Starting phenix.real_space_refine on Sat Feb 7 20:27:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.map" model { file = "/net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7u_53793/02_2026/9r7u_53793.cif" } resolution = 3.31 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= 0.029 sd= 0.164 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 312 5.16 5 C 22536 2.51 5 N 6192 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 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: 35592 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 172} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax Time building chain proxies: 3.34, per 1000 atoms: 0.09 Number of scatterers: 35592 At special positions: 0 Unit cell: (140.156, 140.156, 189.4, 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 312 16.00 O 6552 8.00 N 6192 7.00 C 22536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 48 sheets defined 57.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'Aa' and resid 68 through 73 Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 104 Processing helix chain 'Aa' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAa 112 " --> pdb=" O SERAa 108 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAa 153 " --> pdb=" O PROAa 149 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 157 through 163 Processing helix chain 'Aa' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAa 179 " --> pdb=" O METAa 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAa 180 " --> pdb=" O ARGAa 176 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 184 through 189 Processing helix chain 'Aa' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAa 199 " --> pdb=" O SERAa 196 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 212 through 225 Processing helix chain 'Ab' and resid 68 through 73 Processing helix chain 'Ab' and resid 78 through 82 Processing helix chain 'Ab' and resid 88 through 104 Processing helix chain 'Ab' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAb 112 " --> pdb=" O SERAb 108 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAb 153 " --> pdb=" O PROAb 149 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 157 through 163 Processing helix chain 'Ab' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAb 179 " --> pdb=" O METAb 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAb 180 " --> pdb=" O ARGAb 176 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 184 through 189 Processing helix chain 'Ab' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAb 199 " --> pdb=" O SERAb 196 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 212 through 225 Processing helix chain 'Ac' and resid 68 through 73 Processing helix chain 'Ac' and resid 78 through 82 Processing helix chain 'Ac' and resid 88 through 104 Processing helix chain 'Ac' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAc 112 " --> pdb=" O SERAc 108 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAc 153 " --> pdb=" O PROAc 149 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 157 through 163 Processing helix chain 'Ac' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAc 179 " --> pdb=" O METAc 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAc 180 " --> pdb=" O ARGAc 176 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 184 through 189 Processing helix chain 'Ac' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAc 199 " --> pdb=" O SERAc 196 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 212 through 225 Processing helix chain 'Ad' and resid 68 through 73 Processing helix chain 'Ad' and resid 78 through 82 Processing helix chain 'Ad' and resid 88 through 104 Processing helix chain 'Ad' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAd 112 " --> pdb=" O SERAd 108 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAd 153 " --> pdb=" O PROAd 149 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 157 through 163 Processing helix chain 'Ad' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAd 179 " --> pdb=" O METAd 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAd 180 " --> pdb=" O ARGAd 176 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 184 through 189 Processing helix chain 'Ad' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAd 199 " --> pdb=" O SERAd 196 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 212 through 225 Processing helix chain 'Ae' and resid 68 through 73 Processing helix chain 'Ae' and resid 78 through 82 Processing helix chain 'Ae' and resid 88 through 104 Processing helix chain 'Ae' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAe 153 " --> pdb=" O PROAe 149 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 157 through 163 Processing helix chain 'Ae' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAe 179 " --> pdb=" O METAe 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAe 180 " --> pdb=" O ARGAe 176 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 184 through 189 Processing helix chain 'Ae' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAe 199 " --> pdb=" O SERAe 196 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 212 through 225 Processing helix chain 'Af' and resid 68 through 73 Processing helix chain 'Af' and resid 78 through 82 Processing helix chain 'Af' and resid 88 through 104 Processing helix chain 'Af' and resid 106 through 125 removed outlier: 3.992A pdb=" N ILEAf 112 " --> pdb=" O SERAf 108 " (cutoff:3.500A) Processing helix chain 'Af' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAf 153 " --> pdb=" O PROAf 149 " (cutoff:3.500A) Processing helix chain 'Af' and resid 157 through 163 Processing helix chain 'Af' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAf 179 " --> pdb=" O METAf 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAf 180 " --> pdb=" O ARGAf 176 " (cutoff:3.500A) Processing helix chain 'Af' and resid 184 through 189 Processing helix chain 'Af' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAf 199 " --> pdb=" O SERAf 196 " (cutoff:3.500A) Processing helix chain 'Af' and resid 212 through 225 Processing helix chain 'Ag' and resid 68 through 73 Processing helix chain 'Ag' and resid 78 through 82 Processing helix chain 'Ag' and resid 88 through 104 Processing helix chain 'Ag' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAg 112 " --> pdb=" O SERAg 108 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAg 153 " --> pdb=" O PROAg 149 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 157 through 163 Processing helix chain 'Ag' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAg 179 " --> pdb=" O METAg 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAg 180 " --> pdb=" O ARGAg 176 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 184 through 189 Processing helix chain 'Ag' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAg 199 " --> pdb=" O SERAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 212 through 225 Processing helix chain 'Ah' and resid 68 through 73 Processing helix chain 'Ah' and resid 78 through 82 Processing helix chain 'Ah' and resid 88 through 104 Processing helix chain 'Ah' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAh 112 " --> pdb=" O SERAh 108 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAh 153 " --> pdb=" O PROAh 149 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 157 through 163 Processing helix chain 'Ah' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAh 179 " --> pdb=" O METAh 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAh 180 " --> pdb=" O ARGAh 176 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 184 through 189 Processing helix chain 'Ah' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAh 199 " --> pdb=" O SERAh 196 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 212 through 225 Processing helix chain 'Ai' and resid 68 through 73 Processing helix chain 'Ai' and resid 78 through 82 Processing helix chain 'Ai' and resid 88 through 104 Processing helix chain 'Ai' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAi 112 " --> pdb=" O SERAi 108 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAi 153 " --> pdb=" O PROAi 149 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 157 through 163 Processing helix chain 'Ai' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAi 179 " --> pdb=" O METAi 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAi 180 " --> pdb=" O ARGAi 176 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 184 through 189 Processing helix chain 'Ai' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAi 199 " --> pdb=" O SERAi 196 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 212 through 225 Processing helix chain 'Aj' and resid 68 through 73 Processing helix chain 'Aj' and resid 78 through 82 Processing helix chain 'Aj' and resid 88 through 104 Processing helix chain 'Aj' and resid 106 through 125 removed outlier: 3.994A pdb=" N ILEAj 112 " --> pdb=" O SERAj 108 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAj 153 " --> pdb=" O PROAj 149 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 157 through 163 Processing helix chain 'Aj' and resid 165 through 180 removed outlier: 4.016A pdb=" N GLUAj 179 " --> pdb=" O METAj 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAj 180 " --> pdb=" O ARGAj 176 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 184 through 189 Processing helix chain 'Aj' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAj 199 " --> pdb=" O SERAj 196 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 212 through 225 Processing helix chain 'Ak' and resid 68 through 73 Processing helix chain 'Ak' and resid 78 through 82 Processing helix chain 'Ak' and resid 88 through 104 Processing helix chain 'Ak' and resid 106 through 125 removed outlier: 3.992A pdb=" N ILEAk 112 " --> pdb=" O SERAk 108 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAk 153 " --> pdb=" O PROAk 149 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 157 through 163 Processing helix chain 'Ak' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAk 179 " --> pdb=" O METAk 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSAk 180 " --> pdb=" O ARGAk 176 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 184 through 189 Processing helix chain 'Ak' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAk 199 " --> pdb=" O SERAk 196 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 212 through 225 Processing helix chain 'Al' and resid 68 through 73 Processing helix chain 'Al' and resid 78 through 82 Processing helix chain 'Al' and resid 88 through 104 Processing helix chain 'Al' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAl 112 " --> pdb=" O SERAl 108 " (cutoff:3.500A) Processing helix chain 'Al' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAl 153 " --> pdb=" O PROAl 149 " (cutoff:3.500A) Processing helix chain 'Al' and resid 157 through 163 Processing helix chain 'Al' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAl 179 " --> pdb=" O METAl 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAl 180 " --> pdb=" O ARGAl 176 " (cutoff:3.500A) Processing helix chain 'Al' and resid 184 through 189 Processing helix chain 'Al' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAl 199 " --> pdb=" O SERAl 196 " (cutoff:3.500A) Processing helix chain 'Al' and resid 212 through 225 Processing helix chain 'Am' and resid 68 through 73 Processing helix chain 'Am' and resid 78 through 82 Processing helix chain 'Am' and resid 88 through 104 Processing helix chain 'Am' and resid 106 through 125 removed outlier: 3.992A pdb=" N ILEAm 112 " --> pdb=" O SERAm 108 " (cutoff:3.500A) Processing helix chain 'Am' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAm 153 " --> pdb=" O PROAm 149 " (cutoff:3.500A) Processing helix chain 'Am' and resid 157 through 163 Processing helix chain 'Am' and resid 165 through 180 removed outlier: 4.016A pdb=" N GLUAm 179 " --> pdb=" O METAm 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSAm 180 " --> pdb=" O ARGAm 176 " (cutoff:3.500A) Processing helix chain 'Am' and resid 184 through 189 Processing helix chain 'Am' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAm 199 " --> pdb=" O SERAm 196 " (cutoff:3.500A) Processing helix chain 'Am' and resid 212 through 225 Processing helix chain 'An' and resid 68 through 73 Processing helix chain 'An' and resid 78 through 82 Processing helix chain 'An' and resid 88 through 104 Processing helix chain 'An' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAn 112 " --> pdb=" O SERAn 108 " (cutoff:3.500A) Processing helix chain 'An' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAn 153 " --> pdb=" O PROAn 149 " (cutoff:3.500A) Processing helix chain 'An' and resid 157 through 163 Processing helix chain 'An' and resid 165 through 180 removed outlier: 4.016A pdb=" N GLUAn 179 " --> pdb=" O METAn 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAn 180 " --> pdb=" O ARGAn 176 " (cutoff:3.500A) Processing helix chain 'An' and resid 184 through 189 Processing helix chain 'An' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAn 199 " --> pdb=" O SERAn 196 " (cutoff:3.500A) Processing helix chain 'An' and resid 212 through 225 Processing helix chain 'Ao' and resid 68 through 73 Processing helix chain 'Ao' and resid 78 through 82 Processing helix chain 'Ao' and resid 88 through 104 Processing helix chain 'Ao' and resid 106 through 125 removed outlier: 3.994A pdb=" N ILEAo 112 " --> pdb=" O SERAo 108 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAo 153 " --> pdb=" O PROAo 149 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 157 through 163 Processing helix chain 'Ao' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAo 179 " --> pdb=" O METAo 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSAo 180 " --> pdb=" O ARGAo 176 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 184 through 189 Processing helix chain 'Ao' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAo 199 " --> pdb=" O SERAo 196 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 212 through 225 Processing helix chain 'Ap' and resid 68 through 73 Processing helix chain 'Ap' and resid 78 through 82 Processing helix chain 'Ap' and resid 88 through 104 Processing helix chain 'Ap' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAp 112 " --> pdb=" O SERAp 108 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAp 153 " --> pdb=" O PROAp 149 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 157 through 163 Processing helix chain 'Ap' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAp 179 " --> pdb=" O METAp 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAp 180 " --> pdb=" O ARGAp 176 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 184 through 189 Processing helix chain 'Ap' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAp 199 " --> pdb=" O SERAp 196 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 212 through 225 Processing helix chain 'Aq' and resid 68 through 73 Processing helix chain 'Aq' and resid 78 through 82 Processing helix chain 'Aq' and resid 88 through 104 Processing helix chain 'Aq' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAq 112 " --> pdb=" O SERAq 108 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAq 153 " --> pdb=" O PROAq 149 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 157 through 163 Processing helix chain 'Aq' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAq 179 " --> pdb=" O METAq 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSAq 180 " --> pdb=" O ARGAq 176 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 184 through 189 Processing helix chain 'Aq' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAq 199 " --> pdb=" O SERAq 196 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 212 through 225 Processing helix chain 'Ar' and resid 68 through 73 Processing helix chain 'Ar' and resid 78 through 82 Processing helix chain 'Ar' and resid 88 through 104 Processing helix chain 'Ar' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAr 112 " --> pdb=" O SERAr 108 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAr 153 " --> pdb=" O PROAr 149 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 157 through 163 Processing helix chain 'Ar' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAr 179 " --> pdb=" O METAr 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYSAr 180 " --> pdb=" O ARGAr 176 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 184 through 189 Processing helix chain 'Ar' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAr 199 " --> pdb=" O SERAr 196 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 212 through 225 Processing helix chain 'As' and resid 68 through 73 Processing helix chain 'As' and resid 78 through 82 Processing helix chain 'As' and resid 88 through 104 Processing helix chain 'As' and resid 106 through 125 removed outlier: 3.992A pdb=" N ILEAs 112 " --> pdb=" O SERAs 108 " (cutoff:3.500A) Processing helix chain 'As' and resid 147 through 153 removed outlier: 3.585A pdb=" N HISAs 153 " --> pdb=" O PROAs 149 " (cutoff:3.500A) Processing helix chain 'As' and resid 157 through 163 Processing helix chain 'As' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAs 179 " --> pdb=" O METAs 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAs 180 " --> pdb=" O ARGAs 176 " (cutoff:3.500A) Processing helix chain 'As' and resid 184 through 189 Processing helix chain 'As' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAs 199 " --> pdb=" O SERAs 196 " (cutoff:3.500A) Processing helix chain 'As' and resid 212 through 225 Processing helix chain 'At' and resid 68 through 73 Processing helix chain 'At' and resid 78 through 82 Processing helix chain 'At' and resid 88 through 104 Processing helix chain 'At' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAt 112 " --> pdb=" O SERAt 108 " (cutoff:3.500A) Processing helix chain 'At' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAt 153 " --> pdb=" O PROAt 149 " (cutoff:3.500A) Processing helix chain 'At' and resid 157 through 163 Processing helix chain 'At' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAt 179 " --> pdb=" O METAt 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSAt 180 " --> pdb=" O ARGAt 176 " (cutoff:3.500A) Processing helix chain 'At' and resid 184 through 189 Processing helix chain 'At' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAt 199 " --> pdb=" O SERAt 196 " (cutoff:3.500A) Processing helix chain 'At' and resid 212 through 225 Processing helix chain 'Au' and resid 68 through 73 Processing helix chain 'Au' and resid 78 through 82 Processing helix chain 'Au' and resid 88 through 104 Processing helix chain 'Au' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAu 112 " --> pdb=" O SERAu 108 " (cutoff:3.500A) Processing helix chain 'Au' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAu 153 " --> pdb=" O PROAu 149 " (cutoff:3.500A) Processing helix chain 'Au' and resid 157 through 163 Processing helix chain 'Au' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAu 179 " --> pdb=" O METAu 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAu 180 " --> pdb=" O ARGAu 176 " (cutoff:3.500A) Processing helix chain 'Au' and resid 184 through 189 Processing helix chain 'Au' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAu 199 " --> pdb=" O SERAu 196 " (cutoff:3.500A) Processing helix chain 'Au' and resid 212 through 225 Processing helix chain 'Av' and resid 68 through 73 Processing helix chain 'Av' and resid 78 through 82 Processing helix chain 'Av' and resid 88 through 104 Processing helix chain 'Av' and resid 106 through 125 removed outlier: 3.992A pdb=" N ILEAv 112 " --> pdb=" O SERAv 108 " (cutoff:3.500A) Processing helix chain 'Av' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAv 153 " --> pdb=" O PROAv 149 " (cutoff:3.500A) Processing helix chain 'Av' and resid 157 through 163 Processing helix chain 'Av' and resid 165 through 180 removed outlier: 4.016A pdb=" N GLUAv 179 " --> pdb=" O METAv 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYSAv 180 " --> pdb=" O ARGAv 176 " (cutoff:3.500A) Processing helix chain 'Av' and resid 184 through 189 Processing helix chain 'Av' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAv 199 " --> pdb=" O SERAv 196 " (cutoff:3.500A) Processing helix chain 'Av' and resid 212 through 225 Processing helix chain 'Aw' and resid 68 through 73 Processing helix chain 'Aw' and resid 78 through 82 Processing helix chain 'Aw' and resid 88 through 104 Processing helix chain 'Aw' and resid 106 through 125 removed outlier: 3.993A pdb=" N ILEAw 112 " --> pdb=" O SERAw 108 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAw 153 " --> pdb=" O PROAw 149 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 157 through 163 Processing helix chain 'Aw' and resid 165 through 180 removed outlier: 4.017A pdb=" N GLUAw 179 " --> pdb=" O METAw 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAw 180 " --> pdb=" O ARGAw 176 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 184 through 189 Processing helix chain 'Aw' and resid 194 through 201 removed outlier: 4.459A pdb=" N ARGAw 199 " --> pdb=" O SERAw 196 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 212 through 225 Processing helix chain 'Ax' and resid 68 through 73 Processing helix chain 'Ax' and resid 78 through 82 Processing helix chain 'Ax' and resid 88 through 104 Processing helix chain 'Ax' and resid 106 through 125 removed outlier: 3.994A pdb=" N ILEAx 112 " --> pdb=" O SERAx 108 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 147 through 153 removed outlier: 3.584A pdb=" N HISAx 153 " --> pdb=" O PROAx 149 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 157 through 163 Processing helix chain 'Ax' and resid 165 through 180 removed outlier: 4.018A pdb=" N GLUAx 179 " --> pdb=" O METAx 175 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYSAx 180 " --> pdb=" O ARGAx 176 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 184 through 189 Processing helix chain 'Ax' and resid 194 through 201 removed outlier: 4.460A pdb=" N ARGAx 199 " --> pdb=" O SERAx 196 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 212 through 225 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 133 through 138 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 60 through 61 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 133 through 138 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 133 through 138 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 60 through 61 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 133 through 138 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 133 through 138 Processing sheet with id=AB2, first strand: chain 'Af' and resid 60 through 61 Processing sheet with id=AB3, first strand: chain 'Af' and resid 133 through 138 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 133 through 138 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 60 through 61 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 133 through 138 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 60 through 61 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 133 through 138 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 60 through 61 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 133 through 138 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 60 through 61 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 133 through 138 Processing sheet with id=AC5, first strand: chain 'Al' and resid 60 through 61 Processing sheet with id=AC6, first strand: chain 'Al' and resid 133 through 138 Processing sheet with id=AC7, first strand: chain 'Am' and resid 60 through 61 Processing sheet with id=AC8, first strand: chain 'Am' and resid 133 through 138 Processing sheet with id=AC9, first strand: chain 'An' and resid 60 through 61 Processing sheet with id=AD1, first strand: chain 'An' and resid 133 through 138 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 60 through 61 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 133 through 138 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 60 through 61 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 133 through 138 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 60 through 61 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 133 through 138 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 60 through 61 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 133 through 138 Processing sheet with id=AE1, first strand: chain 'As' and resid 60 through 61 Processing sheet with id=AE2, first strand: chain 'As' and resid 133 through 138 Processing sheet with id=AE3, first strand: chain 'At' and resid 60 through 61 Processing sheet with id=AE4, first strand: chain 'At' and resid 133 through 138 Processing sheet with id=AE5, first strand: chain 'Au' and resid 60 through 61 Processing sheet with id=AE6, first strand: chain 'Au' and resid 133 through 138 Processing sheet with id=AE7, first strand: chain 'Av' and resid 60 through 61 Processing sheet with id=AE8, first strand: chain 'Av' and resid 133 through 138 Processing sheet with id=AE9, first strand: chain 'Aw' and resid 60 through 61 Processing sheet with id=AF1, first strand: chain 'Aw' and resid 133 through 138 Processing sheet with id=AF2, first strand: chain 'Ax' and resid 60 through 61 Processing sheet with id=AF3, first strand: chain 'Ax' and resid 133 through 138 1704 hydrogen bonds defined for protein. 4536 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: 7.38 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11475 1.34 - 1.45: 4958 1.45 - 1.57: 19399 1.57 - 1.69: 0 1.69 - 1.80: 600 Bond restraints: 36432 Sorted by residual: bond pdb=" N GLUAn 140 " pdb=" CA GLUAn 140 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.31e-02 5.83e+03 1.23e+01 bond pdb=" N GLUAv 140 " pdb=" CA GLUAv 140 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.31e-02 5.83e+03 1.19e+01 bond pdb=" N GLUAj 140 " pdb=" CA GLUAj 140 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.31e-02 5.83e+03 1.19e+01 bond pdb=" N GLUAl 140 " pdb=" CA GLUAl 140 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.31e-02 5.83e+03 1.19e+01 bond pdb=" N GLUAf 140 " pdb=" CA GLUAf 140 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.31e-02 5.83e+03 1.19e+01 ... (remaining 36427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 45658 1.40 - 2.80: 2652 2.80 - 4.20: 652 4.20 - 5.59: 166 5.59 - 6.99: 72 Bond angle restraints: 49200 Sorted by residual: angle pdb=" N SERAj 74 " pdb=" CA SERAj 74 " pdb=" C SERAj 74 " ideal model delta sigma weight residual 113.97 108.55 5.42 1.28e+00 6.10e-01 1.79e+01 angle pdb=" N SERAb 74 " pdb=" CA SERAb 74 " pdb=" C SERAb 74 " ideal model delta sigma weight residual 113.97 108.58 5.39 1.28e+00 6.10e-01 1.78e+01 angle pdb=" N SERAr 74 " pdb=" CA SERAr 74 " pdb=" C SERAr 74 " ideal model delta sigma weight residual 113.97 108.58 5.39 1.28e+00 6.10e-01 1.77e+01 angle pdb=" N SERAf 74 " pdb=" CA SERAf 74 " pdb=" C SERAf 74 " ideal model delta sigma weight residual 113.97 108.60 5.37 1.28e+00 6.10e-01 1.76e+01 angle pdb=" N SERAv 74 " pdb=" CA SERAv 74 " pdb=" C SERAv 74 " ideal model delta sigma weight residual 113.97 108.60 5.37 1.28e+00 6.10e-01 1.76e+01 ... (remaining 49195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 19224 17.27 - 34.53: 2328 34.53 - 51.80: 624 51.80 - 69.06: 168 69.06 - 86.33: 96 Dihedral angle restraints: 22440 sinusoidal: 9360 harmonic: 13080 Sorted by residual: dihedral pdb=" CB GLUAs 179 " pdb=" CG GLUAs 179 " pdb=" CD GLUAs 179 " pdb=" OE1 GLUAs 179 " ideal model delta sinusoidal sigma weight residual 0.00 86.33 -86.33 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLUAi 179 " pdb=" CG GLUAi 179 " pdb=" CD GLUAi 179 " pdb=" OE1 GLUAi 179 " ideal model delta sinusoidal sigma weight residual 0.00 86.32 -86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB GLUAc 179 " pdb=" CG GLUAc 179 " pdb=" CD GLUAc 179 " pdb=" OE1 GLUAc 179 " ideal model delta sinusoidal sigma weight residual 0.00 86.31 -86.31 1 3.00e+01 1.11e-03 9.98e+00 ... (remaining 22437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3775 0.049 - 0.097: 1236 0.097 - 0.146: 128 0.146 - 0.195: 69 0.195 - 0.243: 48 Chirality restraints: 5256 Sorted by residual: chirality pdb=" CA SERAo 45 " pdb=" N SERAo 45 " pdb=" C SERAo 45 " pdb=" CB SERAo 45 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA SERAv 45 " pdb=" N SERAv 45 " pdb=" C SERAv 45 " pdb=" CB SERAv 45 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA SERAw 45 " pdb=" N SERAw 45 " pdb=" C SERAw 45 " pdb=" CB SERAw 45 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 5253 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASNAi 139 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C ASNAi 139 " 0.043 2.00e-02 2.50e+03 pdb=" O ASNAi 139 " -0.016 2.00e-02 2.50e+03 pdb=" N GLUAi 140 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASNAk 139 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C ASNAk 139 " 0.043 2.00e-02 2.50e+03 pdb=" O ASNAk 139 " -0.016 2.00e-02 2.50e+03 pdb=" N GLUAk 140 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASNAc 139 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C ASNAc 139 " 0.043 2.00e-02 2.50e+03 pdb=" O ASNAc 139 " -0.016 2.00e-02 2.50e+03 pdb=" N GLUAc 140 " -0.015 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6395 2.76 - 3.30: 32922 3.30 - 3.83: 58202 3.83 - 4.37: 70680 4.37 - 4.90: 120532 Nonbonded interactions: 288731 Sorted by model distance: nonbonded pdb=" OD2 ASPAi 194 " pdb=" OG SERAi 196 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASPAa 194 " pdb=" OG SERAa 196 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASPAr 194 " pdb=" OG SERAr 196 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASPAp 194 " pdb=" OG SERAp 196 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASPAx 194 " pdb=" OG SERAx 196 " model vdw 2.230 3.040 ... (remaining 288726 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: 0.14 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.840 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.046 36432 Z= 0.351 Angle : 0.833 6.992 49200 Z= 0.531 Chirality : 0.052 0.243 5256 Planarity : 0.005 0.034 6312 Dihedral : 17.355 86.326 13944 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 22.84 % Favored : 77.16 % 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: -1.91 (0.12), residues: 4344 helix: -1.65 (0.09), residues: 2232 sheet: -1.15 (0.17), residues: 240 loop : -0.51 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAv 199 TYR 0.019 0.003 TYRAe 186 PHE 0.030 0.004 PHEAj 165 TRP 0.015 0.003 TRPAj 134 HIS 0.002 0.001 HISAo 219 Details of bonding type rmsd covalent geometry : bond 0.00647 (36432) covalent geometry : angle 0.83255 (49200) hydrogen bonds : bond 0.15915 ( 1704) hydrogen bonds : angle 5.81434 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 1.499 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: Ad 110 MET cc_start: 0.8497 (mmm) cc_final: 0.7870 (tpt) REVERT: Am 52 MET cc_start: 0.5638 (mtt) cc_final: 0.4954 (mtm) REVERT: Am 110 MET cc_start: 0.8409 (mmm) cc_final: 0.8138 (tpt) REVERT: Ao 110 MET cc_start: 0.8388 (mmm) cc_final: 0.8142 (tpt) REVERT: Ap 110 MET cc_start: 0.8366 (mmm) cc_final: 0.7837 (tpt) REVERT: As 52 MET cc_start: 0.4693 (mtt) cc_final: 0.4222 (mtm) REVERT: Au 52 MET cc_start: 0.4885 (mtt) cc_final: 0.4330 (mtm) REVERT: Au 118 MET cc_start: 0.7970 (ttp) cc_final: 0.7768 (ttp) REVERT: Av 52 MET cc_start: 0.5029 (mtt) cc_final: 0.4439 (mtm) outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 0.2041 time to fit residues: 251.7793 Evaluate side-chains 646 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ae 160 GLN Ah 124 ASN Al 191 ASN An 191 ASN Aq 124 ASN At 124 ASN Av 191 ASN Aw 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111269 restraints weight = 47923.576| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.99 r_work: 0.3421 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 36432 Z= 0.163 Angle : 0.540 6.652 49200 Z= 0.283 Chirality : 0.039 0.116 5256 Planarity : 0.005 0.061 6312 Dihedral : 4.441 14.787 4848 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.95 % Allowed : 20.24 % Favored : 77.80 % 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: -1.02 (0.12), residues: 4344 helix: -0.64 (0.10), residues: 2376 sheet: -0.75 (0.17), residues: 240 loop : -0.45 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAe 193 TYR 0.013 0.002 TYRAj 205 PHE 0.013 0.002 PHEAh 202 TRP 0.013 0.002 TRPAi 134 HIS 0.002 0.001 HISAe 164 Details of bonding type rmsd covalent geometry : bond 0.00390 (36432) covalent geometry : angle 0.54039 (49200) hydrogen bonds : bond 0.04165 ( 1704) hydrogen bonds : angle 4.46492 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 806 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 90 GLU cc_start: 0.7731 (tp30) cc_final: 0.7347 (mt-10) REVERT: Ab 90 GLU cc_start: 0.7839 (tp30) cc_final: 0.7383 (mt-10) REVERT: Ae 183 MET cc_start: 0.8904 (tpp) cc_final: 0.8657 (tpt) REVERT: Ae 190 ARG cc_start: 0.8926 (mtt90) cc_final: 0.8618 (mtt-85) REVERT: Af 90 GLU cc_start: 0.7744 (tp30) cc_final: 0.7329 (mt-10) REVERT: Ag 52 MET cc_start: 0.6290 (mtt) cc_final: 0.5072 (mtm) REVERT: Ag 90 GLU cc_start: 0.7730 (tp30) cc_final: 0.7284 (mt-10) REVERT: Ag 193 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7294 (mtp85) REVERT: Aj 90 GLU cc_start: 0.7930 (tp30) cc_final: 0.7533 (mt-10) REVERT: Ak 118 MET cc_start: 0.8297 (ttp) cc_final: 0.7921 (ttp) REVERT: Am 90 GLU cc_start: 0.7822 (tp30) cc_final: 0.7324 (mt-10) REVERT: An 52 MET cc_start: 0.5613 (mtp) cc_final: 0.4762 (mtm) REVERT: Ao 193 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7273 (mtp85) REVERT: Ap 90 GLU cc_start: 0.7861 (tp30) cc_final: 0.7337 (mt-10) REVERT: Ap 193 ARG cc_start: 0.7975 (mtt90) cc_final: 0.7253 (mtp85) REVERT: Aq 90 GLU cc_start: 0.7921 (tp30) cc_final: 0.7377 (mt-10) REVERT: Ar 190 ARG cc_start: 0.8798 (mtt90) cc_final: 0.8504 (mtt90) REVERT: Ar 199 ARG cc_start: 0.8560 (ptp-170) cc_final: 0.8339 (ptm-80) REVERT: Ar 214 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7604 (ptm160) REVERT: As 52 MET cc_start: 0.4991 (mtt) cc_final: 0.4348 (mtm) REVERT: Au 52 MET cc_start: 0.5408 (mtt) cc_final: 0.4590 (mtm) REVERT: Av 52 MET cc_start: 0.5329 (mtt) cc_final: 0.4679 (mtm) REVERT: Av 193 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7440 (mtp85) REVERT: Aw 52 MET cc_start: 0.4584 (mtt) cc_final: 0.3961 (mtm) REVERT: Aw 90 GLU cc_start: 0.7809 (tp30) cc_final: 0.7446 (mt-10) REVERT: Aw 193 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7441 (mtp85) REVERT: Ax 141 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7766 (mp0) REVERT: Ax 193 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7575 (mtp85) REVERT: Ax 200 TYR cc_start: 0.8911 (m-80) cc_final: 0.8557 (m-80) outliers start: 76 outliers final: 31 residues processed: 865 average time/residue: 0.2114 time to fit residues: 304.3632 Evaluate side-chains 752 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 721 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ac residue 157 SER Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 219 HIS Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ai residue 157 SER Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 157 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 157 SER Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 157 SER Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 60 MET Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 135 THR Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 414 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 124 ASN ** Ag 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 124 ASN Al 191 ASN Ao 115 ASN Ao 124 ASN Ar 115 ASN ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 139 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107280 restraints weight = 48585.376| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.05 r_work: 0.3362 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 36432 Z= 0.285 Angle : 0.607 8.229 49200 Z= 0.317 Chirality : 0.043 0.152 5256 Planarity : 0.005 0.070 6312 Dihedral : 4.515 15.333 4848 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.67 % Allowed : 20.42 % Favored : 76.90 % 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: -0.39 (0.13), residues: 4344 helix: 0.06 (0.11), residues: 2184 sheet: -0.75 (0.15), residues: 240 loop : -0.40 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAj 178 TYR 0.018 0.003 TYRAb 96 PHE 0.019 0.003 PHEAe 202 TRP 0.013 0.003 TRPAs 134 HIS 0.003 0.001 HISAe 219 Details of bonding type rmsd covalent geometry : bond 0.00692 (36432) covalent geometry : angle 0.60710 (49200) hydrogen bonds : bond 0.04790 ( 1704) hydrogen bonds : angle 4.65062 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 739 time to evaluate : 1.451 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 90 GLU cc_start: 0.7810 (tp30) cc_final: 0.7403 (mt-10) REVERT: Ab 86 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: Ab 90 GLU cc_start: 0.7905 (tp30) cc_final: 0.7431 (mt-10) REVERT: Ad 86 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8073 (ttm170) REVERT: Ad 90 GLU cc_start: 0.7821 (tp30) cc_final: 0.7499 (mt-10) REVERT: Ae 86 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7848 (ttm170) REVERT: Ae 90 GLU cc_start: 0.7761 (tp30) cc_final: 0.7386 (mt-10) REVERT: Af 86 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7749 (ttm170) REVERT: Af 90 GLU cc_start: 0.7908 (tp30) cc_final: 0.7495 (mt-10) REVERT: Ag 52 MET cc_start: 0.6240 (mtt) cc_final: 0.4945 (mtm) REVERT: Ag 86 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7105 (ttm170) REVERT: Ag 90 GLU cc_start: 0.7751 (tp30) cc_final: 0.7245 (mt-10) REVERT: Ag 193 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7284 (mtp85) REVERT: Ah 86 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: Ah 90 GLU cc_start: 0.7990 (tp30) cc_final: 0.7345 (mt-10) REVERT: Ai 86 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8048 (ttm170) REVERT: Ai 90 GLU cc_start: 0.7790 (tp30) cc_final: 0.7281 (mt-10) REVERT: Aj 86 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7932 (ttm170) REVERT: Ak 86 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7292 (ttm170) REVERT: Ak 90 GLU cc_start: 0.7833 (tp30) cc_final: 0.7479 (mt-10) REVERT: Ak 118 MET cc_start: 0.8301 (ttp) cc_final: 0.7935 (ttp) REVERT: Al 52 MET cc_start: 0.5981 (mtt) cc_final: 0.5168 (mtm) REVERT: Al 86 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8256 (ttm170) REVERT: Al 90 GLU cc_start: 0.7866 (tp30) cc_final: 0.7391 (mt-10) REVERT: Al 141 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: Am 86 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: Am 90 GLU cc_start: 0.7840 (tp30) cc_final: 0.7442 (mt-10) REVERT: Am 110 MET cc_start: 0.8541 (mmm) cc_final: 0.8143 (tpt) REVERT: Am 141 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: An 52 MET cc_start: 0.5659 (mtp) cc_final: 0.4742 (mtm) REVERT: An 90 GLU cc_start: 0.7813 (tp30) cc_final: 0.7532 (mt-10) REVERT: Ao 86 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: Ao 90 GLU cc_start: 0.7903 (tp30) cc_final: 0.7532 (mt-10) REVERT: Ao 110 MET cc_start: 0.8525 (mmm) cc_final: 0.8101 (tpt) REVERT: Ao 193 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7192 (mtp85) REVERT: Ap 86 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7557 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7828 (tp30) cc_final: 0.7357 (mt-10) REVERT: Ap 193 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7240 (mtp85) REVERT: Aq 86 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: Aq 90 GLU cc_start: 0.8022 (tp30) cc_final: 0.7545 (mt-10) REVERT: Ar 86 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.6828 (ttm170) REVERT: Ar 90 GLU cc_start: 0.8034 (tp30) cc_final: 0.7518 (mt-10) REVERT: As 52 MET cc_start: 0.4865 (mtt) cc_final: 0.4129 (mtm) REVERT: As 86 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8107 (ttm170) REVERT: As 90 GLU cc_start: 0.7890 (tp30) cc_final: 0.7419 (mt-10) REVERT: As 217 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7977 (mp0) REVERT: At 86 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6824 (ttm170) REVERT: At 90 GLU cc_start: 0.7865 (tp30) cc_final: 0.7456 (mt-10) REVERT: At 193 ARG cc_start: 0.8401 (mtt90) cc_final: 0.7608 (mtp85) REVERT: Au 52 MET cc_start: 0.5565 (mtt) cc_final: 0.4668 (mtm) REVERT: Au 86 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7296 (ttm170) REVERT: Au 90 GLU cc_start: 0.7769 (tp30) cc_final: 0.7389 (mt-10) REVERT: Av 52 MET cc_start: 0.5381 (mtt) cc_final: 0.4690 (mtm) REVERT: Av 86 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7362 (ttm170) REVERT: Av 90 GLU cc_start: 0.7917 (tp30) cc_final: 0.7488 (mt-10) REVERT: Av 193 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7387 (mtp85) REVERT: Aw 52 MET cc_start: 0.4818 (mtt) cc_final: 0.4259 (mtm) REVERT: Aw 86 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7811 (tp30) cc_final: 0.7472 (mt-10) REVERT: Ax 86 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7491 (ttm170) REVERT: Ax 90 GLU cc_start: 0.7927 (tp30) cc_final: 0.7473 (mt-10) REVERT: Ax 193 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7575 (mtp85) outliers start: 104 outliers final: 62 residues processed: 830 average time/residue: 0.2274 time to fit residues: 306.3584 Evaluate side-chains 785 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 700 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 157 SER Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ab residue 124 ASN Chi-restraints excluded: chain Ab residue 143 VAL Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 157 SER Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 143 VAL Chi-restraints excluded: chain Ad residue 157 SER Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 86 ARG Chi-restraints excluded: chain Ae residue 157 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 135 THR Chi-restraints excluded: chain Af residue 143 VAL Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 86 ARG Chi-restraints excluded: chain Ag residue 219 HIS Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 143 VAL Chi-restraints excluded: chain Ah residue 203 ASP Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 143 VAL Chi-restraints excluded: chain Ai residue 157 SER Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 86 ARG Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 157 SER Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 124 ASN Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 86 ARG Chi-restraints excluded: chain Al residue 141 GLU Chi-restraints excluded: chain Al residue 157 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 141 GLU Chi-restraints excluded: chain Am residue 157 SER Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 124 ASN Chi-restraints excluded: chain An residue 157 SER Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 86 ARG Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 124 ASN Chi-restraints excluded: chain Ap residue 157 SER Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 86 ARG Chi-restraints excluded: chain Aq residue 143 VAL Chi-restraints excluded: chain Aq residue 157 SER Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 126 THR Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 86 ARG Chi-restraints excluded: chain As residue 157 SER Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 86 ARG Chi-restraints excluded: chain Au residue 157 SER Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 135 THR Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 86 ARG Chi-restraints excluded: chain Aw residue 157 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 143 VAL Chi-restraints excluded: chain Ax residue 157 SER Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 362 optimal weight: 5.9990 chunk 390 optimal weight: 0.8980 chunk 350 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 364 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ae 124 ASN Af 124 ASN ** Ag 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 124 ASN Ao 124 ASN ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 191 ASN ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116414 restraints weight = 48416.627| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.95 r_work: 0.3406 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 36432 Z= 0.115 Angle : 0.492 6.101 49200 Z= 0.256 Chirality : 0.037 0.113 5256 Planarity : 0.004 0.052 6312 Dihedral : 4.199 14.755 4848 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.49 % Allowed : 20.29 % Favored : 77.21 % 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: -0.21 (0.13), residues: 4344 helix: 0.31 (0.11), residues: 2328 sheet: -0.09 (0.19), residues: 240 loop : -0.60 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAf 178 TYR 0.012 0.001 TYRAb 96 PHE 0.013 0.002 PHEAn 202 TRP 0.013 0.002 TRPAj 134 HIS 0.002 0.000 HISAe 164 Details of bonding type rmsd covalent geometry : bond 0.00273 (36432) covalent geometry : angle 0.49214 (49200) hydrogen bonds : bond 0.03703 ( 1704) hydrogen bonds : angle 4.22943 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 796 time to evaluate : 1.407 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 90 GLU cc_start: 0.7750 (tp30) cc_final: 0.7387 (mt-10) REVERT: Ab 86 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: Ad 86 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (ttm170) REVERT: Ad 137 MET cc_start: 0.8853 (mmm) cc_final: 0.8617 (mmm) REVERT: Ad 190 ARG cc_start: 0.8768 (mtt90) cc_final: 0.8264 (mtt90) REVERT: Ae 86 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: Ae 190 ARG cc_start: 0.8852 (mtt90) cc_final: 0.8523 (mtt180) REVERT: Af 86 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7736 (ttm170) REVERT: Ag 52 MET cc_start: 0.5963 (mtt) cc_final: 0.4730 (mtm) REVERT: Ag 86 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7067 (ttm170) REVERT: Ag 90 GLU cc_start: 0.7723 (tp30) cc_final: 0.7217 (mt-10) REVERT: Ag 150 MET cc_start: 0.8972 (mmt) cc_final: 0.8531 (mmt) REVERT: Ag 193 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7192 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8682 (m-80) cc_final: 0.8420 (m-80) REVERT: Ah 86 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7716 (ttm170) REVERT: Ai 86 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: Aj 52 MET cc_start: 0.5660 (mtt) cc_final: 0.4552 (mtm) REVERT: Ak 86 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: Ak 118 MET cc_start: 0.8226 (ttp) cc_final: 0.7894 (ttp) REVERT: Al 52 MET cc_start: 0.5779 (mtt) cc_final: 0.4880 (mtm) REVERT: Al 86 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8179 (ttm170) REVERT: Al 90 GLU cc_start: 0.7726 (tp30) cc_final: 0.7406 (mt-10) REVERT: Am 86 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7714 (ttm170) REVERT: Am 199 ARG cc_start: 0.8388 (ptp-170) cc_final: 0.8177 (ptm-80) REVERT: An 52 MET cc_start: 0.5870 (mtp) cc_final: 0.4891 (mtm) REVERT: Ao 86 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: Ao 110 MET cc_start: 0.8402 (mmm) cc_final: 0.8058 (tpt) REVERT: Ap 86 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7828 (tp30) cc_final: 0.7378 (mt-10) REVERT: Ap 193 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7164 (mtp85) REVERT: Aq 90 GLU cc_start: 0.7950 (tp30) cc_final: 0.7504 (mt-10) REVERT: Ar 86 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6728 (ttm170) REVERT: As 52 MET cc_start: 0.5096 (mtt) cc_final: 0.4571 (mtm) REVERT: As 86 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: At 86 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.6892 (ttm170) REVERT: Au 52 MET cc_start: 0.5505 (mtt) cc_final: 0.4925 (mtm) REVERT: Au 86 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7182 (ttm170) REVERT: Av 52 MET cc_start: 0.5529 (mtt) cc_final: 0.4837 (mtm) REVERT: Av 86 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7268 (ttm170) REVERT: Av 193 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7328 (mtp85) REVERT: Aw 90 GLU cc_start: 0.7750 (tp30) cc_final: 0.7495 (mt-10) REVERT: Ax 86 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7438 (ttm170) REVERT: Ax 193 ARG cc_start: 0.8043 (mtt90) cc_final: 0.7320 (mtp85) outliers start: 97 outliers final: 38 residues processed: 869 average time/residue: 0.2197 time to fit residues: 314.6684 Evaluate side-chains 817 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 761 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ae residue 86 ARG Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 86 ARG Chi-restraints excluded: chain Ag residue 157 SER Chi-restraints excluded: chain Ag residue 219 HIS Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Al residue 86 ARG Chi-restraints excluded: chain Al residue 157 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 157 SER Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 157 SER Chi-restraints excluded: chain Ao residue 86 ARG Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 157 SER Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 60 MET Chi-restraints excluded: chain As residue 86 ARG Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 86 ARG Chi-restraints excluded: chain Au residue 157 SER Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 138 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 385 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 chunk 413 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 115 ASN ** Ac 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 191 ASN Ae 124 ASN Af 124 ASN ** Ag 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 139 ASN Ai 115 ASN Ak 115 ASN ** Al 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN Ao 115 ASN Ao 124 ASN Ap 115 ASN Aq 115 ASN Ar 115 ASN ** Ar 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 115 ASN ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 115 ASN ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107612 restraints weight = 48272.916| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.03 r_work: 0.3363 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 36432 Z= 0.249 Angle : 0.571 5.770 49200 Z= 0.297 Chirality : 0.041 0.139 5256 Planarity : 0.005 0.057 6312 Dihedral : 4.322 15.877 4848 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.50 % Allowed : 19.73 % Favored : 76.77 % 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: 0.08 (0.13), residues: 4344 helix: 0.60 (0.11), residues: 2184 sheet: -0.22 (0.18), residues: 240 loop : -0.42 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAf 193 TYR 0.018 0.002 TYRAb 96 PHE 0.017 0.003 PHEAb 202 TRP 0.011 0.002 TRPAd 95 HIS 0.003 0.001 HISAe 164 Details of bonding type rmsd covalent geometry : bond 0.00604 (36432) covalent geometry : angle 0.57054 (49200) hydrogen bonds : bond 0.04436 ( 1704) hydrogen bonds : angle 4.43013 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 738 time to evaluate : 1.440 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 90 GLU cc_start: 0.7800 (tp30) cc_final: 0.7432 (mt-10) REVERT: Ab 86 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: Ab 90 GLU cc_start: 0.7928 (tp30) cc_final: 0.7461 (mt-10) REVERT: Ac 52 MET cc_start: 0.6099 (mtt) cc_final: 0.4839 (mtm) REVERT: Ad 86 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8300 (ttm170) REVERT: Ad 90 GLU cc_start: 0.7864 (tp30) cc_final: 0.7518 (mt-10) REVERT: Ae 86 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7830 (ttm170) REVERT: Af 86 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7771 (ttm170) REVERT: Af 90 GLU cc_start: 0.7972 (tp30) cc_final: 0.7588 (mt-10) REVERT: Ag 52 MET cc_start: 0.5982 (mtt) cc_final: 0.5016 (mtm) REVERT: Ag 86 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7160 (ttm170) REVERT: Ag 90 GLU cc_start: 0.7734 (tp30) cc_final: 0.7333 (mt-10) REVERT: Ag 193 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7305 (mtp85) REVERT: Ah 86 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7813 (ttm170) REVERT: Ah 90 GLU cc_start: 0.8030 (tp30) cc_final: 0.7383 (mt-10) REVERT: Ah 222 MET cc_start: 0.7798 (mtm) cc_final: 0.7486 (mtt) REVERT: Ai 86 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: Ai 90 GLU cc_start: 0.7816 (tp30) cc_final: 0.7349 (mt-10) REVERT: Ai 110 MET cc_start: 0.8602 (mmm) cc_final: 0.8393 (tpt) REVERT: Aj 52 MET cc_start: 0.5949 (mtt) cc_final: 0.4766 (mtm) REVERT: Aj 86 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7951 (ttm170) REVERT: Ak 86 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: Ak 90 GLU cc_start: 0.7878 (tp30) cc_final: 0.7540 (mt-10) REVERT: Ak 118 MET cc_start: 0.8295 (ttp) cc_final: 0.7937 (ttp) REVERT: Al 52 MET cc_start: 0.5794 (mtt) cc_final: 0.4856 (mtm) REVERT: Al 86 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: Al 90 GLU cc_start: 0.7789 (tp30) cc_final: 0.7438 (mt-10) REVERT: Am 86 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7719 (ttm170) REVERT: Am 90 GLU cc_start: 0.7827 (tp30) cc_final: 0.7448 (mt-10) REVERT: Am 110 MET cc_start: 0.8545 (mmm) cc_final: 0.8188 (tpt) REVERT: An 52 MET cc_start: 0.5702 (mtp) cc_final: 0.4880 (mtm) REVERT: An 90 GLU cc_start: 0.7876 (tp30) cc_final: 0.7581 (mt-10) REVERT: Ao 86 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7601 (ttm170) REVERT: Ao 90 GLU cc_start: 0.7925 (tp30) cc_final: 0.7566 (mt-10) REVERT: Ao 110 MET cc_start: 0.8500 (mmm) cc_final: 0.8080 (tpt) REVERT: Ao 193 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7247 (mtp180) REVERT: Ap 86 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7606 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7886 (tp30) cc_final: 0.7442 (mt-10) REVERT: Ap 193 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7345 (mtp85) REVERT: Ap 217 GLU cc_start: 0.8244 (mp0) cc_final: 0.8009 (mp0) REVERT: Aq 86 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7255 (ttm170) REVERT: Aq 90 GLU cc_start: 0.8087 (tp30) cc_final: 0.7569 (mt-10) REVERT: Aq 142 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8839 (tt0) REVERT: Ar 86 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6834 (ttm170) REVERT: Ar 90 GLU cc_start: 0.8068 (tp30) cc_final: 0.7603 (mt-10) REVERT: As 52 MET cc_start: 0.5262 (mtt) cc_final: 0.4856 (mtm) REVERT: As 86 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8038 (ttm170) REVERT: As 90 GLU cc_start: 0.7983 (tp30) cc_final: 0.7535 (mt-10) REVERT: At 86 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.6850 (ttm170) REVERT: At 90 GLU cc_start: 0.7906 (tp30) cc_final: 0.7526 (mt-10) REVERT: Au 52 MET cc_start: 0.5759 (mtt) cc_final: 0.5137 (mtm) REVERT: Au 86 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7421 (ttm170) REVERT: Au 90 GLU cc_start: 0.7771 (tp30) cc_final: 0.7431 (mt-10) REVERT: Av 52 MET cc_start: 0.5273 (mtt) cc_final: 0.4905 (mtm) REVERT: Av 86 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7356 (ttm170) REVERT: Av 193 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7441 (mtp85) REVERT: Aw 86 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7821 (tp30) cc_final: 0.7535 (mt-10) REVERT: Aw 193 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7497 (mtp85) REVERT: Ax 86 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7469 (ttm170) REVERT: Ax 90 GLU cc_start: 0.7886 (tp30) cc_final: 0.7407 (mt-10) outliers start: 136 outliers final: 86 residues processed: 849 average time/residue: 0.2177 time to fit residues: 304.9482 Evaluate side-chains 831 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 723 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ab residue 124 ASN Chi-restraints excluded: chain Ab residue 143 VAL Chi-restraints excluded: chain Ab residue 157 SER Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 219 HIS Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 143 VAL Chi-restraints excluded: chain Ad residue 157 SER Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 86 ARG Chi-restraints excluded: chain Ae residue 157 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 143 VAL Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 86 ARG Chi-restraints excluded: chain Ag residue 157 SER Chi-restraints excluded: chain Ag residue 219 HIS Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 143 VAL Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 143 VAL Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 86 ARG Chi-restraints excluded: chain Aj residue 157 SER Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 124 ASN Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 86 ARG Chi-restraints excluded: chain Al residue 157 SER Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 196 SER Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 124 ASN Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 157 SER Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 86 ARG Chi-restraints excluded: chain Ao residue 143 VAL Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 124 ASN Chi-restraints excluded: chain Ap residue 157 SER Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 86 ARG Chi-restraints excluded: chain Aq residue 142 GLN Chi-restraints excluded: chain Aq residue 157 SER Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 60 MET Chi-restraints excluded: chain As residue 86 ARG Chi-restraints excluded: chain As residue 157 SER Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 86 ARG Chi-restraints excluded: chain Au residue 157 SER Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 86 ARG Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 404 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 250 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 312 optimal weight: 6.9990 chunk 427 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ae 124 ASN Af 124 ASN ** Ag 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 139 ASN ** Al 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN Ao 124 ASN As 124 ASN ** At 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117541 restraints weight = 48288.752| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.92 r_work: 0.3426 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36432 Z= 0.100 Angle : 0.467 5.286 49200 Z= 0.243 Chirality : 0.037 0.120 5256 Planarity : 0.004 0.040 6312 Dihedral : 4.020 15.121 4848 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.70 % Allowed : 20.34 % Favored : 76.95 % 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: 0.14 (0.13), residues: 4344 helix: 0.66 (0.11), residues: 2328 sheet: 0.44 (0.21), residues: 240 loop : -0.61 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAd 193 TYR 0.011 0.001 TYRAb 96 PHE 0.014 0.002 PHEAx 202 TRP 0.014 0.001 TRPAs 134 HIS 0.002 0.000 HISAk 219 Details of bonding type rmsd covalent geometry : bond 0.00234 (36432) covalent geometry : angle 0.46723 (49200) hydrogen bonds : bond 0.03378 ( 1704) hydrogen bonds : angle 4.00298 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 791 time to evaluate : 1.254 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 90 GLU cc_start: 0.7742 (tp30) cc_final: 0.7397 (mt-10) REVERT: Ab 86 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7711 (ttm170) REVERT: Ac 52 MET cc_start: 0.5649 (mtt) cc_final: 0.4547 (mtm) REVERT: Ad 86 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8128 (ttm170) REVERT: Af 86 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7700 (ttm170) REVERT: Ag 52 MET cc_start: 0.5693 (mtt) cc_final: 0.4620 (mtm) REVERT: Ag 90 GLU cc_start: 0.7690 (tp30) cc_final: 0.7295 (mt-10) REVERT: Ag 137 MET cc_start: 0.8812 (mmm) cc_final: 0.8592 (mmm) REVERT: Ag 193 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7123 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8630 (m-80) cc_final: 0.8325 (m-80) REVERT: Ah 200 TYR cc_start: 0.8729 (m-80) cc_final: 0.8483 (m-80) REVERT: Ah 222 MET cc_start: 0.7818 (mtm) cc_final: 0.7496 (mtt) REVERT: Aj 52 MET cc_start: 0.5705 (mtt) cc_final: 0.4614 (mtm) REVERT: Ak 86 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7064 (ttm170) REVERT: Ak 118 MET cc_start: 0.8194 (ttp) cc_final: 0.7872 (ttp) REVERT: Al 52 MET cc_start: 0.5809 (mtt) cc_final: 0.4922 (mtm) REVERT: Al 90 GLU cc_start: 0.7707 (tp30) cc_final: 0.7331 (mt-10) REVERT: An 52 MET cc_start: 0.5548 (mtp) cc_final: 0.4792 (mtm) REVERT: An 110 MET cc_start: 0.8362 (mmm) cc_final: 0.8045 (tpt) REVERT: Ao 193 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7167 (mtp180) REVERT: Ap 90 GLU cc_start: 0.7839 (tp30) cc_final: 0.7395 (mt-10) REVERT: Ap 193 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7217 (mtp85) REVERT: Ap 217 GLU cc_start: 0.8187 (mp0) cc_final: 0.7953 (mp0) REVERT: Aq 90 GLU cc_start: 0.8001 (tp30) cc_final: 0.7514 (mt-10) REVERT: Ar 86 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6766 (ttm170) REVERT: As 52 MET cc_start: 0.5283 (mtt) cc_final: 0.4858 (mtm) REVERT: At 86 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6970 (ttm170) REVERT: Au 52 MET cc_start: 0.5698 (mtt) cc_final: 0.5107 (mtm) REVERT: Av 52 MET cc_start: 0.5186 (mtt) cc_final: 0.4904 (mtt) REVERT: Av 86 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7267 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7770 (tp30) cc_final: 0.7547 (mt-10) REVERT: Aw 150 MET cc_start: 0.8862 (mmt) cc_final: 0.8509 (mmt) REVERT: Ax 86 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7399 (ttm170) outliers start: 105 outliers final: 62 residues processed: 878 average time/residue: 0.1973 time to fit residues: 291.9926 Evaluate side-chains 836 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 766 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 219 HIS Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 124 ASN Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 219 HIS Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 219 HIS Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 157 SER Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 303 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 363 optimal weight: 0.0050 chunk 85 optimal weight: 0.7980 chunk 364 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ad 191 ASN Ae 124 ASN ** Af 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 124 ASN Ag 124 ASN ** Ah 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN An 191 ASN Ao 124 ASN Aq 191 ASN Ar 115 ASN As 115 ASN ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 ASN Au 115 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 191 ASN ** Ax 124 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.141591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117736 restraints weight = 48447.941| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.00 r_work: 0.3432 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36432 Z= 0.094 Angle : 0.456 5.250 49200 Z= 0.237 Chirality : 0.036 0.117 5256 Planarity : 0.004 0.040 6312 Dihedral : 3.900 14.536 4848 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.49 % Allowed : 20.65 % Favored : 76.85 % 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: 0.43 (0.13), residues: 4344 helix: 0.93 (0.11), residues: 2328 sheet: 0.92 (0.21), residues: 240 loop : -0.59 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAq 214 TYR 0.012 0.001 TYRAe 96 PHE 0.014 0.002 PHEAe 202 TRP 0.011 0.001 TRPAs 134 HIS 0.002 0.000 HISAq 219 Details of bonding type rmsd covalent geometry : bond 0.00219 (36432) covalent geometry : angle 0.45572 (49200) hydrogen bonds : bond 0.03236 ( 1704) hydrogen bonds : angle 3.91504 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 796 time to evaluate : 1.350 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 90 GLU cc_start: 0.7774 (tp30) cc_final: 0.7412 (mt-10) REVERT: Ab 86 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: Ac 52 MET cc_start: 0.5726 (mtt) cc_final: 0.4776 (mtm) REVERT: Ad 86 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8086 (ttm170) REVERT: Ae 200 TYR cc_start: 0.8814 (m-80) cc_final: 0.8542 (m-80) REVERT: Af 86 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7580 (ttm170) REVERT: Af 151 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8336 (mp) REVERT: Ag 52 MET cc_start: 0.5607 (mtt) cc_final: 0.4589 (mtm) REVERT: Ag 90 GLU cc_start: 0.7742 (tp30) cc_final: 0.7324 (mt-10) REVERT: Ag 137 MET cc_start: 0.8844 (mmm) cc_final: 0.8581 (mmm) REVERT: Ag 193 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7155 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8634 (m-80) cc_final: 0.8391 (m-80) REVERT: Ah 86 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7633 (ttm170) REVERT: Ah 222 MET cc_start: 0.7838 (mtm) cc_final: 0.7514 (mtt) REVERT: Aj 52 MET cc_start: 0.5734 (mtt) cc_final: 0.4659 (mtm) REVERT: Ak 86 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7204 (ttm170) REVERT: Al 52 MET cc_start: 0.5944 (mtt) cc_final: 0.5028 (mtm) REVERT: Al 90 GLU cc_start: 0.7727 (tp30) cc_final: 0.7321 (mt-10) REVERT: Am 86 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: Am 110 MET cc_start: 0.8504 (mmm) cc_final: 0.8166 (tpt) REVERT: An 52 MET cc_start: 0.5622 (mtp) cc_final: 0.4870 (mtm) REVERT: An 110 MET cc_start: 0.8364 (mmm) cc_final: 0.8118 (tpt) REVERT: Ao 110 MET cc_start: 0.8361 (mmm) cc_final: 0.8015 (tpt) REVERT: Ap 86 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7875 (tp30) cc_final: 0.7409 (mt-10) REVERT: Aq 90 GLU cc_start: 0.7993 (tp30) cc_final: 0.7551 (mt-10) REVERT: Aq 217 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8043 (mp0) REVERT: Ar 52 MET cc_start: 0.4982 (mtt) cc_final: 0.4459 (mtm) REVERT: Ar 86 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.6755 (ttm170) REVERT: Ar 199 ARG cc_start: 0.8565 (ptp-170) cc_final: 0.8345 (ptm-80) REVERT: As 52 MET cc_start: 0.5403 (mtt) cc_final: 0.4988 (mtm) REVERT: As 81 ASP cc_start: 0.8353 (m-30) cc_final: 0.8110 (m-30) REVERT: At 86 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6987 (ttm170) REVERT: At 137 MET cc_start: 0.8851 (mmm) cc_final: 0.8484 (mmm) REVERT: Au 52 MET cc_start: 0.5226 (mtt) cc_final: 0.4818 (mtm) REVERT: Au 110 MET cc_start: 0.8304 (mmm) cc_final: 0.8045 (tpt) REVERT: Av 52 MET cc_start: 0.5130 (mtt) cc_final: 0.4851 (mtt) REVERT: Av 86 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7262 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7769 (tp30) cc_final: 0.7484 (mt-10) REVERT: Ax 86 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7402 (ttm170) outliers start: 97 outliers final: 65 residues processed: 875 average time/residue: 0.1995 time to fit residues: 292.6309 Evaluate side-chains 847 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 770 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 219 HIS Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 151 LEU Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 124 ASN Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 219 HIS Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 143 VAL Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 157 SER Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 380 optimal weight: 4.9990 chunk 402 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 160 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 418 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ad 115 ASN Ae 124 ASN ** Af 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 124 ASN Ag 124 ASN ** Ah 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN Ao 115 ASN Ao 124 ASN Ar 115 ASN ** Ar 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 191 ASN Ax 115 ASN ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115724 restraints weight = 48585.863| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.98 r_work: 0.3401 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36432 Z= 0.133 Angle : 0.487 7.784 49200 Z= 0.253 Chirality : 0.038 0.155 5256 Planarity : 0.004 0.058 6312 Dihedral : 3.919 14.861 4848 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.60 % Allowed : 20.81 % Favored : 76.59 % 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: 0.45 (0.13), residues: 4344 helix: 0.93 (0.11), residues: 2328 sheet: 1.11 (0.22), residues: 240 loop : -0.59 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAi 193 TYR 0.014 0.001 TYRAq 96 PHE 0.013 0.002 PHEAa 202 TRP 0.011 0.001 TRPAs 134 HIS 0.002 0.000 HISAf 164 Details of bonding type rmsd covalent geometry : bond 0.00323 (36432) covalent geometry : angle 0.48681 (49200) hydrogen bonds : bond 0.03514 ( 1704) hydrogen bonds : angle 4.05562 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 796 time to evaluate : 1.234 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 90 GLU cc_start: 0.7789 (tp30) cc_final: 0.7423 (mt-10) REVERT: Aa 118 MET cc_start: 0.8448 (ttp) cc_final: 0.8009 (ttp) REVERT: Aa 217 GLU cc_start: 0.8114 (mp0) cc_final: 0.7866 (mp0) REVERT: Ab 86 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: Ab 90 GLU cc_start: 0.7809 (tp30) cc_final: 0.7464 (mt-10) REVERT: Ac 52 MET cc_start: 0.5669 (mtt) cc_final: 0.4600 (mtm) REVERT: Ad 86 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8169 (ttm170) REVERT: Ad 90 GLU cc_start: 0.7754 (tp30) cc_final: 0.7501 (mt-10) REVERT: Ae 86 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: Ae 90 GLU cc_start: 0.7737 (tp30) cc_final: 0.7326 (mt-10) REVERT: Ae 200 TYR cc_start: 0.8818 (m-80) cc_final: 0.8602 (m-80) REVERT: Af 86 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: Af 90 GLU cc_start: 0.7789 (tp30) cc_final: 0.7466 (mt-10) REVERT: Ag 52 MET cc_start: 0.5683 (mtt) cc_final: 0.4637 (mtm) REVERT: Ag 86 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7106 (ttm170) REVERT: Ag 90 GLU cc_start: 0.7705 (tp30) cc_final: 0.7287 (mt-10) REVERT: Ag 137 MET cc_start: 0.8869 (mmm) cc_final: 0.8588 (mmm) REVERT: Ag 193 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7166 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8659 (m-80) cc_final: 0.8303 (m-80) REVERT: Ah 86 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: Ah 90 GLU cc_start: 0.7939 (tp30) cc_final: 0.7407 (mt-10) REVERT: Ah 222 MET cc_start: 0.7837 (mtm) cc_final: 0.7539 (mtt) REVERT: Ai 86 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8009 (ttm170) REVERT: Ai 90 GLU cc_start: 0.7649 (tp30) cc_final: 0.7278 (mt-10) REVERT: Aj 52 MET cc_start: 0.5788 (mtt) cc_final: 0.4787 (mtm) REVERT: Ak 86 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7153 (ttm170) REVERT: Ak 118 MET cc_start: 0.8271 (ttp) cc_final: 0.7939 (ttp) REVERT: Al 86 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (ttm170) REVERT: Al 90 GLU cc_start: 0.7721 (tp30) cc_final: 0.7397 (mt-10) REVERT: Am 86 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: Am 110 MET cc_start: 0.8460 (mmm) cc_final: 0.8150 (tpt) REVERT: Am 142 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: An 52 MET cc_start: 0.5574 (mtp) cc_final: 0.4815 (mtm) REVERT: An 110 MET cc_start: 0.8353 (mmm) cc_final: 0.8148 (tpt) REVERT: Ao 86 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7393 (ttm170) REVERT: Ao 110 MET cc_start: 0.8383 (mmm) cc_final: 0.8122 (tpt) REVERT: Ap 86 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7530 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7861 (tp30) cc_final: 0.7402 (mt-10) REVERT: Ap 193 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7302 (mtp85) REVERT: Ap 217 GLU cc_start: 0.8219 (mp0) cc_final: 0.7978 (mp0) REVERT: Aq 90 GLU cc_start: 0.7975 (tp30) cc_final: 0.7509 (mt-10) REVERT: Ar 86 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6789 (ttm170) REVERT: Ar 199 ARG cc_start: 0.8580 (ptp-170) cc_final: 0.8348 (ptm-80) REVERT: As 52 MET cc_start: 0.5363 (mtt) cc_final: 0.5005 (mtm) REVERT: At 86 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6991 (ttm170) REVERT: At 90 GLU cc_start: 0.7902 (tp30) cc_final: 0.7524 (mt-10) REVERT: Au 52 MET cc_start: 0.5254 (mtt) cc_final: 0.4823 (mtm) REVERT: Au 86 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7458 (ttm170) REVERT: Av 52 MET cc_start: 0.5224 (mtt) cc_final: 0.4982 (mtt) REVERT: Av 86 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: Aw 86 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7247 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7808 (tp30) cc_final: 0.7538 (mt-10) REVERT: Ax 86 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7386 (ttm170) REVERT: Ax 90 GLU cc_start: 0.7883 (tp30) cc_final: 0.7496 (mt-10) outliers start: 101 outliers final: 72 residues processed: 877 average time/residue: 0.1946 time to fit residues: 284.9820 Evaluate side-chains 861 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 770 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 124 ASN Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 219 HIS Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 86 ARG Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 86 ARG Chi-restraints excluded: chain Ag residue 124 ASN Chi-restraints excluded: chain Ag residue 203 ASP Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 219 HIS Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 143 VAL Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 143 VAL Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 86 ARG Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 142 GLN Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 86 ARG Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 67 VAL Chi-restraints excluded: chain Aq residue 157 SER Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 67 VAL Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 67 VAL Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 86 ARG Chi-restraints excluded: chain Au residue 157 SER Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 86 ARG Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 86 ARG Chi-restraints excluded: chain Ax residue 126 THR Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 317 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 122 optimal weight: 0.3980 chunk 311 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 21 optimal weight: 0.0070 chunk 298 optimal weight: 1.9990 chunk 289 optimal weight: 0.0870 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 124 ASN Ae 124 ASN Af 124 ASN ** Ag 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN Ao 115 ASN Ao 124 ASN Ar 115 ASN ** As 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 124 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 115 ASN ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119008 restraints weight = 48158.777| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.94 r_work: 0.3446 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 36432 Z= 0.094 Angle : 0.462 7.330 49200 Z= 0.242 Chirality : 0.037 0.154 5256 Planarity : 0.004 0.044 6312 Dihedral : 3.838 14.569 4848 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.29 % Allowed : 21.48 % Favored : 76.23 % 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: 0.61 (0.13), residues: 4344 helix: 1.05 (0.11), residues: 2328 sheet: 1.46 (0.22), residues: 240 loop : -0.55 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAq 214 TYR 0.011 0.001 TYRAr 200 PHE 0.013 0.002 PHEAv 202 TRP 0.013 0.001 TRPAs 134 HIS 0.002 0.000 HISAa 219 Details of bonding type rmsd covalent geometry : bond 0.00217 (36432) covalent geometry : angle 0.46195 (49200) hydrogen bonds : bond 0.03219 ( 1704) hydrogen bonds : angle 3.96446 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 787 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 52 MET cc_start: 0.5788 (mtt) cc_final: 0.5002 (mtm) REVERT: Aa 90 GLU cc_start: 0.7752 (tp30) cc_final: 0.7418 (mt-10) REVERT: Aa 110 MET cc_start: 0.8438 (tpt) cc_final: 0.7940 (tpt) REVERT: Aa 118 MET cc_start: 0.8408 (ttp) cc_final: 0.7949 (ttp) REVERT: Ab 86 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: Ac 52 MET cc_start: 0.6151 (mtt) cc_final: 0.5246 (mtm) REVERT: Ad 86 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (ttm170) REVERT: Ae 135 THR cc_start: 0.9086 (p) cc_final: 0.8865 (p) REVERT: Af 86 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7681 (ttm170) REVERT: Ag 52 MET cc_start: 0.5605 (mtt) cc_final: 0.4556 (mtm) REVERT: Ag 90 GLU cc_start: 0.7749 (tp30) cc_final: 0.7283 (mt-10) REVERT: Ag 137 MET cc_start: 0.8846 (mmm) cc_final: 0.8544 (mmm) REVERT: Ag 193 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7226 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8588 (m-80) cc_final: 0.8268 (m-80) REVERT: Ah 86 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: Ah 222 MET cc_start: 0.7839 (mtm) cc_final: 0.7580 (mtt) REVERT: Aj 52 MET cc_start: 0.5700 (mtt) cc_final: 0.4499 (mtm) REVERT: Aj 217 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: Ak 86 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7278 (ttm170) REVERT: Al 52 MET cc_start: 0.5805 (mtt) cc_final: 0.4955 (mtm) REVERT: Al 90 GLU cc_start: 0.7730 (tp30) cc_final: 0.7326 (mt-10) REVERT: Am 86 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: Am 110 MET cc_start: 0.8480 (mmm) cc_final: 0.8218 (tpt) REVERT: An 52 MET cc_start: 0.5443 (mtp) cc_final: 0.4681 (mtm) REVERT: Ao 110 MET cc_start: 0.8390 (mmm) cc_final: 0.8095 (tpt) REVERT: Ao 192 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7600 (tp) REVERT: Ao 222 MET cc_start: 0.7645 (mtt) cc_final: 0.7289 (mtt) REVERT: Ap 86 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7572 (ttm170) REVERT: Ap 90 GLU cc_start: 0.7862 (tp30) cc_final: 0.7429 (mt-10) REVERT: Ap 217 GLU cc_start: 0.8129 (mp0) cc_final: 0.7868 (mp0) REVERT: Aq 90 GLU cc_start: 0.7995 (tp30) cc_final: 0.7553 (mt-10) REVERT: Ar 52 MET cc_start: 0.5100 (mtt) cc_final: 0.4696 (mtm) REVERT: Ar 86 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.6829 (ttm170) REVERT: As 52 MET cc_start: 0.4862 (mtt) cc_final: 0.4571 (mtm) REVERT: At 86 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6991 (ttm170) REVERT: At 136 MET cc_start: 0.8652 (ttt) cc_final: 0.8449 (ttt) REVERT: At 193 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7465 (mtp180) REVERT: Av 52 MET cc_start: 0.5069 (mtt) cc_final: 0.4843 (mtt) REVERT: Av 86 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7294 (ttm170) REVERT: Av 110 MET cc_start: 0.8430 (mmm) cc_final: 0.8198 (tpt) REVERT: Aw 86 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7200 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7786 (tp30) cc_final: 0.7520 (mt-10) REVERT: Ax 192 LEU cc_start: 0.7321 (tt) cc_final: 0.6506 (tp) outliers start: 89 outliers final: 67 residues processed: 860 average time/residue: 0.1917 time to fit residues: 278.4418 Evaluate side-chains 858 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 778 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 86 ARG Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 86 ARG Chi-restraints excluded: chain Ad residue 219 HIS Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 124 ASN Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 203 ASP Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 86 ARG Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 219 HIS Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 143 VAL Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 217 GLU Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 86 ARG Chi-restraints excluded: chain Ak residue 143 VAL Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 86 ARG Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 192 LEU Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 86 ARG Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain As residue 219 HIS Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 86 ARG Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 397 optimal weight: 3.9990 chunk 291 optimal weight: 0.6980 chunk 203 optimal weight: 0.8980 chunk 385 optimal weight: 4.9990 chunk 247 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 301 optimal weight: 0.6980 chunk 266 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 139 ASN ** Ac 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 124 ASN ** Af 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 124 ASN Ag 124 ASN Ak 115 ASN ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN Ao 124 ASN Ar 115 ASN As 115 ASN At 124 ASN Au 115 ASN ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 124 ASN ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.144053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118374 restraints weight = 50735.577| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.02 r_work: 0.3453 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36432 Z= 0.090 Angle : 0.459 7.488 49200 Z= 0.240 Chirality : 0.036 0.155 5256 Planarity : 0.004 0.043 6312 Dihedral : 3.798 14.645 4848 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.95 % Allowed : 21.81 % Favored : 76.23 % 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: 0.76 (0.13), residues: 4344 helix: 1.17 (0.11), residues: 2328 sheet: 1.74 (0.23), residues: 240 loop : -0.51 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAe 214 TYR 0.010 0.001 TYRAb 96 PHE 0.013 0.002 PHEAs 202 TRP 0.012 0.001 TRPAp 134 HIS 0.002 0.000 HISAq 219 Details of bonding type rmsd covalent geometry : bond 0.00210 (36432) covalent geometry : angle 0.45914 (49200) hydrogen bonds : bond 0.03115 ( 1704) hydrogen bonds : angle 3.92999 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 784 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 52 MET cc_start: 0.5809 (mtt) cc_final: 0.5078 (mtm) REVERT: Aa 90 GLU cc_start: 0.7757 (tp30) cc_final: 0.7414 (mt-10) REVERT: Aa 110 MET cc_start: 0.8461 (tpt) cc_final: 0.7957 (tpt) REVERT: Aa 118 MET cc_start: 0.8421 (ttp) cc_final: 0.7971 (ttp) REVERT: Ac 52 MET cc_start: 0.6067 (mtt) cc_final: 0.5176 (mtm) REVERT: Ac 203 ASP cc_start: 0.8096 (t0) cc_final: 0.7836 (m-30) REVERT: Af 86 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7620 (ttm170) REVERT: Af 150 MET cc_start: 0.8719 (mmt) cc_final: 0.8484 (mmt) REVERT: Ag 52 MET cc_start: 0.5696 (mtt) cc_final: 0.4653 (mtm) REVERT: Ag 137 MET cc_start: 0.8852 (mmm) cc_final: 0.8545 (mmm) REVERT: Ag 193 ARG cc_start: 0.7792 (mtt90) cc_final: 0.7030 (mtp85) REVERT: Ag 200 TYR cc_start: 0.8588 (m-80) cc_final: 0.8087 (m-80) REVERT: Ah 222 MET cc_start: 0.7825 (mtm) cc_final: 0.7566 (mtt) REVERT: Ai 90 GLU cc_start: 0.7653 (tp30) cc_final: 0.7285 (mt-10) REVERT: Aj 52 MET cc_start: 0.5716 (mtt) cc_final: 0.4554 (mtm) REVERT: Al 52 MET cc_start: 0.5919 (mtt) cc_final: 0.5065 (mtm) REVERT: Al 90 GLU cc_start: 0.7746 (tp30) cc_final: 0.7341 (mt-10) REVERT: Am 110 MET cc_start: 0.8507 (mmm) cc_final: 0.8259 (tpt) REVERT: An 52 MET cc_start: 0.5283 (mtp) cc_final: 0.4592 (mtm) REVERT: Ao 110 MET cc_start: 0.8373 (mmm) cc_final: 0.8152 (tpt) REVERT: Ao 192 LEU cc_start: 0.7922 (tt) cc_final: 0.7570 (tp) REVERT: Ao 222 MET cc_start: 0.7609 (mtt) cc_final: 0.7285 (mtt) REVERT: Ap 90 GLU cc_start: 0.7873 (tp30) cc_final: 0.7442 (mt-10) REVERT: Ap 217 GLU cc_start: 0.8142 (mp0) cc_final: 0.7871 (mp0) REVERT: Aq 90 GLU cc_start: 0.7979 (tp30) cc_final: 0.7551 (mt-10) REVERT: Ar 52 MET cc_start: 0.4997 (mtt) cc_final: 0.4583 (mtm) REVERT: Ar 86 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6827 (ttm170) REVERT: At 86 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: At 136 MET cc_start: 0.8677 (ttt) cc_final: 0.8471 (ttt) REVERT: Av 86 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7304 (ttm170) REVERT: Aw 90 GLU cc_start: 0.7782 (tp30) cc_final: 0.7512 (mt-10) outliers start: 76 outliers final: 66 residues processed: 845 average time/residue: 0.1955 time to fit residues: 285.0082 Evaluate side-chains 840 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 770 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 143 VAL Chi-restraints excluded: chain Ad residue 53 THR Chi-restraints excluded: chain Ad residue 219 HIS Chi-restraints excluded: chain Ae residue 53 THR Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 219 HIS Chi-restraints excluded: chain Af residue 53 THR Chi-restraints excluded: chain Af residue 86 ARG Chi-restraints excluded: chain Af residue 219 HIS Chi-restraints excluded: chain Ag residue 53 THR Chi-restraints excluded: chain Ag residue 124 ASN Chi-restraints excluded: chain Ah residue 53 THR Chi-restraints excluded: chain Ah residue 57 THR Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 219 HIS Chi-restraints excluded: chain Ai residue 53 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 86 ARG Chi-restraints excluded: chain Ai residue 143 VAL Chi-restraints excluded: chain Ai residue 219 HIS Chi-restraints excluded: chain Aj residue 53 THR Chi-restraints excluded: chain Aj residue 219 HIS Chi-restraints excluded: chain Ak residue 53 THR Chi-restraints excluded: chain Ak residue 143 VAL Chi-restraints excluded: chain Ak residue 157 SER Chi-restraints excluded: chain Ak residue 219 HIS Chi-restraints excluded: chain Al residue 53 THR Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 219 HIS Chi-restraints excluded: chain Am residue 53 THR Chi-restraints excluded: chain Am residue 219 HIS Chi-restraints excluded: chain An residue 53 THR Chi-restraints excluded: chain An residue 151 LEU Chi-restraints excluded: chain An residue 219 HIS Chi-restraints excluded: chain Ao residue 53 THR Chi-restraints excluded: chain Ao residue 124 ASN Chi-restraints excluded: chain Ao residue 157 SER Chi-restraints excluded: chain Ao residue 219 HIS Chi-restraints excluded: chain Ap residue 53 THR Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 219 HIS Chi-restraints excluded: chain Aq residue 53 THR Chi-restraints excluded: chain Aq residue 219 HIS Chi-restraints excluded: chain Ar residue 53 THR Chi-restraints excluded: chain Ar residue 86 ARG Chi-restraints excluded: chain Ar residue 157 SER Chi-restraints excluded: chain Ar residue 219 HIS Chi-restraints excluded: chain As residue 53 THR Chi-restraints excluded: chain At residue 53 THR Chi-restraints excluded: chain At residue 86 ARG Chi-restraints excluded: chain At residue 124 ASN Chi-restraints excluded: chain At residue 157 SER Chi-restraints excluded: chain At residue 219 HIS Chi-restraints excluded: chain Au residue 53 THR Chi-restraints excluded: chain Au residue 219 HIS Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 86 ARG Chi-restraints excluded: chain Av residue 157 SER Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 219 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 217 GLU Chi-restraints excluded: chain Ax residue 219 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 411 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 322 optimal weight: 0.6980 chunk 284 optimal weight: 0.6980 chunk 405 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 139 ASN Ac 124 ASN Ae 124 ASN Ae 139 ASN ** Af 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 139 ASN ** Ao 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 115 ASN ** Ar 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117974 restraints weight = 50479.006| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.98 r_work: 0.3461 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 36432 Z= 0.139 Angle : 0.699 59.161 49200 Z= 0.415 Chirality : 0.038 0.645 5256 Planarity : 0.004 0.122 6312 Dihedral : 3.806 18.038 4848 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.83 % Allowed : 22.12 % Favored : 76.05 % Cbeta Deviations : 0.07 % 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: 0.77 (0.13), residues: 4344 helix: 1.18 (0.11), residues: 2328 sheet: 1.76 (0.24), residues: 240 loop : -0.50 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAr 193 TYR 0.014 0.001 TYRAg 186 PHE 0.013 0.002 PHEAs 202 TRP 0.011 0.001 TRPAp 134 HIS 0.002 0.000 HISAq 219 Details of bonding type rmsd covalent geometry : bond 0.00278 (36432) covalent geometry : angle 0.69863 (49200) hydrogen bonds : bond 0.03171 ( 1704) hydrogen bonds : angle 3.95431 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9564.72 seconds wall clock time: 164 minutes 24.61 seconds (9864.61 seconds total)