Starting phenix.real_space_refine on Sat Feb 7 20:27:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7x_53796/02_2026/9r7x_53796.map" } resolution = 2.63 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= 0.027 sd= 0.336 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 288 residue(s): 0.03s 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: 3.15, per 1000 atoms: 0.09 Number of scatterers: 35592 At special positions: 0 Unit cell: (138.116, 139.062, 185.416, 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: 2.70 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 59.0% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'Aa' and resid 68 through 73 Processing helix chain 'Aa' and resid 78 through 83 Processing helix chain 'Aa' and resid 88 through 104 Processing helix chain 'Aa' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAa 112 " --> pdb=" O SERAa 108 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAa 179 " --> pdb=" O METAa 175 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAa 190 " --> pdb=" O TYRAa 186 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ab' and resid 88 through 104 Processing helix chain 'Ab' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAb 112 " --> pdb=" O SERAb 108 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAb 179 " --> pdb=" O METAb 175 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAb 190 " --> pdb=" O TYRAb 186 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ac' and resid 88 through 104 Processing helix chain 'Ac' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAc 112 " --> pdb=" O SERAc 108 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAc 179 " --> pdb=" O METAc 175 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAc 190 " --> pdb=" O TYRAc 186 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ad' and resid 88 through 104 Processing helix chain 'Ad' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAd 112 " --> pdb=" O SERAd 108 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 147 through 153 removed outlier: 3.567A 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: 3.925A pdb=" N GLUAd 179 " --> pdb=" O METAd 175 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAd 190 " --> pdb=" O TYRAd 186 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ae' and resid 88 through 104 Processing helix chain 'Ae' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAe 179 " --> pdb=" O METAe 175 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAe 190 " --> pdb=" O TYRAe 186 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Af' and resid 88 through 104 Processing helix chain 'Af' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAf 112 " --> pdb=" O SERAf 108 " (cutoff:3.500A) Processing helix chain 'Af' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAf 179 " --> pdb=" O METAf 175 " (cutoff:3.500A) Processing helix chain 'Af' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAf 190 " --> pdb=" O TYRAf 186 " (cutoff:3.500A) Processing helix chain 'Af' and resid 194 through 201 removed outlier: 4.498A 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 83 Processing helix chain 'Ag' and resid 88 through 104 Processing helix chain 'Ag' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAg 112 " --> pdb=" O SERAg 108 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAg 179 " --> pdb=" O METAg 175 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAg 190 " --> pdb=" O TYRAg 186 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ah' and resid 88 through 104 Processing helix chain 'Ah' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAh 112 " --> pdb=" O SERAh 108 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAh 179 " --> pdb=" O METAh 175 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAh 190 " --> pdb=" O TYRAh 186 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ai' and resid 88 through 104 Processing helix chain 'Ai' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAi 112 " --> pdb=" O SERAi 108 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAi 179 " --> pdb=" O METAi 175 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAi 190 " --> pdb=" O TYRAi 186 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Aj' and resid 88 through 104 Processing helix chain 'Aj' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAj 112 " --> pdb=" O SERAj 108 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 147 through 153 removed outlier: 3.567A 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: 3.925A pdb=" N GLUAj 179 " --> pdb=" O METAj 175 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAj 190 " --> pdb=" O TYRAj 186 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ak' and resid 88 through 104 Processing helix chain 'Ak' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAk 112 " --> pdb=" O SERAk 108 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAk 179 " --> pdb=" O METAk 175 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAk 190 " --> pdb=" O TYRAk 186 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 194 through 201 removed outlier: 4.498A 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 83 Processing helix chain 'Al' and resid 88 through 104 Processing helix chain 'Al' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAl 112 " --> pdb=" O SERAl 108 " (cutoff:3.500A) Processing helix chain 'Al' and resid 147 through 153 removed outlier: 3.567A 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: 3.925A pdb=" N GLUAl 179 " --> pdb=" O METAl 175 " (cutoff:3.500A) Processing helix chain 'Al' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAl 190 " --> pdb=" O TYRAl 186 " (cutoff:3.500A) Processing helix chain 'Al' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Am' and resid 88 through 104 Processing helix chain 'Am' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAm 112 " --> pdb=" O SERAm 108 " (cutoff:3.500A) Processing helix chain 'Am' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAm 179 " --> pdb=" O METAm 175 " (cutoff:3.500A) Processing helix chain 'Am' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAm 190 " --> pdb=" O TYRAm 186 " (cutoff:3.500A) Processing helix chain 'Am' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'An' and resid 88 through 104 Processing helix chain 'An' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAn 112 " --> pdb=" O SERAn 108 " (cutoff:3.500A) Processing helix chain 'An' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAn 179 " --> pdb=" O METAn 175 " (cutoff:3.500A) Processing helix chain 'An' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAn 190 " --> pdb=" O TYRAn 186 " (cutoff:3.500A) Processing helix chain 'An' and resid 194 through 201 removed outlier: 4.498A 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 83 Processing helix chain 'Ao' and resid 88 through 104 Processing helix chain 'Ao' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAo 112 " --> pdb=" O SERAo 108 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAo 179 " --> pdb=" O METAo 175 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAo 190 " --> pdb=" O TYRAo 186 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ap' and resid 88 through 104 Processing helix chain 'Ap' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAp 112 " --> pdb=" O SERAp 108 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAp 179 " --> pdb=" O METAp 175 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAp 190 " --> pdb=" O TYRAp 186 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Aq' and resid 88 through 104 Processing helix chain 'Aq' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAq 112 " --> pdb=" O SERAq 108 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAq 179 " --> pdb=" O METAq 175 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAq 190 " --> pdb=" O TYRAq 186 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ar' and resid 88 through 104 Processing helix chain 'Ar' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAr 112 " --> pdb=" O SERAr 108 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 147 through 153 removed outlier: 3.568A 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: 3.924A pdb=" N GLUAr 179 " --> pdb=" O METAr 175 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAr 190 " --> pdb=" O TYRAr 186 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 194 through 201 removed outlier: 4.498A 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 83 Processing helix chain 'As' and resid 88 through 104 Processing helix chain 'As' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAs 112 " --> pdb=" O SERAs 108 " (cutoff:3.500A) Processing helix chain 'As' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAs 179 " --> pdb=" O METAs 175 " (cutoff:3.500A) Processing helix chain 'As' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAs 190 " --> pdb=" O TYRAs 186 " (cutoff:3.500A) Processing helix chain 'As' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'At' and resid 88 through 104 Processing helix chain 'At' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAt 112 " --> pdb=" O SERAt 108 " (cutoff:3.500A) Processing helix chain 'At' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAt 179 " --> pdb=" O METAt 175 " (cutoff:3.500A) Processing helix chain 'At' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAt 190 " --> pdb=" O TYRAt 186 " (cutoff:3.500A) Processing helix chain 'At' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Au' and resid 88 through 104 Processing helix chain 'Au' and resid 106 through 125 removed outlier: 3.904A pdb=" N ILEAu 112 " --> pdb=" O SERAu 108 " (cutoff:3.500A) Processing helix chain 'Au' and resid 147 through 153 removed outlier: 3.567A 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: 3.924A pdb=" N GLUAu 179 " --> pdb=" O METAu 175 " (cutoff:3.500A) Processing helix chain 'Au' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAu 190 " --> pdb=" O TYRAu 186 " (cutoff:3.500A) Processing helix chain 'Au' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Av' and resid 88 through 104 Processing helix chain 'Av' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAv 112 " --> pdb=" O SERAv 108 " (cutoff:3.500A) Processing helix chain 'Av' and resid 147 through 153 removed outlier: 3.568A 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: 3.925A pdb=" N GLUAv 179 " --> pdb=" O METAv 175 " (cutoff:3.500A) Processing helix chain 'Av' and resid 184 through 190 removed outlier: 3.550A pdb=" N ARGAv 190 " --> pdb=" O TYRAv 186 " (cutoff:3.500A) Processing helix chain 'Av' and resid 194 through 201 removed outlier: 4.498A 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 83 Processing helix chain 'Aw' and resid 88 through 104 Processing helix chain 'Aw' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAw 112 " --> pdb=" O SERAw 108 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 147 through 153 removed outlier: 3.569A 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: 3.924A pdb=" N GLUAw 179 " --> pdb=" O METAw 175 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 184 through 190 removed outlier: 3.552A pdb=" N ARGAw 190 " --> pdb=" O TYRAw 186 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 194 through 201 removed outlier: 4.499A 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 83 Processing helix chain 'Ax' and resid 88 through 104 Processing helix chain 'Ax' and resid 106 through 125 removed outlier: 3.903A pdb=" N ILEAx 112 " --> pdb=" O SERAx 108 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 147 through 153 removed outlier: 3.569A 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: 3.924A pdb=" N GLUAx 179 " --> pdb=" O METAx 175 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 184 through 190 removed outlier: 3.551A pdb=" N ARGAx 190 " --> pdb=" O TYRAx 186 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 194 through 201 removed outlier: 4.499A 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 1728 hydrogen bonds defined for protein. 4752 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: 6.59 Time building geometry restraints manager: 3.69 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: 11330 1.34 - 1.45: 4762 1.45 - 1.57: 19740 1.57 - 1.69: 0 1.69 - 1.80: 600 Bond restraints: 36432 Sorted by residual: bond pdb=" N ASNAx 124 " pdb=" CA ASNAx 124 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 9.71e+00 bond pdb=" N ASNAq 124 " pdb=" CA ASNAq 124 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.14e-02 7.69e+03 9.66e+00 bond pdb=" N ASNAh 124 " pdb=" CA ASNAh 124 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.14e-02 7.69e+03 9.65e+00 bond pdb=" N ASNAp 124 " pdb=" CA ASNAp 124 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.14e-02 7.69e+03 9.64e+00 bond pdb=" N ASNAo 124 " pdb=" CA ASNAo 124 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.14e-02 7.69e+03 9.60e+00 ... (remaining 36427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 44555 1.23 - 2.45: 3473 2.45 - 3.68: 941 3.68 - 4.91: 183 4.91 - 6.13: 48 Bond angle restraints: 49200 Sorted by residual: angle pdb=" N ASPAw 138 " pdb=" CA ASPAw 138 " pdb=" C ASPAw 138 " ideal model delta sigma weight residual 107.73 101.60 6.13 1.80e+00 3.09e-01 1.16e+01 angle pdb=" N ASPAo 138 " pdb=" CA ASPAo 138 " pdb=" C ASPAo 138 " ideal model delta sigma weight residual 107.73 101.60 6.13 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA SERAr 127 " pdb=" C SERAr 127 " pdb=" N PROAr 128 " ideal model delta sigma weight residual 117.44 120.57 -3.13 9.20e-01 1.18e+00 1.16e+01 angle pdb=" N ASPAg 138 " pdb=" CA ASPAg 138 " pdb=" C ASPAg 138 " ideal model delta sigma weight residual 107.73 101.61 6.12 1.80e+00 3.09e-01 1.16e+01 angle pdb=" N ASPAu 138 " pdb=" CA ASPAu 138 " pdb=" C ASPAu 138 " ideal model delta sigma weight residual 107.73 101.62 6.11 1.80e+00 3.09e-01 1.15e+01 ... (remaining 49195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 19565 17.32 - 34.65: 1962 34.65 - 51.97: 625 51.97 - 69.29: 216 69.29 - 86.61: 72 Dihedral angle restraints: 22440 sinusoidal: 9360 harmonic: 13080 Sorted by residual: dihedral pdb=" CB LYSAo 76 " pdb=" CG LYSAo 76 " pdb=" CD LYSAo 76 " pdb=" CE LYSAo 76 " ideal model delta sinusoidal sigma weight residual -60.00 -119.56 59.56 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYSAw 76 " pdb=" CG LYSAw 76 " pdb=" CD LYSAw 76 " pdb=" CE LYSAw 76 " ideal model delta sinusoidal sigma weight residual -60.00 -119.54 59.54 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYSAg 76 " pdb=" CG LYSAg 76 " pdb=" CD LYSAg 76 " pdb=" CE LYSAg 76 " ideal model delta sinusoidal sigma weight residual -60.00 -119.54 59.54 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 22437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3113 0.038 - 0.077: 1670 0.077 - 0.115: 402 0.115 - 0.153: 23 0.153 - 0.191: 48 Chirality restraints: 5256 Sorted by residual: chirality pdb=" CA TYRAx 200 " pdb=" N TYRAx 200 " pdb=" C TYRAx 200 " pdb=" CB TYRAx 200 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA TYRAt 200 " pdb=" N TYRAt 200 " pdb=" C TYRAt 200 " pdb=" CB TYRAt 200 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA TYRAl 200 " pdb=" N TYRAl 200 " pdb=" C TYRAl 200 " pdb=" CB TYRAl 200 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 5253 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METAk 137 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C METAk 137 " -0.063 2.00e-02 2.50e+03 pdb=" O METAk 137 " 0.024 2.00e-02 2.50e+03 pdb=" N ASPAk 138 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAt 137 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C METAt 137 " -0.063 2.00e-02 2.50e+03 pdb=" O METAt 137 " 0.024 2.00e-02 2.50e+03 pdb=" N ASPAt 138 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAs 137 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.31e+01 pdb=" C METAs 137 " -0.062 2.00e-02 2.50e+03 pdb=" O METAs 137 " 0.024 2.00e-02 2.50e+03 pdb=" N ASPAs 138 " 0.021 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 12503 2.87 - 3.38: 32490 3.38 - 3.89: 63991 3.89 - 4.39: 74202 4.39 - 4.90: 120427 Nonbonded interactions: 303613 Sorted by model distance: nonbonded pdb=" OE2 GLUAl 123 " pdb=" OH TYRAl 182 " model vdw 2.367 3.040 nonbonded pdb=" OE2 GLUAv 123 " pdb=" OH TYRAv 182 " model vdw 2.367 3.040 nonbonded pdb=" OE2 GLUAf 123 " pdb=" OH TYRAf 182 " model vdw 2.367 3.040 nonbonded pdb=" OE2 GLUAn 123 " pdb=" OH TYRAn 182 " model vdw 2.367 3.040 nonbonded pdb=" OE2 GLUAr 123 " pdb=" OH TYRAr 182 " model vdw 2.368 3.040 ... (remaining 303608 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: 0.13 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.480 Find NCS groups from input model: 0.340 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.007 0.036 36432 Z= 0.371 Angle : 0.797 6.133 49200 Z= 0.499 Chirality : 0.047 0.191 5256 Planarity : 0.005 0.036 6312 Dihedral : 17.129 86.615 13944 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 17.90 % Favored : 82.10 % 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: -1.38 (0.12), residues: 4344 helix: -1.12 (0.09), residues: 2184 sheet: 1.16 (0.22), residues: 240 loop : -0.76 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGAw 190 TYR 0.019 0.003 TYRAm 145 PHE 0.014 0.003 PHEAr 165 TRP 0.012 0.002 TRPAu 134 HIS 0.007 0.002 HISAo 89 Details of bonding type rmsd covalent geometry : bond 0.00713 (36432) covalent geometry : angle 0.79685 (49200) hydrogen bonds : bond 0.15032 ( 1728) hydrogen bonds : angle 6.22977 ( 4752) *********************** 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 1267 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1267 time to evaluate : 1.529 Fit side-chains REVERT: Aa 193 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7113 (mtp-110) REVERT: Ab 100 MET cc_start: 0.9040 (ttp) cc_final: 0.8794 (ttm) REVERT: Ab 190 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8388 (mtt90) REVERT: Ab 193 ARG cc_start: 0.7493 (mtm180) cc_final: 0.7113 (mtp-110) REVERT: Ac 159 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8617 (ttm170) REVERT: Ac 193 ARG cc_start: 0.7358 (mtm180) cc_final: 0.7022 (mtp-110) REVERT: Ac 194 ASP cc_start: 0.8559 (t0) cc_final: 0.8349 (t0) REVERT: Ad 55 LYS cc_start: 0.7750 (tptm) cc_final: 0.7321 (ttpp) REVERT: Ad 100 MET cc_start: 0.9042 (ttp) cc_final: 0.8785 (ttm) REVERT: Ad 193 ARG cc_start: 0.7454 (mtm180) cc_final: 0.7105 (mtp-110) REVERT: Ad 214 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7302 (mtp85) REVERT: Ae 79 GLN cc_start: 0.8693 (mt0) cc_final: 0.8461 (mt0) REVERT: Ae 100 MET cc_start: 0.8963 (ttp) cc_final: 0.8659 (ttm) REVERT: Ae 139 ASN cc_start: 0.8058 (m-40) cc_final: 0.7843 (m-40) REVERT: Ae 159 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8669 (ttm170) REVERT: Ae 162 MET cc_start: 0.8958 (mmm) cc_final: 0.8312 (mmm) REVERT: Ae 214 ARG cc_start: 0.7641 (mtp-110) cc_final: 0.7403 (mtp85) REVERT: Af 100 MET cc_start: 0.9018 (ttp) cc_final: 0.8762 (ttm) REVERT: Af 136 MET cc_start: 0.9267 (ttt) cc_final: 0.9017 (ttt) REVERT: Af 190 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8455 (mtt90) REVERT: Af 193 ARG cc_start: 0.7442 (mtm180) cc_final: 0.7178 (mpp-170) REVERT: Af 214 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7542 (mtp85) REVERT: Ag 55 LYS cc_start: 0.7881 (tptm) cc_final: 0.7463 (ttpp) REVERT: Ag 150 MET cc_start: 0.8672 (mmt) cc_final: 0.7810 (mmt) REVERT: Ag 162 MET cc_start: 0.8943 (mmm) cc_final: 0.8452 (mmm) REVERT: Ag 214 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7418 (mtp85) REVERT: Ah 118 MET cc_start: 0.9179 (ttp) cc_final: 0.8820 (ttp) REVERT: Ah 162 MET cc_start: 0.8953 (mmm) cc_final: 0.8660 (mmm) REVERT: Ah 170 GLU cc_start: 0.8532 (tt0) cc_final: 0.8242 (tt0) REVERT: Ah 193 ARG cc_start: 0.7435 (mtm180) cc_final: 0.7148 (mpp-170) REVERT: Ai 118 MET cc_start: 0.9187 (ttp) cc_final: 0.8982 (ttp) REVERT: Ai 162 MET cc_start: 0.8943 (mmm) cc_final: 0.8584 (mmm) REVERT: Ai 190 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8310 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7338 (mpp-170) REVERT: Ai 214 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7292 (mtp85) REVERT: Aj 55 LYS cc_start: 0.7777 (tptm) cc_final: 0.7205 (ttpp) REVERT: Aj 118 MET cc_start: 0.9186 (ttp) cc_final: 0.8852 (ttp) REVERT: Aj 190 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8520 (mtt90) REVERT: Aj 193 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7273 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7784 (tptm) cc_final: 0.7338 (ttpp) REVERT: Ak 118 MET cc_start: 0.9200 (ttp) cc_final: 0.8978 (ttp) REVERT: Ak 190 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8393 (mtt90) REVERT: Ak 193 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7451 (mtp-110) REVERT: Al 55 LYS cc_start: 0.7702 (tptm) cc_final: 0.7259 (ttpp) REVERT: Al 162 MET cc_start: 0.8939 (mmm) cc_final: 0.8556 (mmm) REVERT: Al 193 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7231 (mtp-110) REVERT: Al 214 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7422 (mtp85) REVERT: Am 55 LYS cc_start: 0.7858 (tptm) cc_final: 0.7430 (ttpp) REVERT: Am 78 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8476 (mttp) REVERT: Am 214 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.7377 (mtm110) REVERT: An 162 MET cc_start: 0.8951 (mmm) cc_final: 0.8528 (mmm) REVERT: An 193 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7161 (mpp-170) REVERT: Ao 55 LYS cc_start: 0.7805 (tptm) cc_final: 0.7425 (ttpp) REVERT: Ao 100 MET cc_start: 0.9068 (ttp) cc_final: 0.8821 (ttm) REVERT: Ao 193 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7293 (mpp-170) REVERT: Ap 55 LYS cc_start: 0.7855 (tptm) cc_final: 0.7425 (ttpp) REVERT: Ap 193 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7296 (mpp-170) REVERT: Aq 110 MET cc_start: 0.9017 (mmm) cc_final: 0.8752 (mmp) REVERT: Aq 217 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7559 (mt-10) REVERT: Ar 78 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8497 (mttp) REVERT: Ar 162 MET cc_start: 0.8991 (mmm) cc_final: 0.8531 (mmm) REVERT: Ar 193 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7213 (mpp-170) REVERT: As 78 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8450 (mttp) REVERT: At 55 LYS cc_start: 0.7819 (tptm) cc_final: 0.7509 (ttpp) REVERT: At 170 GLU cc_start: 0.8398 (tt0) cc_final: 0.8136 (tt0) REVERT: Au 159 ARG cc_start: 0.8801 (ttm170) cc_final: 0.8537 (ttm170) REVERT: Av 55 LYS cc_start: 0.7837 (tptm) cc_final: 0.7605 (ttpp) REVERT: Av 90 GLU cc_start: 0.7941 (tt0) cc_final: 0.7594 (tm-30) REVERT: Aw 78 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8515 (mttm) REVERT: Aw 90 GLU cc_start: 0.8030 (tt0) cc_final: 0.7822 (tm-30) REVERT: Aw 193 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7260 (mpp-170) REVERT: Ax 76 LYS cc_start: 0.9182 (mtmm) cc_final: 0.7894 (mmpt) outliers start: 0 outliers final: 1 residues processed: 1267 average time/residue: 0.9621 time to fit residues: 1385.8256 Evaluate side-chains 1004 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1003 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 160 GLN Ag 160 GLN Ah 79 GLN Ah 160 GLN Ai 79 GLN Aj 160 GLN Ak 79 GLN An 160 GLN As 160 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.095224 restraints weight = 39863.786| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.72 r_work: 0.2879 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 36432 Z= 0.126 Angle : 0.488 4.803 49200 Z= 0.258 Chirality : 0.038 0.123 5256 Planarity : 0.004 0.044 6312 Dihedral : 4.442 41.032 4850 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.06 % Allowed : 20.14 % 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: -0.23 (0.12), residues: 4344 helix: -0.14 (0.10), residues: 2376 sheet: 1.95 (0.24), residues: 240 loop : -0.26 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAm 190 TYR 0.012 0.001 TYRAs 186 PHE 0.015 0.002 PHEAi 202 TRP 0.010 0.001 TRPAx 134 HIS 0.003 0.001 HISAa 219 Details of bonding type rmsd covalent geometry : bond 0.00293 (36432) covalent geometry : angle 0.48772 (49200) hydrogen bonds : bond 0.04359 ( 1728) hydrogen bonds : angle 4.61235 ( 4752) *********************** 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 1085 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1005 time to evaluate : 1.278 Fit side-chains REVERT: Aa 60 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8351 (mtt) REVERT: Aa 190 ARG cc_start: 0.8434 (mtt90) cc_final: 0.8009 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7491 (mtm180) cc_final: 0.6848 (mtp-110) REVERT: Ab 100 MET cc_start: 0.9270 (ttp) cc_final: 0.9031 (ttm) REVERT: Ab 190 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8196 (mtt90) REVERT: Ab 193 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6810 (mtp-110) REVERT: Ab 214 ARG cc_start: 0.7646 (mtp-110) cc_final: 0.7410 (mtp85) REVERT: Ac 55 LYS cc_start: 0.7986 (tptm) cc_final: 0.7374 (ttpm) REVERT: Ac 193 ARG cc_start: 0.7430 (mtm180) cc_final: 0.6691 (mtp-110) REVERT: Ad 55 LYS cc_start: 0.7800 (tptm) cc_final: 0.7196 (ttpm) REVERT: Ad 100 MET cc_start: 0.9292 (ttp) cc_final: 0.9056 (ttm) REVERT: Ad 179 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7985 (mp0) REVERT: Ad 186 TYR cc_start: 0.8942 (t80) cc_final: 0.8456 (t80) REVERT: Ad 193 ARG cc_start: 0.7438 (mtm180) cc_final: 0.6756 (mtp-110) REVERT: Ae 55 LYS cc_start: 0.7790 (tppt) cc_final: 0.7069 (ttpp) REVERT: Ae 100 MET cc_start: 0.9214 (ttp) cc_final: 0.8906 (ttm) REVERT: Ae 162 MET cc_start: 0.9217 (mmm) cc_final: 0.8561 (mmm) REVERT: Af 78 LYS cc_start: 0.8235 (mtmm) cc_final: 0.8008 (mttm) REVERT: Af 100 MET cc_start: 0.9213 (ttp) cc_final: 0.8940 (ttm) REVERT: Af 136 MET cc_start: 0.9410 (ttt) cc_final: 0.9155 (ttt) REVERT: Af 193 ARG cc_start: 0.7481 (mtm180) cc_final: 0.7231 (mpp-170) REVERT: Af 214 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.7302 (mtp85) REVERT: Ag 55 LYS cc_start: 0.7924 (tptm) cc_final: 0.7207 (ttpp) REVERT: Ag 150 MET cc_start: 0.8979 (mmt) cc_final: 0.8378 (mmt) REVERT: Ag 162 MET cc_start: 0.9186 (mmm) cc_final: 0.8821 (mmm) REVERT: Ag 193 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6856 (mtp-110) REVERT: Ag 214 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7237 (mtp85) REVERT: Ah 55 LYS cc_start: 0.7651 (tptm) cc_final: 0.7126 (ttpm) REVERT: Ah 78 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8105 (mttm) REVERT: Ah 148 LYS cc_start: 0.8470 (tttp) cc_final: 0.8218 (tptp) REVERT: Ah 170 GLU cc_start: 0.8967 (tt0) cc_final: 0.8563 (tt0) REVERT: Ah 180 LYS cc_start: 0.7735 (tttm) cc_final: 0.7385 (ttmm) REVERT: Ah 193 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6889 (mtp-110) REVERT: Ah 214 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7138 (mtp85) REVERT: Ai 55 LYS cc_start: 0.7846 (tptm) cc_final: 0.7151 (ttpp) REVERT: Ai 78 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8107 (mttm) REVERT: Ai 193 ARG cc_start: 0.7553 (mtm180) cc_final: 0.7327 (mpp-170) REVERT: Ai 214 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7250 (mtp85) REVERT: Aj 55 LYS cc_start: 0.7873 (tptm) cc_final: 0.7282 (ttpm) REVERT: Aj 78 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7999 (mttp) REVERT: Aj 118 MET cc_start: 0.9263 (ttp) cc_final: 0.9039 (ttp) REVERT: Aj 190 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8239 (mtt90) REVERT: Aj 193 ARG cc_start: 0.7659 (mtm180) cc_final: 0.7018 (mtp-110) REVERT: Aj 194 ASP cc_start: 0.8695 (t0) cc_final: 0.8477 (t0) REVERT: Ak 55 LYS cc_start: 0.7946 (tptm) cc_final: 0.7326 (ttpm) REVERT: Ak 118 MET cc_start: 0.9281 (ttp) cc_final: 0.8996 (ttp) REVERT: Ak 190 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8175 (mtt90) REVERT: Ak 193 ARG cc_start: 0.7705 (mtm180) cc_final: 0.7052 (mtp-110) REVERT: Al 55 LYS cc_start: 0.7703 (tptm) cc_final: 0.7178 (ttpm) REVERT: Al 162 MET cc_start: 0.9195 (mmm) cc_final: 0.8856 (mmm) REVERT: Al 193 ARG cc_start: 0.7664 (mtm180) cc_final: 0.6930 (mtp-110) REVERT: Am 78 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7943 (mttp) REVERT: Am 214 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7222 (mtp85) REVERT: An 50 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8114 (pttm) REVERT: An 193 ARG cc_start: 0.7481 (mtm180) cc_final: 0.6784 (mtp-110) REVERT: Ao 55 LYS cc_start: 0.7811 (tptm) cc_final: 0.7112 (ttpp) REVERT: Ao 78 LYS cc_start: 0.8284 (mtmm) cc_final: 0.8028 (mttm) REVERT: Ao 193 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6857 (mtp-110) REVERT: Ap 55 LYS cc_start: 0.8012 (tptm) cc_final: 0.7393 (ttpm) REVERT: Aq 50 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7976 (pttm) REVERT: Aq 55 LYS cc_start: 0.7784 (tppt) cc_final: 0.7569 (tptm) REVERT: Aq 141 GLU cc_start: 0.7994 (tp30) cc_final: 0.7701 (mm-30) REVERT: Aq 174 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7763 (tm-30) REVERT: Aq 178 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7809 (mtm110) REVERT: Aq 179 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7696 (pt0) REVERT: Aq 217 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7776 (mt-10) REVERT: Ar 55 LYS cc_start: 0.7987 (tptm) cc_final: 0.7294 (ttpm) REVERT: Ar 78 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8051 (mttp) REVERT: Ar 162 MET cc_start: 0.9195 (mmm) cc_final: 0.8757 (mmm) REVERT: Ar 214 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7191 (mtp85) REVERT: As 55 LYS cc_start: 0.7991 (tptm) cc_final: 0.7290 (ttpm) REVERT: As 78 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7904 (mttp) REVERT: As 183 MET cc_start: 0.9195 (tpp) cc_final: 0.8811 (tpp) REVERT: At 50 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8239 (pttm) REVERT: At 55 LYS cc_start: 0.7829 (tptm) cc_final: 0.7194 (ttpm) REVERT: At 183 MET cc_start: 0.9264 (tpp) cc_final: 0.8892 (tpp) REVERT: At 190 ARG cc_start: 0.8452 (mtt90) cc_final: 0.8124 (mtt90) REVERT: Au 55 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7322 (ttpm) REVERT: Au 78 LYS cc_start: 0.8330 (mttt) cc_final: 0.7944 (mttm) REVERT: Au 123 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: Au 214 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7015 (mtp-110) REVERT: Au 217 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: Av 55 LYS cc_start: 0.7791 (tptm) cc_final: 0.7442 (ttpp) REVERT: Av 78 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8121 (mttp) REVERT: Av 90 GLU cc_start: 0.8490 (tt0) cc_final: 0.8122 (tm-30) REVERT: Av 174 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7735 (tm-30) REVERT: Av 214 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.7281 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: Aw 52 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7232 (mtt) REVERT: Aw 55 LYS cc_start: 0.7840 (tptm) cc_final: 0.7307 (ttpp) REVERT: Aw 78 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8088 (mttp) REVERT: Aw 90 GLU cc_start: 0.8466 (tt0) cc_final: 0.8141 (tm-30) REVERT: Aw 214 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7365 (mtm110) REVERT: Ax 55 LYS cc_start: 0.7859 (tptm) cc_final: 0.7092 (ttpm) REVERT: Ax 76 LYS cc_start: 0.9237 (mttm) cc_final: 0.7553 (mmtt) REVERT: Ax 78 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8077 (mttm) REVERT: Ax 148 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8277 (tptp) REVERT: Ax 214 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7318 (mtp-110) outliers start: 80 outliers final: 17 residues processed: 1018 average time/residue: 0.9493 time to fit residues: 1102.6527 Evaluate side-chains 975 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 948 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 60 MET Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Ak residue 199 ARG Chi-restraints excluded: chain Am residue 60 MET Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain Ao residue 60 MET Chi-restraints excluded: chain Aq residue 50 LYS Chi-restraints excluded: chain As residue 175 MET Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Ax residue 126 THR Chi-restraints excluded: chain Ax residue 148 LYS 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: 6.9990 chunk 389 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 164 HIS Ah 164 HIS Aj 164 HIS Al 164 HIS An 164 HIS Aq 164 HIS As 164 HIS Au 164 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.091586 restraints weight = 40037.214| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.73 r_work: 0.2830 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 36432 Z= 0.240 Angle : 0.561 5.188 49200 Z= 0.297 Chirality : 0.042 0.124 5256 Planarity : 0.005 0.049 6312 Dihedral : 4.595 16.809 4848 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.22 % Allowed : 17.46 % Favored : 78.32 % 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: -0.49 (0.12), residues: 4344 helix: -0.01 (0.10), residues: 2472 sheet: 2.05 (0.24), residues: 240 loop : -1.05 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAv 190 TYR 0.013 0.002 TYRAs 186 PHE 0.020 0.003 PHEAi 202 TRP 0.013 0.002 TRPAl 134 HIS 0.008 0.002 HISAa 89 Details of bonding type rmsd covalent geometry : bond 0.00570 (36432) covalent geometry : angle 0.56097 (49200) hydrogen bonds : bond 0.05099 ( 1728) hydrogen bonds : angle 4.69037 ( 4752) *********************** 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 1101 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 937 time to evaluate : 1.361 Fit side-chains REVERT: Aa 193 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6867 (mtp-110) REVERT: Ab 100 MET cc_start: 0.9292 (ttp) cc_final: 0.9060 (ttm) REVERT: Ab 107 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7484 (tt0) REVERT: Ab 193 ARG cc_start: 0.7531 (mtm180) cc_final: 0.6871 (mtp-110) REVERT: Ab 214 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: Ac 107 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: Ac 193 ARG cc_start: 0.7451 (mtm180) cc_final: 0.6733 (mtp-110) REVERT: Ad 55 LYS cc_start: 0.7833 (tptm) cc_final: 0.7223 (ttpm) REVERT: Ad 100 MET cc_start: 0.9294 (ttp) cc_final: 0.9048 (ttm) REVERT: Ad 178 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7685 (mtm110) REVERT: Ad 179 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7980 (mp0) REVERT: Ad 186 TYR cc_start: 0.9023 (t80) cc_final: 0.8611 (t80) REVERT: Ad 193 ARG cc_start: 0.7547 (mtm180) cc_final: 0.6803 (mtp-110) REVERT: Ae 55 LYS cc_start: 0.7841 (tppt) cc_final: 0.7627 (tptp) REVERT: Ae 100 MET cc_start: 0.9238 (ttp) cc_final: 0.8928 (ttm) REVERT: Ae 162 MET cc_start: 0.9237 (mmm) cc_final: 0.8565 (mmm) REVERT: Ae 214 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7359 (mtp85) REVERT: Af 100 MET cc_start: 0.9305 (ttp) cc_final: 0.9062 (ttm) REVERT: Af 123 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: Af 136 MET cc_start: 0.9431 (ttt) cc_final: 0.9174 (ttt) REVERT: Af 174 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7699 (tm-30) REVERT: Af 193 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7327 (mpp-170) REVERT: Af 217 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: Ag 52 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7167 (mtt) REVERT: Ag 55 LYS cc_start: 0.7926 (tptm) cc_final: 0.7162 (ttpp) REVERT: Ag 150 MET cc_start: 0.8970 (mmt) cc_final: 0.8369 (mmt) REVERT: Ag 162 MET cc_start: 0.9167 (mmm) cc_final: 0.8779 (mmm) REVERT: Ag 193 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6876 (mtp-110) REVERT: Ag 214 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7312 (mtp85) REVERT: Ag 219 HIS cc_start: 0.8136 (m-70) cc_final: 0.7825 (m-70) REVERT: Ah 78 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8287 (mttm) REVERT: Ah 180 LYS cc_start: 0.8008 (tttm) cc_final: 0.7628 (ttmm) REVERT: Ah 188 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8055 (tp) REVERT: Ah 193 ARG cc_start: 0.7510 (mtm180) cc_final: 0.6932 (mtp-110) REVERT: Ah 214 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7335 (mtp85) REVERT: Ai 55 LYS cc_start: 0.7821 (tptm) cc_final: 0.7108 (ttpp) REVERT: Ai 60 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: Ai 78 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8185 (mttm) REVERT: Ai 100 MET cc_start: 0.9159 (ttp) cc_final: 0.8932 (ttm) REVERT: Ai 190 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8295 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7416 (mpp-170) REVERT: Ai 194 ASP cc_start: 0.8606 (t0) cc_final: 0.8394 (t0) REVERT: Ai 214 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7423 (mtp85) REVERT: Aj 55 LYS cc_start: 0.7952 (tptm) cc_final: 0.7323 (ttpm) REVERT: Aj 78 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8168 (mttm) REVERT: Aj 179 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7870 (pt0) REVERT: Aj 190 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8331 (mtt90) REVERT: Aj 193 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6907 (mtp-110) REVERT: Aj 217 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: Ak 55 LYS cc_start: 0.7855 (tptm) cc_final: 0.7174 (ttpm) REVERT: Ak 118 MET cc_start: 0.9289 (ttp) cc_final: 0.9062 (ttp) REVERT: Ak 193 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6973 (mtp-110) REVERT: Ak 217 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: Al 52 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7167 (mtt) REVERT: Al 55 LYS cc_start: 0.7738 (tptm) cc_final: 0.7220 (ttpm) REVERT: Al 60 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8385 (mtt) REVERT: Al 78 LYS cc_start: 0.8503 (mttp) cc_final: 0.8126 (mttm) REVERT: Al 148 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8281 (tttm) REVERT: Al 162 MET cc_start: 0.9197 (mmm) cc_final: 0.8918 (mmm) REVERT: Al 188 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8009 (tp) REVERT: Al 193 ARG cc_start: 0.7660 (mtm180) cc_final: 0.6919 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: Am 60 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8602 (mtt) REVERT: Am 193 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7317 (mpp-170) REVERT: Am 214 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7333 (mtp85) REVERT: An 60 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: An 180 LYS cc_start: 0.7954 (tttp) cc_final: 0.7669 (ttmm) REVERT: An 193 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6886 (mtp-110) REVERT: An 214 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7405 (mtp85) REVERT: An 217 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: Ao 55 LYS cc_start: 0.7864 (tptm) cc_final: 0.7348 (tttm) REVERT: Ao 78 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8227 (mttm) REVERT: Ao 193 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7010 (mtp-110) REVERT: Ap 55 LYS cc_start: 0.8054 (tptm) cc_final: 0.7356 (ttpm) REVERT: Ap 188 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8077 (tp) REVERT: Ap 213 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7855 (mm) REVERT: Ap 217 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: Aq 141 GLU cc_start: 0.8197 (tp30) cc_final: 0.7952 (mm-30) REVERT: Aq 174 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7766 (tm-30) REVERT: Aq 178 ARG cc_start: 0.8128 (mtm110) cc_final: 0.7900 (mtm110) REVERT: Aq 179 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7779 (pt0) REVERT: Ar 55 LYS cc_start: 0.7924 (tptm) cc_final: 0.7214 (ttpm) REVERT: Ar 78 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8180 (mttp) REVERT: Ar 180 LYS cc_start: 0.7708 (tttp) cc_final: 0.7271 (ttmm) REVERT: As 78 LYS cc_start: 0.8453 (mtmt) cc_final: 0.8084 (mttp) REVERT: As 148 LYS cc_start: 0.8751 (tptp) cc_final: 0.8541 (tptp) REVERT: At 50 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8198 (pttm) REVERT: At 55 LYS cc_start: 0.7869 (tptm) cc_final: 0.7415 (ttpm) REVERT: At 123 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: At 217 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: Au 55 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7291 (ttpm) REVERT: Au 78 LYS cc_start: 0.8486 (mttt) cc_final: 0.8115 (mttm) REVERT: Au 123 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: Au 188 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8095 (tp) REVERT: Au 217 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: Av 52 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7148 (mtt) REVERT: Av 55 LYS cc_start: 0.7838 (tptm) cc_final: 0.7355 (tttm) REVERT: Av 78 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8232 (mttp) REVERT: Av 90 GLU cc_start: 0.8627 (tt0) cc_final: 0.8327 (tm-30) REVERT: Av 123 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: Av 174 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7815 (tm-30) REVERT: Av 214 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.7350 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: Aw 52 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7277 (mtt) REVERT: Aw 55 LYS cc_start: 0.7862 (tptm) cc_final: 0.7293 (ttpm) REVERT: Aw 78 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8292 (mttm) REVERT: Aw 90 GLU cc_start: 0.8559 (tt0) cc_final: 0.8246 (tm-30) REVERT: Aw 214 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7010 (mtp-110) REVERT: Ax 52 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6615 (mtt) REVERT: Ax 76 LYS cc_start: 0.9247 (mttm) cc_final: 0.7776 (mmmt) REVERT: Ax 78 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8215 (mttm) REVERT: Ax 123 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: Ax 148 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (tptp) REVERT: Ax 188 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8083 (tp) REVERT: Ax 217 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7635 (mt-10) outliers start: 164 outliers final: 63 residues processed: 998 average time/residue: 0.8916 time to fit residues: 1017.2834 Evaluate side-chains 1007 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 901 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 188 LEU Chi-restraints excluded: chain Aa residue 193 ARG Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ab residue 214 ARG Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 188 LEU Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Ae residue 188 LEU Chi-restraints excluded: chain Ae residue 193 ARG Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 123 GLU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 193 ARG Chi-restraints excluded: chain Af residue 217 GLU Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 188 LEU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 64 LYS Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 60 MET Chi-restraints excluded: chain Ai residue 126 THR Chi-restraints excluded: chain Ai residue 188 LEU Chi-restraints excluded: chain Ai residue 193 ARG Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 73 LEU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 188 LEU Chi-restraints excluded: chain Aj residue 193 ARG Chi-restraints excluded: chain Aj residue 217 GLU Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Ak residue 193 ARG Chi-restraints excluded: chain Ak residue 217 GLU Chi-restraints excluded: chain Al residue 52 MET Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 60 MET Chi-restraints excluded: chain Al residue 73 LEU Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 148 LYS Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 60 MET Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 193 ARG Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 188 LEU Chi-restraints excluded: chain Ao residue 193 ARG Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Ap residue 217 GLU Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 188 LEU Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain As residue 188 LEU Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 52 MET Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 188 LEU Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 216 LYS Chi-restraints excluded: chain Ax residue 52 MET Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 148 LYS Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 362 optimal weight: 4.9990 chunk 390 optimal weight: 0.8980 chunk 350 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 430 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 164 HIS Af 44 HIS Ak 44 HIS Am 164 HIS At 164 HIS Av 164 HIS Ax 164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097461 restraints weight = 40112.284| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.69 r_work: 0.2895 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 36432 Z= 0.208 Angle : 0.535 5.232 49200 Z= 0.283 Chirality : 0.040 0.123 5256 Planarity : 0.005 0.046 6312 Dihedral : 4.546 17.653 4848 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 4.76 % Allowed : 17.59 % Favored : 77.65 % 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: -0.22 (0.12), residues: 4344 helix: 0.22 (0.10), residues: 2472 sheet: 2.21 (0.24), residues: 240 loop : -0.96 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAo 190 TYR 0.015 0.002 TYRAs 186 PHE 0.018 0.003 PHEAi 202 TRP 0.013 0.002 TRPAl 134 HIS 0.006 0.002 HISAa 89 Details of bonding type rmsd covalent geometry : bond 0.00494 (36432) covalent geometry : angle 0.53514 (49200) hydrogen bonds : bond 0.04794 ( 1728) hydrogen bonds : angle 4.55543 ( 4752) *********************** 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 1098 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 913 time to evaluate : 1.254 Fit side-chains REVERT: Aa 55 LYS cc_start: 0.7914 (tptp) cc_final: 0.7683 (tptp) REVERT: Aa 190 ARG cc_start: 0.8608 (mtt90) cc_final: 0.8145 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6961 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.5508 (t-90) REVERT: Ab 100 MET cc_start: 0.9326 (ttp) cc_final: 0.9126 (ttm) REVERT: Ab 107 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7522 (tt0) REVERT: Ab 188 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8152 (tp) REVERT: Ab 193 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6949 (mtp-110) REVERT: Ac 178 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7825 (mtm110) REVERT: Ac 193 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6846 (mtp-110) REVERT: Ad 44 HIS cc_start: 0.6449 (OUTLIER) cc_final: 0.5659 (t-90) REVERT: Ad 100 MET cc_start: 0.9295 (ttp) cc_final: 0.9059 (ttm) REVERT: Ad 178 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7750 (mtt90) REVERT: Ad 190 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8215 (mtt90) REVERT: Ad 193 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6816 (mtp-110) REVERT: Ae 100 MET cc_start: 0.9276 (ttp) cc_final: 0.8990 (ttm) REVERT: Ae 162 MET cc_start: 0.9246 (mmm) cc_final: 0.8693 (mmm) REVERT: Ae 193 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6971 (mtp-110) REVERT: Ae 214 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7446 (mtp85) REVERT: Af 100 MET cc_start: 0.9323 (ttp) cc_final: 0.9073 (ttm) REVERT: Af 136 MET cc_start: 0.9397 (ttt) cc_final: 0.9173 (ttt) REVERT: Af 193 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7302 (mpp-170) REVERT: Af 214 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7419 (mtp85) REVERT: Ag 52 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7155 (mtt) REVERT: Ag 55 LYS cc_start: 0.7973 (tptm) cc_final: 0.7197 (ttpp) REVERT: Ag 60 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8500 (mtt) REVERT: Ag 150 MET cc_start: 0.8954 (mmt) cc_final: 0.8379 (mmt) REVERT: Ag 162 MET cc_start: 0.9190 (mmm) cc_final: 0.8763 (mmm) REVERT: Ag 219 HIS cc_start: 0.8189 (m-70) cc_final: 0.7884 (m-70) REVERT: Ah 162 MET cc_start: 0.9152 (mmm) cc_final: 0.8819 (mmm) REVERT: Ah 188 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8118 (tp) REVERT: Ah 193 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7012 (mtp-110) REVERT: Ah 214 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7481 (mtp85) REVERT: Ai 78 LYS cc_start: 0.8567 (mtmm) cc_final: 0.8291 (mttm) REVERT: Ai 100 MET cc_start: 0.9246 (ttp) cc_final: 0.9036 (ttm) REVERT: Ai 190 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8339 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7448 (mpp-170) REVERT: Ai 194 ASP cc_start: 0.8799 (t0) cc_final: 0.8543 (t0) REVERT: Ai 214 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7360 (mtp85) REVERT: Aj 55 LYS cc_start: 0.7950 (tptm) cc_final: 0.7332 (ttpm) REVERT: Aj 78 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8241 (mttm) REVERT: Aj 193 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7009 (mtp-110) REVERT: Aj 217 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: Ak 55 LYS cc_start: 0.7905 (tptm) cc_final: 0.7190 (ttpm) REVERT: Ak 193 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7040 (mtp-110) REVERT: Ak 214 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7573 (mtp85) REVERT: Ak 217 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: Al 52 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7167 (mtt) REVERT: Al 55 LYS cc_start: 0.7789 (tptm) cc_final: 0.7214 (ttpm) REVERT: Al 78 LYS cc_start: 0.8545 (mttp) cc_final: 0.8219 (mttm) REVERT: Al 148 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8390 (tttm) REVERT: Al 162 MET cc_start: 0.9219 (mmm) cc_final: 0.8922 (mmm) REVERT: Al 188 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8063 (tp) REVERT: Al 193 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6984 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: Am 60 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (mtt) REVERT: Am 78 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8208 (mttp) REVERT: Am 193 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7287 (mpp-170) REVERT: Am 214 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7578 (mtm110) REVERT: An 50 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8146 (pttm) REVERT: An 60 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: An 78 LYS cc_start: 0.8520 (mttp) cc_final: 0.8134 (mttm) REVERT: An 180 LYS cc_start: 0.7958 (tttp) cc_final: 0.7701 (ttmm) REVERT: An 193 ARG cc_start: 0.7622 (mtm180) cc_final: 0.6957 (mtp-110) REVERT: An 217 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: Ao 78 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8293 (mttm) REVERT: Ao 193 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7017 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.5965 (OUTLIER) cc_final: 0.5196 (t-90) REVERT: Ap 55 LYS cc_start: 0.7951 (tptm) cc_final: 0.7239 (ttpm) REVERT: Ap 73 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8004 (mp) REVERT: Ap 188 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8118 (tp) REVERT: Ap 217 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: Ap 222 MET cc_start: 0.8255 (mtm) cc_final: 0.7938 (mtm) REVERT: Aq 44 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: Aq 52 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: Aq 217 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: Ar 44 HIS cc_start: 0.6388 (OUTLIER) cc_final: 0.6163 (t-90) REVERT: Ar 55 LYS cc_start: 0.7947 (tptm) cc_final: 0.7232 (ttpm) REVERT: Ar 73 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7964 (mp) REVERT: Ar 78 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8273 (mttp) REVERT: As 44 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5454 (t-90) REVERT: As 55 LYS cc_start: 0.7936 (tptm) cc_final: 0.7308 (ttpm) REVERT: As 78 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8192 (mttp) REVERT: At 44 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5550 (t-90) REVERT: At 50 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8104 (pttm) REVERT: At 52 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: At 55 LYS cc_start: 0.7797 (tptm) cc_final: 0.7293 (ttpm) REVERT: At 123 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: At 217 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: Au 55 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7298 (ttpm) REVERT: Au 78 LYS cc_start: 0.8557 (mttt) cc_final: 0.8209 (mttm) REVERT: Au 123 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: Au 148 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8271 (tptp) REVERT: Au 188 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8223 (tp) REVERT: Au 217 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: Av 52 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7161 (mtt) REVERT: Av 55 LYS cc_start: 0.7812 (tptm) cc_final: 0.7338 (tttm) REVERT: Av 78 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8272 (mttp) REVERT: Av 90 GLU cc_start: 0.8614 (tt0) cc_final: 0.8271 (tm-30) REVERT: Av 123 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: Av 174 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7857 (tm-30) REVERT: Av 214 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7313 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: Aw 52 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7211 (mtt) REVERT: Aw 55 LYS cc_start: 0.7797 (tptm) cc_final: 0.7258 (ttpm) REVERT: Aw 78 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8383 (mttm) REVERT: Aw 90 GLU cc_start: 0.8564 (tt0) cc_final: 0.8239 (tm-30) REVERT: Aw 136 MET cc_start: 0.9428 (ttt) cc_final: 0.9190 (ttt) REVERT: Aw 214 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7160 (mtp-110) REVERT: Ax 44 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5368 (t-90) REVERT: Ax 52 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6685 (mtt) REVERT: Ax 76 LYS cc_start: 0.9279 (mttm) cc_final: 0.7787 (mmmt) REVERT: Ax 78 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8248 (mttm) REVERT: Ax 123 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: Ax 214 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7554 (mtp-110) REVERT: Ax 217 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7594 (mt-10) outliers start: 185 outliers final: 69 residues processed: 1002 average time/residue: 0.9074 time to fit residues: 1044.5965 Evaluate side-chains 1009 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 888 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 188 LEU Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ab residue 193 ARG Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 144 SER Chi-restraints excluded: chain Ac residue 188 LEU Chi-restraints excluded: chain Ac residue 193 ARG Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ad residue 193 ARG Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Ae residue 188 LEU Chi-restraints excluded: chain Ae residue 193 ARG Chi-restraints excluded: chain Af residue 50 LYS Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 60 MET Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 179 GLU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ah residue 193 ARG Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 126 THR Chi-restraints excluded: chain Ai residue 188 LEU Chi-restraints excluded: chain Ai residue 193 ARG Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 188 LEU Chi-restraints excluded: chain Aj residue 217 GLU Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Ak residue 217 GLU Chi-restraints excluded: chain Al residue 52 MET Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 73 LEU Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 148 LYS Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 193 ARG Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 60 MET Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain Am residue 193 ARG Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 73 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 179 GLU Chi-restraints excluded: chain Ao residue 188 LEU Chi-restraints excluded: chain Ao residue 193 ARG Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 217 GLU Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 50 LYS Chi-restraints excluded: chain Aq residue 52 MET Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 188 LEU Chi-restraints excluded: chain Aq residue 217 GLU Chi-restraints excluded: chain Ar residue 44 HIS Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 188 LEU Chi-restraints excluded: chain As residue 44 HIS Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain At residue 44 HIS Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 52 MET Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 52 MET Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 188 LEU Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 188 LEU Chi-restraints excluded: chain Aw residue 216 LYS Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 52 MET Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 138 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 369 optimal weight: 0.8980 chunk 413 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 164 HIS Af 44 HIS Af 164 HIS Ak 44 HIS Ak 164 HIS Ar 164 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097609 restraints weight = 40020.381| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.74 r_work: 0.2909 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 36432 Z= 0.155 Angle : 0.495 5.161 49200 Z= 0.261 Chirality : 0.039 0.121 5256 Planarity : 0.004 0.042 6312 Dihedral : 4.408 17.889 4848 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 4.42 % Allowed : 18.31 % Favored : 77.26 % 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: 0.70 (0.13), residues: 4344 helix: 0.79 (0.11), residues: 2328 sheet: 2.51 (0.24), residues: 240 loop : -0.13 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAv 190 TYR 0.018 0.001 TYRAs 186 PHE 0.016 0.002 PHEAi 202 TRP 0.012 0.002 TRPAl 134 HIS 0.004 0.001 HISAt 89 Details of bonding type rmsd covalent geometry : bond 0.00366 (36432) covalent geometry : angle 0.49473 (49200) hydrogen bonds : bond 0.04319 ( 1728) hydrogen bonds : angle 4.34913 ( 4752) *********************** 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 1087 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 915 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.5932 (t-90) REVERT: Aa 52 MET cc_start: 0.7217 (mtt) cc_final: 0.6561 (mtt) REVERT: Aa 55 LYS cc_start: 0.7937 (tptp) cc_final: 0.7688 (tptp) REVERT: Aa 190 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8173 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6969 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5533 (t-90) REVERT: Ab 100 MET cc_start: 0.9325 (ttp) cc_final: 0.9121 (ttm) REVERT: Ab 107 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7506 (tt0) REVERT: Ab 188 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8102 (tp) REVERT: Ab 193 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6921 (mtp-110) REVERT: Ac 44 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.5695 (t-90) REVERT: Ac 52 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6661 (mtt) REVERT: Ac 55 LYS cc_start: 0.7880 (tptm) cc_final: 0.7319 (ttpm) REVERT: Ac 193 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6879 (mtp-110) REVERT: Ad 44 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.5633 (t-90) REVERT: Ad 100 MET cc_start: 0.9305 (ttp) cc_final: 0.9080 (ttm) REVERT: Ad 186 TYR cc_start: 0.9036 (t80) cc_final: 0.8547 (t80) REVERT: Ae 44 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5429 (t-90) REVERT: Ae 73 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8351 (mt) REVERT: Ae 100 MET cc_start: 0.9273 (ttp) cc_final: 0.9030 (ttm) REVERT: Ae 162 MET cc_start: 0.9244 (mmm) cc_final: 0.8672 (mmm) REVERT: Ae 193 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6943 (mtp-110) REVERT: Ae 214 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7406 (mtp85) REVERT: Af 100 MET cc_start: 0.9325 (ttp) cc_final: 0.9101 (ttm) REVERT: Af 123 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: Ag 44 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.5547 (t-90) REVERT: Ag 52 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7170 (mtt) REVERT: Ag 55 LYS cc_start: 0.7926 (tptm) cc_final: 0.7164 (ttpp) REVERT: Ag 162 MET cc_start: 0.9188 (mmm) cc_final: 0.8748 (mmm) REVERT: Ag 193 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7029 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8220 (m-70) cc_final: 0.7853 (m-70) REVERT: Ah 44 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5039 (t-90) REVERT: Ah 162 MET cc_start: 0.9159 (mmm) cc_final: 0.8856 (mmm) REVERT: Ah 188 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (tp) REVERT: Ah 193 ARG cc_start: 0.7466 (mtm180) cc_final: 0.6951 (mtp-110) REVERT: Ai 44 HIS cc_start: 0.6380 (OUTLIER) cc_final: 0.5627 (t-90) REVERT: Ai 78 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8243 (mttm) REVERT: Ai 190 ARG cc_start: 0.8669 (mtt90) cc_final: 0.8388 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7483 (mpp-170) REVERT: Ai 194 ASP cc_start: 0.8796 (t0) cc_final: 0.8544 (t0) REVERT: Ai 214 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7288 (mtp85) REVERT: Ai 219 HIS cc_start: 0.8250 (m-70) cc_final: 0.7935 (m-70) REVERT: Aj 44 HIS cc_start: 0.6450 (OUTLIER) cc_final: 0.5625 (t-90) REVERT: Aj 55 LYS cc_start: 0.7935 (tptm) cc_final: 0.7360 (tttm) REVERT: Aj 78 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8167 (mttm) REVERT: Aj 193 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6986 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7869 (tptm) cc_final: 0.7203 (ttpm) REVERT: Ak 193 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7040 (mtp-110) REVERT: Al 44 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5496 (t-90) REVERT: Al 55 LYS cc_start: 0.7752 (tptm) cc_final: 0.7210 (ttpm) REVERT: Al 60 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: Al 78 LYS cc_start: 0.8479 (mttp) cc_final: 0.8209 (mttm) REVERT: Al 162 MET cc_start: 0.9211 (mmm) cc_final: 0.8893 (mmm) REVERT: Al 188 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8065 (tp) REVERT: Al 193 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6988 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: Am 78 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8063 (mttp) REVERT: Am 188 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8285 (tp) REVERT: An 44 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.5721 (t-90) REVERT: An 50 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8129 (pttm) REVERT: An 60 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: An 78 LYS cc_start: 0.8450 (mttp) cc_final: 0.8095 (mttm) REVERT: An 180 LYS cc_start: 0.7889 (tttp) cc_final: 0.7663 (ttmm) REVERT: An 193 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6979 (mtp-110) REVERT: An 217 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: Ao 148 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8462 (tptp) REVERT: Ao 193 ARG cc_start: 0.7631 (mtm180) cc_final: 0.6993 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5036 (t-90) REVERT: Ap 73 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (mp) REVERT: Ap 188 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8146 (tp) REVERT: Ap 193 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7522 (mtp180) REVERT: Ap 213 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7643 (tp) REVERT: Ap 222 MET cc_start: 0.8265 (mtm) cc_final: 0.7863 (mtm) REVERT: Aq 44 HIS cc_start: 0.6188 (OUTLIER) cc_final: 0.5573 (t-90) REVERT: Aq 52 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7247 (mtt) REVERT: Aq 110 MET cc_start: 0.9179 (mmm) cc_final: 0.8795 (mmp) REVERT: Aq 191 ASN cc_start: 0.8564 (m-40) cc_final: 0.8256 (m-40) REVERT: Ar 44 HIS cc_start: 0.6347 (OUTLIER) cc_final: 0.6087 (t-90) REVERT: Ar 55 LYS cc_start: 0.7906 (tptm) cc_final: 0.7199 (ttpm) REVERT: Ar 73 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7999 (mp) REVERT: Ar 78 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8224 (mttp) REVERT: As 55 LYS cc_start: 0.7959 (tptm) cc_final: 0.7231 (ttpm) REVERT: As 78 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8131 (mttp) REVERT: As 123 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: As 214 ARG cc_start: 0.7379 (mtp-110) cc_final: 0.7004 (mtp-110) REVERT: At 44 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5444 (t-90) REVERT: At 50 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8203 (pttm) REVERT: At 55 LYS cc_start: 0.7774 (tptm) cc_final: 0.7297 (ttpm) REVERT: At 123 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: At 190 ARG cc_start: 0.8507 (mtt90) cc_final: 0.8217 (mtt90) REVERT: At 217 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: Au 44 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5060 (t-90) REVERT: Au 55 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7337 (ttpm) REVERT: Au 78 LYS cc_start: 0.8480 (mttt) cc_final: 0.8124 (mttm) REVERT: Au 123 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: Au 148 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8208 (tptp) REVERT: Au 188 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8199 (tp) REVERT: Au 217 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: Av 52 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7447 (mtt) REVERT: Av 55 LYS cc_start: 0.7783 (tptm) cc_final: 0.7339 (tttm) REVERT: Av 78 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8253 (mttp) REVERT: Av 90 GLU cc_start: 0.8641 (tt0) cc_final: 0.8297 (tm-30) REVERT: Av 123 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: Av 174 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7815 (tm-30) REVERT: Av 193 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7020 (mtp180) REVERT: Av 214 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7447 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: Aw 52 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7208 (mtt) REVERT: Aw 55 LYS cc_start: 0.7761 (tptm) cc_final: 0.7209 (ttpm) REVERT: Aw 78 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8351 (mttm) REVERT: Aw 90 GLU cc_start: 0.8563 (tt0) cc_final: 0.8249 (tm-30) REVERT: Aw 214 ARG cc_start: 0.7691 (mtp-110) cc_final: 0.7316 (mtm110) REVERT: Ax 44 HIS cc_start: 0.5831 (OUTLIER) cc_final: 0.5217 (t-90) REVERT: Ax 52 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6611 (mtt) REVERT: Ax 55 LYS cc_start: 0.7720 (tptm) cc_final: 0.7038 (ttpm) REVERT: Ax 73 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7718 (mp) REVERT: Ax 76 LYS cc_start: 0.9275 (mttm) cc_final: 0.7805 (mmmt) REVERT: Ax 78 LYS cc_start: 0.8539 (mtmm) cc_final: 0.8218 (mttm) REVERT: Ax 123 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: Ax 214 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7559 (mtp-110) REVERT: Ax 217 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7634 (mt-10) outliers start: 172 outliers final: 64 residues processed: 983 average time/residue: 0.8947 time to fit residues: 1010.6024 Evaluate side-chains 1000 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 873 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Aa residue 188 LEU Chi-restraints excluded: chain Aa residue 193 ARG Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ab residue 193 ARG Chi-restraints excluded: chain Ac residue 44 HIS Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 188 LEU Chi-restraints excluded: chain Ac residue 193 ARG Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ae residue 44 HIS Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Ae residue 193 ARG Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 123 GLU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 188 LEU Chi-restraints excluded: chain Ag residue 44 HIS Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 57 THR Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 179 GLU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 44 HIS Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ai residue 44 HIS Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 126 THR Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Ai residue 188 LEU Chi-restraints excluded: chain Aj residue 44 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 193 ARG Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 193 ARG Chi-restraints excluded: chain Ak residue 199 ARG Chi-restraints excluded: chain Al residue 44 HIS Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 60 MET Chi-restraints excluded: chain Al residue 73 LEU Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 148 LYS Chi-restraints excluded: chain Al residue 174 GLU Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 193 ARG Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 44 HIS Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 193 ARG Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 73 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 148 LYS Chi-restraints excluded: chain Ao residue 179 GLU Chi-restraints excluded: chain Ao residue 188 LEU Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 193 ARG Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 52 MET Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 188 LEU Chi-restraints excluded: chain Ar residue 44 HIS Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 188 LEU Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain As residue 123 GLU Chi-restraints excluded: chain At residue 44 HIS Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 126 THR Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 44 HIS Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 52 MET Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 193 ARG Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 188 LEU Chi-restraints excluded: chain Aw residue 216 LYS Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 52 MET Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 404 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 44 HIS Ak 44 HIS Ao 164 HIS Ap 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.095489 restraints weight = 40110.775| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.73 r_work: 0.2916 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 36432 Z= 0.261 Angle : 0.570 5.307 49200 Z= 0.302 Chirality : 0.043 0.126 5256 Planarity : 0.005 0.051 6312 Dihedral : 4.629 18.849 4848 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.76 % Allowed : 18.60 % Favored : 76.65 % 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: -0.07 (0.12), residues: 4344 helix: 0.33 (0.10), residues: 2472 sheet: 2.40 (0.23), residues: 240 loop : -0.91 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAh 190 TYR 0.020 0.002 TYRAs 186 PHE 0.020 0.003 PHEAi 202 TRP 0.014 0.002 TRPAl 134 HIS 0.007 0.002 HISAj 89 Details of bonding type rmsd covalent geometry : bond 0.00622 (36432) covalent geometry : angle 0.57035 (49200) hydrogen bonds : bond 0.05077 ( 1728) hydrogen bonds : angle 4.60605 ( 4752) *********************** 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 1061 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 876 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5876 (t-90) REVERT: Aa 55 LYS cc_start: 0.7981 (tptp) cc_final: 0.7700 (tptp) REVERT: Aa 193 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.6907 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5638 (t-90) REVERT: Ab 107 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7536 (tt0) REVERT: Ab 188 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8141 (tp) REVERT: Ab 193 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6932 (mtp-110) REVERT: Ab 213 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7258 (mm) REVERT: Ac 44 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5590 (t-90) REVERT: Ac 52 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6730 (mtt) REVERT: Ac 107 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: Ac 193 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6869 (mtp-110) REVERT: Ad 44 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.5655 (t-90) REVERT: Ad 100 MET cc_start: 0.9286 (ttp) cc_final: 0.9057 (ttm) REVERT: Ad 186 TYR cc_start: 0.9048 (t80) cc_final: 0.8608 (t80) REVERT: Ae 44 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.5501 (t-90) REVERT: Ae 100 MET cc_start: 0.9272 (ttp) cc_final: 0.8993 (ttm) REVERT: Ae 162 MET cc_start: 0.9272 (mmm) cc_final: 0.8566 (mmm) REVERT: Ae 193 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6909 (mtp-110) REVERT: Af 100 MET cc_start: 0.9310 (ttp) cc_final: 0.9034 (ttm) REVERT: Af 123 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: Af 193 ARG cc_start: 0.7618 (mpp-170) cc_final: 0.6959 (mtp-110) REVERT: Ag 44 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.5482 (t-90) REVERT: Ag 52 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7215 (mtt) REVERT: Ag 55 LYS cc_start: 0.7966 (tptm) cc_final: 0.7161 (ttpp) REVERT: Ag 60 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8500 (mtt) REVERT: Ag 107 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: Ag 162 MET cc_start: 0.9202 (mmm) cc_final: 0.8763 (mmm) REVERT: Ag 193 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7048 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8223 (m-70) cc_final: 0.7863 (m-70) REVERT: Ah 44 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.4977 (t-90) REVERT: Ah 162 MET cc_start: 0.9158 (mmm) cc_final: 0.8936 (mmm) REVERT: Ah 188 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8139 (tp) REVERT: Ah 193 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6848 (mtp-110) REVERT: Ai 44 HIS cc_start: 0.6394 (OUTLIER) cc_final: 0.5625 (t-90) REVERT: Ai 190 ARG cc_start: 0.8702 (mtt90) cc_final: 0.8290 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7462 (mpp-170) REVERT: Ai 194 ASP cc_start: 0.8789 (t0) cc_final: 0.8528 (t0) REVERT: Ai 214 ARG cc_start: 0.7646 (mtp-110) cc_final: 0.7254 (mtp85) REVERT: Ai 216 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.6998 (mtmm) REVERT: Aj 44 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5653 (t-90) REVERT: Aj 55 LYS cc_start: 0.7882 (tptm) cc_final: 0.7282 (tttm) REVERT: Aj 78 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8256 (mttm) REVERT: Aj 193 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7000 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7904 (tptm) cc_final: 0.7168 (ttpm) REVERT: Ak 123 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: Ak 188 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8103 (tp) REVERT: Ak 193 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7006 (mtp-110) REVERT: Ak 217 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: Al 44 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5469 (t-90) REVERT: Al 55 LYS cc_start: 0.7788 (tptm) cc_final: 0.7220 (ttpm) REVERT: Al 78 LYS cc_start: 0.8617 (mttp) cc_final: 0.8295 (mttm) REVERT: Al 148 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8392 (tttm) REVERT: Al 162 MET cc_start: 0.9205 (mmm) cc_final: 0.8889 (mmm) REVERT: Al 188 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8057 (tp) REVERT: Al 193 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7003 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: Am 78 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8223 (mttp) REVERT: An 44 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.5702 (t-90) REVERT: An 60 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: An 123 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: An 193 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6959 (mtp-110) REVERT: An 217 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: Ao 193 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6981 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.6025 (OUTLIER) cc_final: 0.5023 (t-90) REVERT: Ap 73 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8115 (mp) REVERT: Ap 188 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8132 (tp) REVERT: Ap 193 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7476 (mtp180) REVERT: Ap 213 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7649 (tp) REVERT: Ap 222 MET cc_start: 0.8238 (mtm) cc_final: 0.7790 (mtm) REVERT: Aq 44 HIS cc_start: 0.6247 (OUTLIER) cc_final: 0.5566 (t-90) REVERT: Aq 52 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6868 (mtt) REVERT: Aq 110 MET cc_start: 0.9177 (mmm) cc_final: 0.8797 (mmp) REVERT: Aq 191 ASN cc_start: 0.8505 (m-40) cc_final: 0.8227 (m-40) REVERT: Ar 55 LYS cc_start: 0.7962 (tptm) cc_final: 0.7247 (ttpm) REVERT: Ar 73 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7941 (mp) REVERT: Ar 78 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8295 (mttp) REVERT: Ar 180 LYS cc_start: 0.7775 (tttm) cc_final: 0.7352 (ttmm) REVERT: Ar 193 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7347 (mpp-170) REVERT: As 44 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5226 (t-90) REVERT: As 55 LYS cc_start: 0.7923 (tptm) cc_final: 0.7246 (ttpm) REVERT: As 78 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8209 (mttp) REVERT: As 188 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8229 (tp) REVERT: At 44 HIS cc_start: 0.6220 (OUTLIER) cc_final: 0.5402 (t-90) REVERT: At 50 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8212 (pttm) REVERT: At 55 LYS cc_start: 0.7776 (tptm) cc_final: 0.7278 (ttpm) REVERT: At 123 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: At 193 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7225 (mpp-170) REVERT: At 217 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: Au 44 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.4790 (t-90) REVERT: Au 55 LYS cc_start: 0.7604 (ttmm) cc_final: 0.7323 (ttpm) REVERT: Au 78 LYS cc_start: 0.8599 (mttt) cc_final: 0.8240 (mttm) REVERT: Au 123 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: Au 148 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8225 (tptp) REVERT: Au 188 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8220 (tp) REVERT: Au 217 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: Av 52 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7137 (mtt) REVERT: Av 55 LYS cc_start: 0.7871 (tptm) cc_final: 0.7326 (tttm) REVERT: Av 60 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: Av 78 LYS cc_start: 0.8789 (mtmm) cc_final: 0.8340 (mttp) REVERT: Av 90 GLU cc_start: 0.8640 (tt0) cc_final: 0.8285 (tm-30) REVERT: Av 106 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: Av 123 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: Av 174 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7780 (tm-30) REVERT: Av 193 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6935 (mtp180) REVERT: Av 214 ARG cc_start: 0.7621 (mtp-110) cc_final: 0.7363 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: Aw 52 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7068 (mtt) REVERT: Aw 55 LYS cc_start: 0.7840 (tptm) cc_final: 0.7263 (ttpm) REVERT: Aw 78 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8318 (mttm) REVERT: Aw 90 GLU cc_start: 0.8581 (tt0) cc_final: 0.8293 (tm-30) REVERT: Aw 193 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: Aw 214 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7392 (mtp-110) REVERT: Ax 44 HIS cc_start: 0.5880 (OUTLIER) cc_final: 0.5254 (t-90) REVERT: Ax 52 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6687 (mtt) REVERT: Ax 73 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7721 (mp) REVERT: Ax 76 LYS cc_start: 0.9288 (mttm) cc_final: 0.7792 (mmmt) REVERT: Ax 123 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: Ax 217 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7625 (mt-10) outliers start: 185 outliers final: 72 residues processed: 960 average time/residue: 0.8629 time to fit residues: 954.1795 Evaluate side-chains 1016 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 868 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Aa residue 188 LEU Chi-restraints excluded: chain Aa residue 193 ARG Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 144 SER Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ab residue 193 ARG Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 44 HIS Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 144 SER Chi-restraints excluded: chain Ac residue 188 LEU Chi-restraints excluded: chain Ac residue 193 ARG Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ad residue 193 ARG Chi-restraints excluded: chain Ae residue 44 HIS Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Ae residue 188 LEU Chi-restraints excluded: chain Ae residue 193 ARG Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 123 GLU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 144 SER Chi-restraints excluded: chain Af residue 188 LEU Chi-restraints excluded: chain Ag residue 44 HIS Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 60 MET Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 179 GLU Chi-restraints excluded: chain Ag residue 188 LEU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 44 HIS Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ah residue 193 ARG Chi-restraints excluded: chain Ai residue 44 HIS Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Ai residue 188 LEU Chi-restraints excluded: chain Ai residue 193 ARG Chi-restraints excluded: chain Ai residue 216 LYS Chi-restraints excluded: chain Aj residue 44 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 188 LEU Chi-restraints excluded: chain Aj residue 193 ARG Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 123 GLU Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Ak residue 193 ARG Chi-restraints excluded: chain Ak residue 199 ARG Chi-restraints excluded: chain Ak residue 217 GLU Chi-restraints excluded: chain Al residue 44 HIS Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 73 LEU Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 148 LYS Chi-restraints excluded: chain Al residue 174 GLU Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 193 ARG Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 44 HIS Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 123 GLU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 193 ARG Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 73 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 179 GLU Chi-restraints excluded: chain Ao residue 188 LEU Chi-restraints excluded: chain Ao residue 193 ARG Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 193 ARG Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 52 MET Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 188 LEU Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 188 LEU Chi-restraints excluded: chain Ar residue 193 ARG Chi-restraints excluded: chain As residue 44 HIS Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain As residue 188 LEU Chi-restraints excluded: chain At residue 44 HIS Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 193 ARG Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 44 HIS Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 52 MET Chi-restraints excluded: chain Av residue 53 THR Chi-restraints excluded: chain Av residue 60 MET Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 188 LEU Chi-restraints excluded: chain Av residue 193 ARG Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 53 THR Chi-restraints excluded: chain Aw residue 188 LEU Chi-restraints excluded: chain Aw residue 193 ARG Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 52 MET Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 303 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 349 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 363 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 364 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 44 HIS Ak 44 HIS An 44 HIS Aw 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096276 restraints weight = 39254.572| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.76 r_work: 0.2927 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 36432 Z= 0.117 Angle : 0.467 5.241 49200 Z= 0.246 Chirality : 0.037 0.115 5256 Planarity : 0.004 0.046 6312 Dihedral : 4.313 17.951 4848 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.70 % Allowed : 20.29 % Favored : 76.00 % 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: 0.98 (0.13), residues: 4344 helix: 1.02 (0.11), residues: 2328 sheet: 2.69 (0.24), residues: 240 loop : -0.01 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAo 190 TYR 0.021 0.001 TYRAs 186 PHE 0.014 0.002 PHEAa 202 TRP 0.011 0.001 TRPAl 134 HIS 0.003 0.001 HISAp 219 Details of bonding type rmsd covalent geometry : bond 0.00275 (36432) covalent geometry : angle 0.46661 (49200) hydrogen bonds : bond 0.03904 ( 1728) hydrogen bonds : angle 4.17804 ( 4752) *********************** 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 1036 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 892 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6165 (OUTLIER) cc_final: 0.5513 (t-90) REVERT: Aa 55 LYS cc_start: 0.7911 (tptp) cc_final: 0.7612 (tptp) REVERT: Aa 190 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8097 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7453 (mtm180) cc_final: 0.6903 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5673 (t-90) REVERT: Ab 193 ARG cc_start: 0.7483 (mtm180) cc_final: 0.6908 (mtp-110) REVERT: Ac 44 HIS cc_start: 0.6446 (OUTLIER) cc_final: 0.5520 (t-90) REVERT: Ac 52 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6476 (mtt) REVERT: Ac 90 GLU cc_start: 0.8592 (tt0) cc_final: 0.8064 (tm-30) REVERT: Ac 107 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: Ac 214 ARG cc_start: 0.7669 (mtp85) cc_final: 0.7294 (mtm180) REVERT: Ad 44 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.5679 (t-90) REVERT: Ad 100 MET cc_start: 0.9284 (ttp) cc_final: 0.9062 (ttm) REVERT: Ad 186 TYR cc_start: 0.9022 (t80) cc_final: 0.8515 (t80) REVERT: Ad 190 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8373 (mtt90) REVERT: Ae 44 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5352 (t-90) REVERT: Ae 73 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8319 (mt) REVERT: Ae 100 MET cc_start: 0.9277 (ttp) cc_final: 0.9009 (ttm) REVERT: Ae 162 MET cc_start: 0.9229 (mmm) cc_final: 0.8651 (mmm) REVERT: Ae 193 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6863 (mtp-110) REVERT: Af 100 MET cc_start: 0.9307 (ttp) cc_final: 0.9060 (ttm) REVERT: Af 123 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: Af 193 ARG cc_start: 0.7553 (mpp-170) cc_final: 0.6926 (mtp-110) REVERT: Af 219 HIS cc_start: 0.8141 (m-70) cc_final: 0.7858 (m-70) REVERT: Ag 44 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.5235 (t-90) REVERT: Ag 52 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7135 (mtt) REVERT: Ag 55 LYS cc_start: 0.7885 (tptm) cc_final: 0.7144 (ttpp) REVERT: Ag 60 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: Ag 193 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7035 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8133 (m-70) cc_final: 0.7850 (m-70) REVERT: Ah 44 HIS cc_start: 0.6099 (OUTLIER) cc_final: 0.5032 (t-90) REVERT: Ah 148 LYS cc_start: 0.8668 (tttp) cc_final: 0.8355 (tptp) REVERT: Ah 162 MET cc_start: 0.9150 (mmm) cc_final: 0.8939 (mmm) REVERT: Ah 188 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8082 (tp) REVERT: Ah 193 ARG cc_start: 0.7404 (mtm180) cc_final: 0.6921 (mtp-110) REVERT: Ai 44 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5423 (t-90) REVERT: Ai 190 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8366 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7423 (mpp-170) REVERT: Ai 214 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7334 (mtp85) REVERT: Ai 219 HIS cc_start: 0.8175 (m-70) cc_final: 0.7815 (m-70) REVERT: Aj 44 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5526 (t-90) REVERT: Aj 55 LYS cc_start: 0.7898 (tptm) cc_final: 0.7345 (tttm) REVERT: Aj 78 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8118 (mttm) REVERT: Aj 193 ARG cc_start: 0.7528 (mtm180) cc_final: 0.6947 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7868 (tptm) cc_final: 0.7134 (tttm) REVERT: Ak 123 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: Ak 188 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8052 (tp) REVERT: Ak 193 ARG cc_start: 0.7564 (mtm180) cc_final: 0.6945 (mtp-110) REVERT: Ak 194 ASP cc_start: 0.8676 (t0) cc_final: 0.8444 (t0) REVERT: Ak 214 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7362 (mtp85) REVERT: Ak 219 HIS cc_start: 0.8226 (m-70) cc_final: 0.7907 (m-70) REVERT: Al 44 HIS cc_start: 0.6213 (OUTLIER) cc_final: 0.5321 (t-90) REVERT: Al 55 LYS cc_start: 0.7758 (tptm) cc_final: 0.7178 (ttpm) REVERT: Al 78 LYS cc_start: 0.8437 (mttp) cc_final: 0.8168 (mttm) REVERT: Al 162 MET cc_start: 0.9183 (mmm) cc_final: 0.8844 (mmm) REVERT: Al 188 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8036 (tp) REVERT: Al 193 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6905 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: Am 78 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7990 (mttp) REVERT: Am 188 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8260 (tp) REVERT: Am 214 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7102 (ttp80) REVERT: An 44 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.5966 (t70) REVERT: An 50 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8045 (pttm) REVERT: An 60 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: An 217 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: Ao 44 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5586 (t-90) REVERT: Ao 148 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8457 (tptp) REVERT: Ao 193 ARG cc_start: 0.7604 (mtm180) cc_final: 0.6962 (mtp-110) REVERT: Ao 214 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7445 (ttp80) REVERT: Ap 44 HIS cc_start: 0.5927 (OUTLIER) cc_final: 0.4718 (t-90) REVERT: Ap 73 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8055 (mp) REVERT: Ap 188 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8088 (tp) REVERT: Ap 213 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7600 (tp) REVERT: Ap 222 MET cc_start: 0.8162 (mtm) cc_final: 0.7644 (mtm) REVERT: Aq 44 HIS cc_start: 0.6225 (OUTLIER) cc_final: 0.5445 (t-90) REVERT: Aq 52 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6982 (mtt) REVERT: Aq 73 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7775 (mp) REVERT: Aq 191 ASN cc_start: 0.8540 (m-40) cc_final: 0.8219 (m110) REVERT: Ar 44 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6196 (t-90) REVERT: Ar 78 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8174 (mttp) REVERT: Ar 193 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7316 (mpp-170) REVERT: Ar 213 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7315 (mp) REVERT: As 44 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5185 (t-90) REVERT: As 55 LYS cc_start: 0.7944 (tptm) cc_final: 0.7228 (ttpm) REVERT: As 78 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8065 (mttp) REVERT: As 183 MET cc_start: 0.9332 (tpp) cc_final: 0.9121 (tpp) REVERT: As 214 ARG cc_start: 0.7523 (mtp-110) cc_final: 0.7181 (mtp-110) REVERT: At 50 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8169 (pttm) REVERT: At 55 LYS cc_start: 0.7777 (tptm) cc_final: 0.7271 (ttpm) REVERT: At 78 LYS cc_start: 0.8386 (mttt) cc_final: 0.8098 (mttm) REVERT: At 123 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: At 190 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8164 (mtt90) REVERT: At 214 ARG cc_start: 0.7413 (mtp85) cc_final: 0.7142 (ttp80) REVERT: At 217 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: Au 78 LYS cc_start: 0.8434 (mttt) cc_final: 0.8066 (mttm) REVERT: Au 148 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8171 (tptp) REVERT: Au 188 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8199 (tp) REVERT: Au 214 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7408 (mtp-110) REVERT: Au 217 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: Av 90 GLU cc_start: 0.8620 (tt0) cc_final: 0.8193 (tm-30) REVERT: Av 106 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: Av 123 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: Av 174 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7756 (tm-30) REVERT: Av 214 ARG cc_start: 0.7638 (mtp-110) cc_final: 0.7427 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: Aw 52 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7127 (mtt) REVERT: Aw 90 GLU cc_start: 0.8545 (tt0) cc_final: 0.8227 (tm-30) REVERT: Aw 136 MET cc_start: 0.9357 (ttt) cc_final: 0.9120 (ttt) REVERT: Aw 214 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7254 (mtm110) REVERT: Ax 44 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.5278 (t-90) REVERT: Ax 55 LYS cc_start: 0.7711 (tptm) cc_final: 0.6986 (ttpm) REVERT: Ax 73 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7672 (mp) REVERT: Ax 76 LYS cc_start: 0.9259 (mttm) cc_final: 0.7781 (mmmt) REVERT: Ax 78 LYS cc_start: 0.8513 (mttt) cc_final: 0.8178 (mttm) REVERT: Ax 123 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: Ax 217 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7636 (mt-10) outliers start: 144 outliers final: 46 residues processed: 955 average time/residue: 0.9419 time to fit residues: 1034.7139 Evaluate side-chains 967 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 866 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 144 SER Chi-restraints excluded: chain Ac residue 44 HIS Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 144 SER Chi-restraints excluded: chain Ae residue 44 HIS Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 193 ARG Chi-restraints excluded: chain Af residue 50 LYS Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 123 GLU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Ag residue 44 HIS Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 60 MET Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 44 HIS Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ai residue 44 HIS Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Aj residue 44 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 107 GLU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 123 GLU Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Al residue 44 HIS Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 174 GLU Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 44 HIS Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 44 HIS Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 148 LYS Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 50 LYS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 52 MET Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Ar residue 44 HIS Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 193 ARG Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 44 HIS Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 188 LEU Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 380 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 418 optimal weight: 4.9990 chunk 155 optimal weight: 0.0670 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 164 HIS Af 44 HIS Ak 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095743 restraints weight = 40143.197| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.72 r_work: 0.2881 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 36432 Z= 0.239 Angle : 0.558 5.337 49200 Z= 0.295 Chirality : 0.042 0.131 5256 Planarity : 0.005 0.047 6312 Dihedral : 4.564 19.182 4848 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.09 % Allowed : 20.19 % Favored : 75.72 % 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 (0.12), residues: 4344 helix: 0.49 (0.10), residues: 2472 sheet: 2.55 (0.24), residues: 240 loop : -0.81 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAp 190 TYR 0.024 0.002 TYRAs 186 PHE 0.019 0.003 PHEAi 202 TRP 0.013 0.002 TRPAl 134 HIS 0.008 0.002 HISAn 44 Details of bonding type rmsd covalent geometry : bond 0.00570 (36432) covalent geometry : angle 0.55834 (49200) hydrogen bonds : bond 0.04890 ( 1728) hydrogen bonds : angle 4.52612 ( 4752) *********************** 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 1028 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 869 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6191 (OUTLIER) cc_final: 0.5358 (t-90) REVERT: Aa 55 LYS cc_start: 0.7915 (tptp) cc_final: 0.7631 (tptp) REVERT: Aa 107 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: Aa 190 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8173 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6870 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.5667 (t-90) REVERT: Ab 188 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8140 (tp) REVERT: Ab 193 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6910 (mtp-110) REVERT: Ac 44 HIS cc_start: 0.6468 (OUTLIER) cc_final: 0.5521 (t-90) REVERT: Ac 52 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6582 (mtt) REVERT: Ac 107 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: Ac 193 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6886 (mtp-110) REVERT: Ad 44 HIS cc_start: 0.6492 (OUTLIER) cc_final: 0.5729 (t-90) REVERT: Ad 100 MET cc_start: 0.9282 (ttp) cc_final: 0.9050 (ttm) REVERT: Ad 186 TYR cc_start: 0.9049 (t80) cc_final: 0.8566 (t80) REVERT: Ad 190 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8376 (mtt90) REVERT: Ae 44 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5306 (t-90) REVERT: Ae 73 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8248 (mt) REVERT: Ae 100 MET cc_start: 0.9274 (ttp) cc_final: 0.9003 (ttm) REVERT: Ae 162 MET cc_start: 0.9267 (mmm) cc_final: 0.8708 (mmm) REVERT: Af 100 MET cc_start: 0.9309 (ttp) cc_final: 0.9044 (ttm) REVERT: Af 123 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: Af 193 ARG cc_start: 0.7617 (mpp-170) cc_final: 0.6968 (mtp-110) REVERT: Af 219 HIS cc_start: 0.8135 (m-70) cc_final: 0.7788 (m-70) REVERT: Ag 44 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5227 (t-90) REVERT: Ag 52 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: Ag 55 LYS cc_start: 0.7949 (tptm) cc_final: 0.7130 (ttpp) REVERT: Ag 60 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: Ag 193 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7073 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8219 (m-70) cc_final: 0.7928 (m-70) REVERT: Ah 44 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5165 (t-90) REVERT: Ah 162 MET cc_start: 0.9150 (mmm) cc_final: 0.8921 (mmm) REVERT: Ah 188 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8136 (tp) REVERT: Ah 193 ARG cc_start: 0.7405 (mtm180) cc_final: 0.6845 (mtp-110) REVERT: Ai 44 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5488 (t-90) REVERT: Ai 60 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8539 (mtt) REVERT: Ai 190 ARG cc_start: 0.8690 (mtt90) cc_final: 0.8311 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7489 (mpp-170) REVERT: Ai 214 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7334 (mtp85) REVERT: Ai 219 HIS cc_start: 0.8256 (m-70) cc_final: 0.7914 (m-70) REVERT: Aj 44 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.5500 (t-90) REVERT: Aj 55 LYS cc_start: 0.7871 (tptm) cc_final: 0.7293 (tttm) REVERT: Aj 78 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8225 (mttm) REVERT: Aj 193 ARG cc_start: 0.7627 (mtm180) cc_final: 0.6997 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7906 (tptm) cc_final: 0.7186 (ttpm) REVERT: Ak 188 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8126 (tp) REVERT: Ak 193 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6986 (mtp-110) REVERT: Al 44 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5314 (t-90) REVERT: Al 52 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7230 (mtt) REVERT: Al 55 LYS cc_start: 0.7727 (tptm) cc_final: 0.7144 (ttpm) REVERT: Al 60 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: Al 78 LYS cc_start: 0.8582 (mttp) cc_final: 0.8283 (mttm) REVERT: Al 180 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (tttp) REVERT: Al 188 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8061 (tp) REVERT: Al 193 ARG cc_start: 0.7634 (mtm180) cc_final: 0.6976 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: An 60 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8381 (mtt) REVERT: An 217 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: Ao 44 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5610 (t-90) REVERT: Ao 148 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8443 (tptp) REVERT: Ao 193 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7035 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.4864 (t-90) REVERT: Ap 60 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8337 (mtt) REVERT: Ap 73 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8056 (mp) REVERT: Ap 188 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (tp) REVERT: Ap 213 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7748 (tp) REVERT: Ap 222 MET cc_start: 0.8213 (mtm) cc_final: 0.7755 (mtm) REVERT: Aq 44 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5467 (t-90) REVERT: Aq 73 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7782 (mp) REVERT: Aq 110 MET cc_start: 0.9178 (mmm) cc_final: 0.8796 (mmp) REVERT: Aq 191 ASN cc_start: 0.8498 (m-40) cc_final: 0.8224 (m-40) REVERT: Ar 44 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6228 (t-90) REVERT: Ar 55 LYS cc_start: 0.7939 (tptm) cc_final: 0.7250 (ttpm) REVERT: Ar 78 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8307 (mttp) REVERT: Ar 180 LYS cc_start: 0.7750 (tttm) cc_final: 0.7351 (ttmm) REVERT: Ar 193 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7331 (mpp-170) REVERT: Ar 213 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7445 (mp) REVERT: As 44 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5225 (t-90) REVERT: As 55 LYS cc_start: 0.7930 (tptm) cc_final: 0.7263 (ttpm) REVERT: As 78 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8218 (mttp) REVERT: At 44 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.5076 (t-90) REVERT: At 50 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8101 (pttm) REVERT: At 55 LYS cc_start: 0.7792 (tptm) cc_final: 0.7284 (ttpm) REVERT: At 123 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: At 193 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7277 (mpp-170) REVERT: At 217 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: Au 78 LYS cc_start: 0.8582 (mttt) cc_final: 0.8231 (mttm) REVERT: Au 123 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: Au 148 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8243 (tptp) REVERT: Au 188 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8232 (tp) REVERT: Au 217 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: Av 55 LYS cc_start: 0.7867 (tptm) cc_final: 0.7318 (tttm) REVERT: Av 60 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8480 (mtt) REVERT: Av 78 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8339 (mttp) REVERT: Av 90 GLU cc_start: 0.8643 (tt0) cc_final: 0.8270 (tm-30) REVERT: Av 106 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: Av 123 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: Av 174 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7817 (tm-30) REVERT: Av 193 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: Av 214 ARG cc_start: 0.7616 (mtp-110) cc_final: 0.7399 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: Aw 44 HIS cc_start: 0.6151 (OUTLIER) cc_final: 0.4802 (t-90) REVERT: Aw 52 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7099 (mtt) REVERT: Aw 55 LYS cc_start: 0.7840 (tptm) cc_final: 0.7251 (ttpm) REVERT: Aw 78 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8403 (mttm) REVERT: Aw 90 GLU cc_start: 0.8583 (tt0) cc_final: 0.8261 (tm-30) REVERT: Aw 136 MET cc_start: 0.9427 (ttt) cc_final: 0.9206 (ttt) REVERT: Aw 193 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7535 (mpp-170) REVERT: Aw 214 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.7383 (mtm110) REVERT: Ax 44 HIS cc_start: 0.5932 (OUTLIER) cc_final: 0.5233 (t-90) REVERT: Ax 73 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7654 (mp) REVERT: Ax 76 LYS cc_start: 0.9280 (mttm) cc_final: 0.7786 (mmmt) REVERT: Ax 123 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: Ax 217 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7621 (mt-10) outliers start: 159 outliers final: 62 residues processed: 944 average time/residue: 0.8876 time to fit residues: 964.1978 Evaluate side-chains 988 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 858 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Aa residue 193 ARG Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 144 SER Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ab residue 193 ARG Chi-restraints excluded: chain Ac residue 44 HIS Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 193 ARG Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 144 SER Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ad residue 193 ARG Chi-restraints excluded: chain Ae residue 44 HIS Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Af residue 50 LYS Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 123 GLU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 188 LEU Chi-restraints excluded: chain Ag residue 44 HIS Chi-restraints excluded: chain Ag residue 50 LYS Chi-restraints excluded: chain Ag residue 52 MET Chi-restraints excluded: chain Ag residue 60 MET Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ag residue 188 LEU Chi-restraints excluded: chain Ag residue 193 ARG Chi-restraints excluded: chain Ah residue 44 HIS Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ai residue 44 HIS Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 60 MET Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Ai residue 188 LEU Chi-restraints excluded: chain Ai residue 193 ARG Chi-restraints excluded: chain Aj residue 44 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 107 GLU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 148 LYS Chi-restraints excluded: chain Aj residue 188 LEU Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Ak residue 193 ARG Chi-restraints excluded: chain Al residue 44 HIS Chi-restraints excluded: chain Al residue 52 MET Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 60 MET Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 174 GLU Chi-restraints excluded: chain Al residue 180 LYS Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 73 LEU Chi-restraints excluded: chain Am residue 106 GLU Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 44 HIS Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 148 LYS Chi-restraints excluded: chain Ao residue 188 LEU Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 60 MET Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Aq residue 188 LEU Chi-restraints excluded: chain Ar residue 44 HIS Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 193 ARG Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 44 HIS Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain As residue 188 LEU Chi-restraints excluded: chain At residue 44 HIS Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain At residue 193 ARG Chi-restraints excluded: chain At residue 217 GLU Chi-restraints excluded: chain Au residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 60 MET Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 188 LEU Chi-restraints excluded: chain Av residue 193 ARG Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Aw residue 44 HIS Chi-restraints excluded: chain Aw residue 52 MET Chi-restraints excluded: chain Aw residue 188 LEU Chi-restraints excluded: chain Aw residue 193 ARG Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 53 THR Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 317 optimal weight: 0.7980 chunk 406 optimal weight: 0.9990 chunk 348 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 410 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 289 optimal weight: 0.2980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 164 HIS Af 44 HIS Aj 44 HIS Ak 44 HIS Ak 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100664 restraints weight = 39856.931| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.70 r_work: 0.2960 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 36432 Z= 0.096 Angle : 0.450 5.296 49200 Z= 0.237 Chirality : 0.036 0.114 5256 Planarity : 0.004 0.043 6312 Dihedral : 4.219 18.073 4848 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.67 % Allowed : 21.68 % Favored : 75.64 % 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: 1.22 (0.13), residues: 4344 helix: 1.22 (0.11), residues: 2328 sheet: 2.91 (0.25), residues: 240 loop : 0.07 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAt 190 TYR 0.025 0.001 TYRAs 186 PHE 0.013 0.002 PHEAl 202 TRP 0.011 0.001 TRPAl 134 HIS 0.002 0.001 HISAr 219 Details of bonding type rmsd covalent geometry : bond 0.00222 (36432) covalent geometry : angle 0.44975 (49200) hydrogen bonds : bond 0.03598 ( 1728) hydrogen bonds : angle 4.03336 ( 4752) *********************** 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 982 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 878 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5243 (t-90) REVERT: Aa 55 LYS cc_start: 0.7877 (tptp) cc_final: 0.7610 (tptp) REVERT: Aa 190 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8180 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7432 (mtm180) cc_final: 0.6911 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5472 (t-90) REVERT: Ab 188 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8057 (tp) REVERT: Ab 193 ARG cc_start: 0.7452 (mtm180) cc_final: 0.6895 (mtp-110) REVERT: Ac 52 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6445 (mtt) REVERT: Ac 55 LYS cc_start: 0.7712 (tptp) cc_final: 0.7143 (ttpm) REVERT: Ac 90 GLU cc_start: 0.8579 (tt0) cc_final: 0.8030 (tm-30) REVERT: Ac 107 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: Ac 193 ARG cc_start: 0.7459 (mtm180) cc_final: 0.6914 (mtp-110) REVERT: Ac 214 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7326 (mtm180) REVERT: Ad 44 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.5703 (t-90) REVERT: Ad 100 MET cc_start: 0.9263 (ttp) cc_final: 0.9045 (ttm) REVERT: Ad 186 TYR cc_start: 0.8997 (t80) cc_final: 0.8466 (t80) REVERT: Ad 190 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8337 (mtt90) REVERT: Ae 73 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8288 (mt) REVERT: Ae 100 MET cc_start: 0.9279 (ttp) cc_final: 0.9022 (ttm) REVERT: Ae 162 MET cc_start: 0.9199 (mmm) cc_final: 0.8611 (mmm) REVERT: Ae 214 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7438 (ttp80) REVERT: Af 100 MET cc_start: 0.9279 (ttp) cc_final: 0.9059 (ttm) REVERT: Af 193 ARG cc_start: 0.7557 (mpp-170) cc_final: 0.6944 (mtp-110) REVERT: Af 214 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7179 (ttp80) REVERT: Af 219 HIS cc_start: 0.8104 (m-70) cc_final: 0.7804 (m-70) REVERT: Ag 55 LYS cc_start: 0.7863 (tptm) cc_final: 0.7245 (ttpm) REVERT: Ag 178 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7788 (mtm110) REVERT: Ag 193 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7109 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8118 (m-70) cc_final: 0.7765 (m-70) REVERT: Ah 148 LYS cc_start: 0.8629 (tttp) cc_final: 0.8339 (tptt) REVERT: Ah 162 MET cc_start: 0.9142 (mmm) cc_final: 0.8927 (mmm) REVERT: Ah 188 LEU cc_start: 0.8401 (mt) cc_final: 0.8061 (tp) REVERT: Ah 193 ARG cc_start: 0.7393 (mtm180) cc_final: 0.6909 (mtp-110) REVERT: Ah 219 HIS cc_start: 0.8150 (m-70) cc_final: 0.7858 (m-70) REVERT: Ai 60 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8326 (mtt) REVERT: Ai 78 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8192 (mttm) REVERT: Ai 193 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7489 (mpp-170) REVERT: Ai 219 HIS cc_start: 0.8176 (m-70) cc_final: 0.7816 (m-70) REVERT: Aj 44 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5791 (t70) REVERT: Aj 55 LYS cc_start: 0.7850 (tptm) cc_final: 0.7255 (ttpm) REVERT: Aj 78 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8084 (mttm) REVERT: Aj 193 ARG cc_start: 0.7518 (mtm180) cc_final: 0.6931 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7855 (tptm) cc_final: 0.7183 (tttm) REVERT: Ak 188 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8061 (tp) REVERT: Ak 193 ARG cc_start: 0.7584 (mtm180) cc_final: 0.6919 (mtp-110) REVERT: Ak 219 HIS cc_start: 0.8232 (m-70) cc_final: 0.7908 (m-70) REVERT: Al 55 LYS cc_start: 0.7744 (tptm) cc_final: 0.7121 (tttm) REVERT: Al 78 LYS cc_start: 0.8370 (mttp) cc_final: 0.8092 (mttm) REVERT: Al 180 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: Al 188 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8028 (tp) REVERT: Al 193 ARG cc_start: 0.7523 (mtm180) cc_final: 0.6896 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: Am 44 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.5804 (t-90) REVERT: Am 188 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8223 (tp) REVERT: An 50 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8042 (pttm) REVERT: An 60 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: An 78 LYS cc_start: 0.8357 (mttp) cc_final: 0.8034 (mttm) REVERT: An 193 ARG cc_start: 0.7574 (mpp-170) cc_final: 0.6881 (mtp-110) REVERT: An 217 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: Ao 44 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5609 (t-90) REVERT: Ao 148 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (tptp) REVERT: Ao 193 ARG cc_start: 0.7578 (mtm180) cc_final: 0.6977 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.4789 (t-90) REVERT: Ap 188 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8150 (tp) REVERT: Ap 222 MET cc_start: 0.8181 (mtm) cc_final: 0.7645 (mtm) REVERT: Aq 44 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5010 (t-90) REVERT: Aq 73 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7907 (mp) REVERT: Aq 188 LEU cc_start: 0.8347 (mt) cc_final: 0.8102 (tp) REVERT: Aq 191 ASN cc_start: 0.8451 (m-40) cc_final: 0.8109 (m110) REVERT: Ar 78 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8180 (mttp) REVERT: Ar 213 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7363 (mp) REVERT: As 55 LYS cc_start: 0.7923 (tptm) cc_final: 0.7228 (ttpm) REVERT: As 78 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8087 (mttp) REVERT: As 183 MET cc_start: 0.9311 (tpp) cc_final: 0.8981 (tpp) REVERT: At 50 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8216 (pttm) REVERT: At 55 LYS cc_start: 0.7782 (tptm) cc_final: 0.7272 (ttpm) REVERT: At 60 MET cc_start: 0.8864 (mmm) cc_final: 0.8646 (mmt) REVERT: At 78 LYS cc_start: 0.8314 (mttt) cc_final: 0.8054 (mttm) REVERT: At 214 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7246 (ttp80) REVERT: Au 78 LYS cc_start: 0.8402 (mttt) cc_final: 0.8075 (mttm) REVERT: Au 148 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8195 (tptp) REVERT: Au 188 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8173 (tp) REVERT: Au 214 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7442 (mtp-110) REVERT: Au 217 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: Av 90 GLU cc_start: 0.8606 (tt0) cc_final: 0.8164 (tm-30) REVERT: Av 106 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: Av 174 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7713 (tm-30) REVERT: Av 214 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7332 (mtp-110) REVERT: Av 217 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: Aw 90 GLU cc_start: 0.8509 (tt0) cc_final: 0.8197 (tm-30) REVERT: Aw 136 MET cc_start: 0.9325 (ttt) cc_final: 0.9077 (ttt) REVERT: Aw 214 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7423 (mtp-110) REVERT: Ax 44 HIS cc_start: 0.5970 (OUTLIER) cc_final: 0.5194 (t-90) REVERT: Ax 76 LYS cc_start: 0.9246 (mttm) cc_final: 0.7789 (mmmt) REVERT: Ax 217 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7552 (mt-10) outliers start: 104 outliers final: 46 residues processed: 920 average time/residue: 0.8750 time to fit residues: 928.0163 Evaluate side-chains 937 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 858 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 144 SER Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 144 SER Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ae residue 50 LYS Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Af residue 50 LYS Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 60 MET Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Aj residue 44 HIS Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 107 GLU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 180 LYS Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 44 HIS Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 44 HIS Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 148 LYS Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 50 LYS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 188 LEU Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 106 GLU Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 397 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 301 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 44 HIS Ai 164 HIS Ak 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097831 restraints weight = 40120.897| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.69 r_work: 0.2907 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 36432 Z= 0.184 Angle : 0.524 5.361 49200 Z= 0.276 Chirality : 0.040 0.130 5256 Planarity : 0.004 0.049 6312 Dihedral : 4.432 19.130 4848 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.88 % Allowed : 21.73 % Favored : 75.39 % 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: 0.44 (0.12), residues: 4344 helix: 0.71 (0.10), residues: 2472 sheet: 2.76 (0.25), residues: 240 loop : -0.65 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAt 190 TYR 0.026 0.001 TYRAs 186 PHE 0.017 0.002 PHEAi 202 TRP 0.012 0.002 TRPAl 134 HIS 0.004 0.001 HISAj 89 Details of bonding type rmsd covalent geometry : bond 0.00438 (36432) covalent geometry : angle 0.52399 (49200) hydrogen bonds : bond 0.04474 ( 1728) hydrogen bonds : angle 4.32971 ( 4752) ********************** 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 999 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 887 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 44 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5285 (t-90) REVERT: Aa 55 LYS cc_start: 0.7922 (tptp) cc_final: 0.7651 (tptp) REVERT: Aa 190 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8200 (mtt90) REVERT: Aa 193 ARG cc_start: 0.7510 (mtm180) cc_final: 0.6975 (mtp-110) REVERT: Ab 44 HIS cc_start: 0.6119 (OUTLIER) cc_final: 0.5475 (t-90) REVERT: Ab 188 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8099 (tp) REVERT: Ab 193 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6876 (mtp-110) REVERT: Ab 214 ARG cc_start: 0.7482 (mtp85) cc_final: 0.7272 (mtp85) REVERT: Ac 52 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6524 (mtt) REVERT: Ac 90 GLU cc_start: 0.8646 (tt0) cc_final: 0.8138 (tm-30) REVERT: Ac 107 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: Ac 193 ARG cc_start: 0.7465 (mtm180) cc_final: 0.6911 (mtp-110) REVERT: Ad 44 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5364 (t-90) REVERT: Ad 100 MET cc_start: 0.9296 (ttp) cc_final: 0.9068 (ttm) REVERT: Ad 186 TYR cc_start: 0.9054 (t80) cc_final: 0.8599 (t80) REVERT: Ad 190 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8372 (mtt90) REVERT: Ae 44 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5120 (t-90) REVERT: Ae 73 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8288 (mt) REVERT: Ae 100 MET cc_start: 0.9259 (ttp) cc_final: 0.8976 (ttm) REVERT: Ae 162 MET cc_start: 0.9245 (mmm) cc_final: 0.8668 (mmm) REVERT: Af 100 MET cc_start: 0.9326 (ttp) cc_final: 0.9072 (ttm) REVERT: Af 193 ARG cc_start: 0.7591 (mpp-170) cc_final: 0.6940 (mtp-110) REVERT: Af 219 HIS cc_start: 0.8154 (m-70) cc_final: 0.7872 (m-70) REVERT: Ag 55 LYS cc_start: 0.7906 (tptm) cc_final: 0.7157 (ttpp) REVERT: Ag 60 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: Ag 178 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7838 (mtm110) REVERT: Ag 193 ARG cc_start: 0.7629 (mtm180) cc_final: 0.7089 (mtp-110) REVERT: Ag 219 HIS cc_start: 0.8237 (m-70) cc_final: 0.7868 (m-70) REVERT: Ah 162 MET cc_start: 0.9151 (mmm) cc_final: 0.8918 (mmm) REVERT: Ah 188 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8090 (tp) REVERT: Ah 193 ARG cc_start: 0.7367 (mtm180) cc_final: 0.6833 (mtp-110) REVERT: Ai 44 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5275 (t-90) REVERT: Ai 60 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: Ai 78 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8316 (mttm) REVERT: Ai 190 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8528 (mtt90) REVERT: Ai 193 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7146 (mtp-110) REVERT: Ai 219 HIS cc_start: 0.8239 (m-70) cc_final: 0.7956 (m-70) REVERT: Aj 55 LYS cc_start: 0.7838 (tptm) cc_final: 0.7284 (tttm) REVERT: Aj 78 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8223 (mttm) REVERT: Aj 193 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7020 (mtp-110) REVERT: Ak 55 LYS cc_start: 0.7863 (tptm) cc_final: 0.7173 (tttm) REVERT: Ak 188 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8106 (tp) REVERT: Ak 193 ARG cc_start: 0.7591 (mtm180) cc_final: 0.6952 (mtp-110) REVERT: Al 55 LYS cc_start: 0.7762 (tptm) cc_final: 0.7183 (ttpm) REVERT: Al 78 LYS cc_start: 0.8530 (mttp) cc_final: 0.8242 (mttm) REVERT: Al 180 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7601 (tttp) REVERT: Al 188 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8071 (tp) REVERT: Al 193 ARG cc_start: 0.7592 (mtm180) cc_final: 0.6916 (mtp-110) REVERT: Al 217 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: Am 44 HIS cc_start: 0.6448 (OUTLIER) cc_final: 0.5871 (t-90) REVERT: An 50 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8143 (pttm) REVERT: An 60 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8374 (mtt) REVERT: An 217 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: Ao 60 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8601 (mtt) REVERT: Ao 148 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8470 (tptp) REVERT: Ao 193 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6966 (mtp-110) REVERT: Ap 44 HIS cc_start: 0.6101 (OUTLIER) cc_final: 0.4891 (t-90) REVERT: Ap 188 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (tp) REVERT: Ap 213 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7700 (tp) REVERT: Ap 222 MET cc_start: 0.8226 (mtm) cc_final: 0.7792 (mtm) REVERT: Aq 44 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5247 (t-90) REVERT: Aq 73 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7822 (mp) REVERT: Aq 191 ASN cc_start: 0.8510 (m-40) cc_final: 0.8191 (m110) REVERT: Ar 55 LYS cc_start: 0.7896 (tptm) cc_final: 0.7178 (ttpm) REVERT: Ar 78 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8241 (mttp) REVERT: As 78 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8214 (mttp) REVERT: At 50 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8091 (pttm) REVERT: At 55 LYS cc_start: 0.7780 (tptm) cc_final: 0.7275 (ttpm) REVERT: At 78 LYS cc_start: 0.8477 (mttt) cc_final: 0.8155 (mttp) REVERT: At 123 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: At 190 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8257 (mtt90) REVERT: Au 78 LYS cc_start: 0.8513 (mttt) cc_final: 0.8156 (mttm) REVERT: Au 123 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: Au 148 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8222 (tptp) REVERT: Au 188 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8197 (tp) REVERT: Au 214 ARG cc_start: 0.7595 (mtp-110) cc_final: 0.7335 (mtp-110) REVERT: Au 217 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: Av 55 LYS cc_start: 0.7911 (tptm) cc_final: 0.7295 (tttm) REVERT: Av 78 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8319 (mttp) REVERT: Av 90 GLU cc_start: 0.8631 (tt0) cc_final: 0.8265 (tm-30) REVERT: Av 123 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: Av 174 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7777 (tm-30) REVERT: Av 193 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7067 (mtp180) REVERT: Av 217 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: Aw 90 GLU cc_start: 0.8593 (tt0) cc_final: 0.8279 (tm-30) REVERT: Aw 136 MET cc_start: 0.9389 (ttt) cc_final: 0.9152 (ttt) REVERT: Aw 214 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7297 (mtm110) REVERT: Ax 44 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5184 (t-90) REVERT: Ax 76 LYS cc_start: 0.9261 (mttm) cc_final: 0.7791 (mmmt) REVERT: Ax 78 LYS cc_start: 0.8557 (mttt) cc_final: 0.8222 (mttm) REVERT: Ax 123 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: Ax 217 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7578 (mt-10) outliers start: 112 outliers final: 51 residues processed: 936 average time/residue: 0.8997 time to fit residues: 967.1347 Evaluate side-chains 973 residues out of total 3888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 881 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 44 HIS Chi-restraints excluded: chain Aa residue 57 THR Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 144 SER Chi-restraints excluded: chain Ab residue 44 HIS Chi-restraints excluded: chain Ab residue 50 LYS Chi-restraints excluded: chain Ab residue 57 THR Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 144 SER Chi-restraints excluded: chain Ab residue 188 LEU Chi-restraints excluded: chain Ac residue 52 MET Chi-restraints excluded: chain Ac residue 57 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 144 SER Chi-restraints excluded: chain Ac residue 188 LEU Chi-restraints excluded: chain Ad residue 44 HIS Chi-restraints excluded: chain Ad residue 57 THR Chi-restraints excluded: chain Ad residue 126 THR Chi-restraints excluded: chain Ad residue 144 SER Chi-restraints excluded: chain Ad residue 188 LEU Chi-restraints excluded: chain Ae residue 44 HIS Chi-restraints excluded: chain Ae residue 57 THR Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 126 THR Chi-restraints excluded: chain Af residue 57 THR Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Ag residue 60 MET Chi-restraints excluded: chain Ag residue 126 THR Chi-restraints excluded: chain Ah residue 126 THR Chi-restraints excluded: chain Ah residue 188 LEU Chi-restraints excluded: chain Ai residue 44 HIS Chi-restraints excluded: chain Ai residue 57 THR Chi-restraints excluded: chain Ai residue 60 MET Chi-restraints excluded: chain Ai residue 126 THR Chi-restraints excluded: chain Ai residue 144 SER Chi-restraints excluded: chain Ai residue 193 ARG Chi-restraints excluded: chain Aj residue 57 THR Chi-restraints excluded: chain Aj residue 107 GLU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 188 LEU Chi-restraints excluded: chain Ak residue 50 LYS Chi-restraints excluded: chain Ak residue 126 THR Chi-restraints excluded: chain Ak residue 188 LEU Chi-restraints excluded: chain Al residue 57 THR Chi-restraints excluded: chain Al residue 126 THR Chi-restraints excluded: chain Al residue 174 GLU Chi-restraints excluded: chain Al residue 180 LYS Chi-restraints excluded: chain Al residue 188 LEU Chi-restraints excluded: chain Al residue 217 GLU Chi-restraints excluded: chain Am residue 44 HIS Chi-restraints excluded: chain Am residue 126 THR Chi-restraints excluded: chain Am residue 188 LEU Chi-restraints excluded: chain An residue 50 LYS Chi-restraints excluded: chain An residue 57 THR Chi-restraints excluded: chain An residue 60 MET Chi-restraints excluded: chain An residue 73 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 217 GLU Chi-restraints excluded: chain Ao residue 57 THR Chi-restraints excluded: chain Ao residue 60 MET Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 148 LYS Chi-restraints excluded: chain Ao residue 193 ARG Chi-restraints excluded: chain Ap residue 44 HIS Chi-restraints excluded: chain Ap residue 57 THR Chi-restraints excluded: chain Ap residue 126 THR Chi-restraints excluded: chain Ap residue 148 LYS Chi-restraints excluded: chain Ap residue 188 LEU Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 44 HIS Chi-restraints excluded: chain Aq residue 57 THR Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Ar residue 57 THR Chi-restraints excluded: chain Ar residue 188 LEU Chi-restraints excluded: chain As residue 57 THR Chi-restraints excluded: chain As residue 188 LEU Chi-restraints excluded: chain At residue 50 LYS Chi-restraints excluded: chain At residue 57 THR Chi-restraints excluded: chain At residue 123 GLU Chi-restraints excluded: chain Au residue 123 GLU Chi-restraints excluded: chain Au residue 148 LYS Chi-restraints excluded: chain Au residue 188 LEU Chi-restraints excluded: chain Au residue 217 GLU Chi-restraints excluded: chain Av residue 123 GLU Chi-restraints excluded: chain Av residue 193 ARG Chi-restraints excluded: chain Av residue 217 GLU Chi-restraints excluded: chain Ax residue 44 HIS Chi-restraints excluded: chain Ax residue 57 THR Chi-restraints excluded: chain Ax residue 123 GLU Chi-restraints excluded: chain Ax residue 188 LEU Chi-restraints excluded: chain Ax residue 217 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 411 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 322 optimal weight: 0.0040 chunk 284 optimal weight: 4.9990 chunk 405 optimal weight: 0.9990 chunk 253 optimal weight: 0.0970 chunk 130 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 44 HIS Ad 44 HIS Af 44 HIS Ak 44 HIS Al 195 GLN An 44 HIS An 195 GLN Ao 195 GLN Aq 195 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100068 restraints weight = 39158.135| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.76 r_work: 0.2985 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 36432 Z= 0.089 Angle : 0.443 5.325 49200 Z= 0.232 Chirality : 0.036 0.116 5256 Planarity : 0.004 0.043 6312 Dihedral : 4.115 18.182 4848 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.01 % Allowed : 22.76 % Favored : 75.23 % 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: 1.39 (0.13), residues: 4344 helix: 1.26 (0.11), residues: 2376 sheet: 2.96 (0.25), residues: 240 loop : 0.29 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAh 190 TYR 0.025 0.001 TYRAs 186 PHE 0.013 0.002 PHEAl 202 TRP 0.010 0.001 TRPAm 134 HIS 0.002 0.001 HISAr 219 Details of bonding type rmsd covalent geometry : bond 0.00206 (36432) covalent geometry : angle 0.44305 (49200) hydrogen bonds : bond 0.03359 ( 1728) hydrogen bonds : angle 3.89198 ( 4752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18081.17 seconds wall clock time: 306 minutes 55.37 seconds (18415.37 seconds total)