Starting phenix.real_space_refine on Sun Feb 8 05:38:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.map" model { file = "/net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7y_53799/02_2026/9r7y_53799.cif" } resolution = 3.89 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= 0.023 sd= 0.245 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 351 5.16 5 C 25596 2.51 5 N 6993 2.21 5 O 7479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40419 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 174} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax, Ay, Az, Ba Time building chain proxies: 3.60, per 1000 atoms: 0.09 Number of scatterers: 40419 At special positions: 0 Unit cell: (155.339, 155.339, 179.164, 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 351 16.00 O 7479 8.00 N 6993 7.00 C 25596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.7 seconds 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9666 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 54 sheets defined 52.4% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'Aa' and resid 68 through 75 Processing helix chain 'Aa' and resid 88 through 103 Processing helix chain 'Aa' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAa 112 " --> pdb=" O SERAa 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAa 115 " --> pdb=" O GLUAa 111 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 148 through 151 Processing helix chain 'Aa' and resid 157 through 162 Processing helix chain 'Aa' and resid 165 through 177 Processing helix chain 'Aa' and resid 184 through 191 Processing helix chain 'Aa' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAa 199 " --> pdb=" O SERAa 196 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAa 220 " --> pdb=" O LYSAa 216 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 68 through 75 Processing helix chain 'Ab' and resid 88 through 103 Processing helix chain 'Ab' and resid 106 through 124 removed outlier: 4.382A pdb=" N ILEAb 112 " --> pdb=" O SERAb 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASNAb 115 " --> pdb=" O GLUAb 111 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 148 through 151 Processing helix chain 'Ab' and resid 157 through 162 Processing helix chain 'Ab' and resid 165 through 177 Processing helix chain 'Ab' and resid 184 through 191 Processing helix chain 'Ab' and resid 194 through 201 removed outlier: 4.716A pdb=" N ARGAb 199 " --> pdb=" O SERAb 196 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAb 220 " --> pdb=" O LYSAb 216 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 68 through 75 Processing helix chain 'Ac' and resid 88 through 103 Processing helix chain 'Ac' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAc 112 " --> pdb=" O SERAc 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAc 115 " --> pdb=" O GLUAc 111 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 148 through 151 Processing helix chain 'Ac' and resid 157 through 162 Processing helix chain 'Ac' and resid 165 through 177 Processing helix chain 'Ac' and resid 184 through 191 Processing helix chain 'Ac' and resid 194 through 201 removed outlier: 4.718A pdb=" N ARGAc 199 " --> pdb=" O SERAc 196 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAc 220 " --> pdb=" O LYSAc 216 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 68 through 75 Processing helix chain 'Ad' and resid 88 through 103 Processing helix chain 'Ad' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAd 112 " --> pdb=" O SERAd 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAd 115 " --> pdb=" O GLUAd 111 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 148 through 151 Processing helix chain 'Ad' and resid 157 through 162 Processing helix chain 'Ad' and resid 165 through 177 Processing helix chain 'Ad' and resid 184 through 191 Processing helix chain 'Ad' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAd 199 " --> pdb=" O SERAd 196 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAd 220 " --> pdb=" O LYSAd 216 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 68 through 75 Processing helix chain 'Ae' and resid 88 through 103 Processing helix chain 'Ae' and resid 106 through 124 removed outlier: 4.382A pdb=" N ILEAe 112 " --> pdb=" O SERAe 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAe 115 " --> pdb=" O GLUAe 111 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 148 through 151 Processing helix chain 'Ae' and resid 157 through 162 Processing helix chain 'Ae' and resid 165 through 177 Processing helix chain 'Ae' and resid 184 through 191 Processing helix chain 'Ae' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAe 199 " --> pdb=" O SERAe 196 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAe 220 " --> pdb=" O LYSAe 216 " (cutoff:3.500A) Processing helix chain 'Af' and resid 68 through 75 Processing helix chain 'Af' and resid 88 through 103 Processing helix chain 'Af' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAf 112 " --> pdb=" O SERAf 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAf 115 " --> pdb=" O GLUAf 111 " (cutoff:3.500A) Processing helix chain 'Af' and resid 148 through 151 Processing helix chain 'Af' and resid 157 through 162 Processing helix chain 'Af' and resid 165 through 177 Processing helix chain 'Af' and resid 184 through 191 Processing helix chain 'Af' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAf 199 " --> pdb=" O SERAf 196 " (cutoff:3.500A) Processing helix chain 'Af' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAf 220 " --> pdb=" O LYSAf 216 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 68 through 75 Processing helix chain 'Ag' and resid 88 through 103 Processing helix chain 'Ag' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAg 112 " --> pdb=" O SERAg 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAg 115 " --> pdb=" O GLUAg 111 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 148 through 151 Processing helix chain 'Ag' and resid 157 through 162 Processing helix chain 'Ag' and resid 165 through 177 Processing helix chain 'Ag' and resid 184 through 191 Processing helix chain 'Ag' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAg 199 " --> pdb=" O SERAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAg 220 " --> pdb=" O LYSAg 216 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 68 through 75 Processing helix chain 'Ah' and resid 88 through 103 Processing helix chain 'Ah' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAh 112 " --> pdb=" O SERAh 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASNAh 115 " --> pdb=" O GLUAh 111 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 148 through 151 Processing helix chain 'Ah' and resid 157 through 162 Processing helix chain 'Ah' and resid 165 through 177 Processing helix chain 'Ah' and resid 184 through 191 Processing helix chain 'Ah' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAh 199 " --> pdb=" O SERAh 196 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 212 through 225 removed outlier: 3.728A pdb=" N LEUAh 220 " --> pdb=" O LYSAh 216 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 68 through 75 Processing helix chain 'Ai' and resid 88 through 103 Processing helix chain 'Ai' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAi 112 " --> pdb=" O SERAi 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAi 115 " --> pdb=" O GLUAi 111 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 148 through 151 Processing helix chain 'Ai' and resid 157 through 162 Processing helix chain 'Ai' and resid 165 through 177 Processing helix chain 'Ai' and resid 184 through 191 Processing helix chain 'Ai' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAi 199 " --> pdb=" O SERAi 196 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAi 220 " --> pdb=" O LYSAi 216 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 68 through 75 Processing helix chain 'Aj' and resid 88 through 103 Processing helix chain 'Aj' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAj 112 " --> pdb=" O SERAj 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAj 115 " --> pdb=" O GLUAj 111 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 148 through 151 Processing helix chain 'Aj' and resid 157 through 162 Processing helix chain 'Aj' and resid 165 through 177 Processing helix chain 'Aj' and resid 184 through 191 Processing helix chain 'Aj' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAj 199 " --> pdb=" O SERAj 196 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAj 220 " --> pdb=" O LYSAj 216 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 68 through 75 Processing helix chain 'Ak' and resid 88 through 103 Processing helix chain 'Ak' and resid 106 through 124 removed outlier: 4.382A pdb=" N ILEAk 112 " --> pdb=" O SERAk 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASNAk 115 " --> pdb=" O GLUAk 111 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 148 through 151 Processing helix chain 'Ak' and resid 157 through 162 Processing helix chain 'Ak' and resid 165 through 177 Processing helix chain 'Ak' and resid 184 through 191 Processing helix chain 'Ak' and resid 194 through 201 removed outlier: 4.716A pdb=" N ARGAk 199 " --> pdb=" O SERAk 196 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 212 through 225 removed outlier: 3.729A pdb=" N LEUAk 220 " --> pdb=" O LYSAk 216 " (cutoff:3.500A) Processing helix chain 'Al' and resid 68 through 75 Processing helix chain 'Al' and resid 88 through 103 Processing helix chain 'Al' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAl 112 " --> pdb=" O SERAl 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAl 115 " --> pdb=" O GLUAl 111 " (cutoff:3.500A) Processing helix chain 'Al' and resid 148 through 151 Processing helix chain 'Al' and resid 157 through 162 Processing helix chain 'Al' and resid 165 through 177 Processing helix chain 'Al' and resid 184 through 191 Processing helix chain 'Al' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAl 199 " --> pdb=" O SERAl 196 " (cutoff:3.500A) Processing helix chain 'Al' and resid 212 through 226 removed outlier: 3.727A pdb=" N LEUAl 220 " --> pdb=" O LYSAl 216 " (cutoff:3.500A) Processing helix chain 'Am' and resid 68 through 75 Processing helix chain 'Am' and resid 88 through 103 Processing helix chain 'Am' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAm 112 " --> pdb=" O SERAm 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAm 115 " --> pdb=" O GLUAm 111 " (cutoff:3.500A) Processing helix chain 'Am' and resid 148 through 151 Processing helix chain 'Am' and resid 157 through 162 Processing helix chain 'Am' and resid 165 through 177 Processing helix chain 'Am' and resid 184 through 191 Processing helix chain 'Am' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAm 199 " --> pdb=" O SERAm 196 " (cutoff:3.500A) Processing helix chain 'Am' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAm 220 " --> pdb=" O LYSAm 216 " (cutoff:3.500A) Processing helix chain 'An' and resid 68 through 75 Processing helix chain 'An' and resid 88 through 103 Processing helix chain 'An' and resid 106 through 124 removed outlier: 4.382A pdb=" N ILEAn 112 " --> pdb=" O SERAn 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASNAn 115 " --> pdb=" O GLUAn 111 " (cutoff:3.500A) Processing helix chain 'An' and resid 148 through 151 Processing helix chain 'An' and resid 157 through 162 Processing helix chain 'An' and resid 165 through 177 Processing helix chain 'An' and resid 184 through 191 Processing helix chain 'An' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAn 199 " --> pdb=" O SERAn 196 " (cutoff:3.500A) Processing helix chain 'An' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAn 220 " --> pdb=" O LYSAn 216 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 68 through 75 Processing helix chain 'Ao' and resid 88 through 103 Processing helix chain 'Ao' and resid 106 through 124 removed outlier: 4.383A pdb=" N ILEAo 112 " --> pdb=" O SERAo 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAo 115 " --> pdb=" O GLUAo 111 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 148 through 151 Processing helix chain 'Ao' and resid 157 through 162 Processing helix chain 'Ao' and resid 165 through 177 Processing helix chain 'Ao' and resid 184 through 191 Processing helix chain 'Ao' and resid 194 through 201 removed outlier: 4.716A pdb=" N ARGAo 199 " --> pdb=" O SERAo 196 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAo 220 " --> pdb=" O LYSAo 216 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 68 through 75 Processing helix chain 'Ap' and resid 88 through 103 Processing helix chain 'Ap' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAp 112 " --> pdb=" O SERAp 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAp 115 " --> pdb=" O GLUAp 111 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 148 through 151 Processing helix chain 'Ap' and resid 157 through 162 Processing helix chain 'Ap' and resid 165 through 177 Processing helix chain 'Ap' and resid 184 through 191 Processing helix chain 'Ap' and resid 194 through 201 removed outlier: 4.718A pdb=" N ARGAp 199 " --> pdb=" O SERAp 196 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAp 220 " --> pdb=" O LYSAp 216 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 68 through 75 Processing helix chain 'Aq' and resid 88 through 103 Processing helix chain 'Aq' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAq 112 " --> pdb=" O SERAq 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASNAq 115 " --> pdb=" O GLUAq 111 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 148 through 151 Processing helix chain 'Aq' and resid 157 through 162 Processing helix chain 'Aq' and resid 165 through 177 Processing helix chain 'Aq' and resid 184 through 191 Processing helix chain 'Aq' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAq 199 " --> pdb=" O SERAq 196 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAq 220 " --> pdb=" O LYSAq 216 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 68 through 75 Processing helix chain 'Ar' and resid 88 through 103 Processing helix chain 'Ar' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAr 112 " --> pdb=" O SERAr 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAr 115 " --> pdb=" O GLUAr 111 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 148 through 151 Processing helix chain 'Ar' and resid 157 through 162 Processing helix chain 'Ar' and resid 165 through 177 Processing helix chain 'Ar' and resid 184 through 191 Processing helix chain 'Ar' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAr 199 " --> pdb=" O SERAr 196 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 212 through 225 removed outlier: 3.728A pdb=" N LEUAr 220 " --> pdb=" O LYSAr 216 " (cutoff:3.500A) Processing helix chain 'As' and resid 68 through 75 Processing helix chain 'As' and resid 88 through 103 Processing helix chain 'As' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAs 112 " --> pdb=" O SERAs 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAs 115 " --> pdb=" O GLUAs 111 " (cutoff:3.500A) Processing helix chain 'As' and resid 148 through 151 Processing helix chain 'As' and resid 157 through 162 Processing helix chain 'As' and resid 165 through 177 Processing helix chain 'As' and resid 184 through 191 Processing helix chain 'As' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAs 199 " --> pdb=" O SERAs 196 " (cutoff:3.500A) Processing helix chain 'As' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAs 220 " --> pdb=" O LYSAs 216 " (cutoff:3.500A) Processing helix chain 'At' and resid 68 through 75 Processing helix chain 'At' and resid 88 through 103 Processing helix chain 'At' and resid 106 through 124 removed outlier: 4.383A pdb=" N ILEAt 112 " --> pdb=" O SERAt 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASNAt 115 " --> pdb=" O GLUAt 111 " (cutoff:3.500A) Processing helix chain 'At' and resid 148 through 151 Processing helix chain 'At' and resid 157 through 162 Processing helix chain 'At' and resid 165 through 177 Processing helix chain 'At' and resid 184 through 191 Processing helix chain 'At' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAt 199 " --> pdb=" O SERAt 196 " (cutoff:3.500A) Processing helix chain 'At' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAt 220 " --> pdb=" O LYSAt 216 " (cutoff:3.500A) Processing helix chain 'Au' and resid 68 through 75 Processing helix chain 'Au' and resid 88 through 103 Processing helix chain 'Au' and resid 106 through 124 removed outlier: 4.380A pdb=" N ILEAu 112 " --> pdb=" O SERAu 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAu 115 " --> pdb=" O GLUAu 111 " (cutoff:3.500A) Processing helix chain 'Au' and resid 148 through 151 Processing helix chain 'Au' and resid 157 through 162 Processing helix chain 'Au' and resid 165 through 177 Processing helix chain 'Au' and resid 184 through 191 Processing helix chain 'Au' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAu 199 " --> pdb=" O SERAu 196 " (cutoff:3.500A) Processing helix chain 'Au' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAu 220 " --> pdb=" O LYSAu 216 " (cutoff:3.500A) Processing helix chain 'Av' and resid 68 through 75 Processing helix chain 'Av' and resid 88 through 103 Processing helix chain 'Av' and resid 106 through 124 removed outlier: 4.380A pdb=" N ILEAv 112 " --> pdb=" O SERAv 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAv 115 " --> pdb=" O GLUAv 111 " (cutoff:3.500A) Processing helix chain 'Av' and resid 148 through 151 Processing helix chain 'Av' and resid 157 through 162 Processing helix chain 'Av' and resid 165 through 177 Processing helix chain 'Av' and resid 184 through 191 Processing helix chain 'Av' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAv 199 " --> pdb=" O SERAv 196 " (cutoff:3.500A) Processing helix chain 'Av' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUAv 220 " --> pdb=" O LYSAv 216 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 68 through 75 Processing helix chain 'Aw' and resid 88 through 103 Processing helix chain 'Aw' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAw 112 " --> pdb=" O SERAw 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAw 115 " --> pdb=" O GLUAw 111 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 148 through 151 Processing helix chain 'Aw' and resid 157 through 162 Processing helix chain 'Aw' and resid 165 through 177 Processing helix chain 'Aw' and resid 184 through 191 Processing helix chain 'Aw' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAw 199 " --> pdb=" O SERAw 196 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAw 220 " --> pdb=" O LYSAw 216 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 68 through 75 Processing helix chain 'Ax' and resid 88 through 103 Processing helix chain 'Ax' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAx 112 " --> pdb=" O SERAx 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAx 115 " --> pdb=" O GLUAx 111 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 148 through 151 Processing helix chain 'Ax' and resid 157 through 162 Processing helix chain 'Ax' and resid 165 through 177 Processing helix chain 'Ax' and resid 184 through 191 Processing helix chain 'Ax' and resid 194 through 201 removed outlier: 4.716A pdb=" N ARGAx 199 " --> pdb=" O SERAx 196 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 212 through 226 removed outlier: 3.728A pdb=" N LEUAx 220 " --> pdb=" O LYSAx 216 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 68 through 75 Processing helix chain 'Ay' and resid 88 through 103 Processing helix chain 'Ay' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEAy 112 " --> pdb=" O SERAy 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAy 115 " --> pdb=" O GLUAy 111 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 148 through 151 Processing helix chain 'Ay' and resid 157 through 162 Processing helix chain 'Ay' and resid 165 through 177 Processing helix chain 'Ay' and resid 184 through 191 Processing helix chain 'Ay' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGAy 199 " --> pdb=" O SERAy 196 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 212 through 226 removed outlier: 3.727A pdb=" N LEUAy 220 " --> pdb=" O LYSAy 216 " (cutoff:3.500A) Processing helix chain 'Az' and resid 68 through 75 Processing helix chain 'Az' and resid 88 through 103 Processing helix chain 'Az' and resid 106 through 124 removed outlier: 4.382A pdb=" N ILEAz 112 " --> pdb=" O SERAz 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAz 115 " --> pdb=" O GLUAz 111 " (cutoff:3.500A) Processing helix chain 'Az' and resid 148 through 151 Processing helix chain 'Az' and resid 157 through 162 Processing helix chain 'Az' and resid 165 through 177 Processing helix chain 'Az' and resid 184 through 191 Processing helix chain 'Az' and resid 194 through 201 removed outlier: 4.716A pdb=" N ARGAz 199 " --> pdb=" O SERAz 196 " (cutoff:3.500A) Processing helix chain 'Az' and resid 212 through 225 removed outlier: 3.728A pdb=" N LEUAz 220 " --> pdb=" O LYSAz 216 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 68 through 75 Processing helix chain 'Ba' and resid 88 through 103 Processing helix chain 'Ba' and resid 106 through 124 removed outlier: 4.381A pdb=" N ILEBa 112 " --> pdb=" O SERBa 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNBa 115 " --> pdb=" O GLUBa 111 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 148 through 151 Processing helix chain 'Ba' and resid 157 through 162 Processing helix chain 'Ba' and resid 165 through 177 Processing helix chain 'Ba' and resid 184 through 191 Processing helix chain 'Ba' and resid 194 through 201 removed outlier: 4.717A pdb=" N ARGBa 199 " --> pdb=" O SERBa 196 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 212 through 226 removed outlier: 3.729A pdb=" N LEUBa 220 " --> pdb=" O LYSBa 216 " (cutoff:3.500A) 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 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 137 Processing sheet with id=AF4, first strand: chain 'Ay' and resid 60 through 61 Processing sheet with id=AF5, first strand: chain 'Ay' and resid 133 through 137 Processing sheet with id=AF6, first strand: chain 'Az' and resid 60 through 61 Processing sheet with id=AF7, first strand: chain 'Az' and resid 133 through 137 Processing sheet with id=AF8, first strand: chain 'Ba' and resid 60 through 61 Processing sheet with id=AF9, first strand: chain 'Ba' and resid 133 through 137 1751 hydrogen bonds defined for protein. 4767 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: 6.97 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10576 1.33 - 1.45: 7389 1.45 - 1.57: 22697 1.57 - 1.69: 0 1.69 - 1.81: 675 Bond restraints: 41337 Sorted by residual: bond pdb=" C LYSAd 76 " pdb=" N PROAd 77 " ideal model delta sigma weight residual 1.329 1.369 -0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" C LYSAt 76 " pdb=" N PROAt 77 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C LYSAk 76 " pdb=" N PROAk 77 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C LYSAv 76 " pdb=" N PROAv 77 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C LYSAp 76 " pdb=" N PROAp 77 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.20e-02 6.94e+03 1.13e+01 ... (remaining 41332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 46995 1.50 - 2.99: 6999 2.99 - 4.49: 1502 4.49 - 5.98: 259 5.98 - 7.48: 54 Bond angle restraints: 55809 Sorted by residual: angle pdb=" N METAt 52 " pdb=" CA METAt 52 " pdb=" C METAt 52 " ideal model delta sigma weight residual 112.89 105.41 7.48 1.24e+00 6.50e-01 3.63e+01 angle pdb=" N METAo 52 " pdb=" CA METAo 52 " pdb=" C METAo 52 " ideal model delta sigma weight residual 112.89 105.42 7.47 1.24e+00 6.50e-01 3.63e+01 angle pdb=" N METAc 52 " pdb=" CA METAc 52 " pdb=" C METAc 52 " ideal model delta sigma weight residual 112.89 105.42 7.47 1.24e+00 6.50e-01 3.63e+01 angle pdb=" N METAl 52 " pdb=" CA METAl 52 " pdb=" C METAl 52 " ideal model delta sigma weight residual 112.89 105.43 7.46 1.24e+00 6.50e-01 3.62e+01 angle pdb=" N METAu 52 " pdb=" CA METAu 52 " pdb=" C METAu 52 " ideal model delta sigma weight residual 112.89 105.44 7.45 1.24e+00 6.50e-01 3.61e+01 ... (remaining 55804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 22490 15.72 - 31.44: 2184 31.44 - 47.16: 706 47.16 - 62.89: 108 62.89 - 78.61: 54 Dihedral angle restraints: 25542 sinusoidal: 10665 harmonic: 14877 Sorted by residual: dihedral pdb=" C TRPAz 134 " pdb=" N TRPAz 134 " pdb=" CA TRPAz 134 " pdb=" CB TRPAz 134 " ideal model delta harmonic sigma weight residual -122.60 -130.39 7.79 0 2.50e+00 1.60e-01 9.72e+00 dihedral pdb=" C TRPAu 134 " pdb=" N TRPAu 134 " pdb=" CA TRPAu 134 " pdb=" CB TRPAu 134 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.65e+00 dihedral pdb=" C TRPAh 134 " pdb=" N TRPAh 134 " pdb=" CA TRPAh 134 " pdb=" CB TRPAh 134 " ideal model delta harmonic sigma weight residual -122.60 -130.35 7.75 0 2.50e+00 1.60e-01 9.61e+00 ... (remaining 25539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4325 0.065 - 0.129: 1131 0.129 - 0.194: 329 0.194 - 0.259: 155 0.259 - 0.323: 27 Chirality restraints: 5967 Sorted by residual: chirality pdb=" CA TYRAw 103 " pdb=" N TYRAw 103 " pdb=" C TYRAw 103 " pdb=" CB TYRAw 103 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA TYRAb 103 " pdb=" N TYRAb 103 " pdb=" C TYRAb 103 " pdb=" CB TYRAb 103 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA TYRAk 103 " pdb=" N TYRAk 103 " pdb=" C TYRAk 103 " pdb=" CB TYRAk 103 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 5964 not shown) Planarity restraints: 7182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUAt 158 " 0.013 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C LEUAt 158 " -0.048 2.00e-02 2.50e+03 pdb=" O LEUAt 158 " 0.018 2.00e-02 2.50e+03 pdb=" N ARGAt 159 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUAu 158 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C LEUAu 158 " -0.048 2.00e-02 2.50e+03 pdb=" O LEUAu 158 " 0.018 2.00e-02 2.50e+03 pdb=" N ARGAu 159 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUAb 158 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C LEUAb 158 " -0.048 2.00e-02 2.50e+03 pdb=" O LEUAb 158 " 0.018 2.00e-02 2.50e+03 pdb=" N ARGAb 159 " 0.017 2.00e-02 2.50e+03 ... (remaining 7179 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 9625 2.79 - 3.32: 38569 3.32 - 3.85: 61842 3.85 - 4.37: 73325 4.37 - 4.90: 120881 Nonbonded interactions: 304242 Sorted by model distance: nonbonded pdb=" OE2 GLUAr 170 " pdb=" OH TYRAr 205 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLUBa 170 " pdb=" OH TYRBa 205 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLUAn 170 " pdb=" OH TYRAn 205 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLUAi 170 " pdb=" OH TYRAi 205 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLUAo 170 " pdb=" OH TYRAo 205 " model vdw 2.268 3.040 ... (remaining 304237 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: 0.12 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 28.020 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 41337 Z= 0.641 Angle : 1.148 7.475 55809 Z= 0.796 Chirality : 0.072 0.323 5967 Planarity : 0.006 0.033 7182 Dihedral : 14.645 78.607 15876 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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: -4.24 (0.10), residues: 4941 helix: -2.79 (0.09), residues: 2430 sheet: -4.11 (0.20), residues: 324 loop : -2.47 (0.11), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAj 86 TYR 0.014 0.002 TYRAs 205 PHE 0.014 0.003 PHEAz 117 TRP 0.023 0.006 TRPAp 95 HIS 0.003 0.001 HISAq 219 Details of bonding type rmsd covalent geometry : bond 0.00979 (41337) covalent geometry : angle 1.14847 (55809) hydrogen bonds : bond 0.19005 ( 1751) hydrogen bonds : angle 7.36252 ( 4767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1505 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1505 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 74 SER cc_start: 0.9213 (m) cc_final: 0.8866 (t) REVERT: Ab 61 LEU cc_start: 0.8510 (tp) cc_final: 0.8259 (tp) REVERT: Ab 74 SER cc_start: 0.9225 (m) cc_final: 0.8856 (t) REVERT: Ab 118 MET cc_start: 0.8710 (tpt) cc_final: 0.8016 (tpt) REVERT: Ab 150 MET cc_start: 0.8531 (mmt) cc_final: 0.8141 (mmt) REVERT: Ab 203 ASP cc_start: 0.8103 (t0) cc_final: 0.7879 (t0) REVERT: Ac 74 SER cc_start: 0.9256 (m) cc_final: 0.8921 (t) REVERT: Ac 93 GLN cc_start: 0.8608 (tp40) cc_final: 0.7816 (tp40) REVERT: Ac 131 ASN cc_start: 0.8486 (p0) cc_final: 0.8239 (p0) REVERT: Ac 203 ASP cc_start: 0.8093 (t0) cc_final: 0.7885 (t0) REVERT: Ad 74 SER cc_start: 0.9177 (m) cc_final: 0.8758 (t) REVERT: Ad 75 TYR cc_start: 0.8574 (t80) cc_final: 0.8086 (t80) REVERT: Ad 138 ASP cc_start: 0.7373 (t70) cc_final: 0.7156 (t70) REVERT: Ad 150 MET cc_start: 0.8555 (mmt) cc_final: 0.8128 (mmt) REVERT: Ad 210 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8244 (mtm180) REVERT: Ae 74 SER cc_start: 0.9261 (m) cc_final: 0.8857 (t) REVERT: Ae 150 MET cc_start: 0.8535 (mmt) cc_final: 0.8152 (mmt) REVERT: Af 74 SER cc_start: 0.9192 (m) cc_final: 0.8796 (t) REVERT: Af 75 TYR cc_start: 0.8600 (t80) cc_final: 0.8040 (t80) REVERT: Af 150 MET cc_start: 0.8534 (mmt) cc_final: 0.8147 (mmt) REVERT: Ag 74 SER cc_start: 0.9241 (m) cc_final: 0.8802 (t) REVERT: Ag 75 TYR cc_start: 0.8536 (t80) cc_final: 0.8160 (t80) REVERT: Ag 93 GLN cc_start: 0.8444 (tp40) cc_final: 0.8231 (tp40) REVERT: Ag 110 MET cc_start: 0.8980 (mmm) cc_final: 0.8753 (tpp) REVERT: Ag 118 MET cc_start: 0.8801 (tpt) cc_final: 0.8239 (tpt) REVERT: Ag 150 MET cc_start: 0.8576 (mmt) cc_final: 0.8364 (mmt) REVERT: Ah 74 SER cc_start: 0.9296 (m) cc_final: 0.8909 (t) REVERT: Ah 118 MET cc_start: 0.8826 (tpt) cc_final: 0.8467 (tpt) REVERT: Ai 74 SER cc_start: 0.9165 (m) cc_final: 0.8765 (t) REVERT: Ai 122 ILE cc_start: 0.9525 (tt) cc_final: 0.9288 (tt) REVERT: Ai 150 MET cc_start: 0.8571 (mmt) cc_final: 0.8273 (mmt) REVERT: Ai 203 ASP cc_start: 0.8141 (t0) cc_final: 0.7859 (t0) REVERT: Aj 56 LEU cc_start: 0.8148 (mp) cc_final: 0.7915 (mt) REVERT: Aj 74 SER cc_start: 0.9237 (m) cc_final: 0.8792 (t) REVERT: Aj 150 MET cc_start: 0.8553 (mmt) cc_final: 0.8212 (mmt) REVERT: Aj 203 ASP cc_start: 0.8230 (t0) cc_final: 0.7966 (t0) REVERT: Ak 56 LEU cc_start: 0.8332 (mp) cc_final: 0.8106 (mt) REVERT: Ak 74 SER cc_start: 0.9152 (m) cc_final: 0.8773 (t) REVERT: Ak 175 MET cc_start: 0.7679 (ptm) cc_final: 0.7461 (ptm) REVERT: Al 74 SER cc_start: 0.9256 (m) cc_final: 0.8847 (t) REVERT: Al 118 MET cc_start: 0.8751 (tpt) cc_final: 0.8202 (tpt) REVERT: Am 74 SER cc_start: 0.9270 (m) cc_final: 0.8771 (t) REVERT: Am 75 TYR cc_start: 0.8513 (t80) cc_final: 0.8056 (t80) REVERT: Am 81 ASP cc_start: 0.8243 (m-30) cc_final: 0.8031 (m-30) REVERT: Am 93 GLN cc_start: 0.8618 (tp40) cc_final: 0.7858 (tp40) REVERT: Am 118 MET cc_start: 0.8786 (tpt) cc_final: 0.8503 (tpt) REVERT: Am 203 ASP cc_start: 0.8234 (t0) cc_final: 0.8031 (t0) REVERT: An 74 SER cc_start: 0.9228 (m) cc_final: 0.8872 (t) REVERT: An 75 TYR cc_start: 0.8465 (t80) cc_final: 0.7836 (t80) REVERT: An 93 GLN cc_start: 0.8627 (tp40) cc_final: 0.8326 (tp40) REVERT: An 137 MET cc_start: 0.8302 (mmm) cc_final: 0.6988 (mmm) REVERT: An 203 ASP cc_start: 0.8344 (t0) cc_final: 0.8090 (t0) REVERT: Ao 74 SER cc_start: 0.9259 (m) cc_final: 0.8869 (t) REVERT: Ao 93 GLN cc_start: 0.8618 (tp40) cc_final: 0.8306 (tp40) REVERT: Ao 203 ASP cc_start: 0.8251 (t0) cc_final: 0.7890 (t0) REVERT: Ap 74 SER cc_start: 0.9220 (m) cc_final: 0.8844 (t) REVERT: Aq 74 SER cc_start: 0.9236 (m) cc_final: 0.8827 (t) REVERT: Ar 74 SER cc_start: 0.9194 (m) cc_final: 0.8865 (t) REVERT: As 74 SER cc_start: 0.9105 (m) cc_final: 0.8814 (t) REVERT: As 75 TYR cc_start: 0.8445 (t80) cc_final: 0.8171 (t80) REVERT: At 74 SER cc_start: 0.9207 (m) cc_final: 0.8843 (t) REVERT: At 203 ASP cc_start: 0.8197 (t0) cc_final: 0.7996 (t0) REVERT: Au 74 SER cc_start: 0.9157 (m) cc_final: 0.8835 (t) REVERT: Av 74 SER cc_start: 0.9076 (m) cc_final: 0.8731 (t) REVERT: Aw 74 SER cc_start: 0.9163 (m) cc_final: 0.8825 (t) REVERT: Ax 74 SER cc_start: 0.9089 (m) cc_final: 0.8845 (t) REVERT: Ay 74 SER cc_start: 0.9244 (m) cc_final: 0.8901 (t) REVERT: Az 74 SER cc_start: 0.9276 (m) cc_final: 0.8896 (t) REVERT: Az 122 ILE cc_start: 0.9436 (tt) cc_final: 0.9221 (tt) REVERT: Az 162 MET cc_start: 0.8069 (tpp) cc_final: 0.7761 (tpt) REVERT: Ba 74 SER cc_start: 0.9033 (m) cc_final: 0.8652 (t) REVERT: Ba 75 TYR cc_start: 0.8421 (t80) cc_final: 0.8094 (t80) REVERT: Ba 76 LYS cc_start: 0.8901 (mttt) cc_final: 0.8584 (tppt) REVERT: Ba 150 MET cc_start: 0.8550 (mmt) cc_final: 0.8180 (mmt) REVERT: Ba 162 MET cc_start: 0.8071 (tpp) cc_final: 0.7728 (tpt) outliers start: 0 outliers final: 0 residues processed: 1505 average time/residue: 0.2359 time to fit residues: 579.4626 Evaluate side-chains 1177 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1177 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 44 HIS Ad 115 ASN Ae 191 ASN Af 124 ASN Ag 91 GLN Ak 124 ASN Al 91 GLN Al 124 ASN Ao 44 HIS Ar 124 ASN As 124 ASN At 124 ASN Au 124 ASN Av 191 ASN Ay 124 ASN Az 124 ASN Ba 71 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101519 restraints weight = 55219.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102682 restraints weight = 45060.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103800 restraints weight = 38823.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104328 restraints weight = 34719.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105055 restraints weight = 32123.389| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 41337 Z= 0.217 Angle : 0.673 6.654 55809 Z= 0.341 Chirality : 0.040 0.122 5967 Planarity : 0.005 0.035 7182 Dihedral : 4.426 14.872 5508 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.50 % Allowed : 14.61 % Favored : 82.89 % 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: -2.61 (0.11), residues: 4941 helix: -1.20 (0.10), residues: 2484 sheet: -3.59 (0.23), residues: 324 loop : -1.94 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAk 48 TYR 0.026 0.002 TYRAt 75 PHE 0.019 0.003 PHEAh 117 TRP 0.021 0.003 TRPAw 95 HIS 0.009 0.002 HISAt 71 Details of bonding type rmsd covalent geometry : bond 0.00531 (41337) covalent geometry : angle 0.67321 (55809) hydrogen bonds : bond 0.04449 ( 1751) hydrogen bonds : angle 5.02300 ( 4767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1316 time to evaluate : 1.536 Fit side-chains REVERT: Aa 50 LYS cc_start: 0.7402 (pttm) cc_final: 0.7048 (mmtt) REVERT: Aa 176 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.8011 (tpt170) REVERT: Ab 126 THR cc_start: 0.8896 (p) cc_final: 0.8597 (m) REVERT: Ab 150 MET cc_start: 0.8268 (mmt) cc_final: 0.7988 (mmt) REVERT: Ab 203 ASP cc_start: 0.8181 (t0) cc_final: 0.7860 (t0) REVERT: Ac 71 HIS cc_start: 0.6779 (t-170) cc_final: 0.6483 (t-170) REVERT: Ac 74 SER cc_start: 0.9106 (m) cc_final: 0.8883 (t) REVERT: Ac 118 MET cc_start: 0.8686 (tpt) cc_final: 0.8472 (tpt) REVERT: Ac 126 THR cc_start: 0.9000 (p) cc_final: 0.8656 (m) REVERT: Ac 176 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7977 (ttt90) REVERT: Ac 203 ASP cc_start: 0.8130 (t0) cc_final: 0.7756 (t0) REVERT: Ad 74 SER cc_start: 0.9035 (m) cc_final: 0.8788 (t) REVERT: Ad 107 GLU cc_start: 0.7793 (tp30) cc_final: 0.7503 (tp30) REVERT: Ad 150 MET cc_start: 0.8191 (mmt) cc_final: 0.7839 (mmt) REVERT: Ad 176 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.7938 (mtp85) REVERT: Ad 210 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7767 (mtm180) REVERT: Ae 74 SER cc_start: 0.8975 (m) cc_final: 0.8734 (t) REVERT: Ae 150 MET cc_start: 0.8153 (mmt) cc_final: 0.7921 (mmt) REVERT: Af 50 LYS cc_start: 0.7497 (pttm) cc_final: 0.7110 (mmtt) REVERT: Af 74 SER cc_start: 0.9045 (m) cc_final: 0.8754 (t) REVERT: Af 93 GLN cc_start: 0.8459 (tp40) cc_final: 0.7974 (tp40) REVERT: Af 137 MET cc_start: 0.8214 (mmm) cc_final: 0.7905 (mmm) REVERT: Ag 74 SER cc_start: 0.9021 (m) cc_final: 0.8781 (t) REVERT: Ag 176 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8085 (ttt90) REVERT: Ah 74 SER cc_start: 0.9004 (m) cc_final: 0.8751 (t) REVERT: Ah 176 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7939 (mtp85) REVERT: Ai 74 SER cc_start: 0.9060 (m) cc_final: 0.8788 (t) REVERT: Ai 118 MET cc_start: 0.8981 (tpt) cc_final: 0.8712 (tpt) REVERT: Ai 137 MET cc_start: 0.8220 (mmm) cc_final: 0.7160 (mmm) REVERT: Ai 148 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8672 (ttpp) REVERT: Ai 150 MET cc_start: 0.8282 (mmt) cc_final: 0.8024 (mmt) REVERT: Ai 176 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8176 (mtp85) REVERT: Ai 203 ASP cc_start: 0.8288 (t0) cc_final: 0.8015 (t0) REVERT: Aj 74 SER cc_start: 0.8990 (m) cc_final: 0.8734 (t) REVERT: Aj 203 ASP cc_start: 0.8229 (t0) cc_final: 0.7879 (t0) REVERT: Aj 207 ILE cc_start: 0.8696 (mm) cc_final: 0.8376 (mt) REVERT: Ak 74 SER cc_start: 0.8915 (m) cc_final: 0.8652 (t) REVERT: Ak 93 GLN cc_start: 0.8497 (tp40) cc_final: 0.8242 (tp40) REVERT: Ak 176 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8270 (tpp80) REVERT: Ak 178 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8255 (mtp180) REVERT: Ak 199 ARG cc_start: 0.8538 (mtp85) cc_final: 0.8333 (mtp85) REVERT: Al 74 SER cc_start: 0.9106 (m) cc_final: 0.8751 (t) REVERT: Al 93 GLN cc_start: 0.8514 (tp40) cc_final: 0.8250 (tp40) REVERT: Al 159 ARG cc_start: 0.8647 (ptm-80) cc_final: 0.8370 (ttt-90) REVERT: Am 74 SER cc_start: 0.9039 (m) cc_final: 0.8752 (t) REVERT: Am 118 MET cc_start: 0.8975 (tpt) cc_final: 0.8721 (tpt) REVERT: Am 176 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8079 (ttt90) REVERT: Am 203 ASP cc_start: 0.8220 (t0) cc_final: 0.7959 (t0) REVERT: An 74 SER cc_start: 0.9062 (m) cc_final: 0.8696 (t) REVERT: An 118 MET cc_start: 0.8858 (tpt) cc_final: 0.8556 (tpt) REVERT: An 159 ARG cc_start: 0.8659 (ptm-80) cc_final: 0.8388 (ttt-90) REVERT: An 203 ASP cc_start: 0.8344 (t0) cc_final: 0.7882 (t0) REVERT: An 207 ILE cc_start: 0.8651 (mm) cc_final: 0.8381 (mt) REVERT: Ao 74 SER cc_start: 0.9033 (m) cc_final: 0.8703 (t) REVERT: Ao 93 GLN cc_start: 0.8562 (tp40) cc_final: 0.8227 (tp40) REVERT: Ao 137 MET cc_start: 0.8418 (mmm) cc_final: 0.7240 (mmm) REVERT: Ao 200 TYR cc_start: 0.8831 (m-80) cc_final: 0.8509 (m-10) REVERT: Ao 203 ASP cc_start: 0.8231 (t0) cc_final: 0.7872 (t0) REVERT: Ap 74 SER cc_start: 0.8960 (m) cc_final: 0.8741 (t) REVERT: Ap 176 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8088 (ttt90) REVERT: Ap 200 TYR cc_start: 0.8886 (m-80) cc_final: 0.8657 (m-80) REVERT: Aq 74 SER cc_start: 0.9069 (m) cc_final: 0.8766 (t) REVERT: Aq 199 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8226 (mtp85) REVERT: Ar 74 SER cc_start: 0.9034 (m) cc_final: 0.8793 (t) REVERT: Ar 159 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8379 (ttt-90) REVERT: As 74 SER cc_start: 0.9083 (m) cc_final: 0.8836 (t) REVERT: At 74 SER cc_start: 0.9095 (m) cc_final: 0.8826 (t) REVERT: At 126 THR cc_start: 0.8914 (p) cc_final: 0.8655 (m) REVERT: At 176 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8308 (tpp-160) REVERT: At 203 ASP cc_start: 0.8225 (t0) cc_final: 0.7908 (t0) REVERT: Au 107 GLU cc_start: 0.7755 (tp30) cc_final: 0.7332 (tp30) REVERT: Av 74 SER cc_start: 0.8891 (m) cc_final: 0.8685 (t) REVERT: Av 118 MET cc_start: 0.8963 (tpt) cc_final: 0.8405 (tmm) REVERT: Av 137 MET cc_start: 0.8216 (mmm) cc_final: 0.6726 (mmm) REVERT: Av 176 ARG cc_start: 0.8329 (mmm-85) cc_final: 0.8085 (mtp85) REVERT: Aw 118 MET cc_start: 0.8859 (tpt) cc_final: 0.8241 (tpt) REVERT: Aw 137 MET cc_start: 0.8124 (mmm) cc_final: 0.7059 (mmm) REVERT: Aw 159 ARG cc_start: 0.8598 (ptm-80) cc_final: 0.8325 (ttp80) REVERT: Aw 176 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.8046 (mtp85) REVERT: Aw 203 ASP cc_start: 0.8335 (t0) cc_final: 0.8121 (t0) REVERT: Ax 50 LYS cc_start: 0.7871 (pttm) cc_final: 0.7186 (mmtt) REVERT: Ax 137 MET cc_start: 0.8154 (mmm) cc_final: 0.6877 (mmm) REVERT: Ax 162 MET cc_start: 0.8488 (tpp) cc_final: 0.7790 (tpt) REVERT: Ay 159 ARG cc_start: 0.8582 (ptm-80) cc_final: 0.8359 (ttt-90) REVERT: Ay 176 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7995 (ttt90) REVERT: Az 81 ASP cc_start: 0.8321 (m-30) cc_final: 0.8064 (t0) REVERT: Az 137 MET cc_start: 0.8122 (mmm) cc_final: 0.6946 (mmm) REVERT: Az 176 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.8017 (ttt90) REVERT: Ba 74 SER cc_start: 0.8956 (m) cc_final: 0.8677 (t) REVERT: Ba 76 LYS cc_start: 0.8764 (mttt) cc_final: 0.8364 (tppt) REVERT: Ba 126 THR cc_start: 0.9051 (p) cc_final: 0.8842 (m) REVERT: Ba 137 MET cc_start: 0.8196 (mmm) cc_final: 0.7652 (mmm) REVERT: Ba 150 MET cc_start: 0.8230 (mmt) cc_final: 0.7984 (mmt) REVERT: Ba 203 ASP cc_start: 0.8236 (t0) cc_final: 0.7965 (t0) outliers start: 110 outliers final: 74 residues processed: 1344 average time/residue: 0.2789 time to fit residues: 575.0125 Evaluate side-chains 1263 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1189 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 61 LEU Chi-restraints excluded: chain Aa residue 135 THR Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 175 MET Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 135 THR Chi-restraints excluded: chain Ab residue 161 ILE Chi-restraints excluded: chain Ab residue 175 MET Chi-restraints excluded: chain Ac residue 161 ILE Chi-restraints excluded: chain Ac residue 175 MET Chi-restraints excluded: chain Ad residue 58 LEU Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 161 ILE Chi-restraints excluded: chain Ad residue 175 MET Chi-restraints excluded: chain Ae residue 69 LEU Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Ae residue 161 ILE Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Ag residue 135 THR Chi-restraints excluded: chain Ag residue 161 ILE Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 161 ILE Chi-restraints excluded: chain Ai residue 135 THR Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 135 THR Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 196 SER Chi-restraints excluded: chain Al residue 69 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 69 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 135 THR Chi-restraints excluded: chain Ao residue 161 ILE Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 161 ILE Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain At residue 73 LEU Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 196 SER Chi-restraints excluded: chain Au residue 73 LEU Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Au residue 161 ILE Chi-restraints excluded: chain Au residue 196 SER Chi-restraints excluded: chain Av residue 135 THR Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Aw residue 135 THR Chi-restraints excluded: chain Aw residue 161 ILE Chi-restraints excluded: chain Ax residue 73 LEU Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 161 ILE Chi-restraints excluded: chain Ay residue 135 THR Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Az residue 73 LEU Chi-restraints excluded: chain Az residue 161 ILE Chi-restraints excluded: chain Az residue 175 MET Chi-restraints excluded: chain Ba residue 61 LEU Chi-restraints excluded: chain Ba residue 161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 65 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 389 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 413 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ah 44 HIS Ai 44 HIS Ai 91 GLN Ai 124 ASN Aj 124 ASN ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 44 HIS Ap 124 ASN Aw 124 ASN Ax 124 ASN Ba 124 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105147 restraints weight = 55255.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106630 restraints weight = 44679.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.107824 restraints weight = 37987.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108650 restraints weight = 33475.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109171 restraints weight = 30678.189| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41337 Z= 0.107 Angle : 0.535 5.448 55809 Z= 0.277 Chirality : 0.036 0.126 5967 Planarity : 0.005 0.071 7182 Dihedral : 4.056 15.355 5508 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.64 % Allowed : 15.47 % Favored : 82.89 % 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: -1.70 (0.12), residues: 4941 helix: -0.36 (0.11), residues: 2484 sheet: -3.38 (0.21), residues: 324 loop : -1.59 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAq 159 TYR 0.035 0.002 TYRAr 75 PHE 0.015 0.002 PHEAg 117 TRP 0.014 0.002 TRPAz 95 HIS 0.009 0.001 HISAp 71 Details of bonding type rmsd covalent geometry : bond 0.00277 (41337) covalent geometry : angle 0.53542 (55809) hydrogen bonds : bond 0.03175 ( 1751) hydrogen bonds : angle 4.28764 ( 4767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1192 time to evaluate : 1.649 Fit side-chains REVERT: Aa 176 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.7968 (tpt170) REVERT: Ab 137 MET cc_start: 0.7637 (mmm) cc_final: 0.6855 (mmm) REVERT: Ab 150 MET cc_start: 0.8242 (mmt) cc_final: 0.7986 (mmt) REVERT: Ac 74 SER cc_start: 0.8934 (m) cc_final: 0.8654 (t) REVERT: Ac 118 MET cc_start: 0.8919 (tpt) cc_final: 0.8673 (tpt) REVERT: Ac 126 THR cc_start: 0.8924 (p) cc_final: 0.8569 (m) REVERT: Ac 137 MET cc_start: 0.7902 (mmm) cc_final: 0.7214 (mmm) REVERT: Ac 138 ASP cc_start: 0.7772 (t0) cc_final: 0.7427 (m-30) REVERT: Ac 176 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7827 (ttt90) REVERT: Ac 203 ASP cc_start: 0.8214 (t0) cc_final: 0.7911 (t0) REVERT: Ad 74 SER cc_start: 0.8808 (m) cc_final: 0.8381 (t) REVERT: Ad 150 MET cc_start: 0.8170 (mmt) cc_final: 0.7931 (mmt) REVERT: Ad 210 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7735 (mtm180) REVERT: Ae 74 SER cc_start: 0.8834 (m) cc_final: 0.8530 (t) REVERT: Ae 137 MET cc_start: 0.7684 (mmm) cc_final: 0.6562 (mmm) REVERT: Ae 138 ASP cc_start: 0.7697 (t0) cc_final: 0.7437 (m-30) REVERT: Ae 150 MET cc_start: 0.8115 (mmt) cc_final: 0.7908 (mmt) REVERT: Ae 200 TYR cc_start: 0.8753 (m-80) cc_final: 0.8543 (m-80) REVERT: Af 74 SER cc_start: 0.8842 (m) cc_final: 0.8573 (t) REVERT: Af 93 GLN cc_start: 0.8296 (tp40) cc_final: 0.7738 (tp40) REVERT: Af 118 MET cc_start: 0.8910 (tpt) cc_final: 0.8310 (tmm) REVERT: Af 203 ASP cc_start: 0.8287 (t0) cc_final: 0.8032 (t0) REVERT: Ag 74 SER cc_start: 0.8800 (m) cc_final: 0.8535 (t) REVERT: Ag 137 MET cc_start: 0.7478 (mmm) cc_final: 0.6298 (mmm) REVERT: Ag 176 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.7042 (mtp85) REVERT: Ah 74 SER cc_start: 0.8851 (m) cc_final: 0.8630 (t) REVERT: Ah 137 MET cc_start: 0.8004 (mmm) cc_final: 0.7046 (mmm) REVERT: Ah 176 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8057 (mtp85) REVERT: Ai 74 SER cc_start: 0.8949 (m) cc_final: 0.8538 (t) REVERT: Ai 137 MET cc_start: 0.8011 (mmm) cc_final: 0.7036 (mmm) REVERT: Ai 176 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8278 (ttt90) REVERT: Aj 74 SER cc_start: 0.8805 (m) cc_final: 0.8461 (t) REVERT: Aj 137 MET cc_start: 0.8250 (mmm) cc_final: 0.7431 (mmm) REVERT: Aj 203 ASP cc_start: 0.8246 (t0) cc_final: 0.8040 (t0) REVERT: Ak 74 SER cc_start: 0.8740 (m) cc_final: 0.8372 (t) REVERT: Ak 93 GLN cc_start: 0.8338 (tp40) cc_final: 0.7840 (tp40) REVERT: Ak 137 MET cc_start: 0.8067 (mmm) cc_final: 0.7179 (mmm) REVERT: Ak 138 ASP cc_start: 0.7697 (t0) cc_final: 0.7454 (m-30) REVERT: Ak 175 MET cc_start: 0.8296 (tmm) cc_final: 0.8054 (tmm) REVERT: Ak 176 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8224 (ttt90) REVERT: Ak 178 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8158 (mtp180) REVERT: Al 74 SER cc_start: 0.8828 (m) cc_final: 0.8538 (t) REVERT: Al 159 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.8381 (ttt-90) REVERT: Am 74 SER cc_start: 0.8832 (m) cc_final: 0.8526 (t) REVERT: Am 137 MET cc_start: 0.7932 (mmm) cc_final: 0.6821 (mmm) REVERT: Am 176 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.7756 (tpp-160) REVERT: Am 200 TYR cc_start: 0.8650 (m-80) cc_final: 0.8357 (m-10) REVERT: An 74 SER cc_start: 0.8833 (m) cc_final: 0.8490 (t) REVERT: An 118 MET cc_start: 0.8993 (tpt) cc_final: 0.8763 (tpt) REVERT: An 137 MET cc_start: 0.8293 (mmm) cc_final: 0.7242 (mmm) REVERT: An 203 ASP cc_start: 0.8222 (t0) cc_final: 0.8004 (t0) REVERT: An 207 ILE cc_start: 0.8654 (mm) cc_final: 0.8335 (mt) REVERT: Ao 44 HIS cc_start: 0.6125 (t-90) cc_final: 0.5900 (t70) REVERT: Ao 74 SER cc_start: 0.8819 (m) cc_final: 0.8481 (t) REVERT: Ao 137 MET cc_start: 0.7794 (mmm) cc_final: 0.7187 (mmm) REVERT: Ao 200 TYR cc_start: 0.8675 (m-80) cc_final: 0.8328 (m-10) REVERT: Ao 203 ASP cc_start: 0.8227 (t0) cc_final: 0.8019 (t0) REVERT: Ao 207 ILE cc_start: 0.8573 (mm) cc_final: 0.8293 (mt) REVERT: Ap 74 SER cc_start: 0.8726 (m) cc_final: 0.8487 (t) REVERT: Ap 176 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8052 (ttt90) REVERT: Ap 199 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8074 (mtp85) REVERT: Aq 74 SER cc_start: 0.8813 (m) cc_final: 0.8499 (t) REVERT: Aq 200 TYR cc_start: 0.8716 (m-80) cc_final: 0.8419 (m-80) REVERT: Ar 74 SER cc_start: 0.8848 (m) cc_final: 0.8579 (t) REVERT: Ar 93 GLN cc_start: 0.8490 (tp40) cc_final: 0.8275 (tp40) REVERT: Ar 150 MET cc_start: 0.8158 (mmt) cc_final: 0.7823 (mmt) REVERT: Ar 159 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8411 (ttt-90) REVERT: At 74 SER cc_start: 0.8922 (m) cc_final: 0.8603 (t) REVERT: At 126 THR cc_start: 0.8943 (p) cc_final: 0.8589 (m) REVERT: At 137 MET cc_start: 0.7810 (mmm) cc_final: 0.6650 (mmm) REVERT: At 176 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.7727 (ttt90) REVERT: At 199 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8104 (mtp-110) REVERT: At 200 TYR cc_start: 0.8465 (m-80) cc_final: 0.8231 (m-10) REVERT: Au 81 ASP cc_start: 0.8341 (t0) cc_final: 0.7670 (t0) REVERT: Au 137 MET cc_start: 0.7913 (mmm) cc_final: 0.7300 (mmm) REVERT: Au 162 MET cc_start: 0.8395 (tpt) cc_final: 0.8147 (tpt) REVERT: Au 200 TYR cc_start: 0.8405 (m-80) cc_final: 0.8166 (m-10) REVERT: Av 118 MET cc_start: 0.9257 (tpt) cc_final: 0.8575 (tpt) REVERT: Av 137 MET cc_start: 0.7559 (mmm) cc_final: 0.7070 (mmm) REVERT: Av 176 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.7878 (tpp-160) REVERT: Av 199 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8119 (mtp-110) REVERT: Av 200 TYR cc_start: 0.8363 (m-10) cc_final: 0.8029 (m-10) REVERT: Aw 110 MET cc_start: 0.8067 (tpp) cc_final: 0.7615 (mmt) REVERT: Aw 137 MET cc_start: 0.7448 (mmm) cc_final: 0.6814 (mmm) REVERT: Aw 176 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8083 (ttt90) REVERT: Ax 137 MET cc_start: 0.7670 (mmm) cc_final: 0.7046 (mmm) REVERT: Ay 81 ASP cc_start: 0.8130 (t0) cc_final: 0.7838 (t0) REVERT: Ay 176 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.7911 (ttt90) REVERT: Az 75 TYR cc_start: 0.8930 (t80) cc_final: 0.8722 (t80) REVERT: Az 110 MET cc_start: 0.8093 (tpp) cc_final: 0.7327 (mmt) REVERT: Az 126 THR cc_start: 0.8975 (p) cc_final: 0.8756 (m) REVERT: Az 137 MET cc_start: 0.7777 (mmm) cc_final: 0.7003 (mmm) REVERT: Az 176 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7775 (ttt90) REVERT: Az 203 ASP cc_start: 0.8167 (t0) cc_final: 0.7952 (t0) REVERT: Ba 74 SER cc_start: 0.8942 (m) cc_final: 0.8584 (t) REVERT: Ba 126 THR cc_start: 0.9073 (p) cc_final: 0.8835 (m) REVERT: Ba 137 MET cc_start: 0.8297 (mmm) cc_final: 0.7369 (mmm) REVERT: Ba 150 MET cc_start: 0.8208 (mmt) cc_final: 0.7910 (mmt) REVERT: Ba 159 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8160 (ttt90) REVERT: Ba 203 ASP cc_start: 0.8309 (t0) cc_final: 0.7989 (t0) outliers start: 72 outliers final: 37 residues processed: 1217 average time/residue: 0.2760 time to fit residues: 529.3390 Evaluate side-chains 1126 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1089 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 58 LEU Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 213 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 213 ILE Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain As residue 58 LEU Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain Au residue 58 LEU Chi-restraints excluded: chain Au residue 74 SER Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Ay residue 69 LEU Chi-restraints excluded: chain Az residue 114 LEU Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 445 optimal weight: 0.0060 chunk 197 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 289 optimal weight: 0.0370 chunk 31 optimal weight: 8.9990 overall best weight: 3.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ai 124 ASN Aj 44 HIS ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 44 HIS Aq 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097057 restraints weight = 56536.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.098562 restraints weight = 45593.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.099726 restraints weight = 38779.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100563 restraints weight = 34537.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101144 restraints weight = 31618.274| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 41337 Z= 0.231 Angle : 0.662 7.472 55809 Z= 0.330 Chirality : 0.039 0.138 5967 Planarity : 0.005 0.052 7182 Dihedral : 4.153 15.485 5508 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.14 % Allowed : 15.61 % Favored : 81.25 % 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: -1.72 (0.11), residues: 4941 helix: -0.31 (0.11), residues: 2457 sheet: -3.17 (0.22), residues: 324 loop : -1.72 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAy 159 TYR 0.032 0.003 TYRAt 75 PHE 0.017 0.003 PHEAl 117 TRP 0.019 0.003 TRPAk 95 HIS 0.010 0.001 HISAn 71 Details of bonding type rmsd covalent geometry : bond 0.00566 (41337) covalent geometry : angle 0.66174 (55809) hydrogen bonds : bond 0.04103 ( 1751) hydrogen bonds : angle 4.49871 ( 4767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1110 time to evaluate : 1.470 Fit side-chains REVERT: Aa 50 LYS cc_start: 0.7922 (pttm) cc_final: 0.7288 (mmtt) REVERT: Aa 176 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8236 (tpt170) REVERT: Ac 50 LYS cc_start: 0.7939 (pttm) cc_final: 0.7345 (mmtt) REVERT: Ac 74 SER cc_start: 0.9160 (m) cc_final: 0.8807 (t) REVERT: Ac 138 ASP cc_start: 0.7931 (t0) cc_final: 0.7424 (m-30) REVERT: Ac 176 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8271 (mtp85) REVERT: Ac 200 TYR cc_start: 0.9004 (m-10) cc_final: 0.8782 (m-10) REVERT: Ac 203 ASP cc_start: 0.8454 (t0) cc_final: 0.8167 (t0) REVERT: Ad 74 SER cc_start: 0.9146 (m) cc_final: 0.8669 (t) REVERT: Ad 150 MET cc_start: 0.8293 (mmt) cc_final: 0.8009 (mmt) REVERT: Ae 74 SER cc_start: 0.9095 (m) cc_final: 0.8752 (t) REVERT: Ae 138 ASP cc_start: 0.7815 (t0) cc_final: 0.7312 (m-30) REVERT: Af 74 SER cc_start: 0.9150 (m) cc_final: 0.8779 (t) REVERT: Af 93 GLN cc_start: 0.8395 (tp40) cc_final: 0.7855 (tp40) REVERT: Af 118 MET cc_start: 0.8895 (tpt) cc_final: 0.7992 (tmm) REVERT: Af 138 ASP cc_start: 0.8136 (t0) cc_final: 0.7494 (m-30) REVERT: Af 159 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8492 (ttt-90) REVERT: Af 203 ASP cc_start: 0.8604 (t0) cc_final: 0.8228 (t0) REVERT: Ag 52 MET cc_start: 0.7047 (mtt) cc_final: 0.6762 (mtt) REVERT: Ag 74 SER cc_start: 0.9100 (m) cc_final: 0.8789 (t) REVERT: Ag 75 TYR cc_start: 0.8899 (t80) cc_final: 0.8333 (t80) REVERT: Ag 176 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.7863 (mtp85) REVERT: Ah 74 SER cc_start: 0.9168 (m) cc_final: 0.8866 (t) REVERT: Ah 176 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8029 (mtp85) REVERT: Ah 203 ASP cc_start: 0.8578 (t0) cc_final: 0.8376 (t0) REVERT: Ai 74 SER cc_start: 0.9256 (m) cc_final: 0.8825 (t) REVERT: Ai 93 GLN cc_start: 0.8522 (tp40) cc_final: 0.8184 (tp40) REVERT: Ai 137 MET cc_start: 0.7794 (mmm) cc_final: 0.7541 (mmm) REVERT: Ai 176 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8481 (ttt90) REVERT: Aj 74 SER cc_start: 0.9148 (m) cc_final: 0.8804 (t) REVERT: Aj 203 ASP cc_start: 0.8429 (t0) cc_final: 0.8097 (t0) REVERT: Ak 74 SER cc_start: 0.9040 (m) cc_final: 0.8603 (t) REVERT: Ak 93 GLN cc_start: 0.8462 (tp40) cc_final: 0.8149 (tp40) REVERT: Ak 138 ASP cc_start: 0.8071 (t0) cc_final: 0.7546 (m-30) REVERT: Ak 176 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.7893 (ttt90) REVERT: Ak 178 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8517 (mtp180) REVERT: Al 74 SER cc_start: 0.9143 (m) cc_final: 0.8773 (t) REVERT: Al 126 THR cc_start: 0.9227 (p) cc_final: 0.8870 (m) REVERT: Al 159 ARG cc_start: 0.8885 (ptm-80) cc_final: 0.8609 (ttt-90) REVERT: Al 203 ASP cc_start: 0.8473 (t0) cc_final: 0.8226 (t0) REVERT: Am 74 SER cc_start: 0.9127 (m) cc_final: 0.8675 (t) REVERT: Am 176 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.7623 (mtp85) REVERT: Am 203 ASP cc_start: 0.8617 (t0) cc_final: 0.8324 (t0) REVERT: An 74 SER cc_start: 0.9115 (m) cc_final: 0.8798 (t) REVERT: An 137 MET cc_start: 0.8469 (mmm) cc_final: 0.7360 (mmm) REVERT: An 203 ASP cc_start: 0.8580 (t0) cc_final: 0.8255 (t0) REVERT: Ao 74 SER cc_start: 0.9138 (m) cc_final: 0.8685 (t) REVERT: Ao 200 TYR cc_start: 0.9041 (m-80) cc_final: 0.8840 (m-80) REVERT: Ao 203 ASP cc_start: 0.8418 (t0) cc_final: 0.8118 (t0) REVERT: Ap 74 SER cc_start: 0.9011 (m) cc_final: 0.8666 (t) REVERT: Ap 93 GLN cc_start: 0.8703 (tp40) cc_final: 0.8189 (tp40) REVERT: Ap 176 ARG cc_start: 0.8914 (mmm-85) cc_final: 0.8404 (mtp85) REVERT: Ap 200 TYR cc_start: 0.8966 (m-80) cc_final: 0.8698 (m-10) REVERT: Aq 74 SER cc_start: 0.9140 (m) cc_final: 0.8718 (t) REVERT: Aq 199 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8314 (mtp85) REVERT: Ar 71 HIS cc_start: 0.7483 (t-170) cc_final: 0.7278 (t-170) REVERT: Ar 74 SER cc_start: 0.9163 (m) cc_final: 0.8786 (t) REVERT: Ar 93 GLN cc_start: 0.8509 (tp40) cc_final: 0.8188 (tp40) REVERT: Ar 140 GLU cc_start: 0.7509 (mp0) cc_final: 0.7309 (mp0) REVERT: As 50 LYS cc_start: 0.8277 (pttm) cc_final: 0.7455 (mmtt) REVERT: As 93 GLN cc_start: 0.8458 (tp40) cc_final: 0.8179 (tp40) REVERT: As 118 MET cc_start: 0.9109 (tpt) cc_final: 0.8865 (tpt) REVERT: At 74 SER cc_start: 0.9145 (m) cc_final: 0.8790 (t) REVERT: At 176 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8213 (tpp-160) REVERT: At 200 TYR cc_start: 0.8855 (m-80) cc_final: 0.8622 (m-10) REVERT: Au 81 ASP cc_start: 0.8551 (t0) cc_final: 0.8088 (t0) REVERT: Au 93 GLN cc_start: 0.8524 (tp40) cc_final: 0.8271 (tp40) REVERT: Au 111 GLU cc_start: 0.8331 (tt0) cc_final: 0.8068 (tt0) REVERT: Au 200 TYR cc_start: 0.8877 (m-80) cc_final: 0.8676 (m-10) REVERT: Av 118 MET cc_start: 0.8943 (tpt) cc_final: 0.8098 (tmm) REVERT: Av 137 MET cc_start: 0.8383 (mmm) cc_final: 0.7487 (mmm) REVERT: Av 176 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8098 (mtp85) REVERT: Aw 176 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8150 (mtp85) REVERT: Ax 100 MET cc_start: 0.7744 (tpp) cc_final: 0.7481 (tpt) REVERT: Ay 81 ASP cc_start: 0.8606 (t0) cc_final: 0.8283 (t0) REVERT: Ay 100 MET cc_start: 0.7658 (tpp) cc_final: 0.7328 (tpt) REVERT: Ay 118 MET cc_start: 0.8872 (tpt) cc_final: 0.8331 (tmm) REVERT: Az 81 ASP cc_start: 0.8497 (t0) cc_final: 0.8142 (t0) REVERT: Az 137 MET cc_start: 0.8416 (mmm) cc_final: 0.7351 (mmm) REVERT: Az 150 MET cc_start: 0.8532 (mmt) cc_final: 0.8164 (mmt) REVERT: Az 176 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8300 (ttt90) REVERT: Az 203 ASP cc_start: 0.8528 (t0) cc_final: 0.8254 (t0) REVERT: Ba 50 LYS cc_start: 0.8150 (pttm) cc_final: 0.7314 (mmtt) REVERT: Ba 74 SER cc_start: 0.9166 (m) cc_final: 0.8849 (t) REVERT: Ba 76 LYS cc_start: 0.8950 (mttt) cc_final: 0.8333 (tppt) REVERT: Ba 137 MET cc_start: 0.8435 (mmm) cc_final: 0.7307 (mmm) REVERT: Ba 203 ASP cc_start: 0.8617 (t0) cc_final: 0.8321 (t0) outliers start: 138 outliers final: 114 residues processed: 1166 average time/residue: 0.2877 time to fit residues: 520.4438 Evaluate side-chains 1194 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1080 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 196 SER Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 73 LEU Chi-restraints excluded: chain Ab residue 135 THR Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 135 THR Chi-restraints excluded: chain Ac residue 161 ILE Chi-restraints excluded: chain Ac residue 196 SER Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 73 LEU Chi-restraints excluded: chain Ad residue 135 THR Chi-restraints excluded: chain Ad residue 161 ILE Chi-restraints excluded: chain Ad residue 213 ILE Chi-restraints excluded: chain Ae residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 135 THR Chi-restraints excluded: chain Ae residue 196 SER Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Af residue 73 LEU Chi-restraints excluded: chain Af residue 122 ILE Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 196 SER Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 135 THR Chi-restraints excluded: chain Ag residue 213 ILE Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 122 ILE Chi-restraints excluded: chain Ah residue 161 ILE Chi-restraints excluded: chain Ah residue 196 SER Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 122 ILE Chi-restraints excluded: chain Ai residue 135 THR Chi-restraints excluded: chain Ai residue 196 SER Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 126 THR Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 73 LEU Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 135 THR Chi-restraints excluded: chain Ak residue 196 SER Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 69 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Al residue 196 SER Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 69 LEU Chi-restraints excluded: chain Am residue 135 THR Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain Am residue 213 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 135 THR Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 69 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 135 THR Chi-restraints excluded: chain Ao residue 196 SER Chi-restraints excluded: chain Ao residue 213 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 73 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 135 THR Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 73 LEU Chi-restraints excluded: chain Aq residue 114 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 196 SER Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 73 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain Ar residue 196 SER Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain At residue 73 LEU Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 196 SER Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 58 LEU Chi-restraints excluded: chain Au residue 74 SER Chi-restraints excluded: chain Au residue 135 THR Chi-restraints excluded: chain Au residue 196 SER Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 135 THR Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 135 THR Chi-restraints excluded: chain Aw residue 196 SER Chi-restraints excluded: chain Aw residue 213 ILE Chi-restraints excluded: chain Ax residue 74 SER Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 196 SER Chi-restraints excluded: chain Ay residue 135 THR Chi-restraints excluded: chain Ay residue 196 SER Chi-restraints excluded: chain Az residue 73 LEU Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Az residue 114 LEU Chi-restraints excluded: chain Az residue 122 ILE Chi-restraints excluded: chain Az residue 196 SER Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 61 LEU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 196 SER Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 475 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 365 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 482 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 181 optimal weight: 0.1980 chunk 435 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 44 HIS Ad 44 HIS Ah 91 GLN Aj 124 ASN Ao 44 HIS Ap 44 HIS ** Aq 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 124 ASN Ba 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117271 restraints weight = 53502.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118139 restraints weight = 45594.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119019 restraints weight = 40472.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119494 restraints weight = 36616.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120114 restraints weight = 34026.301| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41337 Z= 0.102 Angle : 0.535 6.056 55809 Z= 0.273 Chirality : 0.035 0.127 5967 Planarity : 0.004 0.047 7182 Dihedral : 3.869 14.959 5508 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.57 % Allowed : 17.16 % Favored : 81.28 % 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: -0.91 (0.12), residues: 4941 helix: 0.33 (0.11), residues: 2295 sheet: -3.06 (0.21), residues: 324 loop : -1.13 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAk 159 TYR 0.030 0.002 TYRAr 75 PHE 0.015 0.002 PHEAw 202 TRP 0.013 0.002 TRPAo 95 HIS 0.009 0.001 HISAn 71 Details of bonding type rmsd covalent geometry : bond 0.00272 (41337) covalent geometry : angle 0.53535 (55809) hydrogen bonds : bond 0.02959 ( 1751) hydrogen bonds : angle 3.99246 ( 4767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1123 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 176 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.7865 (tpt170) REVERT: Aa 199 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8044 (mtp85) REVERT: Ab 150 MET cc_start: 0.8327 (mmt) cc_final: 0.7836 (mmt) REVERT: Ac 74 SER cc_start: 0.8432 (m) cc_final: 0.8073 (t) REVERT: Ac 176 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7992 (mtp85) REVERT: Ac 200 TYR cc_start: 0.8537 (m-80) cc_final: 0.8241 (m-10) REVERT: Ad 74 SER cc_start: 0.8560 (m) cc_final: 0.8155 (t) REVERT: Ad 150 MET cc_start: 0.8090 (mmt) cc_final: 0.7739 (mmt) REVERT: Ae 74 SER cc_start: 0.8564 (m) cc_final: 0.8124 (t) REVERT: Ae 150 MET cc_start: 0.8043 (mmt) cc_final: 0.7835 (mmt) REVERT: Ae 175 MET cc_start: 0.8628 (tmm) cc_final: 0.8348 (tmm) REVERT: Af 74 SER cc_start: 0.8575 (m) cc_final: 0.8229 (t) REVERT: Af 93 GLN cc_start: 0.8293 (tp40) cc_final: 0.7948 (tp40) REVERT: Af 118 MET cc_start: 0.9094 (tpt) cc_final: 0.8171 (tmm) REVERT: Af 203 ASP cc_start: 0.8298 (t0) cc_final: 0.8071 (t0) REVERT: Ag 74 SER cc_start: 0.8322 (m) cc_final: 0.8093 (t) REVERT: Ag 176 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.7919 (ttt90) REVERT: Ah 74 SER cc_start: 0.8530 (m) cc_final: 0.8236 (t) REVERT: Ah 176 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8075 (mtp85) REVERT: Ah 200 TYR cc_start: 0.8558 (m-80) cc_final: 0.8217 (m-10) REVERT: Ai 74 SER cc_start: 0.8768 (m) cc_final: 0.8323 (t) REVERT: Ai 118 MET cc_start: 0.8769 (tpt) cc_final: 0.8275 (tmm) REVERT: Ai 176 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8443 (ttt90) REVERT: Aj 74 SER cc_start: 0.8529 (m) cc_final: 0.8087 (t) REVERT: Ak 74 SER cc_start: 0.8372 (m) cc_final: 0.8057 (t) REVERT: Ak 93 GLN cc_start: 0.8283 (tp40) cc_final: 0.7873 (tp40) REVERT: Ak 176 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8172 (ttt90) REVERT: Ak 178 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7950 (mtp180) REVERT: Al 74 SER cc_start: 0.8480 (m) cc_final: 0.8127 (t) REVERT: Al 110 MET cc_start: 0.8242 (tpp) cc_final: 0.7964 (mmt) REVERT: Al 126 THR cc_start: 0.9013 (p) cc_final: 0.8620 (m) REVERT: Al 203 ASP cc_start: 0.8157 (t0) cc_final: 0.7813 (t0) REVERT: Am 74 SER cc_start: 0.8459 (m) cc_final: 0.7956 (t) REVERT: Am 175 MET cc_start: 0.8209 (tmm) cc_final: 0.7764 (ttt) REVERT: Am 176 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.7434 (mtp85) REVERT: Am 200 TYR cc_start: 0.8559 (m-80) cc_final: 0.8281 (m-10) REVERT: An 74 SER cc_start: 0.8521 (m) cc_final: 0.8096 (t) REVERT: An 137 MET cc_start: 0.7942 (mmm) cc_final: 0.7616 (mmm) REVERT: An 203 ASP cc_start: 0.8236 (t0) cc_final: 0.7957 (t0) REVERT: Ao 74 SER cc_start: 0.8511 (m) cc_final: 0.8117 (t) REVERT: Ao 200 TYR cc_start: 0.8678 (m-80) cc_final: 0.8422 (m-10) REVERT: Ao 207 ILE cc_start: 0.8540 (mm) cc_final: 0.8224 (mt) REVERT: Ap 74 SER cc_start: 0.8436 (m) cc_final: 0.8209 (t) REVERT: Ap 93 GLN cc_start: 0.8623 (tp40) cc_final: 0.8257 (tp40) REVERT: Ap 176 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8297 (ttt90) REVERT: Aq 74 SER cc_start: 0.8533 (m) cc_final: 0.8215 (t) REVERT: Aq 175 MET cc_start: 0.8497 (tmm) cc_final: 0.8168 (tmm) REVERT: Aq 200 TYR cc_start: 0.8671 (m-80) cc_final: 0.8280 (m-80) REVERT: Ar 74 SER cc_start: 0.8618 (m) cc_final: 0.8337 (t) REVERT: Ar 118 MET cc_start: 0.9014 (tpt) cc_final: 0.8133 (tmm) REVERT: Ar 175 MET cc_start: 0.8279 (tmm) cc_final: 0.8049 (tmm) REVERT: As 175 MET cc_start: 0.8474 (tmm) cc_final: 0.8172 (tmm) REVERT: At 74 SER cc_start: 0.8586 (m) cc_final: 0.8347 (t) REVERT: At 110 MET cc_start: 0.8316 (tpp) cc_final: 0.8033 (mmt) REVERT: At 176 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8250 (ttt90) REVERT: At 200 TYR cc_start: 0.8421 (m-80) cc_final: 0.8173 (m-10) REVERT: Au 81 ASP cc_start: 0.8303 (t0) cc_final: 0.8005 (t0) REVERT: Au 175 MET cc_start: 0.8476 (tmm) cc_final: 0.8200 (tmm) REVERT: Au 200 TYR cc_start: 0.8499 (m-80) cc_final: 0.8231 (m-10) REVERT: Av 137 MET cc_start: 0.8255 (mmm) cc_final: 0.7396 (mmm) REVERT: Av 176 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7915 (mtp85) REVERT: Aw 176 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8096 (ttt90) REVERT: Ay 110 MET cc_start: 0.8135 (tpp) cc_final: 0.7884 (mmt) REVERT: Ay 118 MET cc_start: 0.9137 (tpt) cc_final: 0.8397 (tmm) REVERT: Az 110 MET cc_start: 0.7976 (tpp) cc_final: 0.7408 (mmt) REVERT: Az 150 MET cc_start: 0.8282 (mmt) cc_final: 0.7999 (mmt) REVERT: Az 176 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7940 (ttt90) REVERT: Ba 74 SER cc_start: 0.8671 (m) cc_final: 0.8348 (t) REVERT: Ba 150 MET cc_start: 0.8334 (mmt) cc_final: 0.7828 (mmt) REVERT: Ba 175 MET cc_start: 0.8475 (tmm) cc_final: 0.8149 (tmm) outliers start: 69 outliers final: 47 residues processed: 1147 average time/residue: 0.2770 time to fit residues: 498.9710 Evaluate side-chains 1102 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1055 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 126 THR Chi-restraints excluded: chain Ab residue 161 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Af residue 58 LEU Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 138 ASP Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 126 THR Chi-restraints excluded: chain Ao residue 161 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 114 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Ay residue 213 ILE Chi-restraints excluded: chain Az residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 283 optimal weight: 0.7980 chunk 372 optimal weight: 0.9990 chunk 233 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 chunk 479 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 305 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 287 optimal weight: 8.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 91 GLN ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 91 GLN Ba 71 HIS Ba 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107022 restraints weight = 55954.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107662 restraints weight = 49808.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108268 restraints weight = 45617.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108802 restraints weight = 42702.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108993 restraints weight = 40843.785| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41337 Z= 0.122 Angle : 0.564 8.196 55809 Z= 0.284 Chirality : 0.036 0.126 5967 Planarity : 0.005 0.056 7182 Dihedral : 3.817 15.294 5508 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.07 % Allowed : 18.27 % Favored : 79.66 % 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: -0.77 (0.12), residues: 4941 helix: 0.27 (0.11), residues: 2457 sheet: -2.85 (0.21), residues: 324 loop : -0.94 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAg 199 TYR 0.031 0.002 TYRAt 75 PHE 0.019 0.002 PHEAm 117 TRP 0.014 0.002 TRPAo 95 HIS 0.013 0.001 HISAn 71 Details of bonding type rmsd covalent geometry : bond 0.00323 (41337) covalent geometry : angle 0.56382 (55809) hydrogen bonds : bond 0.03221 ( 1751) hydrogen bonds : angle 4.01732 ( 4767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1091 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 176 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8174 (tpt170) REVERT: Ab 118 MET cc_start: 0.9232 (tmm) cc_final: 0.8930 (tmm) REVERT: Ab 150 MET cc_start: 0.8369 (mmt) cc_final: 0.8015 (mmt) REVERT: Ac 74 SER cc_start: 0.8634 (m) cc_final: 0.8342 (t) REVERT: Ac 176 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.7773 (mtp85) REVERT: Ad 74 SER cc_start: 0.8738 (m) cc_final: 0.8324 (t) REVERT: Ad 110 MET cc_start: 0.7872 (mmt) cc_final: 0.7618 (mmt) REVERT: Ad 150 MET cc_start: 0.8187 (mmt) cc_final: 0.7964 (mmt) REVERT: Ad 175 MET cc_start: 0.8376 (tmm) cc_final: 0.8068 (tmm) REVERT: Ae 52 MET cc_start: 0.7383 (mtt) cc_final: 0.7074 (mtt) REVERT: Ae 74 SER cc_start: 0.8770 (m) cc_final: 0.8317 (t) REVERT: Ae 175 MET cc_start: 0.8715 (tmm) cc_final: 0.8469 (tmm) REVERT: Af 74 SER cc_start: 0.8717 (m) cc_final: 0.8373 (t) REVERT: Af 93 GLN cc_start: 0.8361 (tp40) cc_final: 0.7731 (tp40) REVERT: Af 203 ASP cc_start: 0.8378 (t0) cc_final: 0.8083 (t0) REVERT: Ag 74 SER cc_start: 0.8457 (m) cc_final: 0.8134 (t) REVERT: Ag 100 MET cc_start: 0.7576 (tpp) cc_final: 0.7312 (tpt) REVERT: Ag 176 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8044 (ttt90) REVERT: Ah 52 MET cc_start: 0.7338 (mtt) cc_final: 0.7006 (mtt) REVERT: Ah 74 SER cc_start: 0.8721 (m) cc_final: 0.8381 (t) REVERT: Ah 176 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8005 (mtp85) REVERT: Ai 74 SER cc_start: 0.8934 (m) cc_final: 0.8480 (t) REVERT: Ai 176 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8507 (ttt90) REVERT: Aj 74 SER cc_start: 0.8682 (m) cc_final: 0.8269 (t) REVERT: Aj 110 MET cc_start: 0.7970 (mmt) cc_final: 0.7723 (tpp) REVERT: Aj 207 ILE cc_start: 0.8818 (mm) cc_final: 0.8539 (mt) REVERT: Ak 74 SER cc_start: 0.8531 (m) cc_final: 0.8185 (t) REVERT: Ak 93 GLN cc_start: 0.8425 (tp40) cc_final: 0.7963 (tp40) REVERT: Ak 176 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.7953 (ttt90) REVERT: Ak 178 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8164 (mtp180) REVERT: Al 74 SER cc_start: 0.8733 (m) cc_final: 0.8329 (t) REVERT: Al 118 MET cc_start: 0.9065 (tmm) cc_final: 0.8809 (tmm) REVERT: Al 126 THR cc_start: 0.9078 (p) cc_final: 0.8776 (m) REVERT: Al 203 ASP cc_start: 0.8313 (t0) cc_final: 0.7970 (t0) REVERT: Am 74 SER cc_start: 0.8699 (m) cc_final: 0.8185 (t) REVERT: Am 93 GLN cc_start: 0.8504 (tp40) cc_final: 0.7810 (tp40) REVERT: Am 136 MET cc_start: 0.7894 (ttt) cc_final: 0.7684 (ttt) REVERT: Am 137 MET cc_start: 0.8287 (mmm) cc_final: 0.8078 (mmm) REVERT: Am 176 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.7657 (mtp85) REVERT: Am 199 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8135 (mtp85) REVERT: An 74 SER cc_start: 0.8638 (m) cc_final: 0.8129 (t) REVERT: An 110 MET cc_start: 0.8277 (tpp) cc_final: 0.7969 (mmt) REVERT: An 203 ASP cc_start: 0.8330 (t0) cc_final: 0.8045 (t0) REVERT: Ao 52 MET cc_start: 0.6878 (mtt) cc_final: 0.6582 (mtt) REVERT: Ao 74 SER cc_start: 0.8682 (m) cc_final: 0.8262 (t) REVERT: Ao 199 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8098 (mtp85) REVERT: Ap 74 SER cc_start: 0.8721 (m) cc_final: 0.8425 (t) REVERT: Ap 93 GLN cc_start: 0.8609 (tp40) cc_final: 0.8295 (tp40) REVERT: Ap 110 MET cc_start: 0.8315 (mmt) cc_final: 0.8109 (tpt) REVERT: Ap 175 MET cc_start: 0.8388 (tmm) cc_final: 0.7787 (ttt) REVERT: Ap 176 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.7896 (mtp85) REVERT: Ap 199 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7941 (mtp-110) REVERT: Aq 74 SER cc_start: 0.8812 (m) cc_final: 0.8457 (t) REVERT: Aq 175 MET cc_start: 0.8614 (tmm) cc_final: 0.8364 (tmm) REVERT: Aq 200 TYR cc_start: 0.8857 (m-80) cc_final: 0.8614 (m-80) REVERT: Ar 74 SER cc_start: 0.8860 (m) cc_final: 0.8545 (t) REVERT: Ar 93 GLN cc_start: 0.8632 (tp40) cc_final: 0.8344 (tp40) REVERT: Ar 118 MET cc_start: 0.9105 (tpt) cc_final: 0.8227 (tmm) REVERT: As 44 HIS cc_start: 0.6172 (t-90) cc_final: 0.5934 (t70) REVERT: As 93 GLN cc_start: 0.8529 (tp40) cc_final: 0.8310 (tp40) REVERT: As 110 MET cc_start: 0.8581 (tpp) cc_final: 0.8294 (tpp) REVERT: As 126 THR cc_start: 0.9289 (p) cc_final: 0.9088 (t) REVERT: As 137 MET cc_start: 0.8417 (mmm) cc_final: 0.8190 (mmm) REVERT: As 175 MET cc_start: 0.8601 (tmm) cc_final: 0.8345 (tmm) REVERT: At 74 SER cc_start: 0.8817 (m) cc_final: 0.8510 (t) REVERT: At 110 MET cc_start: 0.8361 (tpp) cc_final: 0.8106 (mmt) REVERT: At 175 MET cc_start: 0.8214 (tmm) cc_final: 0.7748 (ttt) REVERT: At 176 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.7983 (ttt90) REVERT: At 199 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7951 (mtp-110) REVERT: At 200 TYR cc_start: 0.8607 (m-80) cc_final: 0.8348 (m-10) REVERT: Au 81 ASP cc_start: 0.8414 (t0) cc_final: 0.8209 (t0) REVERT: Au 175 MET cc_start: 0.8488 (tmm) cc_final: 0.8277 (tmm) REVERT: Av 137 MET cc_start: 0.8449 (mmm) cc_final: 0.7442 (mmm) REVERT: Av 175 MET cc_start: 0.8326 (tmm) cc_final: 0.7819 (ttt) REVERT: Av 176 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.7858 (mtp85) REVERT: Av 199 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8115 (mtp-110) REVERT: Aw 176 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8174 (ttt90) REVERT: Ax 175 MET cc_start: 0.8549 (tmm) cc_final: 0.8238 (tmm) REVERT: Ay 110 MET cc_start: 0.8245 (tpp) cc_final: 0.7997 (mmt) REVERT: Ay 118 MET cc_start: 0.9059 (tpt) cc_final: 0.8306 (tmm) REVERT: Az 52 MET cc_start: 0.6646 (mtt) cc_final: 0.6417 (mtt) REVERT: Az 110 MET cc_start: 0.7979 (tpp) cc_final: 0.7583 (mmt) REVERT: Az 137 MET cc_start: 0.7914 (mmm) cc_final: 0.7584 (mmm) REVERT: Az 150 MET cc_start: 0.8331 (mmt) cc_final: 0.8067 (mmt) REVERT: Az 176 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7751 (mtp85) REVERT: Ba 74 SER cc_start: 0.8909 (m) cc_final: 0.8581 (t) REVERT: Ba 76 LYS cc_start: 0.8773 (mttt) cc_final: 0.8484 (tptt) REVERT: Ba 137 MET cc_start: 0.7921 (mmm) cc_final: 0.7645 (mmm) REVERT: Ba 175 MET cc_start: 0.8631 (tmm) cc_final: 0.8358 (tmm) outliers start: 91 outliers final: 73 residues processed: 1120 average time/residue: 0.2642 time to fit residues: 465.1940 Evaluate side-chains 1111 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1038 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 161 ILE Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 213 ILE Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 161 ILE Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 213 ILE Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 121 CYS Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain Am residue 213 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 161 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 61 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 213 ILE Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 213 ILE Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Az residue 114 LEU Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 61 LEU Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 277 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 473 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 390 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 424 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 91 GLN ** Ak 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 44 HIS ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109822 restraints weight = 55522.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110509 restraints weight = 49021.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111174 restraints weight = 44131.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111174 restraints weight = 40972.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111174 restraints weight = 40972.834| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41337 Z= 0.174 Angle : 0.620 7.322 55809 Z= 0.310 Chirality : 0.038 0.122 5967 Planarity : 0.005 0.050 7182 Dihedral : 3.940 15.563 5508 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.34 % Allowed : 18.52 % Favored : 79.14 % 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: -1.20 (0.12), residues: 4941 helix: -0.01 (0.11), residues: 2619 sheet: -2.77 (0.21), residues: 324 loop : -1.41 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAg 199 TYR 0.031 0.002 TYRAt 75 PHE 0.020 0.003 PHEAr 117 TRP 0.017 0.002 TRPAo 95 HIS 0.011 0.001 HISAa 71 Details of bonding type rmsd covalent geometry : bond 0.00441 (41337) covalent geometry : angle 0.61963 (55809) hydrogen bonds : bond 0.03640 ( 1751) hydrogen bonds : angle 4.16098 ( 4767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1051 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: Aa 176 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8098 (tpt170) REVERT: Ab 118 MET cc_start: 0.9244 (tmm) cc_final: 0.8927 (tmm) REVERT: Ac 74 SER cc_start: 0.8649 (m) cc_final: 0.8358 (t) REVERT: Ac 137 MET cc_start: 0.8532 (mmm) cc_final: 0.8163 (mmm) REVERT: Ac 176 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.7849 (mtp85) REVERT: Ad 74 SER cc_start: 0.8794 (m) cc_final: 0.8371 (t) REVERT: Ad 110 MET cc_start: 0.8022 (mmt) cc_final: 0.7780 (mmt) REVERT: Ae 74 SER cc_start: 0.8762 (m) cc_final: 0.8350 (t) REVERT: Ae 175 MET cc_start: 0.8759 (tmm) cc_final: 0.8524 (tmm) REVERT: Ae 190 ARG cc_start: 0.8651 (mpt180) cc_final: 0.8292 (mmt90) REVERT: Af 74 SER cc_start: 0.8724 (m) cc_final: 0.8379 (t) REVERT: Af 93 GLN cc_start: 0.8417 (tp40) cc_final: 0.7745 (tp40) REVERT: Af 203 ASP cc_start: 0.8346 (t0) cc_final: 0.7981 (t0) REVERT: Ag 74 SER cc_start: 0.8402 (m) cc_final: 0.8111 (t) REVERT: Ag 137 MET cc_start: 0.8215 (mmm) cc_final: 0.7950 (mmm) REVERT: Ag 176 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8294 (ttt90) REVERT: Ah 52 MET cc_start: 0.7379 (mtt) cc_final: 0.7165 (mtt) REVERT: Ah 74 SER cc_start: 0.8674 (m) cc_final: 0.8353 (t) REVERT: Ah 93 GLN cc_start: 0.8557 (tp40) cc_final: 0.7917 (tp40) REVERT: Ah 176 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8084 (mtp85) REVERT: Ah 190 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8485 (mtt90) REVERT: Ai 74 SER cc_start: 0.8938 (m) cc_final: 0.8556 (t) REVERT: Ai 93 GLN cc_start: 0.8483 (tp40) cc_final: 0.8128 (tp40) REVERT: Ai 176 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8304 (mtp85) REVERT: Ai 190 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8423 (mmt90) REVERT: Aj 52 MET cc_start: 0.7213 (mtt) cc_final: 0.6943 (mtt) REVERT: Aj 74 SER cc_start: 0.8675 (m) cc_final: 0.8194 (t) REVERT: Ak 74 SER cc_start: 0.8557 (m) cc_final: 0.8167 (t) REVERT: Ak 93 GLN cc_start: 0.8464 (tp40) cc_final: 0.7967 (tp40) REVERT: Ak 178 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8111 (mtp180) REVERT: Al 74 SER cc_start: 0.8737 (m) cc_final: 0.8337 (t) REVERT: Al 137 MET cc_start: 0.8569 (mmm) cc_final: 0.8368 (mmm) REVERT: Al 203 ASP cc_start: 0.8359 (t0) cc_final: 0.7932 (t0) REVERT: Am 74 SER cc_start: 0.8683 (m) cc_final: 0.8202 (t) REVERT: Am 93 GLN cc_start: 0.8540 (tp40) cc_final: 0.7784 (tp40) REVERT: Am 136 MET cc_start: 0.7930 (ttt) cc_final: 0.7614 (ttt) REVERT: Am 176 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.7754 (mtp85) REVERT: Am 199 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8196 (mtp85) REVERT: An 74 SER cc_start: 0.8702 (m) cc_final: 0.8351 (t) REVERT: An 110 MET cc_start: 0.8185 (tpp) cc_final: 0.7968 (mmt) REVERT: An 203 ASP cc_start: 0.8407 (t0) cc_final: 0.8035 (t0) REVERT: Ao 74 SER cc_start: 0.8777 (m) cc_final: 0.8348 (t) REVERT: Ap 74 SER cc_start: 0.8822 (m) cc_final: 0.8489 (t) REVERT: Ap 93 GLN cc_start: 0.8614 (tp40) cc_final: 0.8247 (tp40) REVERT: Ap 110 MET cc_start: 0.8468 (mmt) cc_final: 0.8258 (mmt) REVERT: Ap 176 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8291 (mtp85) REVERT: Aq 74 SER cc_start: 0.8844 (m) cc_final: 0.8484 (t) REVERT: Aq 110 MET cc_start: 0.8045 (tpp) cc_final: 0.7685 (mmt) REVERT: Aq 175 MET cc_start: 0.8659 (tmm) cc_final: 0.8397 (tmm) REVERT: Aq 199 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7947 (mtp85) REVERT: Ar 74 SER cc_start: 0.8953 (m) cc_final: 0.8646 (t) REVERT: Ar 93 GLN cc_start: 0.8704 (tp40) cc_final: 0.8419 (tp40) REVERT: Ar 118 MET cc_start: 0.9042 (tpt) cc_final: 0.8165 (tmm) REVERT: As 93 GLN cc_start: 0.8626 (tp40) cc_final: 0.8339 (tp40) REVERT: As 126 THR cc_start: 0.9347 (p) cc_final: 0.9110 (t) REVERT: As 137 MET cc_start: 0.8494 (mmm) cc_final: 0.8238 (mmm) REVERT: At 74 SER cc_start: 0.8824 (m) cc_final: 0.8532 (t) REVERT: At 110 MET cc_start: 0.8182 (tpp) cc_final: 0.7861 (mmt) REVERT: At 176 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8087 (mtp85) REVERT: At 199 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7998 (mtp85) REVERT: Au 81 ASP cc_start: 0.8462 (t0) cc_final: 0.8253 (t0) REVERT: Au 175 MET cc_start: 0.8523 (tmm) cc_final: 0.8316 (tmm) REVERT: Av 137 MET cc_start: 0.8536 (mmm) cc_final: 0.7526 (mmm) REVERT: Aw 110 MET cc_start: 0.8191 (mmt) cc_final: 0.7960 (tpt) REVERT: Aw 190 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8427 (mmt90) REVERT: Ax 126 THR cc_start: 0.9247 (p) cc_final: 0.8950 (t) REVERT: Ax 175 MET cc_start: 0.8757 (tmm) cc_final: 0.8538 (tmm) REVERT: Ay 110 MET cc_start: 0.8122 (tpp) cc_final: 0.7821 (mmt) REVERT: Ay 118 MET cc_start: 0.9006 (tpt) cc_final: 0.8455 (tmm) REVERT: Az 137 MET cc_start: 0.8237 (mmm) cc_final: 0.7818 (mmm) REVERT: Az 150 MET cc_start: 0.8248 (mmt) cc_final: 0.8018 (mmt) REVERT: Az 222 MET cc_start: 0.7448 (mtp) cc_final: 0.7221 (ttm) REVERT: Ba 52 MET cc_start: 0.6798 (mtt) cc_final: 0.6231 (mtt) REVERT: Ba 74 SER cc_start: 0.8827 (m) cc_final: 0.8497 (t) REVERT: Ba 137 MET cc_start: 0.8225 (mmm) cc_final: 0.7858 (mmm) REVERT: Ba 175 MET cc_start: 0.8722 (tmm) cc_final: 0.8479 (tmm) outliers start: 103 outliers final: 88 residues processed: 1084 average time/residue: 0.2615 time to fit residues: 444.4953 Evaluate side-chains 1116 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1028 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 126 THR Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 161 ILE Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 196 SER Chi-restraints excluded: chain Ad residue 213 ILE Chi-restraints excluded: chain Ae residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 114 LEU Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 135 THR Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 161 ILE Chi-restraints excluded: chain Ag residue 213 ILE Chi-restraints excluded: chain Ah residue 161 ILE Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 138 ASP Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Aj residue 196 SER Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 69 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain Am residue 213 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 161 ILE Chi-restraints excluded: chain Ao residue 213 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 196 SER Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain At residue 121 CYS Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 58 LEU Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 49 LEU Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 213 ILE Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Ay residue 213 ILE Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Az residue 114 LEU Chi-restraints excluded: chain Az residue 161 ILE Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 378 optimal weight: 10.0000 chunk 441 optimal weight: 0.6980 chunk 286 optimal weight: 0.0770 chunk 153 optimal weight: 0.0670 chunk 472 optimal weight: 9.9990 chunk 232 optimal weight: 0.0870 chunk 395 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 323 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.7856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 44 HIS Ai 44 HIS Am 44 HIS An 44 HIS Ap 44 HIS ** Ap 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101804 restraints weight = 56198.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103474 restraints weight = 45354.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104410 restraints weight = 37373.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105235 restraints weight = 33281.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105471 restraints weight = 30824.328| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41337 Z= 0.138 Angle : 0.584 6.521 55809 Z= 0.295 Chirality : 0.037 0.141 5967 Planarity : 0.005 0.053 7182 Dihedral : 3.921 15.694 5508 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.27 % Allowed : 18.61 % Favored : 79.12 % 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: -0.67 (0.12), residues: 4941 helix: 0.35 (0.11), residues: 2457 sheet: -2.64 (0.21), residues: 324 loop : -0.91 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAi 199 TYR 0.033 0.002 TYRAr 75 PHE 0.018 0.002 PHEAf 117 TRP 0.016 0.002 TRPAo 95 HIS 0.014 0.001 HISAr 71 Details of bonding type rmsd covalent geometry : bond 0.00361 (41337) covalent geometry : angle 0.58447 (55809) hydrogen bonds : bond 0.03347 ( 1751) hydrogen bonds : angle 4.06461 ( 4767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1061 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 50 LYS cc_start: 0.8002 (pttm) cc_final: 0.7319 (mmtt) REVERT: Aa 176 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8233 (tpt170) REVERT: Aa 222 MET cc_start: 0.8268 (tpp) cc_final: 0.7743 (tpp) REVERT: Ab 118 MET cc_start: 0.9223 (tmm) cc_final: 0.8936 (tmm) REVERT: Ab 150 MET cc_start: 0.8273 (mmt) cc_final: 0.7941 (mmt) REVERT: Ac 74 SER cc_start: 0.8656 (m) cc_final: 0.8296 (t) REVERT: Ac 137 MET cc_start: 0.8480 (mmm) cc_final: 0.8170 (mmm) REVERT: Ac 176 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7871 (mtp85) REVERT: Ad 74 SER cc_start: 0.8926 (m) cc_final: 0.8483 (t) REVERT: Ad 110 MET cc_start: 0.8047 (mmt) cc_final: 0.7789 (mmt) REVERT: Ae 74 SER cc_start: 0.8846 (m) cc_final: 0.8458 (t) REVERT: Ae 150 MET cc_start: 0.8403 (mmt) cc_final: 0.7915 (mmt) REVERT: Ae 175 MET cc_start: 0.8792 (tmm) cc_final: 0.8586 (tmm) REVERT: Af 74 SER cc_start: 0.8757 (m) cc_final: 0.8405 (t) REVERT: Af 93 GLN cc_start: 0.8360 (tp40) cc_final: 0.7706 (tp40) REVERT: Af 203 ASP cc_start: 0.8370 (t0) cc_final: 0.8016 (t0) REVERT: Ag 74 SER cc_start: 0.8453 (m) cc_final: 0.8123 (t) REVERT: Ag 137 MET cc_start: 0.8196 (mmm) cc_final: 0.7969 (mmm) REVERT: Ag 176 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8227 (ttt90) REVERT: Ah 74 SER cc_start: 0.8740 (m) cc_final: 0.8417 (t) REVERT: Ah 176 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8129 (tpp-160) REVERT: Ai 74 SER cc_start: 0.9027 (m) cc_final: 0.8615 (t) REVERT: Ai 176 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8364 (mtp85) REVERT: Ai 190 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8491 (mmt90) REVERT: Aj 52 MET cc_start: 0.7224 (mtt) cc_final: 0.6968 (mtt) REVERT: Aj 74 SER cc_start: 0.8680 (m) cc_final: 0.8204 (t) REVERT: Ak 74 SER cc_start: 0.8645 (m) cc_final: 0.8223 (t) REVERT: Ak 93 GLN cc_start: 0.8402 (tp40) cc_final: 0.7914 (tp40) REVERT: Ak 178 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8178 (mtp180) REVERT: Al 52 MET cc_start: 0.6944 (mtt) cc_final: 0.6716 (mtt) REVERT: Al 74 SER cc_start: 0.8789 (m) cc_final: 0.8360 (t) REVERT: Al 93 GLN cc_start: 0.8512 (tp40) cc_final: 0.7975 (tp40) REVERT: Al 137 MET cc_start: 0.8610 (mmm) cc_final: 0.8399 (mmm) REVERT: Al 190 ARG cc_start: 0.8883 (mpt180) cc_final: 0.8656 (mmt90) REVERT: Am 74 SER cc_start: 0.8767 (m) cc_final: 0.8286 (t) REVERT: Am 93 GLN cc_start: 0.8467 (tp40) cc_final: 0.7743 (tp40) REVERT: Am 126 THR cc_start: 0.9034 (p) cc_final: 0.8678 (t) REVERT: Am 175 MET cc_start: 0.8401 (tmm) cc_final: 0.7951 (ttt) REVERT: Am 176 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.7541 (mtp85) REVERT: Am 203 ASP cc_start: 0.7985 (t70) cc_final: 0.7768 (t0) REVERT: An 74 SER cc_start: 0.8702 (m) cc_final: 0.8283 (t) REVERT: An 203 ASP cc_start: 0.8415 (t0) cc_final: 0.8097 (t0) REVERT: Ao 74 SER cc_start: 0.8778 (m) cc_final: 0.8358 (t) REVERT: Ao 137 MET cc_start: 0.8326 (mmm) cc_final: 0.8114 (mmm) REVERT: Ap 74 SER cc_start: 0.8963 (m) cc_final: 0.8615 (t) REVERT: Ap 93 GLN cc_start: 0.8585 (tp40) cc_final: 0.8228 (tp40) REVERT: Ap 175 MET cc_start: 0.8476 (tmm) cc_final: 0.7850 (ttt) REVERT: Ap 176 ARG cc_start: 0.8817 (mmm-85) cc_final: 0.8076 (mtp85) REVERT: Aq 74 SER cc_start: 0.8890 (m) cc_final: 0.8541 (t) REVERT: Aq 199 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7738 (mtp85) REVERT: Ar 74 SER cc_start: 0.8913 (m) cc_final: 0.8537 (t) REVERT: Ar 93 GLN cc_start: 0.8709 (tp40) cc_final: 0.8416 (tp40) REVERT: Ar 118 MET cc_start: 0.9071 (tpt) cc_final: 0.8171 (tmm) REVERT: Ar 126 THR cc_start: 0.9019 (p) cc_final: 0.8663 (t) REVERT: Ar 203 ASP cc_start: 0.7880 (t70) cc_final: 0.7656 (t0) REVERT: As 93 GLN cc_start: 0.8646 (tp40) cc_final: 0.8252 (tp40) REVERT: As 126 THR cc_start: 0.9391 (p) cc_final: 0.9131 (t) REVERT: As 137 MET cc_start: 0.8545 (mmm) cc_final: 0.8236 (mmm) REVERT: As 190 ARG cc_start: 0.8831 (mpt180) cc_final: 0.8494 (mmt90) REVERT: At 74 SER cc_start: 0.8937 (m) cc_final: 0.8644 (t) REVERT: At 110 MET cc_start: 0.8187 (tpp) cc_final: 0.7985 (mmt) REVERT: At 137 MET cc_start: 0.8167 (mmm) cc_final: 0.7847 (mmm) REVERT: At 176 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8140 (mtp85) REVERT: At 199 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8129 (mtp85) REVERT: Av 137 MET cc_start: 0.8532 (mmm) cc_final: 0.7509 (mmm) REVERT: Av 176 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.7895 (mtp85) REVERT: Aw 136 MET cc_start: 0.8054 (ttt) cc_final: 0.7838 (ttt) REVERT: Ax 175 MET cc_start: 0.8821 (tmm) cc_final: 0.8579 (tmm) REVERT: Ay 118 MET cc_start: 0.9030 (tpt) cc_final: 0.8457 (tmm) REVERT: Az 150 MET cc_start: 0.8282 (mmt) cc_final: 0.8001 (mmt) REVERT: Ba 52 MET cc_start: 0.7050 (mtt) cc_final: 0.6678 (mtt) REVERT: Ba 74 SER cc_start: 0.9000 (m) cc_final: 0.8639 (t) REVERT: Ba 137 MET cc_start: 0.8283 (mmm) cc_final: 0.7894 (mmm) REVERT: Ba 150 MET cc_start: 0.8540 (mmt) cc_final: 0.8041 (mmt) outliers start: 100 outliers final: 87 residues processed: 1095 average time/residue: 0.2598 time to fit residues: 446.4564 Evaluate side-chains 1118 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1031 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 135 THR Chi-restraints excluded: chain Ac residue 161 ILE Chi-restraints excluded: chain Ac residue 196 SER Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 196 SER Chi-restraints excluded: chain Ad residue 213 ILE Chi-restraints excluded: chain Ae residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 161 ILE Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 135 THR Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 213 ILE Chi-restraints excluded: chain Ah residue 161 ILE Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 69 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain An residue 196 SER Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 213 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 135 THR Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 196 SER Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain At residue 121 CYS Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 58 LEU Chi-restraints excluded: chain Au residue 161 ILE Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 49 LEU Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 135 THR Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 74 SER Chi-restraints excluded: chain Aw residue 213 ILE Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Ay residue 196 SER Chi-restraints excluded: chain Ay residue 213 ILE Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 161 ILE Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 313 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 317 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 410 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Al 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 44 HIS ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103683 restraints weight = 56559.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104551 restraints weight = 49674.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105020 restraints weight = 44238.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105788 restraints weight = 40698.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.105958 restraints weight = 38725.047| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41337 Z= 0.152 Angle : 0.609 6.663 55809 Z= 0.307 Chirality : 0.037 0.138 5967 Planarity : 0.005 0.059 7182 Dihedral : 3.985 16.319 5508 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.25 % Allowed : 19.02 % Favored : 78.73 % 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: -0.99 (0.12), residues: 4941 helix: 0.11 (0.10), residues: 2619 sheet: -2.47 (0.22), residues: 324 loop : -1.26 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGAg 199 TYR 0.033 0.002 TYRAr 75 PHE 0.019 0.002 PHEAl 117 TRP 0.017 0.002 TRPAo 95 HIS 0.013 0.002 HISAg 71 Details of bonding type rmsd covalent geometry : bond 0.00392 (41337) covalent geometry : angle 0.60893 (55809) hydrogen bonds : bond 0.03488 ( 1751) hydrogen bonds : angle 4.11802 ( 4767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1051 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 50 LYS cc_start: 0.8044 (pttm) cc_final: 0.7386 (mmtt) REVERT: Aa 170 GLU cc_start: 0.8472 (tp30) cc_final: 0.8265 (tp30) REVERT: Aa 176 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8139 (tpt170) REVERT: Ab 118 MET cc_start: 0.9218 (tmm) cc_final: 0.8947 (tmm) REVERT: Ab 175 MET cc_start: 0.8431 (tmm) cc_final: 0.8042 (tmm) REVERT: Ac 74 SER cc_start: 0.8453 (m) cc_final: 0.8109 (t) REVERT: Ac 137 MET cc_start: 0.8394 (mmm) cc_final: 0.8072 (mmm) REVERT: Ac 176 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7774 (mtp85) REVERT: Ad 74 SER cc_start: 0.8658 (m) cc_final: 0.8291 (t) REVERT: Ae 74 SER cc_start: 0.8671 (m) cc_final: 0.8300 (t) REVERT: Ae 150 MET cc_start: 0.8292 (mmt) cc_final: 0.7817 (mmt) REVERT: Af 74 SER cc_start: 0.8586 (m) cc_final: 0.8233 (t) REVERT: Af 93 GLN cc_start: 0.8370 (tp40) cc_final: 0.7681 (tp40) REVERT: Af 162 MET cc_start: 0.8256 (tpp) cc_final: 0.8049 (tpp) REVERT: Af 203 ASP cc_start: 0.8271 (t0) cc_final: 0.7938 (t0) REVERT: Ag 74 SER cc_start: 0.8223 (m) cc_final: 0.7936 (t) REVERT: Ag 176 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8260 (ttt90) REVERT: Ah 74 SER cc_start: 0.8507 (m) cc_final: 0.8214 (t) REVERT: Ah 176 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8078 (tpp-160) REVERT: Ai 74 SER cc_start: 0.8882 (m) cc_final: 0.8480 (t) REVERT: Ai 176 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.7965 (mtp85) REVERT: Ai 190 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8323 (mmt90) REVERT: Aj 52 MET cc_start: 0.7217 (mtt) cc_final: 0.6979 (mtt) REVERT: Aj 74 SER cc_start: 0.8504 (m) cc_final: 0.8030 (t) REVERT: Aj 110 MET cc_start: 0.8164 (mmt) cc_final: 0.7716 (mmt) REVERT: Aj 207 ILE cc_start: 0.8713 (mm) cc_final: 0.8453 (mt) REVERT: Ak 74 SER cc_start: 0.8443 (m) cc_final: 0.8066 (t) REVERT: Ak 93 GLN cc_start: 0.8359 (tp40) cc_final: 0.7932 (tp40) REVERT: Ak 178 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.8009 (mtp180) REVERT: Al 74 SER cc_start: 0.8532 (m) cc_final: 0.8124 (t) REVERT: Al 93 GLN cc_start: 0.8498 (tp40) cc_final: 0.7874 (tp40) REVERT: Am 74 SER cc_start: 0.8557 (m) cc_final: 0.8094 (t) REVERT: Am 93 GLN cc_start: 0.8479 (tp40) cc_final: 0.7840 (tp40) REVERT: Am 126 THR cc_start: 0.8974 (p) cc_final: 0.8685 (t) REVERT: Am 175 MET cc_start: 0.8269 (tmm) cc_final: 0.7804 (ttt) REVERT: Am 176 ARG cc_start: 0.8688 (mmm-85) cc_final: 0.7446 (mtp85) REVERT: Am 203 ASP cc_start: 0.7905 (t70) cc_final: 0.7670 (t0) REVERT: An 50 LYS cc_start: 0.7886 (pttm) cc_final: 0.7318 (mmtt) REVERT: An 60 MET cc_start: 0.7961 (mmt) cc_final: 0.7662 (mmt) REVERT: An 74 SER cc_start: 0.8512 (m) cc_final: 0.8152 (t) REVERT: An 76 LYS cc_start: 0.8405 (mmtp) cc_final: 0.8204 (mmtm) REVERT: An 203 ASP cc_start: 0.8311 (t0) cc_final: 0.7993 (t0) REVERT: Ao 74 SER cc_start: 0.8626 (m) cc_final: 0.8224 (t) REVERT: Ap 74 SER cc_start: 0.8610 (m) cc_final: 0.8246 (t) REVERT: Ap 93 GLN cc_start: 0.8582 (tp40) cc_final: 0.8225 (tp40) REVERT: Ap 176 ARG cc_start: 0.8720 (mmm-85) cc_final: 0.8277 (mtp85) REVERT: Aq 74 SER cc_start: 0.8633 (m) cc_final: 0.8330 (t) REVERT: Ar 74 SER cc_start: 0.8731 (m) cc_final: 0.8482 (t) REVERT: Ar 93 GLN cc_start: 0.8715 (tp40) cc_final: 0.8470 (tp40) REVERT: Ar 118 MET cc_start: 0.9077 (tpt) cc_final: 0.8226 (tmm) REVERT: Ar 126 THR cc_start: 0.9024 (p) cc_final: 0.8763 (t) REVERT: Ar 203 ASP cc_start: 0.7801 (t70) cc_final: 0.7549 (t0) REVERT: As 52 MET cc_start: 0.6701 (mtt) cc_final: 0.6408 (mtt) REVERT: As 93 GLN cc_start: 0.8637 (tp40) cc_final: 0.8315 (tp40) REVERT: As 137 MET cc_start: 0.8490 (mmm) cc_final: 0.8120 (mmm) REVERT: As 175 MET cc_start: 0.8532 (tmm) cc_final: 0.8301 (tmm) REVERT: At 74 SER cc_start: 0.8663 (m) cc_final: 0.8299 (t) REVERT: At 176 ARG cc_start: 0.8517 (mmm-85) cc_final: 0.8075 (mtp85) REVERT: At 190 ARG cc_start: 0.8757 (mpt180) cc_final: 0.8544 (mmt90) REVERT: Au 58 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9033 (mt) REVERT: Au 100 MET cc_start: 0.7488 (tpt) cc_final: 0.7200 (tpt) REVERT: Av 137 MET cc_start: 0.7894 (mmm) cc_final: 0.7587 (mmm) REVERT: Av 175 MET cc_start: 0.8219 (tmm) cc_final: 0.7809 (ttt) REVERT: Av 176 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7795 (mtp85) REVERT: Ax 175 MET cc_start: 0.8733 (tmm) cc_final: 0.8522 (tmm) REVERT: Ay 118 MET cc_start: 0.9005 (tpt) cc_final: 0.8480 (tmm) REVERT: Az 175 MET cc_start: 0.8420 (tmm) cc_final: 0.8060 (tmm) REVERT: Ba 52 MET cc_start: 0.6926 (mtt) cc_final: 0.6574 (mtt) REVERT: Ba 74 SER cc_start: 0.8793 (m) cc_final: 0.8447 (t) REVERT: Ba 137 MET cc_start: 0.8303 (mmm) cc_final: 0.7852 (mmm) REVERT: Ba 150 MET cc_start: 0.8423 (mmt) cc_final: 0.8002 (mmt) outliers start: 99 outliers final: 90 residues processed: 1084 average time/residue: 0.2688 time to fit residues: 455.9022 Evaluate side-chains 1115 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1024 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Ab residue 161 ILE Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 135 THR Chi-restraints excluded: chain Ac residue 161 ILE Chi-restraints excluded: chain Ac residue 196 SER Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ad residue 196 SER Chi-restraints excluded: chain Ad residue 213 ILE Chi-restraints excluded: chain Ae residue 69 LEU Chi-restraints excluded: chain Ae residue 73 LEU Chi-restraints excluded: chain Ae residue 114 LEU Chi-restraints excluded: chain Ae residue 161 ILE Chi-restraints excluded: chain Ae residue 213 ILE Chi-restraints excluded: chain Af residue 126 THR Chi-restraints excluded: chain Af residue 135 THR Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 161 ILE Chi-restraints excluded: chain Ag residue 213 ILE Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 69 LEU Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Aj residue 196 SER Chi-restraints excluded: chain Aj residue 213 ILE Chi-restraints excluded: chain Ak residue 58 LEU Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Al residue 69 LEU Chi-restraints excluded: chain Al residue 161 ILE Chi-restraints excluded: chain Al residue 213 ILE Chi-restraints excluded: chain Am residue 161 ILE Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain An residue 196 SER Chi-restraints excluded: chain An residue 213 ILE Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ao residue 213 ILE Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Ap residue 213 ILE Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 135 THR Chi-restraints excluded: chain As residue 196 SER Chi-restraints excluded: chain As residue 213 ILE Chi-restraints excluded: chain At residue 121 CYS Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 135 THR Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 58 LEU Chi-restraints excluded: chain Au residue 69 LEU Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 49 LEU Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 74 SER Chi-restraints excluded: chain Aw residue 213 ILE Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Ay residue 196 SER Chi-restraints excluded: chain Ay residue 213 ILE Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Az residue 114 LEU Chi-restraints excluded: chain Az residue 161 ILE Chi-restraints excluded: chain Az residue 213 ILE Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 161 ILE Chi-restraints excluded: chain Ba residue 213 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 142 optimal weight: 0.0770 chunk 297 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 408 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Am 44 HIS An 44 HIS Ap 44 HIS ** At 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104615 restraints weight = 55694.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106489 restraints weight = 43035.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107882 restraints weight = 35415.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108794 restraints weight = 30834.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109481 restraints weight = 27826.093| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41337 Z= 0.113 Angle : 0.574 7.023 55809 Z= 0.293 Chirality : 0.036 0.147 5967 Planarity : 0.005 0.074 7182 Dihedral : 3.920 17.877 5508 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.55 % Allowed : 20.04 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4941 helix: 0.50 (0.11), residues: 2457 sheet: -2.31 (0.21), residues: 324 loop : -0.70 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGAg 199 TYR 0.032 0.002 TYRAr 75 PHE 0.015 0.002 PHEAi 202 TRP 0.014 0.002 TRPAh 95 HIS 0.014 0.002 HISAi 71 Details of bonding type rmsd covalent geometry : bond 0.00300 (41337) covalent geometry : angle 0.57398 (55809) hydrogen bonds : bond 0.03036 ( 1751) hydrogen bonds : angle 3.94625 ( 4767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9882 Ramachandran restraints generated. 4941 Oldfield, 0 Emsley, 4941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1096 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 176 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8208 (tpt170) REVERT: Aa 199 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7951 (mtp-110) REVERT: Ab 118 MET cc_start: 0.9209 (tmm) cc_final: 0.8949 (tmm) REVERT: Ab 175 MET cc_start: 0.8591 (tmm) cc_final: 0.8197 (tmm) REVERT: Ac 74 SER cc_start: 0.8715 (m) cc_final: 0.8318 (t) REVERT: Ac 137 MET cc_start: 0.8492 (mmm) cc_final: 0.8166 (mmm) REVERT: Ac 175 MET cc_start: 0.8102 (tmm) cc_final: 0.7454 (ttt) REVERT: Ac 176 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8087 (tpt-90) REVERT: Ad 74 SER cc_start: 0.8942 (m) cc_final: 0.8607 (p) REVERT: Ae 74 SER cc_start: 0.8924 (m) cc_final: 0.8530 (t) REVERT: Ae 150 MET cc_start: 0.8402 (mmt) cc_final: 0.7862 (mmt) REVERT: Af 74 SER cc_start: 0.8836 (m) cc_final: 0.8453 (t) REVERT: Af 93 GLN cc_start: 0.8259 (tp40) cc_final: 0.7576 (tp40) REVERT: Af 118 MET cc_start: 0.9113 (tmm) cc_final: 0.8128 (tmm) REVERT: Ag 118 MET cc_start: 0.9310 (tmm) cc_final: 0.9024 (tmm) REVERT: Ag 176 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.7958 (ttt90) REVERT: Ah 176 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8378 (mtp85) REVERT: Ai 74 SER cc_start: 0.9075 (m) cc_final: 0.8685 (t) REVERT: Ai 176 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8623 (tpt-90) REVERT: Ai 190 ARG cc_start: 0.8755 (mtt90) cc_final: 0.8536 (mmt90) REVERT: Aj 52 MET cc_start: 0.7211 (mtt) cc_final: 0.6886 (mtt) REVERT: Aj 74 SER cc_start: 0.8707 (m) cc_final: 0.8220 (t) REVERT: Aj 110 MET cc_start: 0.8000 (mmt) cc_final: 0.7583 (mmt) REVERT: Aj 207 ILE cc_start: 0.8773 (mm) cc_final: 0.8538 (mt) REVERT: Ak 74 SER cc_start: 0.8721 (m) cc_final: 0.8277 (t) REVERT: Ak 100 MET cc_start: 0.7479 (tpt) cc_final: 0.7198 (tpt) REVERT: Ak 178 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8220 (mtp180) REVERT: Ak 203 ASP cc_start: 0.7552 (t70) cc_final: 0.7340 (t0) REVERT: Al 74 SER cc_start: 0.8819 (m) cc_final: 0.8366 (t) REVERT: Al 93 GLN cc_start: 0.8341 (tp40) cc_final: 0.7821 (tp40) REVERT: Al 100 MET cc_start: 0.7276 (tpt) cc_final: 0.7041 (tpt) REVERT: Am 74 SER cc_start: 0.8760 (m) cc_final: 0.8530 (p) REVERT: Am 93 GLN cc_start: 0.8394 (tp40) cc_final: 0.7823 (tp40) REVERT: Am 126 THR cc_start: 0.9012 (p) cc_final: 0.8724 (t) REVERT: Am 175 MET cc_start: 0.8409 (tmm) cc_final: 0.7924 (ttt) REVERT: Am 176 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.7469 (mtp85) REVERT: Am 190 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8455 (mmt90) REVERT: An 60 MET cc_start: 0.8145 (mmt) cc_final: 0.7938 (mmt) REVERT: An 74 SER cc_start: 0.8732 (m) cc_final: 0.8306 (t) REVERT: An 93 GLN cc_start: 0.8479 (tp40) cc_final: 0.8045 (tp40) REVERT: An 203 ASP cc_start: 0.8384 (t0) cc_final: 0.8101 (t0) REVERT: Ao 74 SER cc_start: 0.8843 (m) cc_final: 0.8434 (t) REVERT: Ao 175 MET cc_start: 0.8166 (tmm) cc_final: 0.7622 (ttt) REVERT: Ap 58 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8798 (mt) REVERT: Ap 74 SER cc_start: 0.8789 (m) cc_final: 0.8321 (t) REVERT: Ap 93 GLN cc_start: 0.8502 (tp40) cc_final: 0.8222 (tp40) REVERT: Ap 110 MET cc_start: 0.8025 (mmt) cc_final: 0.7775 (tpt) REVERT: Ap 170 GLU cc_start: 0.8572 (tp30) cc_final: 0.8278 (tp30) REVERT: Ap 176 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8508 (ttt90) REVERT: Aq 74 SER cc_start: 0.8904 (m) cc_final: 0.8552 (t) REVERT: Aq 199 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8034 (mtp85) REVERT: Ar 74 SER cc_start: 0.8944 (m) cc_final: 0.8660 (t) REVERT: Ar 93 GLN cc_start: 0.8639 (tp40) cc_final: 0.8367 (tp40) REVERT: Ar 118 MET cc_start: 0.9115 (tpt) cc_final: 0.8616 (tpt) REVERT: Ar 126 THR cc_start: 0.9093 (p) cc_final: 0.8863 (t) REVERT: Ar 197 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8316 (mt) REVERT: As 52 MET cc_start: 0.6812 (mtt) cc_final: 0.6489 (mtt) REVERT: As 93 GLN cc_start: 0.8656 (tp40) cc_final: 0.8347 (tp40) REVERT: As 137 MET cc_start: 0.8643 (mmm) cc_final: 0.8301 (mmm) REVERT: As 175 MET cc_start: 0.8665 (tmm) cc_final: 0.8389 (tmm) REVERT: At 74 SER cc_start: 0.8973 (m) cc_final: 0.8678 (t) REVERT: At 176 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8494 (tpt-90) REVERT: At 190 ARG cc_start: 0.8912 (mpt180) cc_final: 0.8701 (mmt90) REVERT: At 197 LEU cc_start: 0.8669 (tp) cc_final: 0.8364 (tp) REVERT: Au 110 MET cc_start: 0.8416 (tpp) cc_final: 0.8127 (mmt) REVERT: Au 175 MET cc_start: 0.8499 (tmm) cc_final: 0.8243 (tmm) REVERT: Av 159 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8287 (ttt-90) REVERT: Av 175 MET cc_start: 0.8386 (tmm) cc_final: 0.7861 (ttt) REVERT: Av 176 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7736 (mtp85) REVERT: Ay 110 MET cc_start: 0.8340 (tpp) cc_final: 0.8070 (mmt) REVERT: Ay 118 MET cc_start: 0.9148 (tpt) cc_final: 0.8248 (tmm) REVERT: Ay 190 ARG cc_start: 0.8867 (mpt180) cc_final: 0.8487 (mmt90) REVERT: Az 75 TYR cc_start: 0.8748 (t80) cc_final: 0.8430 (t80) REVERT: Az 137 MET cc_start: 0.8375 (mmm) cc_final: 0.8063 (mmm) REVERT: Az 175 MET cc_start: 0.8473 (tmm) cc_final: 0.8186 (tmm) REVERT: Ba 52 MET cc_start: 0.7043 (mtt) cc_final: 0.6703 (mtt) REVERT: Ba 74 SER cc_start: 0.9123 (m) cc_final: 0.8726 (t) REVERT: Ba 75 TYR cc_start: 0.8423 (t80) cc_final: 0.8065 (t80) REVERT: Ba 136 MET cc_start: 0.8140 (ttt) cc_final: 0.7921 (ttt) REVERT: Ba 137 MET cc_start: 0.8374 (mmm) cc_final: 0.7981 (mmm) REVERT: Ba 150 MET cc_start: 0.8473 (mmt) cc_final: 0.7980 (mmt) outliers start: 68 outliers final: 58 residues processed: 1124 average time/residue: 0.2710 time to fit residues: 478.0619 Evaluate side-chains 1097 residues out of total 4401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1036 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 58 LEU Chi-restraints excluded: chain Aa residue 161 ILE Chi-restraints excluded: chain Ab residue 126 THR Chi-restraints excluded: chain Ab residue 161 ILE Chi-restraints excluded: chain Ab residue 196 SER Chi-restraints excluded: chain Ab residue 213 ILE Chi-restraints excluded: chain Ac residue 196 SER Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ae residue 114 LEU Chi-restraints excluded: chain Ae residue 161 ILE Chi-restraints excluded: chain Af residue 161 ILE Chi-restraints excluded: chain Af residue 213 ILE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 161 ILE Chi-restraints excluded: chain Ah residue 213 ILE Chi-restraints excluded: chain Ai residue 161 ILE Chi-restraints excluded: chain Ai residue 213 ILE Chi-restraints excluded: chain Aj residue 161 ILE Chi-restraints excluded: chain Ak residue 161 ILE Chi-restraints excluded: chain Ak residue 213 ILE Chi-restraints excluded: chain Al residue 58 LEU Chi-restraints excluded: chain Am residue 190 ARG Chi-restraints excluded: chain An residue 126 THR Chi-restraints excluded: chain An residue 161 ILE Chi-restraints excluded: chain An residue 196 SER Chi-restraints excluded: chain Ao residue 58 LEU Chi-restraints excluded: chain Ap residue 58 LEU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 161 ILE Chi-restraints excluded: chain Ap residue 196 SER Chi-restraints excluded: chain Aq residue 58 LEU Chi-restraints excluded: chain Aq residue 69 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 213 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 161 ILE Chi-restraints excluded: chain Ar residue 197 LEU Chi-restraints excluded: chain Ar residue 213 ILE Chi-restraints excluded: chain As residue 46 VAL Chi-restraints excluded: chain As residue 74 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 196 SER Chi-restraints excluded: chain At residue 121 CYS Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 161 ILE Chi-restraints excluded: chain At residue 213 ILE Chi-restraints excluded: chain Au residue 213 ILE Chi-restraints excluded: chain Av residue 74 SER Chi-restraints excluded: chain Av residue 161 ILE Chi-restraints excluded: chain Av residue 196 SER Chi-restraints excluded: chain Av residue 213 ILE Chi-restraints excluded: chain Aw residue 74 SER Chi-restraints excluded: chain Ax residue 74 SER Chi-restraints excluded: chain Ax residue 135 THR Chi-restraints excluded: chain Ax residue 213 ILE Chi-restraints excluded: chain Ay residue 161 ILE Chi-restraints excluded: chain Ay residue 196 SER Chi-restraints excluded: chain Az residue 74 SER Chi-restraints excluded: chain Ba residue 135 THR Chi-restraints excluded: chain Ba residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 18 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 438 optimal weight: 5.9990 chunk 182 optimal weight: 0.3980 chunk 145 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Am 142 GLN An 44 HIS Ap 44 HIS ** As 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105319 restraints weight = 56203.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107102 restraints weight = 43930.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108430 restraints weight = 36638.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109348 restraints weight = 31957.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110070 restraints weight = 28911.301| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 41337 Z= 0.124 Angle : 0.603 7.371 55809 Z= 0.307 Chirality : 0.037 0.142 5967 Planarity : 0.005 0.059 7182 Dihedral : 3.937 18.169 5508 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.66 % Allowed : 21.02 % Favored : 77.32 % 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: -0.32 (0.12), residues: 4941 helix: 0.51 (0.11), residues: 2457 sheet: -2.11 (0.21), residues: 324 loop : -0.63 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGAz 199 TYR 0.032 0.002 TYRAj 75 PHE 0.015 0.002 PHEAq 117 TRP 0.015 0.002 TRPAr 95 HIS 0.015 0.002 HISAy 71 Details of bonding type rmsd covalent geometry : bond 0.00332 (41337) covalent geometry : angle 0.60263 (55809) hydrogen bonds : bond 0.03268 ( 1751) hydrogen bonds : angle 3.99945 ( 4767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8569.16 seconds wall clock time: 147 minutes 47.79 seconds (8867.79 seconds total)