (tmm) REVERT: An 56 MET cc_start: 0.7699 (mmt) cc_final: 0.7045 (mmp) REVERT: An 72 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: An 77 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7882 (tm-30) REVERT: An 99 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7599 (tp) REVERT: An 151 ASN cc_start: 0.8661 (m-40) cc_final: 0.8022 (m-40) REVERT: An 173 MET cc_start: 0.8346 (tmm) cc_final: 0.8051 (tmm) REVERT: An 201 ASP cc_start: 0.8957 (t0) cc_final: 0.8588 (t0) REVERT: Ao 72 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: Ao 151 ASN cc_start: 0.8579 (m110) cc_final: 0.8052 (m-40) REVERT: Ao 173 MET cc_start: 0.8516 (tmm) cc_final: 0.8162 (tmm) REVERT: Ap 72 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: Ap 99 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (tp) REVERT: Ap 151 ASN cc_start: 0.8666 (m-40) cc_final: 0.8067 (m-40) REVERT: Ap 173 MET cc_start: 0.8338 (tmm) cc_final: 0.8041 (tmm) REVERT: Ap 190 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7751 (tt) REVERT: Ap 201 ASP cc_start: 0.8960 (t0) cc_final: 0.8591 (t0) REVERT: Aq 72 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: Aq 160 MET cc_start: 0.9206 (mmm) cc_final: 0.8936 (mmp) REVERT: Aq 173 MET cc_start: 0.8716 (tmm) cc_final: 0.8487 (tmm) REVERT: Aq 181 MET cc_start: 0.8282 (tpp) cc_final: 0.7560 (tpp) REVERT: Aq 201 ASP cc_start: 0.8871 (t0) cc_final: 0.8373 (t0) REVERT: Ar 72 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: Ar 99 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7382 (tp) REVERT: Ar 129 ASN cc_start: 0.8644 (m-40) cc_final: 0.8373 (m-40) REVERT: Ar 142 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: Ar 190 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7326 (tt) REVERT: Ar 201 ASP cc_start: 0.8809 (t0) cc_final: 0.8592 (t0) REVERT: As 72 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: As 99 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7443 (tp) REVERT: As 142 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: As 151 ASN cc_start: 0.8509 (m-40) cc_final: 0.8284 (m-40) REVERT: As 173 MET cc_start: 0.8365 (tmm) cc_final: 0.8039 (tmm) REVERT: As 201 ASP cc_start: 0.8884 (t0) cc_final: 0.8388 (t0) REVERT: At 72 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: At 76 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8285 (mm110) REVERT: At 99 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7389 (tp) REVERT: At 129 ASN cc_start: 0.8650 (m-40) cc_final: 0.8382 (m-40) REVERT: At 142 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: At 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8628 (t0) REVERT: Au 72 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: Au 99 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7404 (tp) REVERT: Au 160 MET cc_start: 0.9225 (mmm) cc_final: 0.8965 (mmp) REVERT: Au 173 MET cc_start: 0.8372 (tmm) cc_final: 0.8048 (tmm) REVERT: Au 181 MET cc_start: 0.8274 (tpp) cc_final: 0.7577 (tpp) REVERT: Au 201 ASP cc_start: 0.8895 (t0) cc_final: 0.8397 (t0) REVERT: Av 72 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: Av 76 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8429 (mm110) REVERT: Av 99 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7395 (tp) REVERT: Av 129 ASN cc_start: 0.8658 (m-40) cc_final: 0.8379 (m-40) REVERT: Av 142 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: Av 190 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7345 (tt) REVERT: Av 201 ASP cc_start: 0.8792 (t0) cc_final: 0.8571 (t0) REVERT: Aw 55 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8011 (mtp85) REVERT: Aw 72 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: Aw 99 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7427 (tp) REVERT: Aw 142 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: Aw 151 ASN cc_start: 0.8514 (m-40) cc_final: 0.8294 (m-40) REVERT: Aw 173 MET cc_start: 0.8359 (tmm) cc_final: 0.8039 (tmm) REVERT: Aw 201 ASP cc_start: 0.8882 (t0) cc_final: 0.8390 (t0) REVERT: Ax 72 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: Ax 76 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8306 (mm110) REVERT: Ax 99 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7354 (tp) REVERT: Ax 129 ASN cc_start: 0.8643 (m-40) cc_final: 0.8375 (m-40) REVERT: Ax 142 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: Ax 190 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7333 (tt) REVERT: Ax 201 ASP cc_start: 0.8807 (t0) cc_final: 0.8594 (t0) outliers start: 136 outliers final: 72 residues processed: 1095 average time/residue: 0.1998 time to fit residues: 350.9693 Evaluate side-chains 1163 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1038 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 142 GLU Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 142 GLU Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 142 GLU Chi-restraints excluded: chain Af residue 190 LEU Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 121 GLU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 142 GLU Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 121 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 135 MET Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 110 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 121 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 135 MET Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 135 MET Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 116 MET Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 108 MET Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Av residue 190 LEU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 116 MET Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 409 optimal weight: 0.0970 chunk 231 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ag 76 GLN Aj 69 HIS Aj 76 GLN Al 69 HIS An 69 HIS Ap 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.136550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113935 restraints weight = 46429.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118447 restraints weight = 22680.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121549 restraints weight = 13923.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123704 restraints weight = 9774.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125253 restraints weight = 7486.614| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35832 Z= 0.103 Angle : 0.584 12.493 48576 Z= 0.281 Chirality : 0.037 0.124 5304 Planarity : 0.006 0.059 6288 Dihedral : 4.188 23.025 4824 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.01 % Allowed : 21.15 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.13), residues: 4296 helix: 0.67 (0.12), residues: 1800 sheet: 0.58 (0.28), residues: 288 loop : -0.92 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAa 157 TYR 0.021 0.001 TYRAn 73 PHE 0.007 0.001 PHEAc 163 TRP 0.017 0.002 TRPAv 93 HIS 0.002 0.000 HISAc 162 Details of bonding type rmsd covalent geometry : bond 0.00251 (35832) covalent geometry : angle 0.58418 (48576) hydrogen bonds : bond 0.02907 ( 1272) hydrogen bonds : angle 4.62801 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1022 time to evaluate : 0.916 Fit side-chains REVERT: Aa 54 MET cc_start: 0.6869 (ptt) cc_final: 0.6396 (ptt) REVERT: Aa 55 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8033 (mmm-85) REVERT: Aa 76 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8249 (mm-40) REVERT: Aa 99 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7339 (tp) REVERT: Aa 201 ASP cc_start: 0.8916 (t0) cc_final: 0.8648 (t0) REVERT: Ab 76 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8218 (mm110) REVERT: Ab 99 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7433 (tp) REVERT: Ab 201 ASP cc_start: 0.8871 (t0) cc_final: 0.8406 (t0) REVERT: Ac 54 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6255 (ptt) REVERT: Ac 76 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8391 (mm-40) REVERT: Ac 99 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7370 (tp) REVERT: Ac 112 MET cc_start: 0.8901 (mmt) cc_final: 0.8688 (mmt) REVERT: Ac 194 SER cc_start: 0.8738 (t) cc_final: 0.8527 (t) REVERT: Ac 201 ASP cc_start: 0.8852 (t0) cc_final: 0.8400 (t0) REVERT: Ad 60 LYS cc_start: 0.8962 (mttp) cc_final: 0.8762 (mmtp) REVERT: Ad 99 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7467 (tp) REVERT: Ad 201 ASP cc_start: 0.8871 (t0) cc_final: 0.8412 (t0) REVERT: Ae 56 MET cc_start: 0.7389 (mmt) cc_final: 0.6949 (mmp) REVERT: Ae 76 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8383 (mm-40) REVERT: Ae 99 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7346 (tp) REVERT: Ae 112 MET cc_start: 0.9159 (mmt) cc_final: 0.8921 (mmt) REVERT: Ae 201 ASP cc_start: 0.8898 (t0) cc_final: 0.8574 (t0) REVERT: Af 54 MET cc_start: 0.7144 (ptt) cc_final: 0.6650 (ptt) REVERT: Af 60 LYS cc_start: 0.8949 (mttp) cc_final: 0.8732 (mmtp) REVERT: Af 99 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7462 (tp) REVERT: Af 201 ASP cc_start: 0.8871 (t0) cc_final: 0.8432 (t0) REVERT: Ag 54 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6327 (ptt) REVERT: Ag 55 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8240 (mmm-85) REVERT: Ag 76 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8051 (mm-40) REVERT: Ag 99 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7332 (tp) REVERT: Ag 201 ASP cc_start: 0.8881 (t0) cc_final: 0.8559 (t0) REVERT: Ah 54 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6494 (ptt) REVERT: Ah 60 LYS cc_start: 0.8940 (mttp) cc_final: 0.8733 (mmtp) REVERT: Ah 201 ASP cc_start: 0.8888 (t0) cc_final: 0.8456 (t0) REVERT: Ai 72 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: Ai 151 ASN cc_start: 0.8519 (m110) cc_final: 0.7941 (m110) REVERT: Ai 173 MET cc_start: 0.8453 (tmm) cc_final: 0.8107 (tmm) REVERT: Aj 56 MET cc_start: 0.7590 (mmt) cc_final: 0.6829 (mmp) REVERT: Aj 72 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: Aj 77 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8141 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8640 (m-40) cc_final: 0.7926 (m110) REVERT: Aj 173 MET cc_start: 0.8245 (tmm) cc_final: 0.7878 (tmm) REVERT: Aj 201 ASP cc_start: 0.8935 (t0) cc_final: 0.8540 (t0) REVERT: Aj 220 MET cc_start: 0.5137 (mmm) cc_final: 0.4823 (mmm) REVERT: Ak 72 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: Ak 151 ASN cc_start: 0.8446 (m110) cc_final: 0.7857 (m110) REVERT: Ak 173 MET cc_start: 0.8456 (tmm) cc_final: 0.8025 (tmm) REVERT: Al 72 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: Al 99 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7641 (tp) REVERT: Al 151 ASN cc_start: 0.8624 (m-40) cc_final: 0.7908 (m110) REVERT: Al 173 MET cc_start: 0.8258 (tmm) cc_final: 0.7876 (tmm) REVERT: Al 201 ASP cc_start: 0.8924 (t0) cc_final: 0.8522 (t0) REVERT: Al 220 MET cc_start: 0.5136 (mmm) cc_final: 0.4831 (mmm) REVERT: Am 56 MET cc_start: 0.7569 (mmt) cc_final: 0.7140 (mmt) REVERT: Am 72 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: Am 151 ASN cc_start: 0.8509 (m110) cc_final: 0.7939 (m110) REVERT: Am 173 MET cc_start: 0.8463 (tmm) cc_final: 0.8025 (tmm) REVERT: An 56 MET cc_start: 0.7589 (mmt) cc_final: 0.6994 (mmp) REVERT: An 72 GLU cc_start: 0.8579 (tt0) cc_final: 0.8256 (tt0) REVERT: An 77 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7761 (tm-30) REVERT: An 99 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7652 (tp) REVERT: An 151 ASN cc_start: 0.8635 (m-40) cc_final: 0.7917 (m110) REVERT: An 173 MET cc_start: 0.8255 (tmm) cc_final: 0.7885 (tmm) REVERT: An 201 ASP cc_start: 0.8925 (t0) cc_final: 0.8545 (t0) REVERT: An 220 MET cc_start: 0.5137 (mmm) cc_final: 0.4828 (mmm) REVERT: Ao 72 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: Ao 99 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7315 (tp) REVERT: Ao 151 ASN cc_start: 0.8438 (m110) cc_final: 0.7843 (m110) REVERT: Ao 173 MET cc_start: 0.8443 (tmm) cc_final: 0.8008 (tmm) REVERT: Ao 201 ASP cc_start: 0.8896 (t0) cc_final: 0.8516 (t0) REVERT: Ap 56 MET cc_start: 0.7302 (mmt) cc_final: 0.6935 (mmp) REVERT: Ap 72 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: Ap 99 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7646 (tp) REVERT: Ap 151 ASN cc_start: 0.8635 (m-40) cc_final: 0.7925 (m110) REVERT: Ap 173 MET cc_start: 0.8249 (tmm) cc_final: 0.7875 (tmm) REVERT: Ap 190 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7822 (tt) REVERT: Ap 201 ASP cc_start: 0.8929 (t0) cc_final: 0.8528 (t0) REVERT: Aq 72 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: Aq 173 MET cc_start: 0.8534 (tmm) cc_final: 0.8290 (tmm) REVERT: Aq 181 MET cc_start: 0.8192 (tpp) cc_final: 0.7536 (tpp) REVERT: Aq 201 ASP cc_start: 0.8892 (t0) cc_final: 0.8374 (t0) REVERT: Ar 72 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: Ar 99 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7275 (tp) REVERT: Ar 129 ASN cc_start: 0.8642 (m-40) cc_final: 0.8387 (m-40) REVERT: Ar 134 MET cc_start: 0.7023 (ttp) cc_final: 0.6816 (ttp) REVERT: Ar 142 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: Ar 181 MET cc_start: 0.8043 (tpp) cc_final: 0.7830 (tpp) REVERT: Ar 201 ASP cc_start: 0.8849 (t0) cc_final: 0.8600 (t0) REVERT: As 72 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: As 99 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7423 (tp) REVERT: As 142 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: As 201 ASP cc_start: 0.8913 (t0) cc_final: 0.8376 (t0) REVERT: At 72 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: At 99 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7306 (tp) REVERT: At 129 ASN cc_start: 0.8648 (m-40) cc_final: 0.8394 (m-40) REVERT: At 134 MET cc_start: 0.7037 (ttp) cc_final: 0.6805 (ttp) REVERT: At 142 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: At 201 ASP cc_start: 0.8850 (t0) cc_final: 0.8613 (t0) REVERT: Au 72 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: Au 99 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7422 (tp) REVERT: Au 181 MET cc_start: 0.8189 (tpp) cc_final: 0.7567 (tpp) REVERT: Au 201 ASP cc_start: 0.8893 (t0) cc_final: 0.8377 (t0) REVERT: Av 72 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: Av 99 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7271 (tp) REVERT: Av 129 ASN cc_start: 0.8648 (m-40) cc_final: 0.8399 (m-40) REVERT: Av 134 MET cc_start: 0.7031 (ttp) cc_final: 0.6801 (ttp) REVERT: Av 142 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: Av 201 ASP cc_start: 0.8845 (t0) cc_final: 0.8604 (t0) REVERT: Aw 55 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8023 (mtp85) REVERT: Aw 72 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: Aw 99 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7372 (tp) REVERT: Aw 142 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: Aw 201 ASP cc_start: 0.8907 (t0) cc_final: 0.8371 (t0) REVERT: Ax 72 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: Ax 99 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7275 (tp) REVERT: Ax 129 ASN cc_start: 0.8637 (m-40) cc_final: 0.8384 (m-40) REVERT: Ax 134 MET cc_start: 0.7159 (ttp) cc_final: 0.6923 (ttp) REVERT: Ax 142 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: Ax 181 MET cc_start: 0.8047 (tpp) cc_final: 0.7834 (tpp) REVERT: Ax 201 ASP cc_start: 0.8847 (t0) cc_final: 0.8617 (t0) outliers start: 115 outliers final: 57 residues processed: 1075 average time/residue: 0.1993 time to fit residues: 343.8338 Evaluate side-chains 1112 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1012 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 54 MET Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 110 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 110 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 108 MET Chi-restraints excluded: chain Av residue 110 THR Chi-restraints excluded: chain Av residue 116 MET Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 110 THR Chi-restraints excluded: chain Ax residue 116 MET Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 363 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 76 GLN Ah 76 GLN Ai 175 ASN Ak 175 ASN Al 76 GLN Am 175 ASN An 69 HIS An 76 GLN Ap 69 HIS Ap 76 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.131772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108859 restraints weight = 46607.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113247 restraints weight = 23082.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116264 restraints weight = 14335.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118385 restraints weight = 10164.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.119833 restraints weight = 7857.215| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35832 Z= 0.169 Angle : 0.624 12.608 48576 Z= 0.301 Chirality : 0.038 0.121 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.250 22.047 4824 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.96 % Allowed : 21.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.13), residues: 4296 helix: 0.62 (0.12), residues: 1800 sheet: 0.49 (0.29), residues: 288 loop : -0.92 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 157 TYR 0.023 0.001 TYRAd 73 PHE 0.012 0.002 PHEAb 163 TRP 0.008 0.002 TRPAu 93 HIS 0.001 0.000 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00399 (35832) covalent geometry : angle 0.62403 (48576) hydrogen bonds : bond 0.03396 ( 1272) hydrogen bonds : angle 4.76896 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6460.23 seconds wall clock time: 111 minutes 35.16 seconds (6695.16 seconds total)