Starting phenix.real_space_refine on Sun Feb 8 11:44:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7z_53800/02_2026/9r7z_53800.map" } resolution = 3.92 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= 0.024 sd= 0.186 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 390 5.16 5 C 28440 2.51 5 N 7770 2.21 5 O 8310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 270 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44910 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 174} 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, Ay, Az, Ba, Bb, Bc, Bd Time building chain proxies: 3.14, per 1000 atoms: 0.07 Number of scatterers: 44910 At special positions: 0 Unit cell: (166.775, 166.775, 180.117, 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 390 16.00 O 8310 8.00 N 7770 7.00 C 28440 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: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10740 Finding SS restraints... Secondary structure from input PDB file: 300 helices and 30 sheets defined 57.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'Aa' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAa 74 " --> pdb=" O ASPAa 70 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAa 82 " --> pdb=" O LYSAa 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAa 83 " --> pdb=" O GLNAa 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 78 through 83' Processing helix chain 'Aa' and resid 88 through 103 Processing helix chain 'Aa' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAa 112 " --> pdb=" O SERAa 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAa 115 " --> pdb=" O GLUAa 111 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAa 151 " --> pdb=" O LEUAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 158 through 163 Processing helix chain 'Aa' and resid 165 through 177 Processing helix chain 'Aa' and resid 184 through 191 Processing helix chain 'Aa' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAa 199 " --> pdb=" O SERAa 196 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAa 220 " --> pdb=" O LYSAa 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAa 227 " --> pdb=" O LYSAa 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAa 228 " --> pdb=" O ALAAa 224 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAb 74 " --> pdb=" O ASPAb 70 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAb 82 " --> pdb=" O LYSAb 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAb 83 " --> pdb=" O GLNAb 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 78 through 83' Processing helix chain 'Ab' and resid 88 through 103 Processing helix chain 'Ab' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAb 112 " --> pdb=" O SERAb 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAb 115 " --> pdb=" O GLUAb 111 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAb 151 " --> pdb=" O LEUAb 147 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 158 through 163 Processing helix chain 'Ab' and resid 165 through 177 Processing helix chain 'Ab' and resid 184 through 191 Processing helix chain 'Ab' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAb 199 " --> pdb=" O SERAb 196 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAb 220 " --> pdb=" O LYSAb 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAb 227 " --> pdb=" O LYSAb 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAb 228 " --> pdb=" O ALAAb 224 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAc 74 " --> pdb=" O ASPAc 70 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAc 82 " --> pdb=" O LYSAc 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAc 83 " --> pdb=" O GLNAc 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 78 through 83' Processing helix chain 'Ac' and resid 88 through 103 Processing helix chain 'Ac' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAc 112 " --> pdb=" O SERAc 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAc 115 " --> pdb=" O GLUAc 111 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAc 151 " --> pdb=" O LEUAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 158 through 163 Processing helix chain 'Ac' and resid 165 through 177 Processing helix chain 'Ac' and resid 184 through 191 Processing helix chain 'Ac' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAc 199 " --> pdb=" O SERAc 196 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAc 220 " --> pdb=" O LYSAc 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAc 227 " --> pdb=" O LYSAc 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAc 228 " --> pdb=" O ALAAc 224 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAd 74 " --> pdb=" O ASPAd 70 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAd 82 " --> pdb=" O LYSAd 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAd 83 " --> pdb=" O GLNAd 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 78 through 83' Processing helix chain 'Ad' and resid 88 through 103 Processing helix chain 'Ad' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAd 112 " --> pdb=" O SERAd 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAd 115 " --> pdb=" O GLUAd 111 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAd 151 " --> pdb=" O LEUAd 147 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 158 through 163 Processing helix chain 'Ad' and resid 165 through 177 Processing helix chain 'Ad' and resid 184 through 191 Processing helix chain 'Ad' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAd 199 " --> pdb=" O SERAd 196 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAd 220 " --> pdb=" O LYSAd 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAd 227 " --> pdb=" O LYSAd 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAd 228 " --> pdb=" O ALAAd 224 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAe 74 " --> pdb=" O ASPAe 70 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAe 82 " --> pdb=" O LYSAe 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAe 83 " --> pdb=" O GLNAe 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 78 through 83' Processing helix chain 'Ae' and resid 88 through 103 Processing helix chain 'Ae' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAe 115 " --> pdb=" O GLUAe 111 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAe 151 " --> pdb=" O LEUAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 158 through 163 Processing helix chain 'Ae' and resid 165 through 177 Processing helix chain 'Ae' and resid 184 through 191 Processing helix chain 'Ae' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAe 199 " --> pdb=" O SERAe 196 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAe 220 " --> pdb=" O LYSAe 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAe 227 " --> pdb=" O LYSAe 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAe 228 " --> pdb=" O ALAAe 224 " (cutoff:3.500A) Processing helix chain 'Af' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAf 74 " --> pdb=" O ASPAf 70 " (cutoff:3.500A) Processing helix chain 'Af' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAf 82 " --> pdb=" O LYSAf 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAf 83 " --> pdb=" O GLNAf 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Af' and resid 78 through 83' Processing helix chain 'Af' and resid 88 through 103 Processing helix chain 'Af' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAf 112 " --> pdb=" O SERAf 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAf 115 " --> pdb=" O GLUAf 111 " (cutoff:3.500A) Processing helix chain 'Af' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAf 151 " --> pdb=" O LEUAf 147 " (cutoff:3.500A) Processing helix chain 'Af' and resid 158 through 163 Processing helix chain 'Af' and resid 165 through 177 Processing helix chain 'Af' and resid 184 through 191 Processing helix chain 'Af' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAf 199 " --> pdb=" O SERAf 196 " (cutoff:3.500A) Processing helix chain 'Af' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAf 220 " --> pdb=" O LYSAf 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAf 227 " --> pdb=" O LYSAf 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAf 228 " --> pdb=" O ALAAf 224 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAg 74 " --> pdb=" O ASPAg 70 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAg 82 " --> pdb=" O LYSAg 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAg 83 " --> pdb=" O GLNAg 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 78 through 83' Processing helix chain 'Ag' and resid 88 through 103 Processing helix chain 'Ag' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAg 112 " --> pdb=" O SERAg 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAg 115 " --> pdb=" O GLUAg 111 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAg 151 " --> pdb=" O LEUAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 158 through 163 Processing helix chain 'Ag' and resid 165 through 177 Processing helix chain 'Ag' and resid 184 through 191 Processing helix chain 'Ag' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAg 199 " --> pdb=" O SERAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAg 220 " --> pdb=" O LYSAg 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAg 227 " --> pdb=" O LYSAg 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAg 228 " --> pdb=" O ALAAg 224 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAh 74 " --> pdb=" O ASPAh 70 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAh 82 " --> pdb=" O LYSAh 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAh 83 " --> pdb=" O GLNAh 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 78 through 83' Processing helix chain 'Ah' and resid 88 through 103 Processing helix chain 'Ah' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAh 112 " --> pdb=" O SERAh 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAh 115 " --> pdb=" O GLUAh 111 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAh 151 " --> pdb=" O LEUAh 147 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 158 through 163 Processing helix chain 'Ah' and resid 165 through 177 Processing helix chain 'Ah' and resid 184 through 191 Processing helix chain 'Ah' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAh 199 " --> pdb=" O SERAh 196 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAh 220 " --> pdb=" O LYSAh 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAh 227 " --> pdb=" O LYSAh 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAh 228 " --> pdb=" O ALAAh 224 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAi 74 " --> pdb=" O ASPAi 70 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAi 82 " --> pdb=" O LYSAi 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAi 83 " --> pdb=" O GLNAi 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ai' and resid 78 through 83' Processing helix chain 'Ai' and resid 88 through 103 Processing helix chain 'Ai' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAi 112 " --> pdb=" O SERAi 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAi 115 " --> pdb=" O GLUAi 111 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAi 151 " --> pdb=" O LEUAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 158 through 163 Processing helix chain 'Ai' and resid 165 through 177 Processing helix chain 'Ai' and resid 184 through 191 Processing helix chain 'Ai' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAi 199 " --> pdb=" O SERAi 196 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAi 220 " --> pdb=" O LYSAi 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAi 227 " --> pdb=" O LYSAi 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAi 228 " --> pdb=" O ALAAi 224 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAj 74 " --> pdb=" O ASPAj 70 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAj 82 " --> pdb=" O LYSAj 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAj 83 " --> pdb=" O GLNAj 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aj' and resid 78 through 83' Processing helix chain 'Aj' and resid 88 through 103 Processing helix chain 'Aj' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAj 112 " --> pdb=" O SERAj 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAj 115 " --> pdb=" O GLUAj 111 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAj 151 " --> pdb=" O LEUAj 147 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 158 through 163 Processing helix chain 'Aj' and resid 165 through 177 Processing helix chain 'Aj' and resid 184 through 191 Processing helix chain 'Aj' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAj 199 " --> pdb=" O SERAj 196 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAj 220 " --> pdb=" O LYSAj 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAj 227 " --> pdb=" O LYSAj 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAj 228 " --> pdb=" O ALAAj 224 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 68 through 74 removed outlier: 3.655A pdb=" N SERAk 74 " --> pdb=" O ASPAk 70 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAk 82 " --> pdb=" O LYSAk 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAk 83 " --> pdb=" O GLNAk 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 78 through 83' Processing helix chain 'Ak' and resid 88 through 103 Processing helix chain 'Ak' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAk 112 " --> pdb=" O SERAk 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAk 115 " --> pdb=" O GLUAk 111 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAk 151 " --> pdb=" O LEUAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 158 through 163 Processing helix chain 'Ak' and resid 165 through 177 Processing helix chain 'Ak' and resid 184 through 191 Processing helix chain 'Ak' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAk 199 " --> pdb=" O SERAk 196 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAk 220 " --> pdb=" O LYSAk 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAk 227 " --> pdb=" O LYSAk 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAk 228 " --> pdb=" O ALAAk 224 " (cutoff:3.500A) Processing helix chain 'Al' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAl 74 " --> pdb=" O ASPAl 70 " (cutoff:3.500A) Processing helix chain 'Al' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAl 82 " --> pdb=" O LYSAl 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAl 83 " --> pdb=" O GLNAl 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Al' and resid 78 through 83' Processing helix chain 'Al' and resid 88 through 103 Processing helix chain 'Al' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAl 112 " --> pdb=" O SERAl 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAl 115 " --> pdb=" O GLUAl 111 " (cutoff:3.500A) Processing helix chain 'Al' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAl 151 " --> pdb=" O LEUAl 147 " (cutoff:3.500A) Processing helix chain 'Al' and resid 158 through 163 Processing helix chain 'Al' and resid 165 through 177 Processing helix chain 'Al' and resid 184 through 191 Processing helix chain 'Al' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAl 199 " --> pdb=" O SERAl 196 " (cutoff:3.500A) Processing helix chain 'Al' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAl 220 " --> pdb=" O LYSAl 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAl 227 " --> pdb=" O LYSAl 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAl 228 " --> pdb=" O ALAAl 224 " (cutoff:3.500A) Processing helix chain 'Am' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAm 74 " --> pdb=" O ASPAm 70 " (cutoff:3.500A) Processing helix chain 'Am' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAm 82 " --> pdb=" O LYSAm 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAm 83 " --> pdb=" O GLNAm 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Am' and resid 78 through 83' Processing helix chain 'Am' and resid 88 through 103 Processing helix chain 'Am' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAm 112 " --> pdb=" O SERAm 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAm 115 " --> pdb=" O GLUAm 111 " (cutoff:3.500A) Processing helix chain 'Am' and resid 147 through 154 removed outlier: 3.563A pdb=" N LEUAm 151 " --> pdb=" O LEUAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 158 through 163 Processing helix chain 'Am' and resid 165 through 177 Processing helix chain 'Am' and resid 184 through 191 Processing helix chain 'Am' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAm 199 " --> pdb=" O SERAm 196 " (cutoff:3.500A) Processing helix chain 'Am' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAm 220 " --> pdb=" O LYSAm 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAm 227 " --> pdb=" O LYSAm 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAm 228 " --> pdb=" O ALAAm 224 " (cutoff:3.500A) Processing helix chain 'An' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAn 74 " --> pdb=" O ASPAn 70 " (cutoff:3.500A) Processing helix chain 'An' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAn 82 " --> pdb=" O LYSAn 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAn 83 " --> pdb=" O GLNAn 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'An' and resid 78 through 83' Processing helix chain 'An' and resid 88 through 103 Processing helix chain 'An' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAn 112 " --> pdb=" O SERAn 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAn 115 " --> pdb=" O GLUAn 111 " (cutoff:3.500A) Processing helix chain 'An' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAn 151 " --> pdb=" O LEUAn 147 " (cutoff:3.500A) Processing helix chain 'An' and resid 158 through 163 Processing helix chain 'An' and resid 165 through 177 Processing helix chain 'An' and resid 184 through 191 Processing helix chain 'An' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAn 199 " --> pdb=" O SERAn 196 " (cutoff:3.500A) Processing helix chain 'An' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAn 220 " --> pdb=" O LYSAn 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAn 227 " --> pdb=" O LYSAn 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAn 228 " --> pdb=" O ALAAn 224 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAo 74 " --> pdb=" O ASPAo 70 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAo 82 " --> pdb=" O LYSAo 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAo 83 " --> pdb=" O GLNAo 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ao' and resid 78 through 83' Processing helix chain 'Ao' and resid 88 through 103 Processing helix chain 'Ao' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAo 112 " --> pdb=" O SERAo 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAo 115 " --> pdb=" O GLUAo 111 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 147 through 154 removed outlier: 3.560A pdb=" N LEUAo 151 " --> pdb=" O LEUAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 158 through 163 Processing helix chain 'Ao' and resid 165 through 177 Processing helix chain 'Ao' and resid 184 through 191 Processing helix chain 'Ao' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAo 199 " --> pdb=" O SERAo 196 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAo 220 " --> pdb=" O LYSAo 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAo 227 " --> pdb=" O LYSAo 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAo 228 " --> pdb=" O ALAAo 224 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAp 74 " --> pdb=" O ASPAp 70 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAp 82 " --> pdb=" O LYSAp 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAp 83 " --> pdb=" O GLNAp 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ap' and resid 78 through 83' Processing helix chain 'Ap' and resid 88 through 103 Processing helix chain 'Ap' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAp 112 " --> pdb=" O SERAp 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASNAp 115 " --> pdb=" O GLUAp 111 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAp 151 " --> pdb=" O LEUAp 147 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 158 through 163 Processing helix chain 'Ap' and resid 165 through 177 Processing helix chain 'Ap' and resid 184 through 191 Processing helix chain 'Ap' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAp 199 " --> pdb=" O SERAp 196 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAp 220 " --> pdb=" O LYSAp 216 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEUAp 227 " --> pdb=" O LYSAp 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAp 228 " --> pdb=" O ALAAp 224 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAq 74 " --> pdb=" O ASPAq 70 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAq 82 " --> pdb=" O LYSAq 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAq 83 " --> pdb=" O GLNAq 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aq' and resid 78 through 83' Processing helix chain 'Aq' and resid 88 through 103 Processing helix chain 'Aq' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAq 112 " --> pdb=" O SERAq 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAq 115 " --> pdb=" O GLUAq 111 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAq 151 " --> pdb=" O LEUAq 147 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 158 through 163 Processing helix chain 'Aq' and resid 165 through 177 Processing helix chain 'Aq' and resid 184 through 191 Processing helix chain 'Aq' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAq 199 " --> pdb=" O SERAq 196 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAq 220 " --> pdb=" O LYSAq 216 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEUAq 227 " --> pdb=" O LYSAq 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAq 228 " --> pdb=" O ALAAq 224 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAr 74 " --> pdb=" O ASPAr 70 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAr 82 " --> pdb=" O LYSAr 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAr 83 " --> pdb=" O GLNAr 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ar' and resid 78 through 83' Processing helix chain 'Ar' and resid 88 through 103 Processing helix chain 'Ar' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAr 112 " --> pdb=" O SERAr 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAr 115 " --> pdb=" O GLUAr 111 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAr 151 " --> pdb=" O LEUAr 147 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 158 through 163 Processing helix chain 'Ar' and resid 165 through 177 Processing helix chain 'Ar' and resid 184 through 191 Processing helix chain 'Ar' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAr 199 " --> pdb=" O SERAr 196 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAr 220 " --> pdb=" O LYSAr 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAr 227 " --> pdb=" O LYSAr 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAr 228 " --> pdb=" O ALAAr 224 " (cutoff:3.500A) Processing helix chain 'As' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAs 74 " --> pdb=" O ASPAs 70 " (cutoff:3.500A) Processing helix chain 'As' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAs 82 " --> pdb=" O LYSAs 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SERAs 83 " --> pdb=" O GLNAs 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'As' and resid 78 through 83' Processing helix chain 'As' and resid 88 through 103 Processing helix chain 'As' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAs 112 " --> pdb=" O SERAs 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASNAs 115 " --> pdb=" O GLUAs 111 " (cutoff:3.500A) Processing helix chain 'As' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAs 151 " --> pdb=" O LEUAs 147 " (cutoff:3.500A) Processing helix chain 'As' and resid 158 through 163 Processing helix chain 'As' and resid 165 through 177 Processing helix chain 'As' and resid 184 through 191 Processing helix chain 'As' and resid 195 through 201 removed outlier: 4.330A pdb=" N ARGAs 199 " --> pdb=" O SERAs 196 " (cutoff:3.500A) Processing helix chain 'As' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAs 220 " --> pdb=" O LYSAs 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAs 227 " --> pdb=" O LYSAs 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAs 228 " --> pdb=" O ALAAs 224 " (cutoff:3.500A) Processing helix chain 'At' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAt 74 " --> pdb=" O ASPAt 70 " (cutoff:3.500A) Processing helix chain 'At' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAt 82 " --> pdb=" O LYSAt 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAt 83 " --> pdb=" O GLNAt 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'At' and resid 78 through 83' Processing helix chain 'At' and resid 88 through 103 Processing helix chain 'At' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAt 112 " --> pdb=" O SERAt 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAt 115 " --> pdb=" O GLUAt 111 " (cutoff:3.500A) Processing helix chain 'At' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAt 151 " --> pdb=" O LEUAt 147 " (cutoff:3.500A) Processing helix chain 'At' and resid 158 through 163 Processing helix chain 'At' and resid 165 through 177 Processing helix chain 'At' and resid 184 through 191 Processing helix chain 'At' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAt 199 " --> pdb=" O SERAt 196 " (cutoff:3.500A) Processing helix chain 'At' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAt 220 " --> pdb=" O LYSAt 216 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEUAt 227 " --> pdb=" O LYSAt 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAt 228 " --> pdb=" O ALAAt 224 " (cutoff:3.500A) Processing helix chain 'Au' and resid 68 through 74 removed outlier: 3.655A pdb=" N SERAu 74 " --> pdb=" O ASPAu 70 " (cutoff:3.500A) Processing helix chain 'Au' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAu 82 " --> pdb=" O LYSAu 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAu 83 " --> pdb=" O GLNAu 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Au' and resid 78 through 83' Processing helix chain 'Au' and resid 88 through 103 Processing helix chain 'Au' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAu 112 " --> pdb=" O SERAu 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAu 115 " --> pdb=" O GLUAu 111 " (cutoff:3.500A) Processing helix chain 'Au' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAu 151 " --> pdb=" O LEUAu 147 " (cutoff:3.500A) Processing helix chain 'Au' and resid 158 through 163 Processing helix chain 'Au' and resid 165 through 177 Processing helix chain 'Au' and resid 184 through 191 Processing helix chain 'Au' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAu 199 " --> pdb=" O SERAu 196 " (cutoff:3.500A) Processing helix chain 'Au' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAu 220 " --> pdb=" O LYSAu 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAu 227 " --> pdb=" O LYSAu 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAu 228 " --> pdb=" O ALAAu 224 " (cutoff:3.500A) Processing helix chain 'Av' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAv 74 " --> pdb=" O ASPAv 70 " (cutoff:3.500A) Processing helix chain 'Av' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAv 82 " --> pdb=" O LYSAv 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAv 83 " --> pdb=" O GLNAv 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Av' and resid 78 through 83' Processing helix chain 'Av' and resid 88 through 103 Processing helix chain 'Av' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAv 112 " --> pdb=" O SERAv 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASNAv 115 " --> pdb=" O GLUAv 111 " (cutoff:3.500A) Processing helix chain 'Av' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAv 151 " --> pdb=" O LEUAv 147 " (cutoff:3.500A) Processing helix chain 'Av' and resid 158 through 163 Processing helix chain 'Av' and resid 165 through 177 Processing helix chain 'Av' and resid 184 through 191 Processing helix chain 'Av' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAv 199 " --> pdb=" O SERAv 196 " (cutoff:3.500A) Processing helix chain 'Av' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAv 220 " --> pdb=" O LYSAv 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAv 227 " --> pdb=" O LYSAv 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAv 228 " --> pdb=" O ALAAv 224 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAw 74 " --> pdb=" O ASPAw 70 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAw 82 " --> pdb=" O LYSAw 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAw 83 " --> pdb=" O GLNAw 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aw' and resid 78 through 83' Processing helix chain 'Aw' and resid 88 through 103 Processing helix chain 'Aw' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAw 112 " --> pdb=" O SERAw 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAw 115 " --> pdb=" O GLUAw 111 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAw 151 " --> pdb=" O LEUAw 147 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 158 through 163 Processing helix chain 'Aw' and resid 165 through 177 Processing helix chain 'Aw' and resid 184 through 191 Processing helix chain 'Aw' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAw 199 " --> pdb=" O SERAw 196 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAw 220 " --> pdb=" O LYSAw 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAw 227 " --> pdb=" O LYSAw 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAw 228 " --> pdb=" O ALAAw 224 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAx 74 " --> pdb=" O ASPAx 70 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAx 82 " --> pdb=" O LYSAx 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAx 83 " --> pdb=" O GLNAx 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ax' and resid 78 through 83' Processing helix chain 'Ax' and resid 88 through 103 Processing helix chain 'Ax' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAx 112 " --> pdb=" O SERAx 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAx 115 " --> pdb=" O GLUAx 111 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 147 through 154 removed outlier: 3.562A pdb=" N LEUAx 151 " --> pdb=" O LEUAx 147 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 158 through 163 Processing helix chain 'Ax' and resid 165 through 177 Processing helix chain 'Ax' and resid 184 through 191 Processing helix chain 'Ax' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGAx 199 " --> pdb=" O SERAx 196 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAx 220 " --> pdb=" O LYSAx 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAx 227 " --> pdb=" O LYSAx 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAx 228 " --> pdb=" O ALAAx 224 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERAy 74 " --> pdb=" O ASPAy 70 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUAy 82 " --> pdb=" O LYSAy 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAy 83 " --> pdb=" O GLNAy 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ay' and resid 78 through 83' Processing helix chain 'Ay' and resid 88 through 103 Processing helix chain 'Ay' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEAy 112 " --> pdb=" O SERAy 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNAy 115 " --> pdb=" O GLUAy 111 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 147 through 154 removed outlier: 3.560A pdb=" N LEUAy 151 " --> pdb=" O LEUAy 147 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 158 through 163 Processing helix chain 'Ay' and resid 165 through 177 Processing helix chain 'Ay' and resid 184 through 191 Processing helix chain 'Ay' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAy 199 " --> pdb=" O SERAy 196 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUAy 220 " --> pdb=" O LYSAy 216 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEUAy 227 " --> pdb=" O LYSAy 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSAy 228 " --> pdb=" O ALAAy 224 " (cutoff:3.500A) Processing helix chain 'Az' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERAz 74 " --> pdb=" O ASPAz 70 " (cutoff:3.500A) Processing helix chain 'Az' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUAz 82 " --> pdb=" O LYSAz 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERAz 83 " --> pdb=" O GLNAz 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Az' and resid 78 through 83' Processing helix chain 'Az' and resid 88 through 103 Processing helix chain 'Az' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEAz 112 " --> pdb=" O SERAz 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASNAz 115 " --> pdb=" O GLUAz 111 " (cutoff:3.500A) Processing helix chain 'Az' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUAz 151 " --> pdb=" O LEUAz 147 " (cutoff:3.500A) Processing helix chain 'Az' and resid 158 through 163 Processing helix chain 'Az' and resid 165 through 177 Processing helix chain 'Az' and resid 184 through 191 Processing helix chain 'Az' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGAz 199 " --> pdb=" O SERAz 196 " (cutoff:3.500A) Processing helix chain 'Az' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUAz 220 " --> pdb=" O LYSAz 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUAz 227 " --> pdb=" O LYSAz 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSAz 228 " --> pdb=" O ALAAz 224 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERBa 74 " --> pdb=" O ASPBa 70 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 78 through 83 removed outlier: 3.961A pdb=" N LEUBa 82 " --> pdb=" O LYSBa 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERBa 83 " --> pdb=" O GLNBa 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 78 through 83' Processing helix chain 'Ba' and resid 88 through 103 Processing helix chain 'Ba' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEBa 112 " --> pdb=" O SERBa 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNBa 115 " --> pdb=" O GLUBa 111 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUBa 151 " --> pdb=" O LEUBa 147 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 158 through 163 Processing helix chain 'Ba' and resid 165 through 177 Processing helix chain 'Ba' and resid 184 through 191 Processing helix chain 'Ba' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGBa 199 " --> pdb=" O SERBa 196 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 212 through 228 removed outlier: 3.947A pdb=" N LEUBa 220 " --> pdb=" O LYSBa 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUBa 227 " --> pdb=" O LYSBa 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSBa 228 " --> pdb=" O ALABa 224 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 68 through 74 removed outlier: 3.655A pdb=" N SERBb 74 " --> pdb=" O ASPBb 70 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUBb 82 " --> pdb=" O LYSBb 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERBb 83 " --> pdb=" O GLNBb 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 78 through 83' Processing helix chain 'Bb' and resid 88 through 103 Processing helix chain 'Bb' and resid 106 through 124 removed outlier: 4.398A pdb=" N ILEBb 112 " --> pdb=" O SERBb 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNBb 115 " --> pdb=" O GLUBb 111 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUBb 151 " --> pdb=" O LEUBb 147 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 158 through 163 Processing helix chain 'Bb' and resid 165 through 177 Processing helix chain 'Bb' and resid 184 through 191 Processing helix chain 'Bb' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGBb 199 " --> pdb=" O SERBb 196 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUBb 220 " --> pdb=" O LYSBb 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUBb 227 " --> pdb=" O LYSBb 223 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYSBb 228 " --> pdb=" O ALABb 224 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 68 through 74 removed outlier: 3.656A pdb=" N SERBc 74 " --> pdb=" O ASPBc 70 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 78 through 83 removed outlier: 3.959A pdb=" N LEUBc 82 " --> pdb=" O LYSBc 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERBc 83 " --> pdb=" O GLNBc 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 78 through 83' Processing helix chain 'Bc' and resid 88 through 103 Processing helix chain 'Bc' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEBc 112 " --> pdb=" O SERBc 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASNBc 115 " --> pdb=" O GLUBc 111 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 147 through 154 removed outlier: 3.561A pdb=" N LEUBc 151 " --> pdb=" O LEUBc 147 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 158 through 163 Processing helix chain 'Bc' and resid 165 through 177 Processing helix chain 'Bc' and resid 184 through 191 Processing helix chain 'Bc' and resid 195 through 201 removed outlier: 4.329A pdb=" N ARGBc 199 " --> pdb=" O SERBc 196 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUBc 220 " --> pdb=" O LYSBc 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUBc 227 " --> pdb=" O LYSBc 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSBc 228 " --> pdb=" O ALABc 224 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 68 through 74 removed outlier: 3.657A pdb=" N SERBd 74 " --> pdb=" O ASPBd 70 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 78 through 83 removed outlier: 3.960A pdb=" N LEUBd 82 " --> pdb=" O LYSBd 78 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERBd 83 " --> pdb=" O GLNBd 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 78 through 83' Processing helix chain 'Bd' and resid 88 through 103 Processing helix chain 'Bd' and resid 106 through 124 removed outlier: 4.397A pdb=" N ILEBd 112 " --> pdb=" O SERBd 108 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNBd 115 " --> pdb=" O GLUBd 111 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 147 through 154 removed outlier: 3.560A pdb=" N LEUBd 151 " --> pdb=" O LEUBd 147 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 158 through 163 Processing helix chain 'Bd' and resid 165 through 177 Processing helix chain 'Bd' and resid 184 through 191 Processing helix chain 'Bd' and resid 195 through 201 removed outlier: 4.328A pdb=" N ARGBd 199 " --> pdb=" O SERBd 196 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 212 through 228 removed outlier: 3.946A pdb=" N LEUBd 220 " --> pdb=" O LYSBd 216 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEUBd 227 " --> pdb=" O LYSBd 223 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYSBd 228 " --> pdb=" O ALABd 224 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 133 through 138 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 133 through 138 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 133 through 138 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 133 through 138 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 133 through 138 Processing sheet with id=AA6, first strand: chain 'Af' and resid 133 through 138 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 133 through 138 Processing sheet with id=AA8, first strand: chain 'Ah' and resid 133 through 138 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 133 through 138 Processing sheet with id=AB1, first strand: chain 'Aj' and resid 133 through 138 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 133 through 138 Processing sheet with id=AB3, first strand: chain 'Al' and resid 133 through 138 Processing sheet with id=AB4, first strand: chain 'Am' and resid 133 through 138 Processing sheet with id=AB5, first strand: chain 'An' and resid 133 through 138 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 133 through 138 Processing sheet with id=AB7, first strand: chain 'Ap' and resid 133 through 138 Processing sheet with id=AB8, first strand: chain 'Aq' and resid 133 through 138 Processing sheet with id=AB9, first strand: chain 'Ar' and resid 133 through 138 Processing sheet with id=AC1, first strand: chain 'As' and resid 133 through 138 Processing sheet with id=AC2, first strand: chain 'At' and resid 133 through 138 Processing sheet with id=AC3, first strand: chain 'Au' and resid 133 through 138 Processing sheet with id=AC4, first strand: chain 'Av' and resid 133 through 138 Processing sheet with id=AC5, first strand: chain 'Aw' and resid 133 through 138 Processing sheet with id=AC6, first strand: chain 'Ax' and resid 133 through 138 Processing sheet with id=AC7, first strand: chain 'Ay' and resid 133 through 138 Processing sheet with id=AC8, first strand: chain 'Az' and resid 133 through 138 Processing sheet with id=AC9, first strand: chain 'Ba' and resid 133 through 138 Processing sheet with id=AD1, first strand: chain 'Bb' and resid 133 through 138 Processing sheet with id=AD2, first strand: chain 'Bc' and resid 133 through 138 Processing sheet with id=AD3, first strand: chain 'Bd' and resid 133 through 138 1920 hydrogen bonds defined for protein. 5400 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: 8.23 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10069 1.33 - 1.45: 9589 1.45 - 1.57: 25522 1.57 - 1.69: 0 1.69 - 1.81: 750 Bond restraints: 45930 Sorted by residual: bond pdb=" N VALAf 66 " pdb=" CA VALAf 66 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VALAv 66 " pdb=" CA VALAv 66 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VALAl 66 " pdb=" CA VALAl 66 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.23e+01 bond pdb=" N VALAq 66 " pdb=" CA VALAq 66 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.23e+01 bond pdb=" N VALAb 66 " pdb=" CA VALAb 66 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 ... (remaining 45925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 52317 1.51 - 3.02: 7402 3.02 - 4.53: 1791 4.53 - 6.04: 410 6.04 - 7.55: 90 Bond angle restraints: 62010 Sorted by residual: angle pdb=" CA ASNAt 124 " pdb=" C ASNAt 124 " pdb=" O ASNAt 124 " ideal model delta sigma weight residual 121.94 117.21 4.73 1.15e+00 7.56e-01 1.69e+01 angle pdb=" CA ASNAd 124 " pdb=" C ASNAd 124 " pdb=" O ASNAd 124 " ideal model delta sigma weight residual 121.94 117.22 4.72 1.15e+00 7.56e-01 1.69e+01 angle pdb=" CA ASNAx 124 " pdb=" C ASNAx 124 " pdb=" O ASNAx 124 " ideal model delta sigma weight residual 121.94 117.22 4.72 1.15e+00 7.56e-01 1.69e+01 angle pdb=" CA ASNAu 124 " pdb=" C ASNAu 124 " pdb=" O ASNAu 124 " ideal model delta sigma weight residual 121.94 117.22 4.72 1.15e+00 7.56e-01 1.69e+01 angle pdb=" CA ASNBd 124 " pdb=" C ASNBd 124 " pdb=" O ASNBd 124 " ideal model delta sigma weight residual 121.94 117.22 4.72 1.15e+00 7.56e-01 1.68e+01 ... (remaining 62005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 25319 15.99 - 31.98: 2370 31.98 - 47.97: 481 47.97 - 63.97: 150 63.97 - 79.96: 60 Dihedral angle restraints: 28380 sinusoidal: 11850 harmonic: 16530 Sorted by residual: dihedral pdb=" CA LYSAe 155 " pdb=" C LYSAe 155 " pdb=" N PROAe 156 " pdb=" CA PROAe 156 " ideal model delta harmonic sigma weight residual 0.00 -23.69 23.69 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LYSAq 155 " pdb=" C LYSAq 155 " pdb=" N PROAq 156 " pdb=" CA PROAq 156 " ideal model delta harmonic sigma weight residual 0.00 -23.66 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LYSBd 155 " pdb=" C LYSBd 155 " pdb=" N PROBd 156 " pdb=" CA PROBd 156 " ideal model delta harmonic sigma weight residual 0.00 -23.66 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 28377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5398 0.072 - 0.144: 825 0.144 - 0.216: 317 0.216 - 0.288: 60 0.288 - 0.359: 30 Chirality restraints: 6630 Sorted by residual: chirality pdb=" CA TYRAo 103 " pdb=" N TYRAo 103 " pdb=" C TYRAo 103 " pdb=" CB TYRAo 103 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA TYRAk 103 " pdb=" N TYRAk 103 " pdb=" C TYRAk 103 " pdb=" CB TYRAk 103 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA TYRAe 103 " pdb=" N TYRAe 103 " pdb=" C TYRAe 103 " pdb=" CB TYRAe 103 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 6627 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METAl 137 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C METAl 137 " -0.060 2.00e-02 2.50e+03 pdb=" O METAl 137 " 0.023 2.00e-02 2.50e+03 pdb=" N ASPAl 138 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAt 137 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C METAt 137 " 0.060 2.00e-02 2.50e+03 pdb=" O METAt 137 " -0.023 2.00e-02 2.50e+03 pdb=" N ASPAt 138 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAy 137 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C METAy 137 " -0.060 2.00e-02 2.50e+03 pdb=" O METAy 137 " 0.023 2.00e-02 2.50e+03 pdb=" N ASPAy 138 " 0.020 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6325 2.75 - 3.28: 43626 3.28 - 3.82: 68080 3.82 - 4.36: 81701 4.36 - 4.90: 134825 Nonbonded interactions: 334557 Sorted by model distance: nonbonded pdb=" OE2 GLUAt 170 " pdb=" OH TYRAt 205 " model vdw 2.207 3.040 nonbonded pdb=" OE2 GLUAj 170 " pdb=" OH TYRAj 205 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLUAn 170 " pdb=" OH TYRAn 205 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLUBd 170 " pdb=" OH TYRBd 205 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLUAu 170 " pdb=" OH TYRAu 205 " model vdw 2.208 3.040 ... (remaining 334552 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: 0.17 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' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' } 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.130 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.010 0.045 45930 Z= 0.648 Angle : 1.190 7.550 62010 Z= 0.819 Chirality : 0.069 0.359 6630 Planarity : 0.005 0.035 7980 Dihedral : 13.844 79.956 17640 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.10), residues: 5490 helix: -2.00 (0.08), residues: 2850 sheet: -3.66 (0.15), residues: 360 loop : -2.29 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGBc 176 TYR 0.013 0.002 TYRAt 200 PHE 0.012 0.002 PHEAo 165 TRP 0.024 0.004 TRPAt 95 HIS 0.002 0.001 HISAx 71 Details of bonding type rmsd covalent geometry : bond 0.00997 (45930) covalent geometry : angle 1.18956 (62010) hydrogen bonds : bond 0.14606 ( 1920) hydrogen bonds : angle 6.10142 ( 5400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2082 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2082 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 111 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7753 (tm-30) REVERT: Aa 138 ASP cc_start: 0.8042 (t70) cc_final: 0.7592 (t70) REVERT: Aa 141 GLU cc_start: 0.7902 (tt0) cc_final: 0.7681 (tt0) REVERT: Aa 174 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7351 (tm-30) REVERT: Ab 50 LYS cc_start: 0.6931 (mttt) cc_final: 0.6728 (ttmm) REVERT: Ab 76 LYS cc_start: 0.8578 (mttt) cc_final: 0.8354 (ptpp) REVERT: Ab 138 ASP cc_start: 0.7948 (t70) cc_final: 0.7686 (t70) REVERT: Ab 174 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7634 (tm-30) REVERT: Ab 214 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7926 (mtm-85) REVERT: Ac 50 LYS cc_start: 0.6770 (mttt) cc_final: 0.6271 (mtmm) REVERT: Ac 75 TYR cc_start: 0.8778 (t80) cc_final: 0.8560 (t80) REVERT: Ac 91 GLN cc_start: 0.8406 (mt0) cc_final: 0.8201 (mt0) REVERT: Ac 115 ASN cc_start: 0.8859 (m-40) cc_final: 0.8655 (m-40) REVERT: Ac 138 ASP cc_start: 0.8117 (t70) cc_final: 0.7771 (t70) REVERT: Ac 141 GLU cc_start: 0.7889 (tt0) cc_final: 0.7653 (tt0) REVERT: Ac 162 MET cc_start: 0.8854 (tpp) cc_final: 0.8462 (tpt) REVERT: Ac 174 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7512 (tm-30) REVERT: Ac 214 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7903 (mtm-85) REVERT: Ad 50 LYS cc_start: 0.6561 (mttt) cc_final: 0.6274 (mtpp) REVERT: Ad 76 LYS cc_start: 0.8579 (mttt) cc_final: 0.8207 (ptpp) REVERT: Ad 138 ASP cc_start: 0.7984 (t70) cc_final: 0.7624 (t70) REVERT: Ad 174 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7765 (tm-30) REVERT: Ad 197 LEU cc_start: 0.8614 (mt) cc_final: 0.8300 (tp) REVERT: Ae 115 ASN cc_start: 0.8932 (m-40) cc_final: 0.8731 (m110) REVERT: Ae 118 MET cc_start: 0.8983 (tpt) cc_final: 0.8752 (tpt) REVERT: Ae 136 MET cc_start: 0.8253 (ttp) cc_final: 0.7911 (ttp) REVERT: Ae 138 ASP cc_start: 0.7926 (t70) cc_final: 0.7472 (t70) REVERT: Ae 174 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7478 (tm-30) REVERT: Ae 214 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7818 (mtm-85) REVERT: Af 46 VAL cc_start: 0.9418 (t) cc_final: 0.9206 (t) REVERT: Af 50 LYS cc_start: 0.6615 (mttt) cc_final: 0.6383 (mtpp) REVERT: Af 76 LYS cc_start: 0.8684 (mttt) cc_final: 0.8415 (ptpp) REVERT: Af 103 TYR cc_start: 0.7988 (m-10) cc_final: 0.7748 (m-10) REVERT: Af 111 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7859 (mt-10) REVERT: Af 122 ILE cc_start: 0.9400 (tt) cc_final: 0.9200 (tt) REVERT: Af 137 MET cc_start: 0.8476 (mmm) cc_final: 0.7988 (mmm) REVERT: Af 174 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7649 (tm-30) REVERT: Ag 50 LYS cc_start: 0.6561 (mttt) cc_final: 0.6287 (mtpp) REVERT: Ag 75 TYR cc_start: 0.8752 (t80) cc_final: 0.8524 (t80) REVERT: Ag 76 LYS cc_start: 0.8648 (mttt) cc_final: 0.8231 (ptpp) REVERT: Ag 138 ASP cc_start: 0.8014 (t70) cc_final: 0.7609 (t70) REVERT: Ag 174 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7585 (tm-30) REVERT: Ag 197 LEU cc_start: 0.8638 (mt) cc_final: 0.8433 (tp) REVERT: Ah 138 ASP cc_start: 0.8016 (t70) cc_final: 0.7708 (t70) REVERT: Ah 174 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7649 (tm-30) REVERT: Ah 214 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7902 (mtm-85) REVERT: Ai 138 ASP cc_start: 0.8002 (t70) cc_final: 0.7781 (t70) REVERT: Ai 141 GLU cc_start: 0.7892 (tt0) cc_final: 0.7643 (tt0) REVERT: Ai 174 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7529 (tm-30) REVERT: Ai 176 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8095 (mmm-85) REVERT: Aj 50 LYS cc_start: 0.6989 (mttt) cc_final: 0.6777 (ttmm) REVERT: Aj 138 ASP cc_start: 0.8014 (t70) cc_final: 0.7690 (t70) REVERT: Aj 174 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7672 (tm-30) REVERT: Aj 214 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7946 (mtm-85) REVERT: Ak 50 LYS cc_start: 0.6776 (mttt) cc_final: 0.6329 (mtmm) REVERT: Ak 75 TYR cc_start: 0.8832 (t80) cc_final: 0.8544 (t80) REVERT: Ak 76 LYS cc_start: 0.8570 (mttt) cc_final: 0.8342 (mttt) REVERT: Ak 115 ASN cc_start: 0.8889 (m-40) cc_final: 0.8650 (m110) REVERT: Ak 138 ASP cc_start: 0.8059 (t70) cc_final: 0.7798 (t70) REVERT: Ak 141 GLU cc_start: 0.7955 (tt0) cc_final: 0.7729 (tt0) REVERT: Ak 174 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7576 (tm-30) REVERT: Ak 214 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7955 (mtm-85) REVERT: Ak 222 MET cc_start: 0.7494 (mtp) cc_final: 0.7168 (mtm) REVERT: Al 76 LYS cc_start: 0.8507 (mttt) cc_final: 0.8208 (ptpp) REVERT: Al 138 ASP cc_start: 0.7991 (t70) cc_final: 0.7569 (t70) REVERT: Al 174 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7784 (tm-30) REVERT: Al 197 LEU cc_start: 0.8663 (mt) cc_final: 0.8422 (tp) REVERT: Am 118 MET cc_start: 0.8962 (tpt) cc_final: 0.8611 (tpt) REVERT: Am 174 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7484 (tm-30) REVERT: Am 214 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7839 (mtm-85) REVERT: An 46 VAL cc_start: 0.9455 (t) cc_final: 0.9245 (t) REVERT: An 111 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7787 (mt-10) REVERT: An 137 MET cc_start: 0.8481 (mmm) cc_final: 0.7995 (mmm) REVERT: An 174 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7641 (tm-30) REVERT: Ao 50 LYS cc_start: 0.6603 (mttt) cc_final: 0.6292 (mtpp) REVERT: Ao 75 TYR cc_start: 0.8778 (t80) cc_final: 0.8543 (t80) REVERT: Ao 76 LYS cc_start: 0.8649 (mttt) cc_final: 0.8219 (ptpp) REVERT: Ao 197 LEU cc_start: 0.8693 (mt) cc_final: 0.8486 (tp) REVERT: Ap 115 ASN cc_start: 0.8882 (m-40) cc_final: 0.8676 (m-40) REVERT: Ap 174 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7627 (tm-30) REVERT: Ap 214 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7932 (mtm-85) REVERT: Aq 75 TYR cc_start: 0.8901 (t80) cc_final: 0.8659 (t80) REVERT: Aq 174 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7507 (tm-30) REVERT: Ar 50 LYS cc_start: 0.6940 (mttt) cc_final: 0.6671 (ttmm) REVERT: Ar 76 LYS cc_start: 0.8562 (mttt) cc_final: 0.8359 (ptpp) REVERT: Ar 136 MET cc_start: 0.8334 (ttp) cc_final: 0.7939 (ttm) REVERT: Ar 174 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7678 (tm-30) REVERT: Ar 214 ARG cc_start: 0.8177 (mtm180) cc_final: 0.7919 (mtm-85) REVERT: As 76 LYS cc_start: 0.8584 (mttt) cc_final: 0.8347 (mttt) REVERT: As 111 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7775 (mt-10) REVERT: As 174 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7595 (tm-30) REVERT: As 186 TYR cc_start: 0.8538 (t80) cc_final: 0.8274 (t80) REVERT: As 211 THR cc_start: 0.9468 (m) cc_final: 0.9180 (t) REVERT: At 76 LYS cc_start: 0.8577 (mttt) cc_final: 0.8230 (ptpp) REVERT: At 136 MET cc_start: 0.8431 (ttp) cc_final: 0.8102 (ttm) REVERT: At 174 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7699 (tm-30) REVERT: Au 214 ARG cc_start: 0.8325 (mtm180) cc_final: 0.7949 (mtm-85) REVERT: Av 122 ILE cc_start: 0.9355 (tt) cc_final: 0.9152 (tt) REVERT: Av 137 MET cc_start: 0.8488 (mmm) cc_final: 0.7935 (mmm) REVERT: Av 174 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7533 (tm-30) REVERT: Aw 75 TYR cc_start: 0.8802 (t80) cc_final: 0.8577 (t80) REVERT: Aw 76 LYS cc_start: 0.8652 (mttt) cc_final: 0.8222 (ptpp) REVERT: Ax 174 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7597 (tm-30) REVERT: Ax 214 ARG cc_start: 0.8268 (mtm180) cc_final: 0.7961 (mtm-85) REVERT: Ay 174 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7456 (tm-30) REVERT: Az 136 MET cc_start: 0.8337 (ttp) cc_final: 0.8024 (ttm) REVERT: Az 174 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7677 (tm-30) REVERT: Az 214 ARG cc_start: 0.8304 (mtm180) cc_final: 0.8055 (mtm-85) REVERT: Ba 141 GLU cc_start: 0.7897 (tt0) cc_final: 0.7627 (tt0) REVERT: Ba 174 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7841 (tm-30) REVERT: Ba 214 ARG cc_start: 0.8305 (mtm180) cc_final: 0.8041 (mtm-85) REVERT: Bb 76 LYS cc_start: 0.8602 (mttt) cc_final: 0.8350 (ptpp) REVERT: Bb 176 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8261 (mmm-85) REVERT: Bc 86 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7745 (ttm170) REVERT: Bc 214 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7985 (mtm-85) REVERT: Bd 57 THR cc_start: 0.9053 (m) cc_final: 0.8810 (p) REVERT: Bd 76 LYS cc_start: 0.8416 (mttt) cc_final: 0.8182 (tptt) REVERT: Bd 111 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7997 (mt-10) REVERT: Bd 122 ILE cc_start: 0.9390 (tt) cc_final: 0.9156 (tt) REVERT: Bd 174 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7576 (tm-30) outliers start: 0 outliers final: 0 residues processed: 2082 average time/residue: 0.3082 time to fit residues: 988.5675 Evaluate side-chains 1589 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1589 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 44 HIS Ab 44 HIS Ab 115 ASN Ad 71 HIS Ad 115 ASN Ae 71 HIS Ae 160 GLN ** Af 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 115 ASN Ag 44 HIS Ah 71 HIS Ah 115 ASN Aj 44 HIS Aj 115 ASN Al 115 ASN Am 71 HIS Am 115 ASN Am 160 GLN ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 115 ASN ** Ap 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 160 GLN Aq 142 GLN Ar 44 HIS Ar 71 HIS Ar 115 ASN As 71 HIS As 115 ASN At 115 ASN At 142 GLN Au 115 ASN Au 160 GLN Av 71 HIS Av 115 ASN Aw 115 ASN ** Ax 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 115 ASN Ax 160 GLN Ay 142 GLN Az 71 HIS Az 115 ASN ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 115 ASN ** Bb 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 142 GLN Bc 115 ASN Bd 115 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121945 restraints weight = 70079.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125367 restraints weight = 45047.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127772 restraints weight = 32908.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129477 restraints weight = 26199.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130712 restraints weight = 22125.786| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45930 Z= 0.130 Angle : 0.581 5.777 62010 Z= 0.302 Chirality : 0.036 0.131 6630 Planarity : 0.005 0.040 7980 Dihedral : 3.976 13.810 6120 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.27 % Allowed : 17.28 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.11), residues: 5490 helix: -0.42 (0.10), residues: 2700 sheet: -2.40 (0.21), residues: 360 loop : -1.86 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAu 199 TYR 0.022 0.001 TYRAe 75 PHE 0.012 0.002 PHEAi 165 TRP 0.016 0.003 TRPAw 95 HIS 0.005 0.001 HISAr 44 Details of bonding type rmsd covalent geometry : bond 0.00316 (45930) covalent geometry : angle 0.58143 (62010) hydrogen bonds : bond 0.03622 ( 1920) hydrogen bonds : angle 4.56949 ( 5400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1801 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1690 time to evaluate : 1.574 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 81 ASP cc_start: 0.8323 (m-30) cc_final: 0.7969 (t0) REVERT: Aa 118 MET cc_start: 0.9165 (tpt) cc_final: 0.8743 (tpt) REVERT: Aa 138 ASP cc_start: 0.8007 (t70) cc_final: 0.7687 (t70) REVERT: Aa 148 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8408 (ttpp) REVERT: Aa 174 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7256 (tm-30) REVERT: Ab 57 THR cc_start: 0.9164 (m) cc_final: 0.8897 (m) REVERT: Ab 137 MET cc_start: 0.8773 (mmm) cc_final: 0.8246 (mmm) REVERT: Ab 138 ASP cc_start: 0.8021 (t70) cc_final: 0.7648 (t70) REVERT: Ab 174 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7581 (tm-30) REVERT: Ab 176 ARG cc_start: 0.8954 (mmm-85) cc_final: 0.8722 (tpp80) REVERT: Ac 75 TYR cc_start: 0.8874 (t80) cc_final: 0.8494 (t80) REVERT: Ac 81 ASP cc_start: 0.8243 (m-30) cc_final: 0.7873 (t0) REVERT: Ac 91 GLN cc_start: 0.8525 (mt0) cc_final: 0.8316 (mt0) REVERT: Ac 138 ASP cc_start: 0.8140 (t70) cc_final: 0.7758 (t70) REVERT: Ac 162 MET cc_start: 0.8922 (tpp) cc_final: 0.8591 (tpt) REVERT: Ad 108 SER cc_start: 0.9024 (p) cc_final: 0.8703 (t) REVERT: Ad 110 MET cc_start: 0.9096 (tpp) cc_final: 0.8239 (mmt) REVERT: Ad 137 MET cc_start: 0.8760 (mmm) cc_final: 0.8248 (mmm) REVERT: Ad 138 ASP cc_start: 0.7919 (t70) cc_final: 0.7604 (t70) REVERT: Ad 174 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7757 (tm-30) REVERT: Ad 178 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8294 (mtp180) REVERT: Ae 78 LYS cc_start: 0.8798 (mppt) cc_final: 0.8458 (mmmm) REVERT: Ae 108 SER cc_start: 0.8812 (p) cc_final: 0.8436 (t) REVERT: Ae 118 MET cc_start: 0.8959 (tpt) cc_final: 0.8567 (tpt) REVERT: Ae 138 ASP cc_start: 0.7984 (t70) cc_final: 0.7497 (t70) REVERT: Ae 174 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7216 (tm-30) REVERT: Ae 175 MET cc_start: 0.9064 (tmm) cc_final: 0.8853 (tmm) REVERT: Ae 203 ASP cc_start: 0.8120 (t0) cc_final: 0.7828 (t0) REVERT: Af 81 ASP cc_start: 0.8156 (m-30) cc_final: 0.7914 (t0) REVERT: Af 108 SER cc_start: 0.8903 (p) cc_final: 0.8597 (t) REVERT: Af 118 MET cc_start: 0.9340 (tpt) cc_final: 0.9127 (tpt) REVERT: Af 150 MET cc_start: 0.7887 (mmt) cc_final: 0.7515 (mmt) REVERT: Af 222 MET cc_start: 0.7560 (mtp) cc_final: 0.6675 (tmm) REVERT: Ag 75 TYR cc_start: 0.8772 (t80) cc_final: 0.8394 (t80) REVERT: Ag 108 SER cc_start: 0.9076 (p) cc_final: 0.8804 (t) REVERT: Ag 138 ASP cc_start: 0.8126 (t70) cc_final: 0.7690 (t70) REVERT: Ag 214 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.8024 (mtm110) REVERT: Ag 222 MET cc_start: 0.7548 (mtm) cc_final: 0.7100 (mtt) REVERT: Ah 78 LYS cc_start: 0.8905 (mppt) cc_final: 0.8488 (mmmm) REVERT: Ah 81 ASP cc_start: 0.8404 (m-30) cc_final: 0.8072 (t0) REVERT: Ah 108 SER cc_start: 0.8917 (p) cc_final: 0.8655 (t) REVERT: Ah 138 ASP cc_start: 0.8092 (t70) cc_final: 0.7541 (t70) REVERT: Ah 174 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7321 (tm-30) REVERT: Ah 175 MET cc_start: 0.9066 (tmm) cc_final: 0.8783 (tmm) REVERT: Ah 203 ASP cc_start: 0.8160 (t0) cc_final: 0.7929 (t0) REVERT: Ai 75 TYR cc_start: 0.8867 (t80) cc_final: 0.8531 (t80) REVERT: Ai 81 ASP cc_start: 0.8377 (m-30) cc_final: 0.7823 (t0) REVERT: Ai 108 SER cc_start: 0.9001 (p) cc_final: 0.8748 (t) REVERT: Ai 137 MET cc_start: 0.8677 (mmm) cc_final: 0.8015 (mmm) REVERT: Ai 138 ASP cc_start: 0.8013 (t70) cc_final: 0.7694 (t70) REVERT: Ai 174 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7443 (tm-30) REVERT: Ai 222 MET cc_start: 0.7801 (mtm) cc_final: 0.7402 (mtt) REVERT: Aj 57 THR cc_start: 0.9171 (m) cc_final: 0.8887 (m) REVERT: Aj 137 MET cc_start: 0.8773 (mmm) cc_final: 0.8139 (mmm) REVERT: Aj 138 ASP cc_start: 0.8049 (t70) cc_final: 0.7655 (t70) REVERT: Aj 174 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7593 (tm-30) REVERT: Ak 81 ASP cc_start: 0.8331 (m-30) cc_final: 0.7945 (t0) REVERT: Ak 138 ASP cc_start: 0.8207 (t70) cc_final: 0.7805 (t70) REVERT: Ak 199 ARG cc_start: 0.8933 (mtp85) cc_final: 0.8280 (ttm110) REVERT: Ak 222 MET cc_start: 0.7634 (mtp) cc_final: 0.7360 (ttm) REVERT: Al 108 SER cc_start: 0.9001 (p) cc_final: 0.8705 (t) REVERT: Al 110 MET cc_start: 0.9073 (tpp) cc_final: 0.8254 (mmt) REVERT: Al 137 MET cc_start: 0.8699 (mmm) cc_final: 0.8136 (mmm) REVERT: Al 138 ASP cc_start: 0.7933 (t70) cc_final: 0.7591 (t70) REVERT: Al 178 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8214 (mtp180) REVERT: Al 222 MET cc_start: 0.7711 (mtp) cc_final: 0.7050 (tmm) REVERT: Am 57 THR cc_start: 0.9122 (m) cc_final: 0.8903 (m) REVERT: Am 78 LYS cc_start: 0.8767 (mppt) cc_final: 0.8383 (mmmm) REVERT: Am 118 MET cc_start: 0.9004 (tpt) cc_final: 0.8548 (tpt) REVERT: Am 138 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: Am 174 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7310 (tm-30) REVERT: Am 175 MET cc_start: 0.9051 (tmm) cc_final: 0.8777 (tmm) REVERT: An 75 TYR cc_start: 0.8625 (t80) cc_final: 0.8306 (t80) REVERT: An 81 ASP cc_start: 0.8248 (m-30) cc_final: 0.8010 (t0) REVERT: An 108 SER cc_start: 0.8812 (p) cc_final: 0.8548 (t) REVERT: An 138 ASP cc_start: 0.8185 (t70) cc_final: 0.7879 (t0) REVERT: An 222 MET cc_start: 0.7774 (mtm) cc_final: 0.7376 (mtt) REVERT: Ao 75 TYR cc_start: 0.8730 (t80) cc_final: 0.8405 (t80) REVERT: Ao 108 SER cc_start: 0.9026 (p) cc_final: 0.8689 (t) REVERT: Ao 137 MET cc_start: 0.8672 (mmm) cc_final: 0.8285 (mmm) REVERT: Ao 138 ASP cc_start: 0.8191 (t70) cc_final: 0.7921 (t0) REVERT: Ap 78 LYS cc_start: 0.8731 (mppt) cc_final: 0.8306 (mmmm) REVERT: Ap 108 SER cc_start: 0.8959 (p) cc_final: 0.8676 (t) REVERT: Ap 150 MET cc_start: 0.7700 (mmt) cc_final: 0.7379 (mmt) REVERT: Ap 162 MET cc_start: 0.8942 (mmm) cc_final: 0.8731 (mmm) REVERT: Ap 174 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7316 (tm-30) REVERT: Ap 175 MET cc_start: 0.9125 (tmm) cc_final: 0.8889 (tmm) REVERT: Aq 50 LYS cc_start: 0.7158 (mtpp) cc_final: 0.6789 (mtmm) REVERT: Aq 75 TYR cc_start: 0.8868 (t80) cc_final: 0.8570 (t80) REVERT: Aq 81 ASP cc_start: 0.8338 (m-30) cc_final: 0.8054 (t0) REVERT: Aq 138 ASP cc_start: 0.8239 (t70) cc_final: 0.7958 (t0) REVERT: Aq 222 MET cc_start: 0.7673 (mtm) cc_final: 0.7444 (mtm) REVERT: Ar 57 THR cc_start: 0.9118 (m) cc_final: 0.8862 (m) REVERT: Ar 137 MET cc_start: 0.8713 (mmm) cc_final: 0.8353 (mmm) REVERT: Ar 174 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7556 (tm-30) REVERT: As 78 LYS cc_start: 0.8786 (mppt) cc_final: 0.8196 (mmmm) REVERT: As 81 ASP cc_start: 0.8334 (m-30) cc_final: 0.7811 (t0) REVERT: As 138 ASP cc_start: 0.8355 (t70) cc_final: 0.8141 (t0) REVERT: At 108 SER cc_start: 0.9043 (p) cc_final: 0.8690 (t) REVERT: At 110 MET cc_start: 0.9018 (tpp) cc_final: 0.8234 (mmt) REVERT: At 137 MET cc_start: 0.8639 (mmm) cc_final: 0.8090 (mmm) REVERT: At 138 ASP cc_start: 0.8018 (t70) cc_final: 0.7700 (t0) REVERT: At 222 MET cc_start: 0.7717 (mtp) cc_final: 0.7046 (tmm) REVERT: Au 57 THR cc_start: 0.9135 (m) cc_final: 0.8933 (m) REVERT: Au 78 LYS cc_start: 0.8709 (mppt) cc_final: 0.8342 (mmmm) REVERT: Au 108 SER cc_start: 0.8904 (p) cc_final: 0.8661 (t) REVERT: Au 175 MET cc_start: 0.8953 (tmm) cc_final: 0.8729 (tmm) REVERT: Au 203 ASP cc_start: 0.8119 (t0) cc_final: 0.7905 (t0) REVERT: Au 214 ARG cc_start: 0.8358 (mtm180) cc_final: 0.8146 (mtm-85) REVERT: Av 75 TYR cc_start: 0.8630 (t80) cc_final: 0.8220 (t80) REVERT: Av 81 ASP cc_start: 0.8233 (m-30) cc_final: 0.8030 (t0) REVERT: Av 108 SER cc_start: 0.8982 (p) cc_final: 0.8593 (t) REVERT: Av 118 MET cc_start: 0.9358 (tpt) cc_final: 0.9139 (tpt) REVERT: Av 122 ILE cc_start: 0.9217 (tt) cc_final: 0.9003 (tt) REVERT: Av 138 ASP cc_start: 0.8258 (t70) cc_final: 0.7950 (t0) REVERT: Av 222 MET cc_start: 0.7647 (mtp) cc_final: 0.7038 (tmm) REVERT: Aw 75 TYR cc_start: 0.8833 (t80) cc_final: 0.8399 (t80) REVERT: Aw 137 MET cc_start: 0.8691 (mmm) cc_final: 0.8304 (mmm) REVERT: Ax 78 LYS cc_start: 0.8709 (mppt) cc_final: 0.8246 (mmmm) REVERT: Ax 108 SER cc_start: 0.9011 (p) cc_final: 0.8744 (t) REVERT: Ax 150 MET cc_start: 0.7786 (mmt) cc_final: 0.7432 (mmt) REVERT: Ax 162 MET cc_start: 0.8966 (mmm) cc_final: 0.8765 (mmm) REVERT: Ax 174 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7295 (tm-30) REVERT: Ax 175 MET cc_start: 0.9069 (tmm) cc_final: 0.8814 (tmm) REVERT: Ax 203 ASP cc_start: 0.8147 (t0) cc_final: 0.7945 (t0) REVERT: Ax 214 ARG cc_start: 0.8334 (mtm180) cc_final: 0.8122 (mtm-85) REVERT: Ay 64 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7938 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8288 (m-30) cc_final: 0.7963 (t0) REVERT: Ay 108 SER cc_start: 0.9038 (p) cc_final: 0.8706 (t) REVERT: Ay 138 ASP cc_start: 0.8251 (t70) cc_final: 0.7920 (t0) REVERT: Ay 203 ASP cc_start: 0.8265 (t0) cc_final: 0.8044 (t0) REVERT: Az 57 THR cc_start: 0.9158 (m) cc_final: 0.8889 (m) REVERT: Az 104 GLU cc_start: 0.7107 (pt0) cc_final: 0.6846 (pt0) REVERT: Az 137 MET cc_start: 0.8734 (mmm) cc_final: 0.8362 (mmm) REVERT: Az 174 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7518 (tm-30) REVERT: Ba 78 LYS cc_start: 0.8929 (mppt) cc_final: 0.8336 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8360 (m-30) cc_final: 0.7810 (t0) REVERT: Ba 136 MET cc_start: 0.8528 (ttp) cc_final: 0.8263 (ttt) REVERT: Bb 57 THR cc_start: 0.9173 (m) cc_final: 0.8963 (m) REVERT: Bb 110 MET cc_start: 0.9025 (tpp) cc_final: 0.8153 (mmt) REVERT: Bb 137 MET cc_start: 0.8646 (mmm) cc_final: 0.8129 (mmm) REVERT: Bb 138 ASP cc_start: 0.8245 (t70) cc_final: 0.8002 (t0) REVERT: Bc 57 THR cc_start: 0.9098 (m) cc_final: 0.8872 (m) REVERT: Bc 78 LYS cc_start: 0.8705 (mppt) cc_final: 0.8383 (mmmm) REVERT: Bc 136 MET cc_start: 0.8546 (ttp) cc_final: 0.8271 (ttt) REVERT: Bc 214 ARG cc_start: 0.8388 (mtm180) cc_final: 0.8164 (mtm-85) REVERT: Bd 57 THR cc_start: 0.9092 (m) cc_final: 0.8720 (p) REVERT: Bd 76 LYS cc_start: 0.8761 (mttt) cc_final: 0.8224 (tptt) REVERT: Bd 108 SER cc_start: 0.9016 (p) cc_final: 0.8784 (t) REVERT: Bd 118 MET cc_start: 0.9358 (tpt) cc_final: 0.9134 (tpt) REVERT: Bd 122 ILE cc_start: 0.9239 (tt) cc_final: 0.9030 (tt) REVERT: Bd 136 MET cc_start: 0.8324 (ttp) cc_final: 0.8084 (ttt) REVERT: Bd 138 ASP cc_start: 0.8219 (t70) cc_final: 0.7930 (t0) outliers start: 111 outliers final: 68 residues processed: 1734 average time/residue: 0.2605 time to fit residues: 725.8326 Evaluate side-chains 1623 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1555 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 97 ASP Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 115 ASN Chi-restraints excluded: chain Af residue 197 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 62 LYS Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 97 ASP Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 197 LEU Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ap residue 62 LYS Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 97 ASP Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 115 ASN Chi-restraints excluded: chain At residue 142 GLN Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain At residue 197 LEU Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 115 ASN Chi-restraints excluded: chain Av residue 197 LEU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 62 LYS Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 97 ASP Chi-restraints excluded: chain Ay residue 142 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 142 GLN Chi-restraints excluded: chain Bb residue 197 LEU Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 115 ASN Chi-restraints excluded: chain Bd residue 197 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 169 optimal weight: 4.9990 chunk 504 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 348 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 71 HIS Ab 160 GLN Ac 115 ASN Ae 115 ASN ** Af 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 71 HIS Aj 71 HIS Ak 71 HIS Ak 115 ASN Al 71 HIS An 71 HIS Ao 115 ASN Ap 71 HIS Ap 115 ASN Ap 160 GLN Aq 142 GLN ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 71 HIS ** At 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 160 GLN Ay 71 HIS Ay 115 ASN Ay 142 GLN ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113651 restraints weight = 70851.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116860 restraints weight = 47127.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119083 restraints weight = 35250.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120686 restraints weight = 28708.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121843 restraints weight = 24648.181| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 45930 Z= 0.210 Angle : 0.659 7.145 62010 Z= 0.330 Chirality : 0.039 0.125 6630 Planarity : 0.005 0.061 7980 Dihedral : 3.961 14.527 6120 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.23 % Allowed : 19.67 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.11), residues: 5490 helix: -0.20 (0.10), residues: 2700 sheet: -2.47 (0.21), residues: 360 loop : -1.54 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBb 176 TYR 0.024 0.002 TYRAu 75 PHE 0.016 0.003 PHEBa 165 TRP 0.019 0.003 TRPAg 95 HIS 0.003 0.001 HISAv 71 Details of bonding type rmsd covalent geometry : bond 0.00503 (45930) covalent geometry : angle 0.65945 (62010) hydrogen bonds : bond 0.04249 ( 1920) hydrogen bonds : angle 4.51931 ( 5400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1759 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1552 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 ASP cc_start: 0.8371 (m-30) cc_final: 0.8111 (t0) REVERT: Aa 108 SER cc_start: 0.9024 (p) cc_final: 0.8822 (t) REVERT: Aa 118 MET cc_start: 0.9028 (tpt) cc_final: 0.8492 (tpt) REVERT: Aa 138 ASP cc_start: 0.8112 (t70) cc_final: 0.7759 (t0) REVERT: Aa 148 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8569 (ttpp) REVERT: Aa 150 MET cc_start: 0.7971 (mmt) cc_final: 0.7396 (mmt) REVERT: Aa 162 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8605 (tpt) REVERT: Aa 174 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7530 (tm-30) REVERT: Aa 178 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8382 (mtp180) REVERT: Aa 222 MET cc_start: 0.7646 (mtm) cc_final: 0.7240 (mtt) REVERT: Ab 57 THR cc_start: 0.9183 (m) cc_final: 0.8874 (m) REVERT: Ab 136 MET cc_start: 0.8195 (ttp) cc_final: 0.7988 (ttp) REVERT: Ab 137 MET cc_start: 0.8815 (mmm) cc_final: 0.8354 (mmm) REVERT: Ab 138 ASP cc_start: 0.8158 (t70) cc_final: 0.7733 (t70) REVERT: Ab 174 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7683 (tm-30) REVERT: Ab 203 ASP cc_start: 0.8347 (t0) cc_final: 0.8120 (t0) REVERT: Ac 75 TYR cc_start: 0.8870 (t80) cc_final: 0.8525 (t80) REVERT: Ac 81 ASP cc_start: 0.8324 (m-30) cc_final: 0.7984 (t0) REVERT: Ac 91 GLN cc_start: 0.8630 (mt0) cc_final: 0.8340 (mt0) REVERT: Ac 138 ASP cc_start: 0.8343 (t70) cc_final: 0.7884 (t70) REVERT: Ac 162 MET cc_start: 0.8903 (tpp) cc_final: 0.8552 (tpt) REVERT: Ac 222 MET cc_start: 0.7634 (mtm) cc_final: 0.7346 (mtt) REVERT: Ad 137 MET cc_start: 0.8777 (mmm) cc_final: 0.8270 (mmm) REVERT: Ad 138 ASP cc_start: 0.7982 (t70) cc_final: 0.7700 (t70) REVERT: Ad 174 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7690 (tm-30) REVERT: Ad 222 MET cc_start: 0.7816 (mtp) cc_final: 0.7335 (ttm) REVERT: Ae 50 LYS cc_start: 0.6896 (mtmm) cc_final: 0.5442 (ttmm) REVERT: Ae 78 LYS cc_start: 0.9013 (mppt) cc_final: 0.8538 (mmmm) REVERT: Ae 108 SER cc_start: 0.8817 (p) cc_final: 0.8557 (t) REVERT: Ae 118 MET cc_start: 0.9083 (tpt) cc_final: 0.8686 (tpt) REVERT: Ae 136 MET cc_start: 0.8264 (ttp) cc_final: 0.8026 (ttm) REVERT: Ae 138 ASP cc_start: 0.8106 (t70) cc_final: 0.7585 (t70) REVERT: Ae 174 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7252 (tm-30) REVERT: Af 64 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8247 (ttpt) REVERT: Af 108 SER cc_start: 0.9065 (p) cc_final: 0.8744 (t) REVERT: Af 150 MET cc_start: 0.7967 (mmt) cc_final: 0.7517 (mmt) REVERT: Af 222 MET cc_start: 0.7695 (mtp) cc_final: 0.6758 (tmm) REVERT: Ag 75 TYR cc_start: 0.8831 (t80) cc_final: 0.8479 (t80) REVERT: Ag 108 SER cc_start: 0.9122 (p) cc_final: 0.8897 (t) REVERT: Ag 138 ASP cc_start: 0.8243 (t70) cc_final: 0.7803 (t70) REVERT: Ag 174 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7685 (tm-30) REVERT: Ag 222 MET cc_start: 0.7432 (mtm) cc_final: 0.7118 (mtt) REVERT: Ah 78 LYS cc_start: 0.8982 (mppt) cc_final: 0.8669 (mmmm) REVERT: Ah 81 ASP cc_start: 0.8468 (m-30) cc_final: 0.8107 (t0) REVERT: Ah 138 ASP cc_start: 0.8190 (t70) cc_final: 0.7629 (t70) REVERT: Ah 162 MET cc_start: 0.8911 (mmm) cc_final: 0.8710 (mmm) REVERT: Ah 174 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7363 (tm-30) REVERT: Ah 175 MET cc_start: 0.9095 (tmm) cc_final: 0.8863 (tmm) REVERT: Ah 222 MET cc_start: 0.7540 (mtm) cc_final: 0.7301 (mtt) REVERT: Ai 64 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8234 (ttpt) REVERT: Ai 137 MET cc_start: 0.8886 (mmm) cc_final: 0.8259 (mmm) REVERT: Ai 138 ASP cc_start: 0.8100 (t70) cc_final: 0.7838 (t70) REVERT: Ai 210 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8261 (mtt-85) REVERT: Ai 222 MET cc_start: 0.7848 (mtm) cc_final: 0.7626 (ttm) REVERT: Aj 57 THR cc_start: 0.9185 (m) cc_final: 0.8871 (m) REVERT: Aj 137 MET cc_start: 0.8853 (mmm) cc_final: 0.8408 (mmm) REVERT: Aj 138 ASP cc_start: 0.8146 (t70) cc_final: 0.7716 (t70) REVERT: Aj 174 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7651 (tm-30) REVERT: Aj 203 ASP cc_start: 0.8376 (t0) cc_final: 0.8145 (t0) REVERT: Ak 71 HIS cc_start: 0.8122 (t70) cc_final: 0.7899 (t-90) REVERT: Ak 81 ASP cc_start: 0.8475 (m-30) cc_final: 0.8158 (t0) REVERT: Ak 138 ASP cc_start: 0.8315 (t70) cc_final: 0.7857 (t70) REVERT: Ak 199 ARG cc_start: 0.9093 (mtp85) cc_final: 0.8518 (ttm110) REVERT: Ak 222 MET cc_start: 0.7694 (mtp) cc_final: 0.7455 (ttm) REVERT: Al 108 SER cc_start: 0.9007 (p) cc_final: 0.8797 (t) REVERT: Al 137 MET cc_start: 0.8824 (mmm) cc_final: 0.8285 (mmm) REVERT: Al 174 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7724 (tm-30) REVERT: Al 222 MET cc_start: 0.7753 (mtp) cc_final: 0.7064 (tmm) REVERT: Am 78 LYS cc_start: 0.8965 (mppt) cc_final: 0.8494 (mmmm) REVERT: Am 118 MET cc_start: 0.9098 (tpt) cc_final: 0.8674 (tpt) REVERT: Am 138 ASP cc_start: 0.8298 (t0) cc_final: 0.8090 (t0) REVERT: Am 174 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7256 (tm-30) REVERT: Am 194 ASP cc_start: 0.8630 (t70) cc_final: 0.8428 (t0) REVERT: An 64 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8239 (ttpt) REVERT: An 81 ASP cc_start: 0.8423 (m-30) cc_final: 0.8218 (t0) REVERT: An 108 SER cc_start: 0.8898 (p) cc_final: 0.8651 (t) REVERT: An 136 MET cc_start: 0.8437 (ttp) cc_final: 0.8144 (ttt) REVERT: An 138 ASP cc_start: 0.8271 (t70) cc_final: 0.8052 (t0) REVERT: An 150 MET cc_start: 0.7814 (mmt) cc_final: 0.7494 (mmt) REVERT: Ao 75 TYR cc_start: 0.8769 (t80) cc_final: 0.8364 (t80) REVERT: Ao 108 SER cc_start: 0.9113 (p) cc_final: 0.8786 (t) REVERT: Ao 137 MET cc_start: 0.8900 (mmm) cc_final: 0.8567 (mmm) REVERT: Ao 138 ASP cc_start: 0.8162 (t70) cc_final: 0.7922 (t0) REVERT: Ap 78 LYS cc_start: 0.8931 (mppt) cc_final: 0.8403 (mmmm) REVERT: Ap 108 SER cc_start: 0.8984 (p) cc_final: 0.8770 (t) REVERT: Ap 162 MET cc_start: 0.8897 (mmm) cc_final: 0.8664 (mmm) REVERT: Ap 174 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7377 (tm-30) REVERT: Ap 175 MET cc_start: 0.9133 (tmm) cc_final: 0.8905 (tmm) REVERT: Aq 64 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8223 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8886 (t80) cc_final: 0.8583 (t80) REVERT: Aq 107 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6872 (tm-30) REVERT: Aq 108 SER cc_start: 0.9056 (p) cc_final: 0.8850 (t) REVERT: Aq 111 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8036 (mt-10) REVERT: Aq 123 GLU cc_start: 0.8909 (tp30) cc_final: 0.8682 (tp30) REVERT: Aq 138 ASP cc_start: 0.8266 (t70) cc_final: 0.8040 (t0) REVERT: Ar 137 MET cc_start: 0.8815 (mmm) cc_final: 0.8540 (mmm) REVERT: Ar 174 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7543 (tm-30) REVERT: Ar 190 ARG cc_start: 0.8748 (mmt-90) cc_final: 0.8440 (tpt170) REVERT: Ar 203 ASP cc_start: 0.8342 (t0) cc_final: 0.8072 (t0) REVERT: As 55 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8309 (mppt) REVERT: As 78 LYS cc_start: 0.9014 (mppt) cc_final: 0.8430 (mmmm) REVERT: As 81 ASP cc_start: 0.8433 (m-30) cc_final: 0.8016 (t0) REVERT: As 162 MET cc_start: 0.9048 (tpt) cc_final: 0.8841 (tpt) REVERT: As 174 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7716 (tp30) REVERT: At 137 MET cc_start: 0.8750 (mmm) cc_final: 0.8229 (mmm) REVERT: At 138 ASP cc_start: 0.8022 (t70) cc_final: 0.7813 (t0) REVERT: At 174 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7672 (tm-30) REVERT: At 222 MET cc_start: 0.7771 (mtp) cc_final: 0.7363 (ttm) REVERT: Au 78 LYS cc_start: 0.8905 (mppt) cc_final: 0.8426 (mmmm) REVERT: Au 118 MET cc_start: 0.9400 (tpt) cc_final: 0.8591 (tpt) REVERT: Av 64 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7997 (ttpt) REVERT: Av 81 ASP cc_start: 0.8271 (m-30) cc_final: 0.8058 (t0) REVERT: Av 108 SER cc_start: 0.8949 (p) cc_final: 0.8716 (t) REVERT: Av 138 ASP cc_start: 0.8417 (t70) cc_final: 0.8145 (t0) REVERT: Av 222 MET cc_start: 0.7756 (mtp) cc_final: 0.7452 (ttm) REVERT: Aw 75 TYR cc_start: 0.8801 (t80) cc_final: 0.8435 (t80) REVERT: Aw 108 SER cc_start: 0.8958 (p) cc_final: 0.8630 (t) REVERT: Aw 137 MET cc_start: 0.8800 (mmm) cc_final: 0.8438 (mmm) REVERT: Ax 78 LYS cc_start: 0.8901 (mppt) cc_final: 0.8505 (mmmm) REVERT: Ax 108 SER cc_start: 0.8973 (p) cc_final: 0.8735 (t) REVERT: Ax 150 MET cc_start: 0.8025 (mmt) cc_final: 0.7642 (mmt) REVERT: Ax 162 MET cc_start: 0.8943 (mmm) cc_final: 0.8679 (mmm) REVERT: Ax 174 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Ay 64 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8068 (ttpt) REVERT: Ay 107 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6826 (tm-30) REVERT: Ay 108 SER cc_start: 0.9117 (p) cc_final: 0.8888 (t) REVERT: Ay 111 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8064 (mt-10) REVERT: Ay 118 MET cc_start: 0.9346 (tpt) cc_final: 0.9036 (tpt) REVERT: Ay 123 GLU cc_start: 0.8909 (tp30) cc_final: 0.8708 (tp30) REVERT: Ay 138 ASP cc_start: 0.8326 (t70) cc_final: 0.8100 (t0) REVERT: Ay 150 MET cc_start: 0.7745 (mmt) cc_final: 0.7147 (mmt) REVERT: Az 118 MET cc_start: 0.9263 (tpt) cc_final: 0.8543 (tpt) REVERT: Az 137 MET cc_start: 0.8734 (mmm) cc_final: 0.8422 (mmm) REVERT: Az 174 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7557 (tm-30) REVERT: Az 203 ASP cc_start: 0.8359 (t0) cc_final: 0.8132 (t0) REVERT: Ba 78 LYS cc_start: 0.9017 (mppt) cc_final: 0.8506 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8450 (m-30) cc_final: 0.8029 (t0) REVERT: Ba 174 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7426 (tm-30) REVERT: Bb 137 MET cc_start: 0.8809 (mmm) cc_final: 0.8348 (mmm) REVERT: Bb 138 ASP cc_start: 0.8260 (t70) cc_final: 0.7983 (t0) REVERT: Bb 222 MET cc_start: 0.7422 (mtm) cc_final: 0.7157 (mtt) REVERT: Bc 78 LYS cc_start: 0.8923 (mppt) cc_final: 0.8448 (mmmm) REVERT: Bc 118 MET cc_start: 0.9389 (tpt) cc_final: 0.8539 (tpt) REVERT: Bc 136 MET cc_start: 0.8623 (ttp) cc_final: 0.8400 (ttt) REVERT: Bc 194 ASP cc_start: 0.8579 (t70) cc_final: 0.8374 (t0) REVERT: Bd 57 THR cc_start: 0.9108 (m) cc_final: 0.8715 (p) REVERT: Bd 75 TYR cc_start: 0.8807 (t80) cc_final: 0.8580 (t80) REVERT: Bd 76 LYS cc_start: 0.8968 (mttt) cc_final: 0.8364 (tptt) REVERT: Bd 108 SER cc_start: 0.9098 (p) cc_final: 0.8844 (t) REVERT: Bd 136 MET cc_start: 0.8326 (ttp) cc_final: 0.8089 (ttt) outliers start: 207 outliers final: 128 residues processed: 1643 average time/residue: 0.2726 time to fit residues: 722.8991 Evaluate side-chains 1576 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1447 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 97 ASP Chi-restraints excluded: chain Aa residue 162 MET Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ac residue 115 ASN Chi-restraints excluded: chain Ac residue 135 THR Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 160 GLN Chi-restraints excluded: chain Af residue 197 LEU Chi-restraints excluded: chain Ag residue 49 LEU Chi-restraints excluded: chain Ag residue 73 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ah residue 99 VAL Chi-restraints excluded: chain Ah residue 135 THR Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 97 ASP Chi-restraints excluded: chain Ai residue 135 THR Chi-restraints excluded: chain Ai residue 197 LEU Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 135 THR Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 97 ASP Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 160 GLN Chi-restraints excluded: chain An residue 197 LEU Chi-restraints excluded: chain Ao residue 49 LEU Chi-restraints excluded: chain Ao residue 73 LEU Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 115 ASN Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 97 ASP Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Ar residue 69 LEU Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain At residue 197 LEU Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 49 LEU Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 160 GLN Chi-restraints excluded: chain Av residue 197 LEU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 49 LEU Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 97 ASP Chi-restraints excluded: chain Ay residue 142 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 69 LEU Chi-restraints excluded: chain Az residue 73 LEU Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Az residue 135 THR Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 97 ASP Chi-restraints excluded: chain Bb residue 160 GLN Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 135 THR Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 53 THR Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 160 GLN Chi-restraints excluded: chain Bd residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 98 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 428 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 chunk 281 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 71 HIS ** Ab 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 160 GLN Ac 115 ASN Ac 124 ASN Ad 142 GLN ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 124 ASN Ai 124 ASN ** Aj 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 142 GLN ** Am 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 71 HIS Ap 115 ASN Ap 124 ASN Aq 124 ASN ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 71 HIS Ax 160 GLN Ay 124 ASN ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116176 restraints weight = 70570.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119177 restraints weight = 47732.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121333 restraints weight = 36239.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122860 restraints weight = 29829.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123720 restraints weight = 25862.460| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 45930 Z= 0.205 Angle : 0.658 7.669 62010 Z= 0.329 Chirality : 0.038 0.128 6630 Planarity : 0.005 0.054 7980 Dihedral : 4.086 15.738 6120 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.81 % Allowed : 20.41 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.11), residues: 5490 helix: -0.05 (0.10), residues: 2700 sheet: -2.41 (0.22), residues: 360 loop : -1.31 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGBb 176 TYR 0.023 0.002 TYRAu 200 PHE 0.018 0.003 PHEBa 165 TRP 0.018 0.003 TRPAf 95 HIS 0.005 0.001 HISAh 71 Details of bonding type rmsd covalent geometry : bond 0.00494 (45930) covalent geometry : angle 0.65813 (62010) hydrogen bonds : bond 0.04086 ( 1920) hydrogen bonds : angle 4.40871 ( 5400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1765 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 1530 time to evaluate : 1.052 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 108 SER cc_start: 0.9073 (p) cc_final: 0.8833 (t) REVERT: Aa 138 ASP cc_start: 0.8085 (t70) cc_final: 0.7644 (t0) REVERT: Aa 148 LYS cc_start: 0.8771 (ttpp) cc_final: 0.8516 (ttpp) REVERT: Aa 174 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7537 (tm-30) REVERT: Aa 178 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8418 (mtp180) REVERT: Aa 222 MET cc_start: 0.7756 (mtm) cc_final: 0.7377 (ttm) REVERT: Ab 136 MET cc_start: 0.8228 (ttp) cc_final: 0.8005 (ttp) REVERT: Ab 138 ASP cc_start: 0.8147 (t70) cc_final: 0.7737 (t70) REVERT: Ab 174 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7631 (tm-30) REVERT: Ab 190 ARG cc_start: 0.8701 (mpt180) cc_final: 0.8052 (tpp80) REVERT: Ac 75 TYR cc_start: 0.8908 (t80) cc_final: 0.8638 (t80) REVERT: Ac 81 ASP cc_start: 0.8331 (m-30) cc_final: 0.8044 (t0) REVERT: Ac 91 GLN cc_start: 0.8637 (mt0) cc_final: 0.8351 (mt0) REVERT: Ac 106 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: Ac 138 ASP cc_start: 0.8360 (t70) cc_final: 0.7854 (t70) REVERT: Ac 162 MET cc_start: 0.8826 (tpp) cc_final: 0.8482 (tpt) REVERT: Ac 222 MET cc_start: 0.7722 (mtm) cc_final: 0.7341 (mtt) REVERT: Ad 137 MET cc_start: 0.8817 (mmm) cc_final: 0.8315 (mmm) REVERT: Ad 138 ASP cc_start: 0.8032 (t70) cc_final: 0.7722 (t70) REVERT: Ad 174 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7653 (tm-30) REVERT: Ad 222 MET cc_start: 0.7765 (mtp) cc_final: 0.7373 (ttm) REVERT: Ae 78 LYS cc_start: 0.9070 (mppt) cc_final: 0.8618 (mmmm) REVERT: Ae 108 SER cc_start: 0.8890 (p) cc_final: 0.8607 (t) REVERT: Ae 118 MET cc_start: 0.9104 (tpt) cc_final: 0.8699 (tpt) REVERT: Ae 136 MET cc_start: 0.8235 (ttp) cc_final: 0.8012 (ttt) REVERT: Ae 138 ASP cc_start: 0.8099 (t70) cc_final: 0.7596 (t70) REVERT: Ae 174 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7279 (tm-30) REVERT: Af 64 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8258 (ttpt) REVERT: Af 108 SER cc_start: 0.9083 (p) cc_final: 0.8833 (t) REVERT: Af 110 MET cc_start: 0.8624 (tpp) cc_final: 0.8419 (mmt) REVERT: Af 150 MET cc_start: 0.7799 (mmt) cc_final: 0.7290 (mmt) REVERT: Af 222 MET cc_start: 0.7667 (mtp) cc_final: 0.7306 (ttm) REVERT: Ag 75 TYR cc_start: 0.8898 (t80) cc_final: 0.8505 (t80) REVERT: Ag 108 SER cc_start: 0.9085 (p) cc_final: 0.8773 (t) REVERT: Ag 138 ASP cc_start: 0.8258 (t70) cc_final: 0.7841 (t70) REVERT: Ag 174 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7636 (tm-30) REVERT: Ag 222 MET cc_start: 0.7365 (mtm) cc_final: 0.7023 (mtt) REVERT: Ah 78 LYS cc_start: 0.9028 (mppt) cc_final: 0.8636 (mmmm) REVERT: Ah 81 ASP cc_start: 0.8439 (m-30) cc_final: 0.8146 (t0) REVERT: Ah 138 ASP cc_start: 0.8245 (t70) cc_final: 0.7671 (t70) REVERT: Ah 174 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7333 (tm-30) REVERT: Ah 175 MET cc_start: 0.9057 (tmm) cc_final: 0.8820 (tmm) REVERT: Ai 93 GLN cc_start: 0.9066 (tp40) cc_final: 0.8330 (tp40) REVERT: Ai 137 MET cc_start: 0.8912 (mmm) cc_final: 0.8262 (mmm) REVERT: Ai 138 ASP cc_start: 0.8210 (t70) cc_final: 0.7795 (t70) REVERT: Ai 150 MET cc_start: 0.7962 (mmt) cc_final: 0.7490 (mmt) REVERT: Ai 162 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8585 (tpt) REVERT: Ai 174 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7312 (tm-30) REVERT: Ai 222 MET cc_start: 0.7800 (mtm) cc_final: 0.7579 (ttm) REVERT: Aj 57 THR cc_start: 0.9230 (m) cc_final: 0.8925 (m) REVERT: Aj 78 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8813 (mmmm) REVERT: Aj 138 ASP cc_start: 0.8129 (t70) cc_final: 0.7719 (t70) REVERT: Aj 174 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7610 (tm-30) REVERT: Aj 190 ARG cc_start: 0.8779 (mpt180) cc_final: 0.8018 (tpp80) REVERT: Aj 197 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7826 (tt) REVERT: Ak 81 ASP cc_start: 0.8447 (m-30) cc_final: 0.7962 (t0) REVERT: Ak 106 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6895 (pt0) REVERT: Ak 138 ASP cc_start: 0.8244 (t70) cc_final: 0.7816 (t70) REVERT: Ak 199 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8471 (ttm110) REVERT: Ak 222 MET cc_start: 0.7679 (mtp) cc_final: 0.7455 (ttm) REVERT: Al 137 MET cc_start: 0.8805 (mmm) cc_final: 0.8242 (mmm) REVERT: Al 174 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7655 (tm-30) REVERT: Al 222 MET cc_start: 0.7753 (mtp) cc_final: 0.6846 (tmm) REVERT: Am 50 LYS cc_start: 0.6863 (mtmm) cc_final: 0.5335 (ttmm) REVERT: Am 78 LYS cc_start: 0.8991 (mppt) cc_final: 0.8534 (mmmm) REVERT: Am 118 MET cc_start: 0.9122 (tpt) cc_final: 0.8727 (tpt) REVERT: Am 174 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7319 (tm-30) REVERT: An 64 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8326 (ttpt) REVERT: An 108 SER cc_start: 0.8906 (p) cc_final: 0.8669 (t) REVERT: An 136 MET cc_start: 0.8419 (ttp) cc_final: 0.8140 (ttt) REVERT: An 150 MET cc_start: 0.7755 (mmt) cc_final: 0.7389 (mmt) REVERT: An 174 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7294 (tm-30) REVERT: An 222 MET cc_start: 0.7517 (mtm) cc_final: 0.7197 (mtt) REVERT: Ao 75 TYR cc_start: 0.8782 (t80) cc_final: 0.8434 (t80) REVERT: Ao 108 SER cc_start: 0.9112 (p) cc_final: 0.8808 (t) REVERT: Ao 138 ASP cc_start: 0.8243 (t70) cc_final: 0.7984 (t0) REVERT: Ao 174 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7637 (tm-30) REVERT: Ap 78 LYS cc_start: 0.8922 (mppt) cc_final: 0.8491 (mmmm) REVERT: Ap 108 SER cc_start: 0.8912 (p) cc_final: 0.8662 (t) REVERT: Ap 174 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7348 (tm-30) REVERT: Ap 175 MET cc_start: 0.9099 (tmm) cc_final: 0.8833 (tmm) REVERT: Ap 222 MET cc_start: 0.7576 (mtm) cc_final: 0.7245 (mtt) REVERT: Aq 64 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8325 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8891 (t80) cc_final: 0.8486 (t80) REVERT: Aq 93 GLN cc_start: 0.9044 (tp40) cc_final: 0.8326 (tp40) REVERT: Aq 138 ASP cc_start: 0.8355 (t70) cc_final: 0.8059 (t0) REVERT: Aq 162 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8684 (tpt) REVERT: Ar 78 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8749 (mmmm) REVERT: Ar 174 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7619 (tm-30) REVERT: Ar 190 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8258 (mmt-90) REVERT: Ar 197 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7766 (tt) REVERT: Ar 203 ASP cc_start: 0.8352 (t0) cc_final: 0.8132 (t0) REVERT: As 55 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8332 (mppt) REVERT: As 78 LYS cc_start: 0.9043 (mppt) cc_final: 0.8469 (mmmm) REVERT: As 81 ASP cc_start: 0.8379 (m-30) cc_final: 0.8143 (t0) REVERT: As 174 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7683 (tp30) REVERT: At 138 ASP cc_start: 0.8147 (t70) cc_final: 0.7899 (t0) REVERT: At 174 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7635 (tm-30) REVERT: At 222 MET cc_start: 0.7779 (mtp) cc_final: 0.7369 (ttm) REVERT: Au 78 LYS cc_start: 0.8999 (mppt) cc_final: 0.8510 (mmmm) REVERT: Au 108 SER cc_start: 0.8994 (p) cc_final: 0.8695 (t) REVERT: Au 222 MET cc_start: 0.7344 (mtm) cc_final: 0.7130 (mtm) REVERT: Av 64 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8095 (ttpt) REVERT: Av 81 ASP cc_start: 0.8273 (m-30) cc_final: 0.8062 (t0) REVERT: Av 104 GLU cc_start: 0.7412 (pt0) cc_final: 0.7027 (pt0) REVERT: Av 136 MET cc_start: 0.8363 (ttp) cc_final: 0.8020 (ttt) REVERT: Av 222 MET cc_start: 0.7776 (mtp) cc_final: 0.7529 (ttm) REVERT: Aw 75 TYR cc_start: 0.8857 (t80) cc_final: 0.8470 (t80) REVERT: Aw 108 SER cc_start: 0.8944 (p) cc_final: 0.8630 (t) REVERT: Aw 137 MET cc_start: 0.8774 (mmm) cc_final: 0.8405 (mmm) REVERT: Aw 174 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7555 (tm-30) REVERT: Ax 78 LYS cc_start: 0.8893 (mppt) cc_final: 0.8498 (mmmm) REVERT: Ax 108 SER cc_start: 0.8930 (p) cc_final: 0.8708 (t) REVERT: Ax 150 MET cc_start: 0.7936 (mmt) cc_final: 0.7535 (mmt) REVERT: Ax 162 MET cc_start: 0.8885 (mmm) cc_final: 0.8634 (mmm) REVERT: Ax 174 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7356 (tm-30) REVERT: Ay 64 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8287 (ttpt) REVERT: Ay 93 GLN cc_start: 0.9053 (tp40) cc_final: 0.8286 (tp40) REVERT: Ay 118 MET cc_start: 0.9262 (tpt) cc_final: 0.8867 (tpt) REVERT: Ay 138 ASP cc_start: 0.8438 (t70) cc_final: 0.8197 (t0) REVERT: Az 108 SER cc_start: 0.8779 (p) cc_final: 0.8545 (t) REVERT: Az 118 MET cc_start: 0.9197 (tpt) cc_final: 0.8446 (tpt) REVERT: Az 174 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7569 (tm-30) REVERT: Az 178 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8221 (mtp180) REVERT: Az 190 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.7609 (tpp-160) REVERT: Az 197 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8002 (tt) REVERT: Az 203 ASP cc_start: 0.8395 (t0) cc_final: 0.8156 (t0) REVERT: Ba 78 LYS cc_start: 0.9028 (mppt) cc_final: 0.8499 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8454 (m-30) cc_final: 0.8225 (t0) REVERT: Ba 110 MET cc_start: 0.8557 (tpp) cc_final: 0.7979 (mmt) REVERT: Ba 174 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7449 (tm-30) REVERT: Bb 138 ASP cc_start: 0.8200 (t70) cc_final: 0.7996 (t0) REVERT: Bc 78 LYS cc_start: 0.8975 (mppt) cc_final: 0.8521 (mmmm) REVERT: Bc 108 SER cc_start: 0.8942 (p) cc_final: 0.8608 (t) REVERT: Bc 136 MET cc_start: 0.8593 (ttp) cc_final: 0.8342 (ttt) REVERT: Bd 57 THR cc_start: 0.9133 (m) cc_final: 0.8737 (p) REVERT: Bd 75 TYR cc_start: 0.8721 (t80) cc_final: 0.8473 (t80) REVERT: Bd 76 LYS cc_start: 0.9061 (mttt) cc_final: 0.8388 (tptt) REVERT: Bd 136 MET cc_start: 0.8335 (ttp) cc_final: 0.8062 (ttt) REVERT: Bd 222 MET cc_start: 0.7678 (mtm) cc_final: 0.7373 (mtt) outliers start: 235 outliers final: 161 residues processed: 1636 average time/residue: 0.2376 time to fit residues: 623.9371 Evaluate side-chains 1603 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1435 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 97 ASP Chi-restraints excluded: chain Aa residue 106 GLU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 106 GLU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ac residue 106 GLU Chi-restraints excluded: chain Ac residue 115 ASN Chi-restraints excluded: chain Ac residue 135 THR Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 97 ASP Chi-restraints excluded: chain Ad residue 106 GLU Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 52 MET Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 104 GLU Chi-restraints excluded: chain Ae residue 106 GLU Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 106 GLU Chi-restraints excluded: chain Af residue 197 LEU Chi-restraints excluded: chain Ag residue 49 LEU Chi-restraints excluded: chain Ag residue 73 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ah residue 106 GLU Chi-restraints excluded: chain Ah residue 135 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 81 ASP Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 97 ASP Chi-restraints excluded: chain Ai residue 124 ASN Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Ai residue 162 MET Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 106 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 197 LEU Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Ak residue 106 GLU Chi-restraints excluded: chain Ak residue 135 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 97 ASP Chi-restraints excluded: chain Al residue 106 GLU Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 49 LEU Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 106 GLU Chi-restraints excluded: chain An residue 197 LEU Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 49 LEU Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ao residue 106 GLU Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 106 GLU Chi-restraints excluded: chain Ap residue 115 ASN Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 97 ASP Chi-restraints excluded: chain Aq residue 124 ASN Chi-restraints excluded: chain Aq residue 162 MET Chi-restraints excluded: chain Ar residue 49 LEU Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 197 LEU Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 106 GLU Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 49 LEU Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Av residue 197 LEU Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 73 LEU Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Aw residue 106 GLU Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 49 LEU Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 106 GLU Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 97 ASP Chi-restraints excluded: chain Ay residue 124 ASN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 52 MET Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 86 ARG Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Az residue 135 THR Chi-restraints excluded: chain Az residue 197 LEU Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 53 THR Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 106 GLU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 97 ASP Chi-restraints excluded: chain Bb residue 160 GLN Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 135 THR Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 53 THR Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 106 GLU Chi-restraints excluded: chain Bd residue 160 GLN Chi-restraints excluded: chain Bd residue 197 LEU Chi-restraints excluded: chain Bd residue 213 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 37 optimal weight: 4.9990 chunk 367 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 446 optimal weight: 7.9990 chunk 439 optimal weight: 0.9980 chunk 371 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 479 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 160 GLN Ac 124 ASN Ad 71 HIS Ad 142 GLN ** Af 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 ASN ** Aj 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 142 GLN An 71 HIS Aq 124 ASN Au 71 HIS Ay 124 ASN ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 142 GLN ** Bc 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119260 restraints weight = 70532.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122522 restraints weight = 46957.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124840 restraints weight = 35110.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126444 restraints weight = 28397.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127694 restraints weight = 24286.498| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45930 Z= 0.129 Angle : 0.599 9.892 62010 Z= 0.301 Chirality : 0.036 0.130 6630 Planarity : 0.005 0.058 7980 Dihedral : 4.020 15.268 6120 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.66 % Allowed : 22.11 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.11), residues: 5490 helix: 0.19 (0.10), residues: 2700 sheet: -2.30 (0.21), residues: 360 loop : -1.00 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAr 48 TYR 0.027 0.002 TYRAu 200 PHE 0.016 0.002 PHEAy 165 TRP 0.018 0.002 TRPAc 95 HIS 0.005 0.001 HISAb 71 Details of bonding type rmsd covalent geometry : bond 0.00321 (45930) covalent geometry : angle 0.59877 (62010) hydrogen bonds : bond 0.03245 ( 1920) hydrogen bonds : angle 4.22388 ( 5400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1766 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1587 time to evaluate : 2.208 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 108 SER cc_start: 0.8949 (p) cc_final: 0.8683 (t) REVERT: Aa 138 ASP cc_start: 0.8060 (t70) cc_final: 0.7687 (t0) REVERT: Aa 148 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8472 (ttpp) REVERT: Aa 178 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8385 (mtp180) REVERT: Aa 222 MET cc_start: 0.7802 (mtm) cc_final: 0.7483 (ttm) REVERT: Ab 110 MET cc_start: 0.8403 (tpp) cc_final: 0.8198 (mmt) REVERT: Ab 137 MET cc_start: 0.8779 (mmm) cc_final: 0.8537 (mmm) REVERT: Ab 138 ASP cc_start: 0.8085 (t70) cc_final: 0.7699 (t70) REVERT: Ab 190 ARG cc_start: 0.8632 (mpt180) cc_final: 0.8055 (tpp80) REVERT: Ac 75 TYR cc_start: 0.8928 (t80) cc_final: 0.8723 (t80) REVERT: Ac 91 GLN cc_start: 0.8621 (mt0) cc_final: 0.8385 (mt0) REVERT: Ac 93 GLN cc_start: 0.9107 (tp40) cc_final: 0.8725 (tp40) REVERT: Ac 110 MET cc_start: 0.8451 (tpp) cc_final: 0.8035 (mmt) REVERT: Ac 138 ASP cc_start: 0.8250 (t70) cc_final: 0.7863 (t70) REVERT: Ac 162 MET cc_start: 0.8736 (tpp) cc_final: 0.8369 (tpt) REVERT: Ac 214 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: Ad 137 MET cc_start: 0.8827 (mmm) cc_final: 0.8353 (mmm) REVERT: Ad 138 ASP cc_start: 0.7928 (t70) cc_final: 0.7702 (t70) REVERT: Ad 222 MET cc_start: 0.7717 (mtp) cc_final: 0.7463 (ttm) REVERT: Ae 78 LYS cc_start: 0.8990 (mppt) cc_final: 0.8550 (mmmm) REVERT: Ae 108 SER cc_start: 0.8696 (p) cc_final: 0.8425 (t) REVERT: Ae 138 ASP cc_start: 0.8084 (t70) cc_final: 0.7616 (t70) REVERT: Ae 197 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7824 (tt) REVERT: Af 64 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8288 (ttpt) REVERT: Af 93 GLN cc_start: 0.9040 (tp40) cc_final: 0.8568 (tp40) REVERT: Af 108 SER cc_start: 0.8929 (p) cc_final: 0.8612 (t) REVERT: Af 222 MET cc_start: 0.7739 (mtp) cc_final: 0.7337 (ttm) REVERT: Ag 75 TYR cc_start: 0.8890 (t80) cc_final: 0.8549 (t80) REVERT: Ag 108 SER cc_start: 0.9011 (p) cc_final: 0.8686 (t) REVERT: Ag 138 ASP cc_start: 0.8226 (t70) cc_final: 0.7817 (t70) REVERT: Ag 222 MET cc_start: 0.7482 (mtm) cc_final: 0.7156 (mtt) REVERT: Ah 78 LYS cc_start: 0.9019 (mppt) cc_final: 0.8711 (mmmm) REVERT: Ah 138 ASP cc_start: 0.8222 (t70) cc_final: 0.7655 (t70) REVERT: Ai 64 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8277 (ttpt) REVERT: Ai 93 GLN cc_start: 0.9022 (tp40) cc_final: 0.8279 (tp40) REVERT: Ai 137 MET cc_start: 0.8848 (mmm) cc_final: 0.8264 (mmm) REVERT: Ai 138 ASP cc_start: 0.8184 (t70) cc_final: 0.7764 (t70) REVERT: Ai 222 MET cc_start: 0.7673 (mtm) cc_final: 0.7458 (ttm) REVERT: Aj 57 THR cc_start: 0.9191 (m) cc_final: 0.8912 (m) REVERT: Aj 78 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8708 (mmmm) REVERT: Aj 138 ASP cc_start: 0.8138 (t70) cc_final: 0.7725 (t70) REVERT: Ak 75 TYR cc_start: 0.8953 (t80) cc_final: 0.8722 (t80) REVERT: Ak 81 ASP cc_start: 0.8461 (m-30) cc_final: 0.8211 (t0) REVERT: Ak 106 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6701 (pt0) REVERT: Ak 110 MET cc_start: 0.8435 (tpp) cc_final: 0.8040 (mmt) REVERT: Ak 138 ASP cc_start: 0.8206 (t70) cc_final: 0.7850 (t70) REVERT: Ak 214 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8111 (mtm-85) REVERT: Ak 222 MET cc_start: 0.7673 (mtp) cc_final: 0.7438 (ttm) REVERT: Al 137 MET cc_start: 0.8837 (mmm) cc_final: 0.8282 (mmm) REVERT: Al 222 MET cc_start: 0.7780 (mtp) cc_final: 0.7456 (ttm) REVERT: Am 78 LYS cc_start: 0.8940 (mppt) cc_final: 0.8514 (mmmm) REVERT: Am 104 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: An 64 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8342 (ttpt) REVERT: An 76 LYS cc_start: 0.8887 (mttt) cc_final: 0.8569 (mtmm) REVERT: An 93 GLN cc_start: 0.9006 (tp40) cc_final: 0.8570 (tp40) REVERT: An 108 SER cc_start: 0.8781 (p) cc_final: 0.8500 (t) REVERT: An 136 MET cc_start: 0.8368 (ttp) cc_final: 0.8135 (ttt) REVERT: An 222 MET cc_start: 0.7647 (mtm) cc_final: 0.7284 (mtt) REVERT: Ao 75 TYR cc_start: 0.8812 (t80) cc_final: 0.8561 (t80) REVERT: Ao 108 SER cc_start: 0.9006 (p) cc_final: 0.8593 (t) REVERT: Ao 176 ARG cc_start: 0.9129 (mmm-85) cc_final: 0.8477 (mmm-85) REVERT: Ap 78 LYS cc_start: 0.8869 (mppt) cc_final: 0.8544 (mmmm) REVERT: Ap 108 SER cc_start: 0.8875 (p) cc_final: 0.8615 (t) REVERT: Ap 135 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8869 (t) REVERT: Ap 162 MET cc_start: 0.8857 (mmm) cc_final: 0.8638 (mmm) REVERT: Aq 64 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8287 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8928 (t80) cc_final: 0.8573 (t80) REVERT: Aq 81 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8012 (t0) REVERT: Aq 93 GLN cc_start: 0.9018 (tp40) cc_final: 0.8317 (tp40) REVERT: Ar 78 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8673 (mmmm) REVERT: Ar 100 MET cc_start: 0.7765 (tpp) cc_final: 0.7531 (tpp) REVERT: As 55 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8314 (ptpt) REVERT: As 78 LYS cc_start: 0.9016 (mppt) cc_final: 0.8450 (mmmm) REVERT: As 93 GLN cc_start: 0.9035 (tp40) cc_final: 0.8676 (tp40) REVERT: As 110 MET cc_start: 0.8545 (tpp) cc_final: 0.8050 (mmt) REVERT: At 136 MET cc_start: 0.8190 (ttp) cc_final: 0.7915 (ttm) REVERT: At 222 MET cc_start: 0.7826 (mtp) cc_final: 0.7160 (tmm) REVERT: Au 78 LYS cc_start: 0.8941 (mppt) cc_final: 0.8491 (mmmm) REVERT: Au 108 SER cc_start: 0.8918 (p) cc_final: 0.8615 (t) REVERT: Au 118 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.9175 (tmm) REVERT: Au 174 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7576 (tp30) REVERT: Au 176 ARG cc_start: 0.9119 (mmm-85) cc_final: 0.8287 (mmm-85) REVERT: Av 64 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8078 (ttpt) REVERT: Av 93 GLN cc_start: 0.9065 (tp40) cc_final: 0.8548 (tp40) REVERT: Av 136 MET cc_start: 0.8280 (ttp) cc_final: 0.7945 (ttt) REVERT: Av 222 MET cc_start: 0.7810 (mtp) cc_final: 0.7566 (ttm) REVERT: Aw 75 TYR cc_start: 0.8869 (t80) cc_final: 0.8542 (t80) REVERT: Aw 108 SER cc_start: 0.8815 (p) cc_final: 0.8477 (t) REVERT: Aw 137 MET cc_start: 0.8703 (mmm) cc_final: 0.8468 (mmm) REVERT: Aw 176 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8828 (mmm-85) REVERT: Aw 222 MET cc_start: 0.7581 (mtm) cc_final: 0.7301 (mtt) REVERT: Ax 78 LYS cc_start: 0.8830 (mppt) cc_final: 0.8484 (mmmm) REVERT: Ax 108 SER cc_start: 0.8936 (p) cc_final: 0.8691 (t) REVERT: Ax 150 MET cc_start: 0.7786 (mmt) cc_final: 0.7444 (mmt) REVERT: Ax 197 LEU cc_start: 0.7941 (tp) cc_final: 0.7667 (tt) REVERT: Ay 64 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8278 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8027 (t0) REVERT: Ay 93 GLN cc_start: 0.9037 (tp40) cc_final: 0.8296 (tp40) REVERT: Ay 118 MET cc_start: 0.9233 (tpt) cc_final: 0.8832 (tpt) REVERT: Az 108 SER cc_start: 0.8744 (p) cc_final: 0.8468 (t) REVERT: Az 118 MET cc_start: 0.9216 (tpt) cc_final: 0.8486 (tpt) REVERT: Az 176 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8829 (mmm-85) REVERT: Az 190 ARG cc_start: 0.8594 (mmt-90) cc_final: 0.7687 (tpp-160) REVERT: Ba 78 LYS cc_start: 0.8982 (mppt) cc_final: 0.8504 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8441 (m-30) cc_final: 0.8232 (t0) REVERT: Bb 136 MET cc_start: 0.8213 (ttp) cc_final: 0.7872 (ttm) REVERT: Bb 137 MET cc_start: 0.8662 (mmm) cc_final: 0.8239 (mmm) REVERT: Bb 138 ASP cc_start: 0.8279 (t70) cc_final: 0.8053 (t0) REVERT: Bc 78 LYS cc_start: 0.8916 (mppt) cc_final: 0.8489 (mmmm) REVERT: Bc 108 SER cc_start: 0.8894 (p) cc_final: 0.8600 (t) REVERT: Bc 118 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9163 (tmm) REVERT: Bc 176 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8253 (mmm-85) REVERT: Bd 57 THR cc_start: 0.9105 (m) cc_final: 0.8687 (p) REVERT: Bd 75 TYR cc_start: 0.8771 (t80) cc_final: 0.8542 (t80) REVERT: Bd 76 LYS cc_start: 0.9062 (mttt) cc_final: 0.8468 (tptt) REVERT: Bd 93 GLN cc_start: 0.9084 (tp40) cc_final: 0.8605 (tp40) REVERT: Bd 136 MET cc_start: 0.8321 (ttp) cc_final: 0.8025 (ttt) REVERT: Bd 222 MET cc_start: 0.7736 (mtm) cc_final: 0.7461 (mtt) outliers start: 179 outliers final: 115 residues processed: 1666 average time/residue: 0.2554 time to fit residues: 684.7947 Evaluate side-chains 1570 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1447 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 106 GLU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 106 GLU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 106 GLU Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Ae residue 197 LEU Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 106 GLU Chi-restraints excluded: chain Af residue 197 LEU Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 49 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ah residue 106 GLU Chi-restraints excluded: chain Ah residue 135 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 73 LEU Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 106 GLU Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Ak residue 106 GLU Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 106 GLU Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Al residue 197 LEU Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 104 GLU Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 81 ASP Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 49 LEU Chi-restraints excluded: chain Ao residue 73 LEU Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 106 GLU Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 118 MET Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 118 MET Chi-restraints excluded: chain Bc residue 135 THR Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 213 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 393 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 249 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 504 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 160 GLN Ad 124 ASN Ad 142 GLN ** Af 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 160 GLN Ai 71 HIS Ai 124 ASN Ai 142 GLN Aj 71 HIS Al 142 GLN ** Am 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 124 ASN As 44 HIS ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 124 ASN ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 71 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.140562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116307 restraints weight = 71276.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119403 restraints weight = 48539.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121647 restraints weight = 36885.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123193 restraints weight = 30161.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124420 restraints weight = 26023.240| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45930 Z= 0.182 Angle : 0.669 10.841 62010 Z= 0.328 Chirality : 0.038 0.127 6630 Planarity : 0.005 0.063 7980 Dihedral : 4.076 16.380 6120 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.58 % Allowed : 23.64 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.11), residues: 5490 helix: -0.09 (0.10), residues: 2880 sheet: -2.30 (0.22), residues: 360 loop : -0.94 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGBc 199 TYR 0.028 0.002 TYRBc 200 PHE 0.019 0.003 PHEAi 165 TRP 0.016 0.003 TRPAn 95 HIS 0.005 0.001 HISAp 71 Details of bonding type rmsd covalent geometry : bond 0.00446 (45930) covalent geometry : angle 0.66865 (62010) hydrogen bonds : bond 0.03779 ( 1920) hydrogen bonds : angle 4.29579 ( 5400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1456 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7739 (t0) REVERT: Aa 108 SER cc_start: 0.9015 (p) cc_final: 0.8726 (t) REVERT: Aa 138 ASP cc_start: 0.8075 (t70) cc_final: 0.7854 (t70) REVERT: Aa 148 LYS cc_start: 0.8746 (ttpp) cc_final: 0.8504 (ttpp) REVERT: Aa 222 MET cc_start: 0.7846 (mtm) cc_final: 0.7535 (ttm) REVERT: Ab 137 MET cc_start: 0.8650 (mmm) cc_final: 0.8027 (mmm) REVERT: Ab 138 ASP cc_start: 0.8108 (t70) cc_final: 0.7739 (t70) REVERT: Ab 174 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7627 (tm-30) REVERT: Ab 190 ARG cc_start: 0.8665 (mpt180) cc_final: 0.8022 (tpp80) REVERT: Ac 81 ASP cc_start: 0.8255 (t0) cc_final: 0.7761 (t70) REVERT: Ac 91 GLN cc_start: 0.8607 (mt0) cc_final: 0.8360 (mt0) REVERT: Ac 93 GLN cc_start: 0.9108 (tp40) cc_final: 0.8713 (tp40) REVERT: Ac 138 ASP cc_start: 0.8204 (t70) cc_final: 0.7844 (t70) REVERT: Ac 162 MET cc_start: 0.8743 (tpp) cc_final: 0.8383 (tpt) REVERT: Ac 222 MET cc_start: 0.7742 (mtm) cc_final: 0.7376 (mtt) REVERT: Ad 137 MET cc_start: 0.8755 (mmm) cc_final: 0.8352 (tpp) REVERT: Ad 174 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7607 (tm-30) REVERT: Ad 222 MET cc_start: 0.7740 (mtp) cc_final: 0.7102 (tmm) REVERT: Ae 78 LYS cc_start: 0.9069 (mppt) cc_final: 0.8638 (mmmm) REVERT: Ae 106 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6677 (pt0) REVERT: Ae 138 ASP cc_start: 0.8101 (t70) cc_final: 0.7630 (t70) REVERT: Ae 197 LEU cc_start: 0.8249 (tp) cc_final: 0.7983 (tt) REVERT: Af 93 GLN cc_start: 0.9107 (tp40) cc_final: 0.8486 (tp40) REVERT: Af 108 SER cc_start: 0.8962 (p) cc_final: 0.8731 (t) REVERT: Af 222 MET cc_start: 0.7828 (mtp) cc_final: 0.7499 (ttm) REVERT: Ag 75 TYR cc_start: 0.8928 (t80) cc_final: 0.8474 (t80) REVERT: Ag 108 SER cc_start: 0.8960 (p) cc_final: 0.8592 (t) REVERT: Ag 138 ASP cc_start: 0.8280 (t70) cc_final: 0.7848 (t70) REVERT: Ag 174 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7616 (tm-30) REVERT: Ag 176 ARG cc_start: 0.9165 (mmm-85) cc_final: 0.8357 (mmm-85) REVERT: Ag 222 MET cc_start: 0.7487 (mtm) cc_final: 0.7096 (mtt) REVERT: Ah 78 LYS cc_start: 0.9005 (mppt) cc_final: 0.8789 (mmmm) REVERT: Ah 81 ASP cc_start: 0.8144 (t0) cc_final: 0.7703 (t0) REVERT: Ah 138 ASP cc_start: 0.8208 (t70) cc_final: 0.7670 (t70) REVERT: Ah 222 MET cc_start: 0.7677 (mtm) cc_final: 0.7338 (mtt) REVERT: Ai 64 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8307 (ttpt) REVERT: Ai 93 GLN cc_start: 0.9006 (tp40) cc_final: 0.8297 (tp40) REVERT: Ai 138 ASP cc_start: 0.8148 (t70) cc_final: 0.7795 (t70) REVERT: Ai 142 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7853 (tp40) REVERT: Ai 222 MET cc_start: 0.7730 (mtm) cc_final: 0.7503 (ttm) REVERT: Aj 78 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8791 (mmmm) REVERT: Aj 138 ASP cc_start: 0.8143 (t70) cc_final: 0.7755 (t70) REVERT: Aj 174 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7607 (tp30) REVERT: Aj 190 ARG cc_start: 0.8717 (mpt180) cc_final: 0.8037 (tpp80) REVERT: Ak 138 ASP cc_start: 0.8235 (t70) cc_final: 0.7864 (t70) REVERT: Ak 222 MET cc_start: 0.7690 (mtp) cc_final: 0.7468 (ttm) REVERT: Al 137 MET cc_start: 0.8829 (mmm) cc_final: 0.8356 (mmm) REVERT: Al 174 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7605 (tm-30) REVERT: Al 222 MET cc_start: 0.7851 (mtp) cc_final: 0.7428 (ttm) REVERT: Am 78 LYS cc_start: 0.8990 (mppt) cc_final: 0.8583 (mmmm) REVERT: Am 104 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: An 64 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8364 (ttpt) REVERT: An 93 GLN cc_start: 0.9056 (tp40) cc_final: 0.8540 (tp40) REVERT: An 108 SER cc_start: 0.8872 (p) cc_final: 0.8589 (t) REVERT: An 136 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttt) REVERT: An 150 MET cc_start: 0.7849 (mmt) cc_final: 0.7571 (mmt) REVERT: An 174 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7294 (tm-30) REVERT: An 222 MET cc_start: 0.7761 (mtm) cc_final: 0.7518 (ttm) REVERT: Ao 75 TYR cc_start: 0.8864 (t80) cc_final: 0.8508 (t80) REVERT: Ao 108 SER cc_start: 0.9069 (p) cc_final: 0.8618 (t) REVERT: Ap 78 LYS cc_start: 0.8944 (mppt) cc_final: 0.8561 (mmmm) REVERT: Ap 108 SER cc_start: 0.8924 (p) cc_final: 0.8679 (t) REVERT: Ap 222 MET cc_start: 0.7600 (mtm) cc_final: 0.7288 (mtt) REVERT: Aq 64 LYS cc_start: 0.8621 (ttpt) cc_final: 0.8290 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8955 (t80) cc_final: 0.8528 (t80) REVERT: Aq 81 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8019 (t0) REVERT: Aq 93 GLN cc_start: 0.8998 (tp40) cc_final: 0.8282 (tp40) REVERT: Aq 222 MET cc_start: 0.7865 (mtm) cc_final: 0.7556 (mtt) REVERT: Ar 64 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8536 (ttpt) REVERT: Ar 78 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8687 (mmmm) REVERT: Ar 190 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.7973 (mmt90) REVERT: As 55 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8327 (ptpt) REVERT: As 78 LYS cc_start: 0.8985 (mppt) cc_final: 0.8531 (mmmm) REVERT: As 81 ASP cc_start: 0.8014 (t0) cc_final: 0.7466 (t0) REVERT: As 93 GLN cc_start: 0.9051 (tp40) cc_final: 0.8693 (tp40) REVERT: As 174 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7490 (mt-10) REVERT: At 136 MET cc_start: 0.8358 (ttp) cc_final: 0.8048 (ttm) REVERT: At 174 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7547 (tm-30) REVERT: At 222 MET cc_start: 0.7848 (mtp) cc_final: 0.7187 (tmm) REVERT: Au 78 LYS cc_start: 0.8980 (mppt) cc_final: 0.8558 (mmmm) REVERT: Au 108 SER cc_start: 0.8946 (p) cc_final: 0.8712 (t) REVERT: Av 64 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8144 (ttpt) REVERT: Av 93 GLN cc_start: 0.9053 (tp40) cc_final: 0.8594 (tp40) REVERT: Av 136 MET cc_start: 0.8329 (ttp) cc_final: 0.7915 (ttt) REVERT: Av 222 MET cc_start: 0.7920 (mtp) cc_final: 0.7170 (tmm) REVERT: Aw 75 TYR cc_start: 0.8908 (t80) cc_final: 0.8525 (t80) REVERT: Aw 108 SER cc_start: 0.8949 (p) cc_final: 0.8536 (t) REVERT: Aw 176 ARG cc_start: 0.9077 (mmm-85) cc_final: 0.8750 (mmm-85) REVERT: Ax 78 LYS cc_start: 0.8922 (mppt) cc_final: 0.8583 (mmmm) REVERT: Ax 150 MET cc_start: 0.7819 (mmt) cc_final: 0.7403 (mmt) REVERT: Ax 162 MET cc_start: 0.8906 (mmm) cc_final: 0.8691 (mmm) REVERT: Ay 64 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8306 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8016 (t0) REVERT: Ay 93 GLN cc_start: 0.9024 (tp40) cc_final: 0.8302 (tp40) REVERT: Ay 136 MET cc_start: 0.8453 (ttp) cc_final: 0.8141 (ttt) REVERT: Az 108 SER cc_start: 0.8854 (p) cc_final: 0.8546 (t) REVERT: Az 118 MET cc_start: 0.9151 (tpt) cc_final: 0.8451 (tpt) REVERT: Az 190 ARG cc_start: 0.8393 (mmt-90) cc_final: 0.7965 (mmt90) REVERT: Ba 78 LYS cc_start: 0.9023 (mppt) cc_final: 0.8524 (mmmm) REVERT: Ba 110 MET cc_start: 0.8596 (tpp) cc_final: 0.8262 (mmt) REVERT: Ba 174 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7349 (tm-30) REVERT: Bb 136 MET cc_start: 0.8347 (ttp) cc_final: 0.7996 (ttm) REVERT: Bb 137 MET cc_start: 0.8797 (mmm) cc_final: 0.8474 (mmm) REVERT: Bb 138 ASP cc_start: 0.8343 (t70) cc_final: 0.8093 (t0) REVERT: Bb 150 MET cc_start: 0.7900 (mmt) cc_final: 0.7578 (mmt) REVERT: Bc 78 LYS cc_start: 0.8983 (mppt) cc_final: 0.8529 (mmmm) REVERT: Bc 108 SER cc_start: 0.8942 (p) cc_final: 0.8666 (t) REVERT: Bc 174 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7386 (tt0) REVERT: Bd 57 THR cc_start: 0.9134 (m) cc_final: 0.8712 (p) REVERT: Bd 75 TYR cc_start: 0.8807 (t80) cc_final: 0.8592 (t80) REVERT: Bd 76 LYS cc_start: 0.9097 (mttt) cc_final: 0.8519 (tptt) REVERT: Bd 93 GLN cc_start: 0.9120 (tp40) cc_final: 0.8582 (tp40) REVERT: Bd 136 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8053 (ttt) outliers start: 175 outliers final: 139 residues processed: 1536 average time/residue: 0.2470 time to fit residues: 611.7548 Evaluate side-chains 1549 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1403 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 81 ASP Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 106 GLU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 106 GLU Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 106 GLU Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 197 LEU Chi-restraints excluded: chain Ag residue 49 LEU Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 69 LEU Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 142 GLN Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 106 GLU Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 104 GLU Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 49 LEU Chi-restraints excluded: chain An residue 81 ASP Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 106 GLU Chi-restraints excluded: chain An residue 197 LEU Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ao residue 106 GLU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 69 LEU Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 106 GLU Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 49 LEU Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 106 GLU Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 81 ASP Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 49 LEU Chi-restraints excluded: chain Aw residue 73 LEU Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Aw residue 106 GLU Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 106 GLU Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 97 ASP Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 52 MET Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 97 ASP Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 73 LEU Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 106 GLU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 160 GLN Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 106 GLU Chi-restraints excluded: chain Bc residue 135 THR Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 136 MET Chi-restraints excluded: chain Bd residue 160 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 312 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 449 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 464 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 428 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 160 GLN Ad 124 ASN ** Af 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 124 ASN ** Aj 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 142 GLN Aq 124 ASN Aq 142 GLN As 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 142 GLN Bc 71 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119992 restraints weight = 70237.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123170 restraints weight = 47529.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125415 restraints weight = 35854.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127087 restraints weight = 29274.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128216 restraints weight = 25075.026| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45930 Z= 0.137 Angle : 0.635 10.718 62010 Z= 0.312 Chirality : 0.036 0.131 6630 Planarity : 0.005 0.063 7980 Dihedral : 4.057 17.006 6120 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.60 % Allowed : 23.80 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 5490 helix: 0.41 (0.11), residues: 2700 sheet: -2.23 (0.21), residues: 360 loop : -0.82 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGAc 199 TYR 0.035 0.002 TYRAr 186 PHE 0.016 0.002 PHEAf 165 TRP 0.016 0.002 TRPBb 95 HIS 0.004 0.001 HISAh 71 Details of bonding type rmsd covalent geometry : bond 0.00342 (45930) covalent geometry : angle 0.63467 (62010) hydrogen bonds : bond 0.03293 ( 1920) hydrogen bonds : angle 4.18747 ( 5400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1488 time to evaluate : 1.049 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 81 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7687 (t0) REVERT: Aa 136 MET cc_start: 0.8316 (ttp) cc_final: 0.8052 (ttt) REVERT: Aa 148 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8462 (ttpp) REVERT: Aa 222 MET cc_start: 0.7833 (mtm) cc_final: 0.7603 (ttm) REVERT: Ab 137 MET cc_start: 0.8585 (mmm) cc_final: 0.8012 (mmm) REVERT: Ab 138 ASP cc_start: 0.8107 (t70) cc_final: 0.7757 (t70) REVERT: Ac 81 ASP cc_start: 0.8097 (t0) cc_final: 0.7638 (t70) REVERT: Ac 93 GLN cc_start: 0.9105 (tp40) cc_final: 0.8742 (tp40) REVERT: Ac 110 MET cc_start: 0.8566 (tpp) cc_final: 0.8283 (mmt) REVERT: Ac 138 ASP cc_start: 0.8232 (t70) cc_final: 0.7801 (t70) REVERT: Ac 222 MET cc_start: 0.7662 (mtm) cc_final: 0.7243 (mtt) REVERT: Ad 75 TYR cc_start: 0.8864 (t80) cc_final: 0.8614 (t80) REVERT: Ad 137 MET cc_start: 0.8692 (mmm) cc_final: 0.8071 (mmm) REVERT: Ad 189 GLN cc_start: 0.8786 (tt0) cc_final: 0.8554 (tt0) REVERT: Ad 222 MET cc_start: 0.7889 (mtp) cc_final: 0.7550 (ttm) REVERT: Ae 78 LYS cc_start: 0.9032 (mppt) cc_final: 0.8616 (mmmm) REVERT: Ae 138 ASP cc_start: 0.8138 (t70) cc_final: 0.7740 (m-30) REVERT: Ae 197 LEU cc_start: 0.8125 (tp) cc_final: 0.7876 (tt) REVERT: Af 76 LYS cc_start: 0.8865 (mttt) cc_final: 0.8586 (mtmm) REVERT: Af 81 ASP cc_start: 0.8366 (m-30) cc_final: 0.8135 (t0) REVERT: Af 93 GLN cc_start: 0.9031 (tp40) cc_final: 0.8495 (tp40) REVERT: Af 222 MET cc_start: 0.7817 (mtp) cc_final: 0.7281 (ttm) REVERT: Ag 64 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8365 (ttpp) REVERT: Ag 75 TYR cc_start: 0.8903 (t80) cc_final: 0.8459 (t80) REVERT: Ag 108 SER cc_start: 0.8936 (p) cc_final: 0.8619 (t) REVERT: Ag 138 ASP cc_start: 0.8253 (t70) cc_final: 0.7852 (t70) REVERT: Ag 176 ARG cc_start: 0.9126 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: Ag 222 MET cc_start: 0.7479 (mtm) cc_final: 0.7115 (mtt) REVERT: Ah 81 ASP cc_start: 0.8219 (t0) cc_final: 0.7754 (t0) REVERT: Ah 138 ASP cc_start: 0.8222 (t70) cc_final: 0.7663 (t70) REVERT: Ah 222 MET cc_start: 0.7682 (mtm) cc_final: 0.7364 (mtt) REVERT: Ai 64 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8265 (ttpt) REVERT: Ai 93 GLN cc_start: 0.9009 (tp40) cc_final: 0.8300 (tp40) REVERT: Ai 124 ASN cc_start: 0.7750 (m110) cc_final: 0.7492 (t0) REVERT: Ai 138 ASP cc_start: 0.8279 (t70) cc_final: 0.7981 (t70) REVERT: Ai 222 MET cc_start: 0.7728 (mtm) cc_final: 0.7508 (ttm) REVERT: Aj 78 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8773 (mmmm) REVERT: Aj 138 ASP cc_start: 0.8136 (t70) cc_final: 0.7780 (t70) REVERT: Aj 190 ARG cc_start: 0.8674 (mpt180) cc_final: 0.8030 (tpp80) REVERT: Ak 81 ASP cc_start: 0.8189 (t0) cc_final: 0.7573 (t70) REVERT: Ak 138 ASP cc_start: 0.8183 (t70) cc_final: 0.7773 (t70) REVERT: Ak 222 MET cc_start: 0.7663 (mtp) cc_final: 0.7337 (tmm) REVERT: Al 106 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6762 (pm20) REVERT: Al 137 MET cc_start: 0.8746 (mmm) cc_final: 0.8148 (mmm) REVERT: Al 222 MET cc_start: 0.7852 (mtp) cc_final: 0.7479 (ttm) REVERT: Am 78 LYS cc_start: 0.8951 (mppt) cc_final: 0.8542 (mmmm) REVERT: Am 135 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8856 (t) REVERT: Am 190 ARG cc_start: 0.8651 (mpt180) cc_final: 0.7881 (tpp80) REVERT: An 93 GLN cc_start: 0.9023 (tp40) cc_final: 0.8538 (tp40) REVERT: An 106 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: An 108 SER cc_start: 0.8859 (p) cc_final: 0.8545 (t) REVERT: An 136 MET cc_start: 0.8351 (ttp) cc_final: 0.8132 (ttt) REVERT: An 150 MET cc_start: 0.7813 (mmt) cc_final: 0.7452 (mmt) REVERT: Ao 75 TYR cc_start: 0.8845 (t80) cc_final: 0.8497 (t80) REVERT: Ao 108 SER cc_start: 0.9021 (p) cc_final: 0.8573 (t) REVERT: Ap 78 LYS cc_start: 0.8903 (mppt) cc_final: 0.8514 (mmmm) REVERT: Ap 108 SER cc_start: 0.8878 (p) cc_final: 0.8632 (t) REVERT: Ap 222 MET cc_start: 0.7659 (mtm) cc_final: 0.7348 (mtt) REVERT: Aq 64 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8301 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8970 (t80) cc_final: 0.8524 (t80) REVERT: Aq 81 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7989 (t0) REVERT: Aq 93 GLN cc_start: 0.9031 (tp40) cc_final: 0.8330 (tp40) REVERT: Aq 142 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8500 (tp40) REVERT: Aq 222 MET cc_start: 0.7896 (mtm) cc_final: 0.7569 (mtt) REVERT: Ar 64 LYS cc_start: 0.8765 (ttpp) cc_final: 0.8561 (ttpt) REVERT: Ar 78 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8705 (mmmm) REVERT: As 55 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8328 (ptpt) REVERT: As 78 LYS cc_start: 0.8953 (mppt) cc_final: 0.8442 (mmmm) REVERT: As 93 GLN cc_start: 0.9033 (tp40) cc_final: 0.8707 (tp40) REVERT: As 106 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6829 (pm20) REVERT: As 135 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8895 (t) REVERT: As 197 LEU cc_start: 0.7896 (tp) cc_final: 0.7694 (tt) REVERT: At 136 MET cc_start: 0.8311 (ttp) cc_final: 0.8051 (ttm) REVERT: At 222 MET cc_start: 0.7842 (mtp) cc_final: 0.7285 (tmm) REVERT: Au 78 LYS cc_start: 0.8980 (mppt) cc_final: 0.8530 (mmmm) REVERT: Au 108 SER cc_start: 0.8926 (p) cc_final: 0.8653 (t) REVERT: Au 118 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9211 (tmm) REVERT: Au 135 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8799 (t) REVERT: Au 190 ARG cc_start: 0.8687 (mpt180) cc_final: 0.7826 (tpp80) REVERT: Av 64 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8137 (ttpt) REVERT: Av 93 GLN cc_start: 0.9001 (tp40) cc_final: 0.8585 (tp40) REVERT: Av 135 THR cc_start: 0.9285 (p) cc_final: 0.8811 (t) REVERT: Av 136 MET cc_start: 0.8245 (ttp) cc_final: 0.7894 (ttt) REVERT: Av 222 MET cc_start: 0.7910 (mtp) cc_final: 0.7221 (tmm) REVERT: Aw 75 TYR cc_start: 0.8932 (t80) cc_final: 0.8546 (t80) REVERT: Aw 108 SER cc_start: 0.8895 (p) cc_final: 0.8473 (t) REVERT: Aw 176 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8835 (mmm-85) REVERT: Ax 78 LYS cc_start: 0.8859 (mppt) cc_final: 0.8515 (mmmm) REVERT: Ax 150 MET cc_start: 0.7763 (mmt) cc_final: 0.7389 (mmt) REVERT: Ax 162 MET cc_start: 0.8902 (mmm) cc_final: 0.8695 (mmm) REVERT: Ay 64 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8277 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7953 (t0) REVERT: Ay 93 GLN cc_start: 0.9029 (tp40) cc_final: 0.8326 (tp40) REVERT: Ay 124 ASN cc_start: 0.7901 (m-40) cc_final: 0.7652 (t0) REVERT: Ay 222 MET cc_start: 0.7737 (mtm) cc_final: 0.7522 (ttm) REVERT: Az 108 SER cc_start: 0.8850 (p) cc_final: 0.8557 (t) REVERT: Ba 78 LYS cc_start: 0.8924 (mppt) cc_final: 0.8500 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8016 (t0) cc_final: 0.7522 (t70) REVERT: Ba 135 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8848 (t) REVERT: Bb 93 GLN cc_start: 0.9003 (tp40) cc_final: 0.8246 (tp40) REVERT: Bb 110 MET cc_start: 0.8407 (tpp) cc_final: 0.7544 (mmt) REVERT: Bb 137 MET cc_start: 0.8669 (mmm) cc_final: 0.8299 (mmm) REVERT: Bb 138 ASP cc_start: 0.8376 (t70) cc_final: 0.8155 (t0) REVERT: Bb 178 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8202 (mtp180) REVERT: Bc 78 LYS cc_start: 0.8938 (mppt) cc_final: 0.8500 (mmmm) REVERT: Bc 174 GLU cc_start: 0.7920 (tm-30) cc_final: 0.6949 (tt0) REVERT: Bc 199 ARG cc_start: 0.8735 (ttm110) cc_final: 0.7812 (ttm110) REVERT: Bd 57 THR cc_start: 0.9115 (m) cc_final: 0.8676 (p) REVERT: Bd 75 TYR cc_start: 0.8773 (t80) cc_final: 0.8565 (t80) REVERT: Bd 76 LYS cc_start: 0.9086 (mttt) cc_final: 0.8529 (tptt) REVERT: Bd 93 GLN cc_start: 0.9095 (tp40) cc_final: 0.8620 (tp40) REVERT: Bd 136 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7958 (ttt) outliers start: 176 outliers final: 128 residues processed: 1558 average time/residue: 0.1912 time to fit residues: 482.2593 Evaluate side-chains 1553 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1412 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 81 ASP Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 135 THR Chi-restraints excluded: chain Ad residue 138 ASP Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 73 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ag residue 105 LEU Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Ak residue 105 LEU Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 106 GLU Chi-restraints excluded: chain Al residue 135 THR Chi-restraints excluded: chain Al residue 138 ASP Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 106 GLU Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ao residue 106 GLU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 106 GLU Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Ap residue 142 GLN Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 97 ASP Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 222 MET Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 49 LEU Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 106 GLU Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 104 GLU Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 118 MET Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 81 ASP Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Aw residue 106 GLU Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 52 MET Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 97 ASP Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 73 LEU Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 106 GLU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 106 GLU Chi-restraints excluded: chain Bb residue 142 GLN Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 106 GLU Chi-restraints excluded: chain Bc residue 135 THR Chi-restraints excluded: chain Bc residue 190 ARG Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 136 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 248 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 449 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 380 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 424 optimal weight: 1.9990 chunk 357 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 160 GLN Ad 124 ASN Ad 142 GLN Af 71 HIS ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 142 GLN ** Am 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 142 GLN As 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 142 GLN Bb 71 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120768 restraints weight = 70489.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123904 restraints weight = 47630.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126169 restraints weight = 35995.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127806 restraints weight = 29311.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128993 restraints weight = 25088.613| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45930 Z= 0.136 Angle : 0.653 11.383 62010 Z= 0.321 Chirality : 0.037 0.138 6630 Planarity : 0.005 0.070 7980 Dihedral : 4.056 20.307 6120 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.39 % Allowed : 24.31 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 5490 helix: 0.28 (0.10), residues: 2790 sheet: -2.10 (0.22), residues: 360 loop : -0.69 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAc 199 TYR 0.027 0.002 TYRAx 200 PHE 0.014 0.002 PHEAn 165 TRP 0.015 0.002 TRPAc 95 HIS 0.004 0.001 HISAs 71 Details of bonding type rmsd covalent geometry : bond 0.00342 (45930) covalent geometry : angle 0.65275 (62010) hydrogen bonds : bond 0.03220 ( 1920) hydrogen bonds : angle 4.17271 ( 5400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1456 time to evaluate : 1.018 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 81 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7667 (t0) REVERT: Aa 108 SER cc_start: 0.8771 (p) cc_final: 0.8511 (t) REVERT: Aa 148 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8429 (ttpp) REVERT: Aa 222 MET cc_start: 0.7849 (mtm) cc_final: 0.7616 (ttm) REVERT: Ab 137 MET cc_start: 0.8559 (mmm) cc_final: 0.8034 (mmm) REVERT: Ab 138 ASP cc_start: 0.8077 (t70) cc_final: 0.7718 (t70) REVERT: Ac 81 ASP cc_start: 0.8078 (t0) cc_final: 0.7832 (t70) REVERT: Ac 93 GLN cc_start: 0.9093 (tp40) cc_final: 0.8757 (tp40) REVERT: Ac 138 ASP cc_start: 0.8174 (t70) cc_final: 0.7900 (t70) REVERT: Ac 222 MET cc_start: 0.7767 (mtm) cc_final: 0.7342 (mtt) REVERT: Ad 75 TYR cc_start: 0.8836 (t80) cc_final: 0.8593 (t80) REVERT: Ad 137 MET cc_start: 0.8681 (mmm) cc_final: 0.8181 (tpp) REVERT: Ad 142 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7867 (tp40) REVERT: Ad 189 GLN cc_start: 0.8760 (tt0) cc_final: 0.8509 (tt0) REVERT: Ad 222 MET cc_start: 0.7932 (mtp) cc_final: 0.7291 (tmm) REVERT: Ae 78 LYS cc_start: 0.9029 (mppt) cc_final: 0.8612 (mmmm) REVERT: Ae 135 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8775 (t) REVERT: Ae 138 ASP cc_start: 0.8160 (t70) cc_final: 0.7662 (t70) REVERT: Ae 197 LEU cc_start: 0.8093 (tp) cc_final: 0.7827 (tt) REVERT: Af 76 LYS cc_start: 0.8815 (mttt) cc_final: 0.8563 (mtmm) REVERT: Af 93 GLN cc_start: 0.9037 (tp40) cc_final: 0.8514 (tp40) REVERT: Af 222 MET cc_start: 0.7840 (mtp) cc_final: 0.7336 (ttm) REVERT: Ag 64 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8352 (ttpp) REVERT: Ag 108 SER cc_start: 0.8880 (p) cc_final: 0.8673 (t) REVERT: Ag 138 ASP cc_start: 0.8281 (t70) cc_final: 0.7893 (t70) REVERT: Ag 176 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8505 (mmm-85) REVERT: Ag 222 MET cc_start: 0.7531 (mtm) cc_final: 0.7155 (mtt) REVERT: Ah 81 ASP cc_start: 0.8211 (t0) cc_final: 0.7734 (t0) REVERT: Ah 105 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7825 (pp) REVERT: Ah 138 ASP cc_start: 0.8213 (t70) cc_final: 0.7664 (t70) REVERT: Ah 162 MET cc_start: 0.8862 (mmm) cc_final: 0.8449 (tpt) REVERT: Ah 222 MET cc_start: 0.7682 (mtm) cc_final: 0.7465 (mtt) REVERT: Ai 64 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8306 (ttpt) REVERT: Ai 93 GLN cc_start: 0.8996 (tp40) cc_final: 0.8315 (tp40) REVERT: Ai 124 ASN cc_start: 0.7911 (m110) cc_final: 0.7588 (t0) REVERT: Ai 138 ASP cc_start: 0.8262 (t70) cc_final: 0.7964 (t70) REVERT: Ai 222 MET cc_start: 0.7747 (mtm) cc_final: 0.7528 (ttm) REVERT: Aj 78 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8785 (mmmm) REVERT: Aj 138 ASP cc_start: 0.8180 (t70) cc_final: 0.7814 (t70) REVERT: Ak 81 ASP cc_start: 0.8163 (t0) cc_final: 0.7866 (t70) REVERT: Ak 105 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7983 (pp) REVERT: Ak 110 MET cc_start: 0.8603 (tpp) cc_final: 0.8194 (mmt) REVERT: Ak 138 ASP cc_start: 0.8182 (t70) cc_final: 0.7824 (t70) REVERT: Ak 162 MET cc_start: 0.8585 (tpt) cc_final: 0.8245 (tpt) REVERT: Ak 222 MET cc_start: 0.7666 (mtp) cc_final: 0.7334 (tmm) REVERT: Al 137 MET cc_start: 0.8722 (mmm) cc_final: 0.8149 (tpp) REVERT: Al 142 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: Al 222 MET cc_start: 0.7859 (mtp) cc_final: 0.7471 (ttm) REVERT: Am 78 LYS cc_start: 0.8943 (mppt) cc_final: 0.8539 (mmmm) REVERT: Am 135 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8755 (t) REVERT: Am 190 ARG cc_start: 0.8676 (mpt180) cc_final: 0.7850 (tpp80) REVERT: An 81 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7950 (t0) REVERT: An 93 GLN cc_start: 0.9029 (tp40) cc_final: 0.8562 (tp40) REVERT: An 106 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: An 136 MET cc_start: 0.8289 (ttp) cc_final: 0.7990 (ttt) REVERT: An 150 MET cc_start: 0.7932 (mmt) cc_final: 0.7712 (mmt) REVERT: Ao 75 TYR cc_start: 0.8877 (t80) cc_final: 0.8563 (t80) REVERT: Ao 108 SER cc_start: 0.9028 (p) cc_final: 0.8587 (t) REVERT: Ap 78 LYS cc_start: 0.8870 (mppt) cc_final: 0.8568 (mmmm) REVERT: Ap 106 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: Ap 108 SER cc_start: 0.8915 (p) cc_final: 0.8587 (t) REVERT: Aq 64 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8257 (ttpt) REVERT: Aq 75 TYR cc_start: 0.8987 (t80) cc_final: 0.8526 (t80) REVERT: Aq 81 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7892 (t0) REVERT: Aq 93 GLN cc_start: 0.8979 (tp40) cc_final: 0.8294 (tp40) REVERT: Aq 124 ASN cc_start: 0.7961 (m-40) cc_final: 0.7676 (t0) REVERT: Aq 160 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8336 (mm-40) REVERT: Aq 222 MET cc_start: 0.7890 (mtm) cc_final: 0.7684 (mtt) REVERT: Ar 64 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8536 (ttpt) REVERT: Ar 78 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8721 (mmmm) REVERT: Ar 110 MET cc_start: 0.8422 (tpp) cc_final: 0.7856 (mmt) REVERT: As 55 LYS cc_start: 0.8811 (mmtm) cc_final: 0.8319 (ptpt) REVERT: As 78 LYS cc_start: 0.8947 (mppt) cc_final: 0.8450 (mmmm) REVERT: As 81 ASP cc_start: 0.7944 (t0) cc_final: 0.7519 (t70) REVERT: As 93 GLN cc_start: 0.9025 (tp40) cc_final: 0.8699 (tp40) REVERT: As 135 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8914 (t) REVERT: As 162 MET cc_start: 0.8668 (tpt) cc_final: 0.8290 (tpt) REVERT: As 197 LEU cc_start: 0.7934 (tp) cc_final: 0.7725 (tt) REVERT: At 136 MET cc_start: 0.8274 (ttp) cc_final: 0.7984 (ttm) REVERT: At 222 MET cc_start: 0.7884 (mtp) cc_final: 0.7548 (ttm) REVERT: Au 78 LYS cc_start: 0.8850 (mppt) cc_final: 0.8510 (mmmm) REVERT: Au 108 SER cc_start: 0.8918 (p) cc_final: 0.8656 (t) REVERT: Au 135 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8979 (t) REVERT: Au 190 ARG cc_start: 0.8703 (mpt180) cc_final: 0.7791 (tpp80) REVERT: Av 64 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8148 (ttpt) REVERT: Av 81 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7905 (t0) REVERT: Av 93 GLN cc_start: 0.9000 (tp40) cc_final: 0.8557 (tp40) REVERT: Av 106 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6917 (pm20) REVERT: Av 135 THR cc_start: 0.9198 (p) cc_final: 0.8773 (t) REVERT: Av 222 MET cc_start: 0.7939 (mtp) cc_final: 0.7219 (tmm) REVERT: Aw 108 SER cc_start: 0.8948 (p) cc_final: 0.8597 (t) REVERT: Aw 190 ARG cc_start: 0.8691 (mmt-90) cc_final: 0.8465 (mpt180) REVERT: Aw 199 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8645 (ttm110) REVERT: Ax 78 LYS cc_start: 0.8832 (mppt) cc_final: 0.8552 (mmmm) REVERT: Ax 93 GLN cc_start: 0.8997 (tp40) cc_final: 0.8736 (tp40) REVERT: Ay 64 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8265 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7913 (t0) REVERT: Ay 93 GLN cc_start: 0.9016 (tp40) cc_final: 0.8275 (tp40) REVERT: Ay 136 MET cc_start: 0.8317 (ttp) cc_final: 0.7908 (ttt) REVERT: Ay 160 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8293 (mm-40) REVERT: Ay 222 MET cc_start: 0.7761 (mtm) cc_final: 0.7441 (mtt) REVERT: Az 108 SER cc_start: 0.8853 (p) cc_final: 0.8549 (t) REVERT: Ba 78 LYS cc_start: 0.8932 (mppt) cc_final: 0.8547 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8078 (t0) cc_final: 0.7637 (t0) REVERT: Ba 106 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: Ba 135 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8746 (t) REVERT: Ba 162 MET cc_start: 0.8734 (tpt) cc_final: 0.8376 (tpt) REVERT: Bb 93 GLN cc_start: 0.8995 (tp40) cc_final: 0.8220 (tp40) REVERT: Bb 110 MET cc_start: 0.8512 (tpp) cc_final: 0.7740 (mmt) REVERT: Bc 78 LYS cc_start: 0.8958 (mppt) cc_final: 0.8530 (mmmm) REVERT: Bc 104 GLU cc_start: 0.7453 (pm20) cc_final: 0.6609 (pp20) REVERT: Bc 106 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: Bc 124 ASN cc_start: 0.8026 (m-40) cc_final: 0.7711 (t0) REVERT: Bc 174 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7030 (tt0) REVERT: Bc 199 ARG cc_start: 0.8696 (ttm110) cc_final: 0.7957 (ttm110) REVERT: Bc 214 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.8009 (mtm-85) REVERT: Bd 57 THR cc_start: 0.9105 (m) cc_final: 0.8657 (p) REVERT: Bd 75 TYR cc_start: 0.8792 (t80) cc_final: 0.8589 (t80) REVERT: Bd 76 LYS cc_start: 0.9103 (mttt) cc_final: 0.8516 (tptt) REVERT: Bd 93 GLN cc_start: 0.9080 (tp40) cc_final: 0.8608 (tp40) REVERT: Bd 136 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (ttt) outliers start: 166 outliers final: 121 residues processed: 1525 average time/residue: 0.1777 time to fit residues: 438.9915 Evaluate side-chains 1549 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1406 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 81 ASP Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 105 LEU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 73 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ah residue 105 LEU Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 105 LEU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Ak residue 105 LEU Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 67 VAL Chi-restraints excluded: chain An residue 81 ASP Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 106 GLU Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ao residue 106 GLU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 106 GLU Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 97 ASP Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 49 LEU Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 73 LEU Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 81 ASP Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 49 LEU Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 106 GLU Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 53 THR Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 97 ASP Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 73 LEU Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 106 GLU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 142 GLN Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 106 GLU Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 106 GLU Chi-restraints excluded: chain Bc residue 190 ARG Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 136 MET Chi-restraints excluded: chain Bd residue 160 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 436 optimal weight: 5.9990 chunk 514 optimal weight: 5.9990 chunk 496 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 417 optimal weight: 0.0870 chunk 446 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 441 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 71 HIS Ab 160 GLN ** Ac 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 124 ASN Ad 142 GLN Ag 71 HIS ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 142 GLN ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** As 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 71 HIS Ax 142 GLN Ba 71 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116609 restraints weight = 70432.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119701 restraints weight = 47871.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121926 restraints weight = 36403.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123494 restraints weight = 29771.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124645 restraints weight = 25646.467| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 45930 Z= 0.156 Angle : 0.685 14.004 62010 Z= 0.337 Chirality : 0.037 0.152 6630 Planarity : 0.005 0.072 7980 Dihedral : 4.085 17.796 6120 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.48 % Allowed : 24.72 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5490 helix: 0.46 (0.11), residues: 2700 sheet: -2.07 (0.22), residues: 360 loop : -0.81 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAc 199 TYR 0.031 0.002 TYRAc 75 PHE 0.017 0.002 PHEAp 165 TRP 0.014 0.002 TRPAx 95 HIS 0.006 0.001 HISAn 71 Details of bonding type rmsd covalent geometry : bond 0.00387 (45930) covalent geometry : angle 0.68498 (62010) hydrogen bonds : bond 0.03438 ( 1920) hydrogen bonds : angle 4.19491 ( 5400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1424 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7887 (t0) REVERT: Aa 148 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8496 (ttpp) REVERT: Aa 222 MET cc_start: 0.7858 (mtm) cc_final: 0.7631 (ttm) REVERT: Ab 108 SER cc_start: 0.8754 (p) cc_final: 0.8469 (t) REVERT: Ab 137 MET cc_start: 0.8568 (mmm) cc_final: 0.8018 (mmm) REVERT: Ab 138 ASP cc_start: 0.8091 (t70) cc_final: 0.7713 (t70) REVERT: Ac 81 ASP cc_start: 0.8277 (t0) cc_final: 0.7863 (t0) REVERT: Ac 93 GLN cc_start: 0.9091 (tp40) cc_final: 0.8739 (tp40) REVERT: Ac 110 MET cc_start: 0.8520 (tpp) cc_final: 0.8126 (mmt) REVERT: Ac 174 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7337 (mt-10) REVERT: Ac 222 MET cc_start: 0.7844 (mtm) cc_final: 0.7441 (mtt) REVERT: Ad 75 TYR cc_start: 0.8794 (t80) cc_final: 0.8551 (t80) REVERT: Ad 136 MET cc_start: 0.8203 (ttt) cc_final: 0.7997 (ttp) REVERT: Ad 142 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7949 (tp40) REVERT: Ad 178 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8334 (mtp180) REVERT: Ad 189 GLN cc_start: 0.8763 (tt0) cc_final: 0.8495 (tt0) REVERT: Ad 222 MET cc_start: 0.7921 (mtp) cc_final: 0.7311 (tmm) REVERT: Ae 78 LYS cc_start: 0.9061 (mppt) cc_final: 0.8647 (mmmm) REVERT: Ae 138 ASP cc_start: 0.8171 (t70) cc_final: 0.7714 (m-30) REVERT: Ae 197 LEU cc_start: 0.8197 (tp) cc_final: 0.7886 (tt) REVERT: Af 76 LYS cc_start: 0.8844 (mttt) cc_final: 0.8612 (mtmm) REVERT: Af 93 GLN cc_start: 0.9052 (tp40) cc_final: 0.8520 (tp40) REVERT: Af 222 MET cc_start: 0.7850 (mtp) cc_final: 0.7515 (ttm) REVERT: Ag 64 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8368 (ttpp) REVERT: Ag 138 ASP cc_start: 0.8287 (t70) cc_final: 0.7909 (t70) REVERT: Ag 176 ARG cc_start: 0.9185 (mmm-85) cc_final: 0.8628 (mmm-85) REVERT: Ag 222 MET cc_start: 0.7544 (mtm) cc_final: 0.7150 (mtt) REVERT: Ah 81 ASP cc_start: 0.8194 (t0) cc_final: 0.7635 (t0) REVERT: Ah 138 ASP cc_start: 0.8236 (t70) cc_final: 0.7687 (t70) REVERT: Ah 162 MET cc_start: 0.8873 (mmm) cc_final: 0.8354 (tpt) REVERT: Ai 64 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8317 (ttpt) REVERT: Ai 93 GLN cc_start: 0.8986 (tp40) cc_final: 0.8430 (tp40) REVERT: Ai 124 ASN cc_start: 0.7852 (m110) cc_final: 0.7599 (t0) REVERT: Ai 138 ASP cc_start: 0.8246 (t70) cc_final: 0.7835 (t70) REVERT: Ai 160 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8393 (mm-40) REVERT: Ai 222 MET cc_start: 0.7711 (mtm) cc_final: 0.7484 (ttm) REVERT: Aj 64 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8547 (ttpt) REVERT: Aj 108 SER cc_start: 0.8797 (p) cc_final: 0.8498 (t) REVERT: Aj 138 ASP cc_start: 0.8246 (t70) cc_final: 0.7808 (t70) REVERT: Ak 81 ASP cc_start: 0.8319 (t0) cc_final: 0.7787 (t0) REVERT: Ak 110 MET cc_start: 0.8652 (tpp) cc_final: 0.8301 (mmt) REVERT: Ak 138 ASP cc_start: 0.8202 (t70) cc_final: 0.7886 (t70) REVERT: Ak 162 MET cc_start: 0.8615 (tpt) cc_final: 0.8308 (tpt) REVERT: Ak 197 LEU cc_start: 0.7941 (tp) cc_final: 0.7646 (tt) REVERT: Ak 222 MET cc_start: 0.7669 (mtp) cc_final: 0.7307 (tmm) REVERT: Al 142 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7918 (tp40) REVERT: Al 222 MET cc_start: 0.7863 (mtp) cc_final: 0.7187 (tmm) REVERT: Am 78 LYS cc_start: 0.8984 (mppt) cc_final: 0.8577 (mmmm) REVERT: Am 124 ASN cc_start: 0.8096 (m-40) cc_final: 0.7884 (t0) REVERT: Am 190 ARG cc_start: 0.8677 (mpt180) cc_final: 0.7920 (tpp80) REVERT: An 81 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7986 (t0) REVERT: An 93 GLN cc_start: 0.9054 (tp40) cc_final: 0.8576 (tp40) REVERT: An 105 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8198 (pp) REVERT: An 106 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: An 108 SER cc_start: 0.8837 (p) cc_final: 0.8478 (t) REVERT: An 136 MET cc_start: 0.8268 (ttp) cc_final: 0.8033 (ttt) REVERT: An 150 MET cc_start: 0.7917 (mmt) cc_final: 0.7698 (mmt) REVERT: Ao 106 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: Ao 108 SER cc_start: 0.9005 (p) cc_final: 0.8675 (t) REVERT: Ap 78 LYS cc_start: 0.8920 (mppt) cc_final: 0.8579 (mmmm) REVERT: Ap 135 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8647 (t) REVERT: Ap 197 LEU cc_start: 0.7990 (tp) cc_final: 0.7762 (tt) REVERT: Aq 64 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8303 (ttpt) REVERT: Aq 75 TYR cc_start: 0.9006 (t80) cc_final: 0.8522 (t80) REVERT: Aq 81 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7911 (t0) REVERT: Aq 93 GLN cc_start: 0.8986 (tp40) cc_final: 0.8280 (tp40) REVERT: Aq 160 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: Aq 207 ILE cc_start: 0.9154 (mm) cc_final: 0.8918 (mt) REVERT: Aq 222 MET cc_start: 0.7913 (mtm) cc_final: 0.7692 (mtt) REVERT: Ar 64 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8558 (ttpt) REVERT: As 55 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8333 (ptpt) REVERT: As 78 LYS cc_start: 0.9025 (mppt) cc_final: 0.8527 (mmmm) REVERT: As 81 ASP cc_start: 0.7997 (t0) cc_final: 0.7574 (t70) REVERT: As 93 GLN cc_start: 0.9062 (tp40) cc_final: 0.8737 (tp40) REVERT: As 135 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8829 (t) REVERT: As 197 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7792 (tt) REVERT: At 136 MET cc_start: 0.8346 (ttp) cc_final: 0.8046 (ttm) REVERT: At 222 MET cc_start: 0.7885 (mtp) cc_final: 0.7541 (ttm) REVERT: Au 78 LYS cc_start: 0.8907 (mppt) cc_final: 0.8457 (mmmm) REVERT: Au 106 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: Au 190 ARG cc_start: 0.8695 (mpt180) cc_final: 0.7858 (tpp80) REVERT: Av 64 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8148 (ttpt) REVERT: Av 81 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7977 (t0) REVERT: Av 93 GLN cc_start: 0.9050 (tp40) cc_final: 0.8597 (tp40) REVERT: Av 105 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7929 (pp) REVERT: Av 106 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6692 (pm20) REVERT: Av 222 MET cc_start: 0.7950 (mtp) cc_final: 0.7206 (tmm) REVERT: Aw 199 ARG cc_start: 0.8917 (mtp-110) cc_final: 0.8628 (ttm110) REVERT: Ax 78 LYS cc_start: 0.8890 (mppt) cc_final: 0.8563 (mmmm) REVERT: Ax 93 GLN cc_start: 0.9002 (tp40) cc_final: 0.8748 (tp40) REVERT: Ax 106 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: Ay 64 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8312 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7993 (t0) REVERT: Ay 93 GLN cc_start: 0.9023 (tp40) cc_final: 0.8449 (tp40) REVERT: Ay 136 MET cc_start: 0.8390 (ttp) cc_final: 0.7919 (ttt) REVERT: Ay 160 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8268 (mm-40) REVERT: Az 108 SER cc_start: 0.8887 (p) cc_final: 0.8602 (t) REVERT: Az 190 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7515 (mtt90) REVERT: Ba 78 LYS cc_start: 0.8984 (mppt) cc_final: 0.8624 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8236 (t0) cc_final: 0.7718 (t0) REVERT: Ba 135 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8842 (t) REVERT: Ba 162 MET cc_start: 0.8714 (tpt) cc_final: 0.8418 (tpt) REVERT: Bc 78 LYS cc_start: 0.8979 (mppt) cc_final: 0.8562 (mmmm) REVERT: Bc 106 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: Bc 174 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7118 (tt0) REVERT: Bc 199 ARG cc_start: 0.8662 (ttm110) cc_final: 0.7755 (ttm110) REVERT: Bd 57 THR cc_start: 0.9122 (m) cc_final: 0.8686 (p) REVERT: Bd 75 TYR cc_start: 0.8786 (t80) cc_final: 0.8577 (t80) REVERT: Bd 76 LYS cc_start: 0.9107 (mttt) cc_final: 0.8518 (tptt) REVERT: Bd 93 GLN cc_start: 0.9123 (tp40) cc_final: 0.8646 (tp40) REVERT: Bd 136 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: Bd 222 MET cc_start: 0.7933 (tpp) cc_final: 0.7450 (tpp) outliers start: 170 outliers final: 126 residues processed: 1488 average time/residue: 0.1745 time to fit residues: 419.7377 Evaluate side-chains 1534 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1385 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 81 ASP Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 105 LEU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 135 THR Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 67 VAL Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 73 LEU Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 73 LEU Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 135 THR Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 222 MET Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 81 ASP Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 105 LEU Chi-restraints excluded: chain An residue 106 GLU Chi-restraints excluded: chain An residue 222 MET Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ao residue 106 GLU Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Aq residue 81 ASP Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 135 THR Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 97 ASP Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 49 LEU Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 197 LEU Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Au residue 222 MET Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 67 VAL Chi-restraints excluded: chain Av residue 81 ASP Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 105 LEU Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 49 LEU Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 67 VAL Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ax residue 106 GLU Chi-restraints excluded: chain Ax residue 142 GLN Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 53 THR Chi-restraints excluded: chain Ay residue 67 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 97 ASP Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 73 LEU Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 106 GLU Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 106 GLU Chi-restraints excluded: chain Bc residue 190 ARG Chi-restraints excluded: chain Bc residue 222 MET Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 136 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 283 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 405 optimal weight: 0.9990 chunk 321 optimal weight: 7.9990 chunk 57 optimal weight: 0.0370 chunk 177 optimal weight: 10.0000 chunk 458 optimal weight: 0.0970 chunk 224 optimal weight: 9.9990 overall best weight: 3.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 160 GLN Ac 71 HIS Ad 124 ASN Ad 142 GLN Af 142 GLN Ag 71 HIS ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 71 HIS Al 124 ASN Al 142 GLN ** Am 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 124 ASN Aq 142 GLN As 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 142 GLN Ba 142 GLN ** Bc 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107958 restraints weight = 72627.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110917 restraints weight = 48609.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112978 restraints weight = 36541.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114512 restraints weight = 29897.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115624 restraints weight = 25671.421| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 45930 Z= 0.196 Angle : 0.727 11.044 62010 Z= 0.359 Chirality : 0.039 0.156 6630 Planarity : 0.005 0.075 7980 Dihedral : 4.179 18.669 6120 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.31 % Allowed : 25.17 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 5490 helix: 0.39 (0.11), residues: 2700 sheet: -2.02 (0.23), residues: 360 loop : -0.88 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 199 TYR 0.030 0.002 TYRAx 200 PHE 0.021 0.003 PHEAc 165 TRP 0.014 0.003 TRPAw 95 HIS 0.006 0.001 HISAb 71 Details of bonding type rmsd covalent geometry : bond 0.00479 (45930) covalent geometry : angle 0.72741 (62010) hydrogen bonds : bond 0.03898 ( 1920) hydrogen bonds : angle 4.28504 ( 5400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10980 Ramachandran restraints generated. 5490 Oldfield, 0 Emsley, 5490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1405 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 81 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7886 (t0) REVERT: Aa 148 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8559 (ttpp) REVERT: Aa 222 MET cc_start: 0.7828 (mtm) cc_final: 0.7589 (ttm) REVERT: Ab 108 SER cc_start: 0.8762 (p) cc_final: 0.8531 (t) REVERT: Ab 137 MET cc_start: 0.8567 (mmm) cc_final: 0.8022 (mmm) REVERT: Ab 138 ASP cc_start: 0.8116 (t70) cc_final: 0.7740 (t70) REVERT: Ab 174 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7609 (tm-30) REVERT: Ac 81 ASP cc_start: 0.8360 (t0) cc_final: 0.7837 (t70) REVERT: Ac 93 GLN cc_start: 0.9131 (tp40) cc_final: 0.8764 (tp40) REVERT: Ac 174 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7498 (mt-10) REVERT: Ac 222 MET cc_start: 0.7712 (mtm) cc_final: 0.7262 (mtt) REVERT: Ad 136 MET cc_start: 0.8296 (ttt) cc_final: 0.8048 (ttp) REVERT: Ad 142 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8048 (tp40) REVERT: Ad 178 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8318 (mtp180) REVERT: Ad 222 MET cc_start: 0.7873 (mtp) cc_final: 0.7408 (tmm) REVERT: Ae 78 LYS cc_start: 0.9151 (mppt) cc_final: 0.8771 (mmmm) REVERT: Ae 138 ASP cc_start: 0.8053 (t70) cc_final: 0.7803 (m-30) REVERT: Af 76 LYS cc_start: 0.8918 (mttt) cc_final: 0.8609 (mtmm) REVERT: Af 93 GLN cc_start: 0.9075 (tp40) cc_final: 0.8548 (tp40) REVERT: Af 174 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7332 (tm-30) REVERT: Ag 64 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8384 (ttpp) REVERT: Ag 138 ASP cc_start: 0.8280 (t70) cc_final: 0.7938 (t70) REVERT: Ag 176 ARG cc_start: 0.9246 (mmm-85) cc_final: 0.8485 (mmm-85) REVERT: Ag 222 MET cc_start: 0.7457 (mtm) cc_final: 0.7042 (mtt) REVERT: Ah 81 ASP cc_start: 0.8221 (t0) cc_final: 0.7681 (t0) REVERT: Ah 138 ASP cc_start: 0.8277 (t70) cc_final: 0.7730 (t70) REVERT: Ai 64 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8288 (ttpt) REVERT: Ai 93 GLN cc_start: 0.9006 (tp40) cc_final: 0.8391 (tp40) REVERT: Ai 138 ASP cc_start: 0.8273 (t70) cc_final: 0.7895 (t70) REVERT: Ai 222 MET cc_start: 0.7716 (mtm) cc_final: 0.7479 (ttm) REVERT: Aj 108 SER cc_start: 0.8811 (p) cc_final: 0.8541 (t) REVERT: Aj 174 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7588 (tm-30) REVERT: Ak 81 ASP cc_start: 0.8346 (t0) cc_final: 0.7774 (t0) REVERT: Ak 174 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7233 (tm-30) REVERT: Al 142 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8015 (tp40) REVERT: Al 189 GLN cc_start: 0.8812 (tt0) cc_final: 0.8542 (tt0) REVERT: Al 222 MET cc_start: 0.7817 (mtp) cc_final: 0.7526 (ttm) REVERT: Am 78 LYS cc_start: 0.9091 (mppt) cc_final: 0.8699 (mmmm) REVERT: Am 174 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7689 (tp30) REVERT: Am 190 ARG cc_start: 0.8571 (mpt180) cc_final: 0.7969 (tpp80) REVERT: An 81 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7958 (t0) REVERT: An 93 GLN cc_start: 0.9089 (tp40) cc_final: 0.8601 (tp40) REVERT: An 105 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8282 (pp) REVERT: An 108 SER cc_start: 0.8865 (p) cc_final: 0.8520 (t) REVERT: An 136 MET cc_start: 0.8332 (ttp) cc_final: 0.8057 (ttt) REVERT: An 150 MET cc_start: 0.7995 (mmt) cc_final: 0.7780 (mmt) REVERT: An 174 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7230 (tm-30) REVERT: Ap 78 LYS cc_start: 0.9017 (mppt) cc_final: 0.8665 (mmmm) REVERT: Ap 174 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7557 (tt0) REVERT: Ap 197 LEU cc_start: 0.8191 (tp) cc_final: 0.7881 (tt) REVERT: Aq 64 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8300 (ttpt) REVERT: Aq 93 GLN cc_start: 0.9015 (tp40) cc_final: 0.8409 (tp40) REVERT: Aq 222 MET cc_start: 0.7835 (mtm) cc_final: 0.7561 (mtt) REVERT: Ar 110 MET cc_start: 0.8602 (tpp) cc_final: 0.8026 (mmt) REVERT: Ar 222 MET cc_start: 0.7425 (tmm) cc_final: 0.7087 (tpt) REVERT: As 55 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8375 (ptpt) REVERT: As 78 LYS cc_start: 0.9051 (mppt) cc_final: 0.8601 (mmmm) REVERT: As 81 ASP cc_start: 0.7990 (t0) cc_final: 0.7632 (t70) REVERT: As 93 GLN cc_start: 0.9097 (tp40) cc_final: 0.8757 (tp40) REVERT: As 174 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7324 (tm-30) REVERT: As 197 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7914 (tt) REVERT: At 136 MET cc_start: 0.8360 (ttp) cc_final: 0.8044 (ttm) REVERT: At 174 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7539 (tm-30) REVERT: At 222 MET cc_start: 0.7803 (mtp) cc_final: 0.7160 (tmm) REVERT: Au 78 LYS cc_start: 0.8899 (mppt) cc_final: 0.8546 (mmmm) REVERT: Au 106 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: Au 190 ARG cc_start: 0.8601 (mpt180) cc_final: 0.7892 (tpp80) REVERT: Av 64 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8139 (ttpt) REVERT: Av 93 GLN cc_start: 0.9083 (tp40) cc_final: 0.8595 (tp40) REVERT: Av 105 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8137 (pp) REVERT: Av 222 MET cc_start: 0.7883 (mtp) cc_final: 0.7281 (tmm) REVERT: Aw 108 SER cc_start: 0.8978 (p) cc_final: 0.8603 (t) REVERT: Aw 199 ARG cc_start: 0.8945 (mtp-110) cc_final: 0.8681 (ttm110) REVERT: Ax 78 LYS cc_start: 0.9006 (mppt) cc_final: 0.8682 (mmmm) REVERT: Ax 174 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7549 (tt0) REVERT: Ay 64 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8361 (ttpt) REVERT: Ay 81 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8067 (t0) REVERT: Ay 93 GLN cc_start: 0.9036 (tp40) cc_final: 0.8407 (tp40) REVERT: Ay 136 MET cc_start: 0.8396 (ttp) cc_final: 0.8049 (ttt) REVERT: Az 108 SER cc_start: 0.8848 (p) cc_final: 0.8568 (t) REVERT: Ba 78 LYS cc_start: 0.9036 (mppt) cc_final: 0.8688 (mmmm) REVERT: Ba 81 ASP cc_start: 0.8247 (t0) cc_final: 0.7734 (t0) REVERT: Ba 135 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (t) REVERT: Ba 174 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7297 (tm-30) REVERT: Ba 197 LEU cc_start: 0.8153 (tp) cc_final: 0.7803 (tt) REVERT: Bb 174 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7456 (tm-30) REVERT: Bc 78 LYS cc_start: 0.9040 (mppt) cc_final: 0.8591 (mmmm) REVERT: Bc 106 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6824 (pm20) REVERT: Bc 174 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7133 (tt0) REVERT: Bc 190 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8067 (tpp80) REVERT: Bc 199 ARG cc_start: 0.8658 (ttm110) cc_final: 0.7870 (ttm110) REVERT: Bd 57 THR cc_start: 0.9133 (m) cc_final: 0.8704 (p) REVERT: Bd 75 TYR cc_start: 0.8824 (t80) cc_final: 0.8614 (t80) REVERT: Bd 76 LYS cc_start: 0.9080 (mttt) cc_final: 0.8552 (tptt) REVERT: Bd 93 GLN cc_start: 0.9163 (tp40) cc_final: 0.8638 (tp40) REVERT: Bd 136 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7978 (ttt) REVERT: Bd 174 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7303 (tm-30) REVERT: Bd 222 MET cc_start: 0.7935 (tpp) cc_final: 0.7517 (tpp) outliers start: 162 outliers final: 130 residues processed: 1467 average time/residue: 0.1695 time to fit residues: 401.0490 Evaluate side-chains 1527 residues out of total 4890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1384 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 81 ASP Chi-restraints excluded: chain Aa residue 88 THR Chi-restraints excluded: chain Aa residue 105 LEU Chi-restraints excluded: chain Aa residue 160 GLN Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 88 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 73 LEU Chi-restraints excluded: chain Ac residue 88 THR Chi-restraints excluded: chain Ac residue 97 ASP Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 88 THR Chi-restraints excluded: chain Ad residue 135 THR Chi-restraints excluded: chain Ad residue 142 GLN Chi-restraints excluded: chain Ad residue 160 GLN Chi-restraints excluded: chain Ae residue 49 LEU Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 88 THR Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 67 VAL Chi-restraints excluded: chain Af residue 81 ASP Chi-restraints excluded: chain Af residue 88 THR Chi-restraints excluded: chain Af residue 97 ASP Chi-restraints excluded: chain Af residue 142 GLN Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 88 THR Chi-restraints excluded: chain Ah residue 49 LEU Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 88 THR Chi-restraints excluded: chain Ai residue 73 LEU Chi-restraints excluded: chain Ai residue 88 THR Chi-restraints excluded: chain Ai residue 160 GLN Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 88 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 88 THR Chi-restraints excluded: chain Ak residue 97 ASP Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 88 THR Chi-restraints excluded: chain Al residue 135 THR Chi-restraints excluded: chain Al residue 142 GLN Chi-restraints excluded: chain Al residue 160 GLN Chi-restraints excluded: chain Am residue 49 LEU Chi-restraints excluded: chain Am residue 88 THR Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 67 VAL Chi-restraints excluded: chain An residue 81 ASP Chi-restraints excluded: chain An residue 88 THR Chi-restraints excluded: chain An residue 97 ASP Chi-restraints excluded: chain An residue 105 LEU Chi-restraints excluded: chain An residue 222 MET Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 88 THR Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 88 THR Chi-restraints excluded: chain Aq residue 88 THR Chi-restraints excluded: chain Aq residue 135 THR Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Aq residue 160 GLN Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 88 THR Chi-restraints excluded: chain Ar residue 97 ASP Chi-restraints excluded: chain Ar residue 106 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 49 LEU Chi-restraints excluded: chain As residue 67 VAL Chi-restraints excluded: chain As residue 73 LEU Chi-restraints excluded: chain As residue 88 THR Chi-restraints excluded: chain As residue 97 ASP Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 197 LEU Chi-restraints excluded: chain At residue 46 VAL Chi-restraints excluded: chain At residue 88 THR Chi-restraints excluded: chain At residue 106 GLU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 160 GLN Chi-restraints excluded: chain Au residue 46 VAL Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 88 THR Chi-restraints excluded: chain Au residue 97 ASP Chi-restraints excluded: chain Au residue 106 GLU Chi-restraints excluded: chain Au residue 211 THR Chi-restraints excluded: chain Av residue 46 VAL Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 67 VAL Chi-restraints excluded: chain Av residue 88 THR Chi-restraints excluded: chain Av residue 97 ASP Chi-restraints excluded: chain Av residue 105 LEU Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 88 THR Chi-restraints excluded: chain Ax residue 46 VAL Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 67 VAL Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 88 THR Chi-restraints excluded: chain Ay residue 46 VAL Chi-restraints excluded: chain Ay residue 53 THR Chi-restraints excluded: chain Ay residue 67 VAL Chi-restraints excluded: chain Ay residue 81 ASP Chi-restraints excluded: chain Ay residue 88 THR Chi-restraints excluded: chain Ay residue 97 ASP Chi-restraints excluded: chain Ay residue 142 GLN Chi-restraints excluded: chain Ay residue 160 GLN Chi-restraints excluded: chain Ay residue 197 LEU Chi-restraints excluded: chain Az residue 46 VAL Chi-restraints excluded: chain Az residue 52 MET Chi-restraints excluded: chain Az residue 53 THR Chi-restraints excluded: chain Az residue 88 THR Chi-restraints excluded: chain Az residue 97 ASP Chi-restraints excluded: chain Az residue 106 GLU Chi-restraints excluded: chain Az residue 133 VAL Chi-restraints excluded: chain Ba residue 46 VAL Chi-restraints excluded: chain Ba residue 49 LEU Chi-restraints excluded: chain Ba residue 67 VAL Chi-restraints excluded: chain Ba residue 73 LEU Chi-restraints excluded: chain Ba residue 88 THR Chi-restraints excluded: chain Ba residue 97 ASP Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 142 GLN Chi-restraints excluded: chain Bb residue 46 VAL Chi-restraints excluded: chain Bb residue 53 THR Chi-restraints excluded: chain Bb residue 81 ASP Chi-restraints excluded: chain Bb residue 88 THR Chi-restraints excluded: chain Bb residue 106 GLU Chi-restraints excluded: chain Bc residue 46 VAL Chi-restraints excluded: chain Bc residue 53 THR Chi-restraints excluded: chain Bc residue 88 THR Chi-restraints excluded: chain Bc residue 97 ASP Chi-restraints excluded: chain Bc residue 106 GLU Chi-restraints excluded: chain Bc residue 190 ARG Chi-restraints excluded: chain Bd residue 46 VAL Chi-restraints excluded: chain Bd residue 88 THR Chi-restraints excluded: chain Bd residue 97 ASP Chi-restraints excluded: chain Bd residue 136 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 459 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 324 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 160 GLN Ac 44 HIS Ac 71 HIS Ad 124 ASN Ad 142 GLN ** Ag 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 124 ASN Al 142 GLN ** An 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 142 GLN As 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 142 GLN Bb 142 GLN ** Bc 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111221 restraints weight = 71903.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114498 restraints weight = 46180.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116918 restraints weight = 33808.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118596 restraints weight = 26981.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119807 restraints weight = 22804.356| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 45930 Z= 0.135 Angle : 0.685 10.986 62010 Z= 0.340 Chirality : 0.037 0.150 6630 Planarity : 0.005 0.073 7980 Dihedral : 4.124 20.204 6120 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 26.22 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 5490 helix: 0.32 (0.11), residues: 2760 sheet: -1.95 (0.23), residues: 360 loop : -0.80 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 199 TYR 0.033 0.002 TYRAc 75 PHE 0.015 0.002 PHEAp 165 TRP 0.017 0.002 TRPAl 95 HIS 0.007 0.001 HISAb 71 Details of bonding type rmsd covalent geometry : bond 0.00336 (45930) covalent geometry : angle 0.68534 (62010) hydrogen bonds : bond 0.03187 ( 1920) hydrogen bonds : angle 4.17100 ( 5400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9187.32 seconds wall clock time: 157 minutes 56.82 seconds (9476.82 seconds total)