Starting phenix.real_space_refine on Sun Feb 8 05:54:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.map" model { file = "/net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r9y_53864/02_2026/9r9y_53864.cif" } resolution = 4.32 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= 0.014 sd= 0.100 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 405 5.16 5 C 25569 2.51 5 N 7101 2.21 5 O 7452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 351 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: 40527 Number of models: 1 Model: "" Number of chains: 27 Chain: "Aa" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ab" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ac" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ad" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ae" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Af" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ag" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ah" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ai" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Aj" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ak" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Al" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Am" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "An" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ao" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ap" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Aq" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ar" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "As" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "At" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Au" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Av" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Aw" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ax" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ay" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Az" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Chain: "Ba" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1501 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 175} Time building chain proxies: 9.05, per 1000 atoms: 0.22 Number of scatterers: 40527 At special positions: 0 Unit cell: (150.1, 151.05, 136.8, 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 405 16.00 O 7452 8.00 N 7101 7.00 C 25569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 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: 9558 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 54 sheets defined 53.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'Aa' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAa 78 " --> pdb=" O ALAAa 74 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 92 through 107 Processing helix chain 'Aa' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAa 115 " --> pdb=" O GLUAa 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAa 116 " --> pdb=" O GLUAa 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAa 117 " --> pdb=" O ALAAa 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAa 123 " --> pdb=" O ASNAa 119 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAa 156 " --> pdb=" O LYSAa 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAa 157 " --> pdb=" O PROAa 153 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 162 through 167 Processing helix chain 'Aa' and resid 169 through 182 removed outlier: 3.729A pdb=" N LYSAa 182 " --> pdb=" O GLUAa 178 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 188 through 194 Processing helix chain 'Aa' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAa 203 " --> pdb=" O GLYAa 200 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 216 through 228 Processing helix chain 'Ab' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAb 78 " --> pdb=" O ALAAb 74 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 92 through 107 Processing helix chain 'Ab' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAb 115 " --> pdb=" O GLUAb 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAb 116 " --> pdb=" O GLUAb 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAb 117 " --> pdb=" O ALAAb 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAb 123 " --> pdb=" O ASNAb 119 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAb 156 " --> pdb=" O LYSAb 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAb 157 " --> pdb=" O PROAb 153 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 161 through 167 Processing helix chain 'Ab' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAb 182 " --> pdb=" O GLUAb 178 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 188 through 194 Processing helix chain 'Ab' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAb 203 " --> pdb=" O GLYAb 200 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 216 through 228 Processing helix chain 'Ac' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAc 78 " --> pdb=" O ALAAc 74 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 92 through 107 Processing helix chain 'Ac' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAc 115 " --> pdb=" O GLUAc 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAc 116 " --> pdb=" O GLUAc 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAc 117 " --> pdb=" O ALAAc 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAc 123 " --> pdb=" O ASNAc 119 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAc 156 " --> pdb=" O LYSAc 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAc 157 " --> pdb=" O PROAc 153 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 162 through 167 Processing helix chain 'Ac' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAc 182 " --> pdb=" O GLUAc 178 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 188 through 194 Processing helix chain 'Ac' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAc 203 " --> pdb=" O GLYAc 200 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 216 through 228 Processing helix chain 'Ad' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAd 78 " --> pdb=" O ALAAd 74 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 92 through 107 Processing helix chain 'Ad' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAd 115 " --> pdb=" O GLUAd 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAd 116 " --> pdb=" O GLUAd 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAd 117 " --> pdb=" O ALAAd 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALAd 123 " --> pdb=" O ASNAd 119 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAd 156 " --> pdb=" O LYSAd 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAd 157 " --> pdb=" O PROAd 153 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 161 through 167 Processing helix chain 'Ad' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAd 182 " --> pdb=" O GLUAd 178 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 188 through 194 Processing helix chain 'Ad' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAd 203 " --> pdb=" O GLYAd 200 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 216 through 228 Processing helix chain 'Ae' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAe 78 " --> pdb=" O ALAAe 74 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 92 through 107 Processing helix chain 'Ae' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAe 115 " --> pdb=" O GLUAe 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAe 116 " --> pdb=" O GLUAe 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAe 117 " --> pdb=" O ALAAe 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAe 123 " --> pdb=" O ASNAe 119 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAe 156 " --> pdb=" O LYSAe 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAe 157 " --> pdb=" O PROAe 153 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 162 through 167 Processing helix chain 'Ae' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAe 182 " --> pdb=" O GLUAe 178 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 188 through 194 Processing helix chain 'Ae' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAe 203 " --> pdb=" O GLYAe 200 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 216 through 228 Processing helix chain 'Af' and resid 72 through 79 removed outlier: 3.718A pdb=" N GLUAf 78 " --> pdb=" O ALAAf 74 " (cutoff:3.500A) Processing helix chain 'Af' and resid 92 through 107 Processing helix chain 'Af' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAf 115 " --> pdb=" O GLUAf 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAf 116 " --> pdb=" O GLUAf 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAf 117 " --> pdb=" O ALAAf 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAf 123 " --> pdb=" O ASNAf 119 " (cutoff:3.500A) Processing helix chain 'Af' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAf 156 " --> pdb=" O LYSAf 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAf 157 " --> pdb=" O PROAf 153 " (cutoff:3.500A) Processing helix chain 'Af' and resid 162 through 167 Processing helix chain 'Af' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAf 182 " --> pdb=" O GLUAf 178 " (cutoff:3.500A) Processing helix chain 'Af' and resid 188 through 194 Processing helix chain 'Af' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAf 203 " --> pdb=" O GLYAf 200 " (cutoff:3.500A) Processing helix chain 'Af' and resid 216 through 228 Processing helix chain 'Ag' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAg 78 " --> pdb=" O ALAAg 74 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 92 through 107 Processing helix chain 'Ag' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAg 115 " --> pdb=" O GLUAg 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAg 116 " --> pdb=" O GLUAg 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAg 117 " --> pdb=" O ALAAg 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAg 123 " --> pdb=" O ASNAg 119 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAg 156 " --> pdb=" O LYSAg 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAg 157 " --> pdb=" O PROAg 153 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 161 through 167 Processing helix chain 'Ag' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAg 182 " --> pdb=" O GLUAg 178 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 188 through 194 Processing helix chain 'Ag' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAg 203 " --> pdb=" O GLYAg 200 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 216 through 228 Processing helix chain 'Ah' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAh 78 " --> pdb=" O ALAAh 74 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 92 through 107 Processing helix chain 'Ah' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAh 115 " --> pdb=" O GLUAh 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAh 116 " --> pdb=" O GLUAh 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAh 117 " --> pdb=" O ALAAh 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAh 123 " --> pdb=" O ASNAh 119 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAh 156 " --> pdb=" O LYSAh 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAh 157 " --> pdb=" O PROAh 153 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 162 through 167 Processing helix chain 'Ah' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAh 182 " --> pdb=" O GLUAh 178 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 188 through 194 Processing helix chain 'Ah' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAh 203 " --> pdb=" O GLYAh 200 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 216 through 228 Processing helix chain 'Ai' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAi 78 " --> pdb=" O ALAAi 74 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 92 through 107 Processing helix chain 'Ai' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAi 115 " --> pdb=" O GLUAi 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAi 116 " --> pdb=" O GLUAi 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALAi 117 " --> pdb=" O ALAAi 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAi 123 " --> pdb=" O ASNAi 119 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAi 156 " --> pdb=" O LYSAi 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAi 157 " --> pdb=" O PROAi 153 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 162 through 167 Processing helix chain 'Ai' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAi 182 " --> pdb=" O GLUAi 178 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 188 through 194 Processing helix chain 'Ai' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAi 203 " --> pdb=" O GLYAi 200 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 216 through 228 Processing helix chain 'Aj' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAj 78 " --> pdb=" O ALAAj 74 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 92 through 107 Processing helix chain 'Aj' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAj 115 " --> pdb=" O GLUAj 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAj 116 " --> pdb=" O GLUAj 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAj 117 " --> pdb=" O ALAAj 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAj 123 " --> pdb=" O ASNAj 119 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAj 156 " --> pdb=" O LYSAj 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAj 157 " --> pdb=" O PROAj 153 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 162 through 167 Processing helix chain 'Aj' and resid 169 through 182 removed outlier: 3.729A pdb=" N LYSAj 182 " --> pdb=" O GLUAj 178 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 188 through 194 Processing helix chain 'Aj' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAj 203 " --> pdb=" O GLYAj 200 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 216 through 228 Processing helix chain 'Ak' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAk 78 " --> pdb=" O ALAAk 74 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 92 through 107 Processing helix chain 'Ak' and resid 110 through 128 removed outlier: 3.674A pdb=" N GLYAk 115 " --> pdb=" O GLUAk 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAk 116 " --> pdb=" O GLUAk 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAk 117 " --> pdb=" O ALAAk 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAk 123 " --> pdb=" O ASNAk 119 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAk 156 " --> pdb=" O LYSAk 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAk 157 " --> pdb=" O PROAk 153 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 161 through 167 Processing helix chain 'Ak' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAk 182 " --> pdb=" O GLUAk 178 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 188 through 194 Processing helix chain 'Ak' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAk 203 " --> pdb=" O GLYAk 200 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 216 through 228 Processing helix chain 'Al' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAl 78 " --> pdb=" O ALAAl 74 " (cutoff:3.500A) Processing helix chain 'Al' and resid 92 through 107 Processing helix chain 'Al' and resid 110 through 128 removed outlier: 3.671A pdb=" N GLYAl 115 " --> pdb=" O GLUAl 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAl 116 " --> pdb=" O GLUAl 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAl 117 " --> pdb=" O ALAAl 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAl 123 " --> pdb=" O ASNAl 119 " (cutoff:3.500A) Processing helix chain 'Al' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAl 156 " --> pdb=" O LYSAl 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAl 157 " --> pdb=" O PROAl 153 " (cutoff:3.500A) Processing helix chain 'Al' and resid 162 through 167 Processing helix chain 'Al' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAl 182 " --> pdb=" O GLUAl 178 " (cutoff:3.500A) Processing helix chain 'Al' and resid 188 through 194 Processing helix chain 'Al' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAl 203 " --> pdb=" O GLYAl 200 " (cutoff:3.500A) Processing helix chain 'Al' and resid 216 through 228 Processing helix chain 'Am' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAm 78 " --> pdb=" O ALAAm 74 " (cutoff:3.500A) Processing helix chain 'Am' and resid 92 through 107 Processing helix chain 'Am' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAm 115 " --> pdb=" O GLUAm 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAm 116 " --> pdb=" O GLUAm 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAm 117 " --> pdb=" O ALAAm 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAm 123 " --> pdb=" O ASNAm 119 " (cutoff:3.500A) Processing helix chain 'Am' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAm 156 " --> pdb=" O LYSAm 152 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASNAm 157 " --> pdb=" O PROAm 153 " (cutoff:3.500A) Processing helix chain 'Am' and resid 162 through 167 Processing helix chain 'Am' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAm 182 " --> pdb=" O GLUAm 178 " (cutoff:3.500A) Processing helix chain 'Am' and resid 188 through 194 Processing helix chain 'Am' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAm 203 " --> pdb=" O GLYAm 200 " (cutoff:3.500A) Processing helix chain 'Am' and resid 216 through 228 Processing helix chain 'An' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAn 78 " --> pdb=" O ALAAn 74 " (cutoff:3.500A) Processing helix chain 'An' and resid 92 through 107 Processing helix chain 'An' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAn 115 " --> pdb=" O GLUAn 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAn 116 " --> pdb=" O GLUAn 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAn 117 " --> pdb=" O ALAAn 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAn 123 " --> pdb=" O ASNAn 119 " (cutoff:3.500A) Processing helix chain 'An' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAn 156 " --> pdb=" O LYSAn 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAn 157 " --> pdb=" O PROAn 153 " (cutoff:3.500A) Processing helix chain 'An' and resid 162 through 167 Processing helix chain 'An' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAn 182 " --> pdb=" O GLUAn 178 " (cutoff:3.500A) Processing helix chain 'An' and resid 188 through 194 Processing helix chain 'An' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAn 203 " --> pdb=" O GLYAn 200 " (cutoff:3.500A) Processing helix chain 'An' and resid 216 through 228 Processing helix chain 'Ao' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAo 78 " --> pdb=" O ALAAo 74 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 92 through 107 Processing helix chain 'Ao' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAo 115 " --> pdb=" O GLUAo 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAo 116 " --> pdb=" O GLUAo 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAo 117 " --> pdb=" O ALAAo 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAo 123 " --> pdb=" O ASNAo 119 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 151 through 157 removed outlier: 3.930A pdb=" N GLUAo 156 " --> pdb=" O LYSAo 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAo 157 " --> pdb=" O PROAo 153 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 162 through 167 Processing helix chain 'Ao' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAo 182 " --> pdb=" O GLUAo 178 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 188 through 194 Processing helix chain 'Ao' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAo 203 " --> pdb=" O GLYAo 200 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 216 through 228 Processing helix chain 'Ap' and resid 72 through 79 removed outlier: 3.718A pdb=" N GLUAp 78 " --> pdb=" O ALAAp 74 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 92 through 107 Processing helix chain 'Ap' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAp 115 " --> pdb=" O GLUAp 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAp 116 " --> pdb=" O GLUAp 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAp 117 " --> pdb=" O ALAAp 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAp 123 " --> pdb=" O ASNAp 119 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAp 156 " --> pdb=" O LYSAp 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAp 157 " --> pdb=" O PROAp 153 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 161 through 167 Processing helix chain 'Ap' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAp 182 " --> pdb=" O GLUAp 178 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 188 through 194 Processing helix chain 'Ap' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAp 203 " --> pdb=" O GLYAp 200 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 216 through 228 Processing helix chain 'Aq' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAq 78 " --> pdb=" O ALAAq 74 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 92 through 107 Processing helix chain 'Aq' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAq 115 " --> pdb=" O GLUAq 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAq 116 " --> pdb=" O GLUAq 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALAq 117 " --> pdb=" O ALAAq 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAq 123 " --> pdb=" O ASNAq 119 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 151 through 157 removed outlier: 3.930A pdb=" N GLUAq 156 " --> pdb=" O LYSAq 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAq 157 " --> pdb=" O PROAq 153 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 162 through 167 Processing helix chain 'Aq' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAq 182 " --> pdb=" O GLUAq 178 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 188 through 194 Processing helix chain 'Aq' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAq 203 " --> pdb=" O GLYAq 200 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 216 through 228 Processing helix chain 'Ar' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAr 78 " --> pdb=" O ALAAr 74 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 92 through 107 Processing helix chain 'Ar' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAr 115 " --> pdb=" O GLUAr 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAr 116 " --> pdb=" O GLUAr 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALAr 117 " --> pdb=" O ALAAr 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAr 123 " --> pdb=" O ASNAr 119 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAr 156 " --> pdb=" O LYSAr 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAr 157 " --> pdb=" O PROAr 153 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 162 through 167 Processing helix chain 'Ar' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAr 182 " --> pdb=" O GLUAr 178 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 188 through 194 Processing helix chain 'Ar' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAr 203 " --> pdb=" O GLYAr 200 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 216 through 228 Processing helix chain 'As' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAs 78 " --> pdb=" O ALAAs 74 " (cutoff:3.500A) Processing helix chain 'As' and resid 92 through 107 Processing helix chain 'As' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAs 115 " --> pdb=" O GLUAs 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAs 116 " --> pdb=" O GLUAs 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAs 117 " --> pdb=" O ALAAs 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAs 123 " --> pdb=" O ASNAs 119 " (cutoff:3.500A) Processing helix chain 'As' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAs 156 " --> pdb=" O LYSAs 152 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASNAs 157 " --> pdb=" O PROAs 153 " (cutoff:3.500A) Processing helix chain 'As' and resid 162 through 167 Processing helix chain 'As' and resid 169 through 182 removed outlier: 3.729A pdb=" N LYSAs 182 " --> pdb=" O GLUAs 178 " (cutoff:3.500A) Processing helix chain 'As' and resid 188 through 194 Processing helix chain 'As' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAs 203 " --> pdb=" O GLYAs 200 " (cutoff:3.500A) Processing helix chain 'As' and resid 216 through 228 Processing helix chain 'At' and resid 72 through 79 removed outlier: 3.718A pdb=" N GLUAt 78 " --> pdb=" O ALAAt 74 " (cutoff:3.500A) Processing helix chain 'At' and resid 92 through 107 Processing helix chain 'At' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAt 115 " --> pdb=" O GLUAt 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAt 116 " --> pdb=" O GLUAt 112 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALAt 117 " --> pdb=" O ALAAt 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALAt 123 " --> pdb=" O ASNAt 119 " (cutoff:3.500A) Processing helix chain 'At' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAt 156 " --> pdb=" O LYSAt 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAt 157 " --> pdb=" O PROAt 153 " (cutoff:3.500A) Processing helix chain 'At' and resid 161 through 167 Processing helix chain 'At' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAt 182 " --> pdb=" O GLUAt 178 " (cutoff:3.500A) Processing helix chain 'At' and resid 188 through 194 Processing helix chain 'At' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAt 203 " --> pdb=" O GLYAt 200 " (cutoff:3.500A) Processing helix chain 'At' and resid 216 through 228 Processing helix chain 'Au' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAu 78 " --> pdb=" O ALAAu 74 " (cutoff:3.500A) Processing helix chain 'Au' and resid 92 through 107 Processing helix chain 'Au' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAu 115 " --> pdb=" O GLUAu 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAu 116 " --> pdb=" O GLUAu 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAu 117 " --> pdb=" O ALAAu 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAu 123 " --> pdb=" O ASNAu 119 " (cutoff:3.500A) Processing helix chain 'Au' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAu 156 " --> pdb=" O LYSAu 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAu 157 " --> pdb=" O PROAu 153 " (cutoff:3.500A) Processing helix chain 'Au' and resid 162 through 167 Processing helix chain 'Au' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAu 182 " --> pdb=" O GLUAu 178 " (cutoff:3.500A) Processing helix chain 'Au' and resid 188 through 194 Processing helix chain 'Au' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAu 203 " --> pdb=" O GLYAu 200 " (cutoff:3.500A) Processing helix chain 'Au' and resid 216 through 228 Processing helix chain 'Av' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAv 78 " --> pdb=" O ALAAv 74 " (cutoff:3.500A) Processing helix chain 'Av' and resid 92 through 107 Processing helix chain 'Av' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAv 115 " --> pdb=" O GLUAv 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAv 116 " --> pdb=" O GLUAv 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALAv 117 " --> pdb=" O ALAAv 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALAv 123 " --> pdb=" O ASNAv 119 " (cutoff:3.500A) Processing helix chain 'Av' and resid 151 through 157 removed outlier: 3.930A pdb=" N GLUAv 156 " --> pdb=" O LYSAv 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAv 157 " --> pdb=" O PROAv 153 " (cutoff:3.500A) Processing helix chain 'Av' and resid 162 through 167 Processing helix chain 'Av' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAv 182 " --> pdb=" O GLUAv 178 " (cutoff:3.500A) Processing helix chain 'Av' and resid 188 through 194 Processing helix chain 'Av' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAv 203 " --> pdb=" O GLYAv 200 " (cutoff:3.500A) Processing helix chain 'Av' and resid 216 through 228 Processing helix chain 'Aw' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUAw 78 " --> pdb=" O ALAAw 74 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 92 through 107 Processing helix chain 'Aw' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAw 115 " --> pdb=" O GLUAw 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAw 116 " --> pdb=" O GLUAw 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAw 117 " --> pdb=" O ALAAw 113 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VALAw 123 " --> pdb=" O ASNAw 119 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAw 156 " --> pdb=" O LYSAw 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAw 157 " --> pdb=" O PROAw 153 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 162 through 167 Processing helix chain 'Aw' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAw 182 " --> pdb=" O GLUAw 178 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 188 through 194 Processing helix chain 'Aw' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAw 203 " --> pdb=" O GLYAw 200 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 216 through 228 Processing helix chain 'Ax' and resid 72 through 79 removed outlier: 3.718A pdb=" N GLUAx 78 " --> pdb=" O ALAAx 74 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 92 through 107 Processing helix chain 'Ax' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAx 115 " --> pdb=" O GLUAx 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAx 116 " --> pdb=" O GLUAx 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAx 117 " --> pdb=" O ALAAx 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAx 123 " --> pdb=" O ASNAx 119 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAx 156 " --> pdb=" O LYSAx 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAx 157 " --> pdb=" O PROAx 153 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 161 through 167 Processing helix chain 'Ax' and resid 169 through 182 removed outlier: 3.728A pdb=" N LYSAx 182 " --> pdb=" O GLUAx 178 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 188 through 194 Processing helix chain 'Ax' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAx 203 " --> pdb=" O GLYAx 200 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 216 through 228 Processing helix chain 'Ay' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAy 78 " --> pdb=" O ALAAy 74 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 92 through 107 Processing helix chain 'Ay' and resid 110 through 128 removed outlier: 3.672A pdb=" N GLYAy 115 " --> pdb=" O GLUAy 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THRAy 116 " --> pdb=" O GLUAy 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALAy 117 " --> pdb=" O ALAAy 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAy 123 " --> pdb=" O ASNAy 119 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 151 through 157 removed outlier: 3.932A pdb=" N GLUAy 156 " --> pdb=" O LYSAy 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNAy 157 " --> pdb=" O PROAy 153 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 161 through 167 Processing helix chain 'Ay' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAy 182 " --> pdb=" O GLUAy 178 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 188 through 194 Processing helix chain 'Ay' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGAy 203 " --> pdb=" O GLYAy 200 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 216 through 228 Processing helix chain 'Az' and resid 72 through 79 removed outlier: 3.720A pdb=" N GLUAz 78 " --> pdb=" O ALAAz 74 " (cutoff:3.500A) Processing helix chain 'Az' and resid 92 through 107 Processing helix chain 'Az' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYAz 115 " --> pdb=" O GLUAz 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRAz 116 " --> pdb=" O GLUAz 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALAz 117 " --> pdb=" O ALAAz 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALAz 123 " --> pdb=" O ASNAz 119 " (cutoff:3.500A) Processing helix chain 'Az' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUAz 156 " --> pdb=" O LYSAz 152 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASNAz 157 " --> pdb=" O PROAz 153 " (cutoff:3.500A) Processing helix chain 'Az' and resid 162 through 167 Processing helix chain 'Az' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSAz 182 " --> pdb=" O GLUAz 178 " (cutoff:3.500A) Processing helix chain 'Az' and resid 188 through 194 Processing helix chain 'Az' and resid 198 through 205 removed outlier: 3.797A pdb=" N ARGAz 203 " --> pdb=" O GLYAz 200 " (cutoff:3.500A) Processing helix chain 'Az' and resid 216 through 228 Processing helix chain 'Ba' and resid 72 through 79 removed outlier: 3.719A pdb=" N GLUBa 78 " --> pdb=" O ALABa 74 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 92 through 107 Processing helix chain 'Ba' and resid 110 through 128 removed outlier: 3.673A pdb=" N GLYBa 115 " --> pdb=" O GLUBa 111 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THRBa 116 " --> pdb=" O GLUBa 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALBa 117 " --> pdb=" O ALABa 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VALBa 123 " --> pdb=" O ASNBa 119 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 151 through 157 removed outlier: 3.931A pdb=" N GLUBa 156 " --> pdb=" O LYSBa 152 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASNBa 157 " --> pdb=" O PROBa 153 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 162 through 167 Processing helix chain 'Ba' and resid 169 through 182 removed outlier: 3.727A pdb=" N LYSBa 182 " --> pdb=" O GLUBa 178 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 188 through 194 Processing helix chain 'Ba' and resid 198 through 205 removed outlier: 3.796A pdb=" N ARGBa 203 " --> pdb=" O GLYBa 200 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 216 through 228 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAa 138 " --> pdb=" O PHEAa 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAa 147 " --> pdb=" O METAa 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ab' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAb 138 " --> pdb=" O PHEAb 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAb 147 " --> pdb=" O METAb 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ac' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAc 138 " --> pdb=" O PHEAc 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAc 147 " --> pdb=" O METAc 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ad' and resid 64 through 65 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAd 138 " --> pdb=" O PHEAd 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAd 147 " --> pdb=" O METAd 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ae' and resid 64 through 65 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAe 138 " --> pdb=" O PHEAe 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAe 147 " --> pdb=" O METAe 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Af' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'Af' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAf 138 " --> pdb=" O PHEAf 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAf 147 " --> pdb=" O METAf 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ag' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 137 through 141 removed outlier: 3.676A pdb=" N TRPAg 138 " --> pdb=" O PHEAg 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAg 147 " --> pdb=" O METAg 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ah' and resid 64 through 65 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAh 138 " --> pdb=" O PHEAh 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAh 147 " --> pdb=" O METAh 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ai' and resid 64 through 65 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAi 138 " --> pdb=" O PHEAi 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAi 147 " --> pdb=" O METAi 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Aj' and resid 64 through 65 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAj 138 " --> pdb=" O PHEAj 149 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VALAj 147 " --> pdb=" O METAj 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ak' and resid 64 through 65 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAk 138 " --> pdb=" O PHEAk 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAk 147 " --> pdb=" O METAk 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Al' and resid 64 through 65 Processing sheet with id=AC6, first strand: chain 'Al' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAl 138 " --> pdb=" O PHEAl 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAl 147 " --> pdb=" O METAl 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Am' and resid 64 through 65 Processing sheet with id=AC8, first strand: chain 'Am' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAm 138 " --> pdb=" O PHEAm 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAm 147 " --> pdb=" O METAm 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'An' and resid 64 through 65 Processing sheet with id=AD1, first strand: chain 'An' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAn 138 " --> pdb=" O PHEAn 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAn 147 " --> pdb=" O METAn 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Ao' and resid 64 through 65 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAo 138 " --> pdb=" O PHEAo 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAo 147 " --> pdb=" O METAo 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Ap' and resid 64 through 65 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAp 138 " --> pdb=" O PHEAp 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAp 147 " --> pdb=" O METAp 140 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Aq' and resid 64 through 65 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAq 138 " --> pdb=" O PHEAq 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAq 147 " --> pdb=" O METAq 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Ar' and resid 64 through 65 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAr 138 " --> pdb=" O PHEAr 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAr 147 " --> pdb=" O METAr 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'As' and resid 64 through 65 Processing sheet with id=AE2, first strand: chain 'As' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAs 138 " --> pdb=" O PHEAs 149 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VALAs 147 " --> pdb=" O METAs 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'At' and resid 64 through 65 Processing sheet with id=AE4, first strand: chain 'At' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAt 138 " --> pdb=" O PHEAt 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAt 147 " --> pdb=" O METAt 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Au' and resid 64 through 65 Processing sheet with id=AE6, first strand: chain 'Au' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAu 138 " --> pdb=" O PHEAu 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAu 147 " --> pdb=" O METAu 140 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Av' and resid 64 through 65 Processing sheet with id=AE8, first strand: chain 'Av' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAv 138 " --> pdb=" O PHEAv 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAv 147 " --> pdb=" O METAv 140 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Aw' and resid 64 through 65 Processing sheet with id=AF1, first strand: chain 'Aw' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAw 138 " --> pdb=" O PHEAw 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAw 147 " --> pdb=" O METAw 140 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Ax' and resid 64 through 65 Processing sheet with id=AF3, first strand: chain 'Ax' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPAx 138 " --> pdb=" O PHEAx 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALAx 147 " --> pdb=" O METAx 140 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Ay' and resid 64 through 65 Processing sheet with id=AF5, first strand: chain 'Ay' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAy 138 " --> pdb=" O PHEAy 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAy 147 " --> pdb=" O METAy 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Az' and resid 64 through 65 Processing sheet with id=AF7, first strand: chain 'Az' and resid 137 through 141 removed outlier: 3.675A pdb=" N TRPAz 138 " --> pdb=" O PHEAz 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALAz 147 " --> pdb=" O METAz 140 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Ba' and resid 64 through 65 Processing sheet with id=AF9, first strand: chain 'Ba' and resid 137 through 141 removed outlier: 3.674A pdb=" N TRPBa 138 " --> pdb=" O PHEBa 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VALBa 147 " --> pdb=" O METBa 140 " (cutoff:3.500A) 1574 hydrogen bonds defined for protein. 4317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7320 1.32 - 1.44: 10284 1.44 - 1.57: 23031 1.57 - 1.69: 0 1.69 - 1.81: 756 Bond restraints: 41391 Sorted by residual: bond pdb=" C GLUAg 184 " pdb=" N PROAg 185 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.12e-02 7.97e+03 1.19e+01 bond pdb=" N VALAy 84 " pdb=" CA VALAy 84 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.17e+01 bond pdb=" C GLUAk 184 " pdb=" N PROAk 185 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.12e-02 7.97e+03 1.17e+01 bond pdb=" N VALAu 84 " pdb=" CA VALAu 84 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.17e+01 bond pdb=" N VALAv 84 " pdb=" CA VALAv 84 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.17e+01 ... (remaining 41386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 41030 1.17 - 2.34: 9164 2.34 - 3.51: 3811 3.51 - 4.67: 1280 4.67 - 5.84: 497 Bond angle restraints: 55782 Sorted by residual: angle pdb=" N ASNAl 157 " pdb=" CA ASNAl 157 " pdb=" C ASNAl 157 " ideal model delta sigma weight residual 113.21 108.03 5.18 1.15e+00 7.56e-01 2.03e+01 angle pdb=" N ASNAp 157 " pdb=" CA ASNAp 157 " pdb=" C ASNAp 157 " ideal model delta sigma weight residual 113.21 108.03 5.18 1.15e+00 7.56e-01 2.03e+01 angle pdb=" N ASNAc 157 " pdb=" CA ASNAc 157 " pdb=" C ASNAc 157 " ideal model delta sigma weight residual 113.21 108.04 5.17 1.15e+00 7.56e-01 2.02e+01 angle pdb=" N ASNAu 157 " pdb=" CA ASNAu 157 " pdb=" C ASNAu 157 " ideal model delta sigma weight residual 113.21 108.05 5.16 1.15e+00 7.56e-01 2.01e+01 angle pdb=" N ASNAm 157 " pdb=" CA ASNAm 157 " pdb=" C ASNAm 157 " ideal model delta sigma weight residual 113.21 108.05 5.16 1.15e+00 7.56e-01 2.01e+01 ... (remaining 55777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 22518 16.85 - 33.70: 2349 33.70 - 50.54: 378 50.54 - 67.39: 189 67.39 - 84.24: 81 Dihedral angle restraints: 25515 sinusoidal: 10773 harmonic: 14742 Sorted by residual: dihedral pdb=" CA ASPAo 171 " pdb=" CB ASPAo 171 " pdb=" CG ASPAo 171 " pdb=" OD1 ASPAo 171 " ideal model delta sinusoidal sigma weight residual -30.00 -87.04 57.04 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASPAr 171 " pdb=" CB ASPAr 171 " pdb=" CG ASPAr 171 " pdb=" OD1 ASPAr 171 " ideal model delta sinusoidal sigma weight residual -30.00 -87.03 57.03 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASPAf 171 " pdb=" CB ASPAf 171 " pdb=" CG ASPAf 171 " pdb=" OD1 ASPAf 171 " ideal model delta sinusoidal sigma weight residual -30.00 -87.01 57.01 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 25512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3359 0.057 - 0.114: 1534 0.114 - 0.171: 608 0.171 - 0.228: 250 0.228 - 0.284: 189 Chirality restraints: 5940 Sorted by residual: chirality pdb=" CA ILEAy 50 " pdb=" N ILEAy 50 " pdb=" C ILEAy 50 " pdb=" CB ILEAy 50 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ILEAp 50 " pdb=" N ILEAp 50 " pdb=" C ILEAp 50 " pdb=" CB ILEAp 50 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA ILEAj 50 " pdb=" N ILEAj 50 " pdb=" C ILEAj 50 " pdb=" CB ILEAj 50 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 5937 not shown) Planarity restraints: 7209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALAAc 167 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ALAAc 167 " -0.040 2.00e-02 2.50e+03 pdb=" O ALAAc 167 " 0.015 2.00e-02 2.50e+03 pdb=" N HISAc 168 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAAu 167 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C ALAAu 167 " -0.039 2.00e-02 2.50e+03 pdb=" O ALAAu 167 " 0.014 2.00e-02 2.50e+03 pdb=" N HISAu 168 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAAw 167 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C ALAAw 167 " -0.039 2.00e-02 2.50e+03 pdb=" O ALAAw 167 " 0.014 2.00e-02 2.50e+03 pdb=" N HISAw 168 " 0.014 2.00e-02 2.50e+03 ... (remaining 7206 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 12761 2.83 - 3.35: 40489 3.35 - 3.86: 64620 3.86 - 4.38: 74023 4.38 - 4.90: 118702 Nonbonded interactions: 310595 Sorted by model distance: nonbonded pdb=" O ARGAm 214 " pdb=" OE1 GLUAv 156 " model vdw 2.310 3.040 nonbonded pdb=" O ARGAo 214 " pdb=" OE1 GLUAx 156 " model vdw 2.314 3.040 nonbonded pdb=" O ASPAt 144 " pdb=" OD1 ASPAt 144 " model vdw 2.314 3.040 nonbonded pdb=" O ASPAk 144 " pdb=" OD1 ASPAk 144 " model vdw 2.315 3.040 nonbonded pdb=" O ASPAf 144 " pdb=" OD1 ASPAf 144 " model vdw 2.315 3.040 ... (remaining 310590 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: 0.15 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.210 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.140 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.044 41391 Z= 0.736 Angle : 1.361 5.842 55782 Z= 0.983 Chirality : 0.089 0.284 5940 Planarity : 0.005 0.030 7209 Dihedral : 14.946 84.241 15957 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -4.15 (0.09), residues: 4941 helix: -2.38 (0.09), residues: 2025 sheet: None (None), residues: 0 loop : -3.19 (0.09), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAu 90 TYR 0.010 0.002 TYRAf 190 PHE 0.018 0.003 PHEAp 149 TRP 0.026 0.005 TRPAk 138 HIS 0.004 0.001 HISAb 168 Details of bonding type rmsd covalent geometry : bond 0.01031 (41391) covalent geometry : angle 1.36138 (55782) hydrogen bonds : bond 0.21771 ( 1574) hydrogen bonds : angle 7.76992 ( 4317) *********************** 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 2319 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2319 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 66 LYS cc_start: 0.9097 (mttm) cc_final: 0.8866 (mttm) REVERT: Aa 98 ASN cc_start: 0.8595 (t0) cc_final: 0.8109 (t0) REVERT: Aa 108 ASP cc_start: 0.8712 (t70) cc_final: 0.8346 (t0) REVERT: Aa 128 ASN cc_start: 0.8483 (t0) cc_final: 0.8159 (p0) REVERT: Aa 142 ASP cc_start: 0.8791 (t0) cc_final: 0.8570 (t0) REVERT: Aa 166 MET cc_start: 0.8119 (mmp) cc_final: 0.7543 (tpp) REVERT: Aa 190 TYR cc_start: 0.9030 (t80) cc_final: 0.8473 (t80) REVERT: Ab 50 ILE cc_start: 0.9534 (mm) cc_final: 0.9191 (tp) REVERT: Ab 108 ASP cc_start: 0.8688 (t70) cc_final: 0.8277 (t0) REVERT: Ab 162 PHE cc_start: 0.8845 (t80) cc_final: 0.8639 (t80) REVERT: Ab 166 MET cc_start: 0.8214 (mmp) cc_final: 0.7342 (tpp) REVERT: Ab 190 TYR cc_start: 0.8749 (t80) cc_final: 0.8380 (t80) REVERT: Ac 86 ILE cc_start: 0.9239 (mp) cc_final: 0.9033 (pt) REVERT: Ac 98 ASN cc_start: 0.8592 (t0) cc_final: 0.8345 (t0) REVERT: Ac 108 ASP cc_start: 0.8825 (t70) cc_final: 0.8535 (t0) REVERT: Ac 128 ASN cc_start: 0.8462 (t0) cc_final: 0.8215 (p0) REVERT: Ac 166 MET cc_start: 0.8279 (mmp) cc_final: 0.7457 (tpp) REVERT: Ac 190 TYR cc_start: 0.9004 (t80) cc_final: 0.8457 (t80) REVERT: Ac 199 MET cc_start: 0.8817 (tpp) cc_final: 0.8292 (tpp) REVERT: Ad 77 LEU cc_start: 0.8625 (mt) cc_final: 0.8290 (mt) REVERT: Ad 78 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7784 (mm-30) REVERT: Ad 79 TYR cc_start: 0.8320 (t80) cc_final: 0.8050 (t80) REVERT: Ad 86 ILE cc_start: 0.9338 (mp) cc_final: 0.8963 (pt) REVERT: Ad 98 ASN cc_start: 0.8482 (t0) cc_final: 0.8151 (t0) REVERT: Ad 108 ASP cc_start: 0.8792 (t70) cc_final: 0.8434 (t0) REVERT: Ad 142 ASP cc_start: 0.8900 (t0) cc_final: 0.8695 (t0) REVERT: Ad 166 MET cc_start: 0.8199 (mmp) cc_final: 0.7454 (tpp) REVERT: Ad 190 TYR cc_start: 0.8930 (t80) cc_final: 0.8557 (t80) REVERT: Ad 199 MET cc_start: 0.8944 (tpp) cc_final: 0.8558 (tpp) REVERT: Ad 226 MET cc_start: 0.8817 (mtm) cc_final: 0.8496 (mtp) REVERT: Ae 66 LYS cc_start: 0.9088 (mttm) cc_final: 0.8846 (mttm) REVERT: Ae 72 ASN cc_start: 0.8925 (t0) cc_final: 0.8615 (t0) REVERT: Ae 77 LEU cc_start: 0.8499 (mt) cc_final: 0.8122 (mt) REVERT: Ae 78 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7932 (mm-30) REVERT: Ae 98 ASN cc_start: 0.8609 (t0) cc_final: 0.8131 (t0) REVERT: Ae 108 ASP cc_start: 0.8816 (t70) cc_final: 0.8465 (t0) REVERT: Ae 128 ASN cc_start: 0.8461 (t0) cc_final: 0.7917 (p0) REVERT: Ae 142 ASP cc_start: 0.8857 (t0) cc_final: 0.8653 (t0) REVERT: Ae 166 MET cc_start: 0.8153 (mmp) cc_final: 0.7270 (tpp) REVERT: Ae 190 TYR cc_start: 0.8945 (t80) cc_final: 0.8583 (t80) REVERT: Ae 199 MET cc_start: 0.8833 (tpp) cc_final: 0.8224 (tpp) REVERT: Af 50 ILE cc_start: 0.9487 (mm) cc_final: 0.9140 (tp) REVERT: Af 72 ASN cc_start: 0.8951 (t0) cc_final: 0.8700 (t0) REVERT: Af 78 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8029 (mm-30) REVERT: Af 98 ASN cc_start: 0.8446 (t0) cc_final: 0.8101 (t0) REVERT: Af 108 ASP cc_start: 0.8698 (t70) cc_final: 0.8362 (t0) REVERT: Af 128 ASN cc_start: 0.8481 (t0) cc_final: 0.8271 (p0) REVERT: Af 166 MET cc_start: 0.8281 (mmp) cc_final: 0.7712 (tpp) REVERT: Af 190 TYR cc_start: 0.8986 (t80) cc_final: 0.8442 (t80) REVERT: Af 199 MET cc_start: 0.8860 (tpp) cc_final: 0.8363 (tpp) REVERT: Ag 50 ILE cc_start: 0.9534 (mm) cc_final: 0.9077 (tp) REVERT: Ag 72 ASN cc_start: 0.8936 (t0) cc_final: 0.8716 (t0) REVERT: Ag 77 LEU cc_start: 0.8409 (mt) cc_final: 0.8037 (mt) REVERT: Ag 78 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7894 (mm-30) REVERT: Ag 86 ILE cc_start: 0.9256 (mp) cc_final: 0.8895 (pt) REVERT: Ag 98 ASN cc_start: 0.8505 (t0) cc_final: 0.8094 (t0) REVERT: Ag 108 ASP cc_start: 0.8719 (t70) cc_final: 0.8355 (t0) REVERT: Ag 166 MET cc_start: 0.8190 (mmp) cc_final: 0.7385 (tpp) REVERT: Ag 190 TYR cc_start: 0.8830 (t80) cc_final: 0.8311 (t80) REVERT: Ag 199 MET cc_start: 0.8828 (tpp) cc_final: 0.8426 (tpp) REVERT: Ag 226 MET cc_start: 0.8889 (mtm) cc_final: 0.8651 (mtp) REVERT: Ah 79 TYR cc_start: 0.8170 (t80) cc_final: 0.7865 (t80) REVERT: Ah 98 ASN cc_start: 0.8539 (t0) cc_final: 0.8198 (t0) REVERT: Ah 108 ASP cc_start: 0.8819 (t70) cc_final: 0.8482 (t0) REVERT: Ah 142 ASP cc_start: 0.8894 (t0) cc_final: 0.8655 (t0) REVERT: Ah 166 MET cc_start: 0.8269 (mmp) cc_final: 0.7508 (tpp) REVERT: Ah 190 TYR cc_start: 0.9030 (t80) cc_final: 0.8684 (t80) REVERT: Ai 66 LYS cc_start: 0.9124 (mttm) cc_final: 0.8851 (mttm) REVERT: Ai 72 ASN cc_start: 0.8893 (t0) cc_final: 0.8505 (t0) REVERT: Ai 98 ASN cc_start: 0.8504 (t0) cc_final: 0.8069 (t0) REVERT: Ai 108 ASP cc_start: 0.8761 (t70) cc_final: 0.8451 (t0) REVERT: Ai 128 ASN cc_start: 0.8498 (t0) cc_final: 0.8084 (p0) REVERT: Ai 142 ASP cc_start: 0.8843 (t0) cc_final: 0.8620 (t0) REVERT: Ai 162 PHE cc_start: 0.8962 (t80) cc_final: 0.8713 (t80) REVERT: Ai 166 MET cc_start: 0.8268 (mmp) cc_final: 0.7534 (tpp) REVERT: Ai 190 TYR cc_start: 0.8974 (t80) cc_final: 0.8649 (t80) REVERT: Ai 199 MET cc_start: 0.8799 (tpp) cc_final: 0.8470 (tpp) REVERT: Ai 226 MET cc_start: 0.8882 (mtm) cc_final: 0.8676 (mtp) REVERT: Aj 72 ASN cc_start: 0.9052 (t0) cc_final: 0.8783 (t0) REVERT: Aj 79 TYR cc_start: 0.8441 (t80) cc_final: 0.7995 (t80) REVERT: Aj 98 ASN cc_start: 0.8318 (t0) cc_final: 0.7906 (t0) REVERT: Aj 166 MET cc_start: 0.7982 (mmp) cc_final: 0.7239 (tpp) REVERT: Aj 190 TYR cc_start: 0.9049 (t80) cc_final: 0.8675 (t80) REVERT: Aj 226 MET cc_start: 0.8912 (mtm) cc_final: 0.8420 (mtp) REVERT: Ak 77 LEU cc_start: 0.8171 (mt) cc_final: 0.7757 (mt) REVERT: Ak 78 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7871 (mm-30) REVERT: Ak 98 ASN cc_start: 0.8330 (t0) cc_final: 0.7966 (t0) REVERT: Ak 108 ASP cc_start: 0.8493 (t70) cc_final: 0.8161 (t0) REVERT: Ak 128 ASN cc_start: 0.8382 (t0) cc_final: 0.8149 (p0) REVERT: Ak 166 MET cc_start: 0.8125 (mmp) cc_final: 0.7405 (tpp) REVERT: Ak 190 TYR cc_start: 0.8819 (t80) cc_final: 0.8532 (t80) REVERT: Ak 226 MET cc_start: 0.8901 (mtm) cc_final: 0.8564 (mtp) REVERT: Al 72 ASN cc_start: 0.8937 (t0) cc_final: 0.8681 (t0) REVERT: Al 86 ILE cc_start: 0.9224 (mp) cc_final: 0.8837 (pt) REVERT: Al 98 ASN cc_start: 0.8429 (t0) cc_final: 0.8112 (t0) REVERT: Al 108 ASP cc_start: 0.8548 (t70) cc_final: 0.8290 (t0) REVERT: Al 166 MET cc_start: 0.7969 (mmp) cc_final: 0.7322 (tpp) REVERT: Al 190 TYR cc_start: 0.8820 (t80) cc_final: 0.8542 (t80) REVERT: Al 226 MET cc_start: 0.8963 (mtm) cc_final: 0.8643 (mtp) REVERT: Am 77 LEU cc_start: 0.8390 (mt) cc_final: 0.7983 (mt) REVERT: Am 78 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7784 (mm-30) REVERT: Am 98 ASN cc_start: 0.8400 (t0) cc_final: 0.8073 (t0) REVERT: Am 108 ASP cc_start: 0.8632 (t70) cc_final: 0.8295 (t0) REVERT: Am 116 THR cc_start: 0.8537 (t) cc_final: 0.8317 (t) REVERT: Am 166 MET cc_start: 0.8142 (mmp) cc_final: 0.7101 (tpp) REVERT: Am 199 MET cc_start: 0.8752 (tpp) cc_final: 0.8388 (tpp) REVERT: An 60 MET cc_start: 0.7264 (tpt) cc_final: 0.7043 (tpp) REVERT: An 72 ASN cc_start: 0.8963 (t0) cc_final: 0.8724 (t0) REVERT: An 98 ASN cc_start: 0.8451 (t0) cc_final: 0.8051 (t0) REVERT: An 108 ASP cc_start: 0.8572 (t70) cc_final: 0.8304 (t0) REVERT: An 166 MET cc_start: 0.8287 (mmp) cc_final: 0.7544 (tpp) REVERT: An 190 TYR cc_start: 0.8945 (t80) cc_final: 0.8521 (t80) REVERT: An 199 MET cc_start: 0.8752 (tpp) cc_final: 0.8046 (tpp) REVERT: An 226 MET cc_start: 0.8970 (mtm) cc_final: 0.8358 (mtp) REVERT: Ao 50 ILE cc_start: 0.9466 (mm) cc_final: 0.9072 (tp) REVERT: Ao 72 ASN cc_start: 0.8948 (t0) cc_final: 0.8709 (t0) REVERT: Ao 79 TYR cc_start: 0.8223 (t80) cc_final: 0.7910 (t80) REVERT: Ao 98 ASN cc_start: 0.8559 (t0) cc_final: 0.8098 (t0) REVERT: Ao 108 ASP cc_start: 0.8617 (t70) cc_final: 0.8372 (t0) REVERT: Ao 162 PHE cc_start: 0.8953 (t80) cc_final: 0.8364 (t80) REVERT: Ao 166 MET cc_start: 0.8086 (mmp) cc_final: 0.7516 (tpp) REVERT: Ao 190 TYR cc_start: 0.8946 (t80) cc_final: 0.8646 (t80) REVERT: Ao 199 MET cc_start: 0.8808 (tpp) cc_final: 0.8384 (tpp) REVERT: Ao 226 MET cc_start: 0.8957 (mtm) cc_final: 0.8681 (mtp) REVERT: Ap 60 MET cc_start: 0.7527 (tpt) cc_final: 0.7237 (tpp) REVERT: Ap 72 ASN cc_start: 0.8929 (t0) cc_final: 0.8696 (t0) REVERT: Ap 77 LEU cc_start: 0.8419 (mt) cc_final: 0.7970 (mt) REVERT: Ap 78 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8084 (mm-30) REVERT: Ap 86 ILE cc_start: 0.9237 (mp) cc_final: 0.8926 (pt) REVERT: Ap 98 ASN cc_start: 0.8453 (t0) cc_final: 0.8155 (t0) REVERT: Ap 108 ASP cc_start: 0.8657 (t70) cc_final: 0.8364 (t0) REVERT: Ap 128 ASN cc_start: 0.8393 (t0) cc_final: 0.8073 (p0) REVERT: Ap 140 MET cc_start: 0.6912 (ttm) cc_final: 0.6695 (ttm) REVERT: Ap 166 MET cc_start: 0.7969 (mmp) cc_final: 0.7161 (tpp) REVERT: Ap 190 TYR cc_start: 0.8877 (t80) cc_final: 0.8647 (t80) REVERT: Ap 199 MET cc_start: 0.8881 (tpp) cc_final: 0.8482 (tpp) REVERT: Aq 66 LYS cc_start: 0.9051 (mttm) cc_final: 0.8807 (mttp) REVERT: Aq 72 ASN cc_start: 0.9006 (t0) cc_final: 0.8551 (t0) REVERT: Aq 98 ASN cc_start: 0.8400 (t0) cc_final: 0.8099 (t0) REVERT: Aq 108 ASP cc_start: 0.8569 (t70) cc_final: 0.8303 (t0) REVERT: Aq 128 ASN cc_start: 0.8532 (t0) cc_final: 0.8268 (p0) REVERT: Aq 166 MET cc_start: 0.8057 (mmp) cc_final: 0.7281 (tpp) REVERT: Ar 50 ILE cc_start: 0.9540 (mm) cc_final: 0.9162 (tp) REVERT: Ar 72 ASN cc_start: 0.8966 (t0) cc_final: 0.8518 (t0) REVERT: Ar 98 ASN cc_start: 0.8347 (t0) cc_final: 0.7965 (t0) REVERT: Ar 108 ASP cc_start: 0.8559 (t70) cc_final: 0.8337 (t0) REVERT: Ar 166 MET cc_start: 0.7994 (mmp) cc_final: 0.7268 (tpp) REVERT: Ar 190 TYR cc_start: 0.9031 (t80) cc_final: 0.8751 (t80) REVERT: Ar 199 MET cc_start: 0.8781 (tpp) cc_final: 0.8558 (tpp) REVERT: As 60 MET cc_start: 0.7244 (tpt) cc_final: 0.7034 (tpp) REVERT: As 72 ASN cc_start: 0.8969 (t0) cc_final: 0.8654 (t0) REVERT: As 79 TYR cc_start: 0.8204 (t80) cc_final: 0.7843 (t80) REVERT: As 98 ASN cc_start: 0.8475 (t0) cc_final: 0.8103 (t0) REVERT: As 108 ASP cc_start: 0.8576 (t70) cc_final: 0.8370 (t0) REVERT: As 133 ASN cc_start: 0.7893 (p0) cc_final: 0.7685 (t0) REVERT: As 140 MET cc_start: 0.6932 (ttm) cc_final: 0.6527 (ttm) REVERT: As 142 ASP cc_start: 0.8734 (t0) cc_final: 0.8527 (t0) REVERT: As 190 TYR cc_start: 0.9042 (t80) cc_final: 0.8753 (t80) REVERT: As 218 ARG cc_start: 0.8888 (ttt90) cc_final: 0.8610 (ttm170) REVERT: As 226 MET cc_start: 0.8929 (mtm) cc_final: 0.8625 (mtp) REVERT: At 60 MET cc_start: 0.7676 (tpt) cc_final: 0.7406 (tpp) REVERT: At 76 LEU cc_start: 0.8420 (tp) cc_final: 0.8085 (tp) REVERT: At 77 LEU cc_start: 0.8232 (mt) cc_final: 0.7700 (mt) REVERT: At 78 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7808 (mm-30) REVERT: At 98 ASN cc_start: 0.8462 (t0) cc_final: 0.8045 (t0) REVERT: At 108 ASP cc_start: 0.8595 (t70) cc_final: 0.8330 (t0) REVERT: At 133 ASN cc_start: 0.7904 (p0) cc_final: 0.7546 (t0) REVERT: At 166 MET cc_start: 0.8028 (mmp) cc_final: 0.7493 (tpp) REVERT: At 218 ARG cc_start: 0.8992 (ttt90) cc_final: 0.8791 (ttm170) REVERT: Au 72 ASN cc_start: 0.9032 (t0) cc_final: 0.8820 (t0) REVERT: Au 79 TYR cc_start: 0.8193 (t80) cc_final: 0.7489 (t80) REVERT: Au 98 ASN cc_start: 0.8505 (t0) cc_final: 0.8081 (t0) REVERT: Au 108 ASP cc_start: 0.8751 (t70) cc_final: 0.8394 (t0) REVERT: Au 128 ASN cc_start: 0.8588 (t0) cc_final: 0.8210 (p0) REVERT: Au 162 PHE cc_start: 0.8906 (t80) cc_final: 0.8650 (t80) REVERT: Au 166 MET cc_start: 0.8101 (mmp) cc_final: 0.7514 (tpp) REVERT: Au 218 ARG cc_start: 0.8948 (ttt90) cc_final: 0.8657 (ttp-170) REVERT: Au 226 MET cc_start: 0.8919 (mtm) cc_final: 0.8635 (mtp) REVERT: Av 98 ASN cc_start: 0.8459 (t0) cc_final: 0.8075 (t0) REVERT: Av 128 ASN cc_start: 0.8486 (t0) cc_final: 0.7899 (p0) REVERT: Av 142 ASP cc_start: 0.8689 (t0) cc_final: 0.8438 (t0) REVERT: Av 166 MET cc_start: 0.8017 (mmp) cc_final: 0.7623 (tpp) REVERT: Av 188 PRO cc_start: 0.8647 (Cg_exo) cc_final: 0.8351 (Cg_endo) REVERT: Av 190 TYR cc_start: 0.9040 (t80) cc_final: 0.8690 (t80) REVERT: Av 199 MET cc_start: 0.8829 (tpp) cc_final: 0.8586 (tpp) REVERT: Av 226 MET cc_start: 0.8893 (mtm) cc_final: 0.8186 (mtp) REVERT: Aw 60 MET cc_start: 0.7308 (tpt) cc_final: 0.7044 (tpp) REVERT: Aw 72 ASN cc_start: 0.8974 (t0) cc_final: 0.8746 (t0) REVERT: Aw 79 TYR cc_start: 0.8180 (t80) cc_final: 0.7878 (t80) REVERT: Aw 98 ASN cc_start: 0.8462 (t0) cc_final: 0.8194 (t0) REVERT: Aw 108 ASP cc_start: 0.8631 (t70) cc_final: 0.8316 (t0) REVERT: Aw 128 ASN cc_start: 0.8533 (t0) cc_final: 0.8308 (p0) REVERT: Aw 166 MET cc_start: 0.8109 (mmp) cc_final: 0.7317 (tpp) REVERT: Aw 199 MET cc_start: 0.8907 (tpp) cc_final: 0.8570 (tpp) REVERT: Aw 226 MET cc_start: 0.8872 (mtm) cc_final: 0.8566 (mtp) REVERT: Ax 77 LEU cc_start: 0.8315 (mt) cc_final: 0.7983 (mt) REVERT: Ax 78 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7801 (mm-30) REVERT: Ax 98 ASN cc_start: 0.8443 (t0) cc_final: 0.7939 (t0) REVERT: Ax 111 GLU cc_start: 0.8309 (tp30) cc_final: 0.8109 (tp30) REVERT: Ax 166 MET cc_start: 0.7943 (mmp) cc_final: 0.7366 (tpp) REVERT: Ax 188 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.7861 (Cg_endo) REVERT: Ax 190 TYR cc_start: 0.8814 (t80) cc_final: 0.8353 (t80) REVERT: Ax 218 ARG cc_start: 0.8971 (ttt90) cc_final: 0.8767 (ttp-170) REVERT: Ay 72 ASN cc_start: 0.8961 (t0) cc_final: 0.8755 (t0) REVERT: Ay 77 LEU cc_start: 0.8299 (mt) cc_final: 0.8037 (mt) REVERT: Ay 98 ASN cc_start: 0.8466 (t0) cc_final: 0.8127 (t0) REVERT: Ay 108 ASP cc_start: 0.8629 (t70) cc_final: 0.8314 (t0) REVERT: Ay 128 ASN cc_start: 0.8435 (t0) cc_final: 0.8098 (p0) REVERT: Ay 140 MET cc_start: 0.6759 (ttm) cc_final: 0.6212 (ttm) REVERT: Ay 166 MET cc_start: 0.8145 (mmp) cc_final: 0.7509 (tpp) REVERT: Az 60 MET cc_start: 0.7019 (tpt) cc_final: 0.6794 (tpp) REVERT: Az 72 ASN cc_start: 0.9060 (t0) cc_final: 0.8848 (t0) REVERT: Az 79 TYR cc_start: 0.8265 (t80) cc_final: 0.7373 (t80) REVERT: Az 98 ASN cc_start: 0.8521 (t0) cc_final: 0.7918 (t0) REVERT: Az 108 ASP cc_start: 0.8665 (t70) cc_final: 0.8437 (t0) REVERT: Az 128 ASN cc_start: 0.8538 (t0) cc_final: 0.8198 (p0) REVERT: Az 166 MET cc_start: 0.8104 (mmp) cc_final: 0.7221 (tpp) REVERT: Az 190 TYR cc_start: 0.9065 (t80) cc_final: 0.8783 (t80) REVERT: Az 199 MET cc_start: 0.8739 (tpp) cc_final: 0.8328 (tpp) REVERT: Az 218 ARG cc_start: 0.8958 (ttt90) cc_final: 0.8715 (ttp-170) REVERT: Az 226 MET cc_start: 0.8967 (mtm) cc_final: 0.8377 (mtp) REVERT: Ba 72 ASN cc_start: 0.9064 (t0) cc_final: 0.8814 (t0) REVERT: Ba 79 TYR cc_start: 0.8376 (t80) cc_final: 0.7974 (t80) REVERT: Ba 98 ASN cc_start: 0.8503 (t0) cc_final: 0.8046 (t0) REVERT: Ba 108 ASP cc_start: 0.8660 (t70) cc_final: 0.8416 (t0) REVERT: Ba 128 ASN cc_start: 0.8437 (t0) cc_final: 0.8083 (p0) REVERT: Ba 166 MET cc_start: 0.8255 (mmp) cc_final: 0.7500 (tpp) REVERT: Ba 190 TYR cc_start: 0.9025 (t80) cc_final: 0.8821 (t80) outliers start: 0 outliers final: 0 residues processed: 2319 average time/residue: 0.2354 time to fit residues: 921.4065 Evaluate side-chains 1748 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1748 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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: 10.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 146 GLN Ab 146 GLN Ac 146 GLN Ad 146 GLN Ae 146 GLN Af 146 GLN Ag 146 GLN Ah 146 GLN ** Ai 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 146 GLN Aj 146 GLN Ak 146 GLN Al 146 GLN Am 146 GLN An 146 GLN Ao 146 GLN Ap 146 GLN Aq 146 GLN Ar 146 GLN As 146 GLN ** At 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 146 GLN Au 146 GLN Av 98 ASN ** Av 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 146 GLN Aw 146 GLN Ax 98 ASN ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 146 GLN ** Ay 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 146 GLN Az 146 GLN Ba 98 ASN Ba 146 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107451 restraints weight = 66092.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110789 restraints weight = 42908.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113206 restraints weight = 30728.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114990 restraints weight = 23588.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116363 restraints weight = 19063.828| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 41391 Z= 0.222 Angle : 0.659 5.888 55782 Z= 0.360 Chirality : 0.043 0.286 5940 Planarity : 0.005 0.057 7209 Dihedral : 4.579 21.605 5535 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.62 (0.12), residues: 4941 helix: -0.79 (0.10), residues: 2187 sheet: -0.48 (0.30), residues: 270 loop : -1.35 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAk 90 TYR 0.022 0.002 TYRAk 79 PHE 0.024 0.002 PHEAn 208 TRP 0.025 0.004 TRPAk 99 HIS 0.011 0.003 HISAw 168 Details of bonding type rmsd covalent geometry : bond 0.00498 (41391) covalent geometry : angle 0.65888 (55782) hydrogen bonds : bond 0.04092 ( 1574) hydrogen bonds : angle 4.86676 ( 4317) *********************** 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 2042 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2042 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Aa 98 ASN cc_start: 0.8660 (t0) cc_final: 0.8357 (t0) REVERT: Aa 110 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8900 (mm-40) REVERT: Aa 128 ASN cc_start: 0.8458 (t0) cc_final: 0.7985 (t0) REVERT: Aa 166 MET cc_start: 0.8029 (mmp) cc_final: 0.7594 (tpp) REVERT: Aa 190 TYR cc_start: 0.8788 (t80) cc_final: 0.8526 (t80) REVERT: Ab 76 LEU cc_start: 0.8401 (tp) cc_final: 0.7875 (tp) REVERT: Ab 91 SER cc_start: 0.8830 (m) cc_final: 0.8619 (t) REVERT: Ab 95 GLN cc_start: 0.8138 (mt0) cc_final: 0.7898 (mt0) REVERT: Ab 108 ASP cc_start: 0.8619 (t70) cc_final: 0.8351 (t0) REVERT: Ab 166 MET cc_start: 0.8073 (mmp) cc_final: 0.7659 (tpp) REVERT: Ab 190 TYR cc_start: 0.8698 (t80) cc_final: 0.8230 (t80) REVERT: Ab 196 LEU cc_start: 0.9034 (mt) cc_final: 0.8662 (mt) REVERT: Ac 76 LEU cc_start: 0.8534 (tp) cc_final: 0.8317 (tp) REVERT: Ac 83 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Ac 91 SER cc_start: 0.8812 (m) cc_final: 0.8600 (t) REVERT: Ac 95 GLN cc_start: 0.8389 (mt0) cc_final: 0.8032 (mt0) REVERT: Ac 98 ASN cc_start: 0.8620 (t0) cc_final: 0.8080 (t0) REVERT: Ac 142 ASP cc_start: 0.8642 (t0) cc_final: 0.8202 (t0) REVERT: Ac 166 MET cc_start: 0.8148 (mmp) cc_final: 0.7560 (tpp) REVERT: Ac 190 TYR cc_start: 0.8746 (t80) cc_final: 0.8428 (t80) REVERT: Ac 199 MET cc_start: 0.8760 (tpp) cc_final: 0.8495 (tpp) REVERT: Ac 207 ASP cc_start: 0.8465 (t70) cc_final: 0.8003 (t70) REVERT: Ad 50 ILE cc_start: 0.9440 (tp) cc_final: 0.8858 (tp) REVERT: Ad 72 ASN cc_start: 0.8743 (t0) cc_final: 0.8496 (t0) REVERT: Ad 76 LEU cc_start: 0.8399 (tp) cc_final: 0.7850 (tp) REVERT: Ad 108 ASP cc_start: 0.8672 (t70) cc_final: 0.8468 (t0) REVERT: Ad 128 ASN cc_start: 0.9218 (p0) cc_final: 0.8932 (p0) REVERT: Ad 142 ASP cc_start: 0.8888 (t0) cc_final: 0.8145 (t0) REVERT: Ad 166 MET cc_start: 0.8257 (mmp) cc_final: 0.7994 (tpp) REVERT: Ad 190 TYR cc_start: 0.8645 (t80) cc_final: 0.8188 (t80) REVERT: Ad 226 MET cc_start: 0.8884 (mtm) cc_final: 0.8623 (mtp) REVERT: Ae 72 ASN cc_start: 0.8684 (t0) cc_final: 0.8443 (t0) REVERT: Ae 76 LEU cc_start: 0.8529 (tp) cc_final: 0.7854 (tp) REVERT: Ae 80 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8527 (mtpp) REVERT: Ae 91 SER cc_start: 0.8883 (m) cc_final: 0.8644 (t) REVERT: Ae 98 ASN cc_start: 0.8448 (t0) cc_final: 0.8175 (t0) REVERT: Ae 105 LYS cc_start: 0.9134 (tppp) cc_final: 0.8809 (tppt) REVERT: Ae 108 ASP cc_start: 0.8714 (t70) cc_final: 0.8463 (t0) REVERT: Ae 122 MET cc_start: 0.9370 (ttm) cc_final: 0.9147 (ttp) REVERT: Ae 128 ASN cc_start: 0.8491 (t0) cc_final: 0.8192 (t0) REVERT: Ae 166 MET cc_start: 0.8227 (mmp) cc_final: 0.7332 (tpp) REVERT: Ae 190 TYR cc_start: 0.8702 (t80) cc_final: 0.8302 (t80) REVERT: Ae 199 MET cc_start: 0.8650 (tpp) cc_final: 0.8405 (tpp) REVERT: Ae 208 PHE cc_start: 0.8786 (p90) cc_final: 0.8443 (p90) REVERT: Af 76 LEU cc_start: 0.8483 (tp) cc_final: 0.7932 (tp) REVERT: Af 78 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7689 (mm-30) REVERT: Af 98 ASN cc_start: 0.8636 (t0) cc_final: 0.8402 (t0) REVERT: Af 105 LYS cc_start: 0.9257 (tppp) cc_final: 0.8841 (tppt) REVERT: Af 128 ASN cc_start: 0.8508 (t0) cc_final: 0.8244 (t0) REVERT: Af 142 ASP cc_start: 0.8624 (t0) cc_final: 0.8145 (t0) REVERT: Af 166 MET cc_start: 0.8134 (mmp) cc_final: 0.7882 (tpp) REVERT: Af 190 TYR cc_start: 0.8770 (t80) cc_final: 0.8495 (t80) REVERT: Af 195 ASN cc_start: 0.9065 (t0) cc_final: 0.8839 (t0) REVERT: Af 212 THR cc_start: 0.9481 (t) cc_final: 0.9129 (p) REVERT: Ag 76 LEU cc_start: 0.8421 (tp) cc_final: 0.7951 (tp) REVERT: Ag 83 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8362 (tm-30) REVERT: Ag 86 ILE cc_start: 0.9271 (mp) cc_final: 0.9029 (pt) REVERT: Ag 98 ASN cc_start: 0.8430 (t0) cc_final: 0.8097 (t0) REVERT: Ag 108 ASP cc_start: 0.8522 (t70) cc_final: 0.8320 (t0) REVERT: Ag 128 ASN cc_start: 0.9257 (p0) cc_final: 0.8998 (p0) REVERT: Ag 166 MET cc_start: 0.8204 (mmp) cc_final: 0.7584 (tpp) REVERT: Ag 190 TYR cc_start: 0.8618 (t80) cc_final: 0.8194 (t80) REVERT: Ag 195 ASN cc_start: 0.9177 (t0) cc_final: 0.8952 (t0) REVERT: Ag 199 MET cc_start: 0.8653 (tpp) cc_final: 0.8405 (tpp) REVERT: Ag 226 MET cc_start: 0.8932 (mtm) cc_final: 0.8627 (mtp) REVERT: Ah 83 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8292 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8511 (t0) cc_final: 0.8066 (t0) REVERT: Ah 141 MET cc_start: 0.7656 (tpp) cc_final: 0.7038 (tpp) REVERT: Ah 166 MET cc_start: 0.8302 (mmp) cc_final: 0.7785 (tpp) REVERT: Ah 190 TYR cc_start: 0.8710 (t80) cc_final: 0.8376 (t80) REVERT: Ah 192 LEU cc_start: 0.9559 (mt) cc_final: 0.9177 (mt) REVERT: Ai 76 LEU cc_start: 0.8498 (tp) cc_final: 0.7960 (tp) REVERT: Ai 80 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8654 (mtpp) REVERT: Ai 98 ASN cc_start: 0.8429 (t0) cc_final: 0.8167 (t0) REVERT: Ai 105 LYS cc_start: 0.9258 (tppp) cc_final: 0.8863 (tppt) REVERT: Ai 166 MET cc_start: 0.8277 (mmp) cc_final: 0.7568 (tpp) REVERT: Ai 190 TYR cc_start: 0.8836 (t80) cc_final: 0.8483 (t80) REVERT: Ai 208 PHE cc_start: 0.8752 (p90) cc_final: 0.8510 (p90) REVERT: Ai 226 MET cc_start: 0.8975 (mtm) cc_final: 0.8705 (mtp) REVERT: Aj 50 ILE cc_start: 0.9294 (tp) cc_final: 0.8662 (tp) REVERT: Aj 83 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8167 (tm-30) REVERT: Aj 98 ASN cc_start: 0.8466 (t0) cc_final: 0.7892 (t0) REVERT: Aj 142 ASP cc_start: 0.8815 (t0) cc_final: 0.8240 (t0) REVERT: Aj 146 GLN cc_start: 0.8531 (pt0) cc_final: 0.8106 (pt0) REVERT: Aj 166 MET cc_start: 0.8210 (mmp) cc_final: 0.7712 (tpp) REVERT: Aj 187 MET cc_start: 0.8096 (tmm) cc_final: 0.7604 (tmm) REVERT: Aj 190 TYR cc_start: 0.8787 (t80) cc_final: 0.8535 (t80) REVERT: Aj 226 MET cc_start: 0.8910 (mtm) cc_final: 0.8697 (mtp) REVERT: Ak 98 ASN cc_start: 0.8448 (t0) cc_final: 0.7738 (t0) REVERT: Ak 121 LEU cc_start: 0.9529 (tp) cc_final: 0.9108 (tp) REVERT: Ak 166 MET cc_start: 0.8386 (mmp) cc_final: 0.7752 (tpp) REVERT: Ak 187 MET cc_start: 0.7849 (ttm) cc_final: 0.7542 (ttm) REVERT: Ak 199 MET cc_start: 0.8694 (tpp) cc_final: 0.8481 (tpp) REVERT: Ak 207 ASP cc_start: 0.8582 (p0) cc_final: 0.7885 (t0) REVERT: Al 72 ASN cc_start: 0.8758 (t0) cc_final: 0.8455 (t0) REVERT: Al 78 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7890 (tm-30) REVERT: Al 83 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8248 (tm-30) REVERT: Al 98 ASN cc_start: 0.8582 (t0) cc_final: 0.8271 (t0) REVERT: Al 121 LEU cc_start: 0.9205 (tt) cc_final: 0.9001 (tt) REVERT: Al 166 MET cc_start: 0.8400 (mmp) cc_final: 0.7568 (tpp) REVERT: Al 190 TYR cc_start: 0.8584 (t80) cc_final: 0.8334 (t80) REVERT: Al 192 LEU cc_start: 0.9462 (mm) cc_final: 0.8676 (mm) REVERT: Al 199 MET cc_start: 0.8785 (tpp) cc_final: 0.8438 (tpp) REVERT: Al 226 MET cc_start: 0.9082 (mtm) cc_final: 0.8768 (mtp) REVERT: Am 83 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8060 (tm-30) REVERT: Am 98 ASN cc_start: 0.8583 (t0) cc_final: 0.7867 (t0) REVERT: An 72 ASN cc_start: 0.8695 (t0) cc_final: 0.8449 (t0) REVERT: An 98 ASN cc_start: 0.8520 (t0) cc_final: 0.7854 (t0) REVERT: An 141 MET cc_start: 0.7589 (tpp) cc_final: 0.7099 (tpp) REVERT: An 142 ASP cc_start: 0.8932 (t0) cc_final: 0.8656 (t70) REVERT: An 146 GLN cc_start: 0.8595 (pt0) cc_final: 0.8249 (pt0) REVERT: An 166 MET cc_start: 0.8257 (mmp) cc_final: 0.7579 (tpp) REVERT: An 187 MET cc_start: 0.8108 (ttm) cc_final: 0.7827 (ttm) REVERT: An 199 MET cc_start: 0.8606 (tpp) cc_final: 0.8248 (tpp) REVERT: An 207 ASP cc_start: 0.8674 (p0) cc_final: 0.7904 (t0) REVERT: An 226 MET cc_start: 0.9045 (mtm) cc_final: 0.8726 (mtp) REVERT: Ao 72 ASN cc_start: 0.8821 (t0) cc_final: 0.8555 (t0) REVERT: Ao 98 ASN cc_start: 0.8582 (t0) cc_final: 0.7932 (t0) REVERT: Ao 142 ASP cc_start: 0.8842 (t0) cc_final: 0.8168 (t0) REVERT: Ao 166 MET cc_start: 0.8220 (mmp) cc_final: 0.7843 (tpp) REVERT: Ao 187 MET cc_start: 0.8092 (ttm) cc_final: 0.7619 (ttm) REVERT: Ap 72 ASN cc_start: 0.8714 (t0) cc_final: 0.8510 (t0) REVERT: Ap 83 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8029 (tm-30) REVERT: Ap 91 SER cc_start: 0.8810 (m) cc_final: 0.8470 (t) REVERT: Ap 95 GLN cc_start: 0.8294 (mt0) cc_final: 0.7817 (mt0) REVERT: Ap 98 ASN cc_start: 0.8583 (t0) cc_final: 0.8032 (t0) REVERT: Ap 207 ASP cc_start: 0.8685 (p0) cc_final: 0.7983 (t0) REVERT: Aq 50 ILE cc_start: 0.9386 (tp) cc_final: 0.9119 (mm) REVERT: Aq 72 ASN cc_start: 0.8593 (t0) cc_final: 0.8241 (t0) REVERT: Aq 98 ASN cc_start: 0.8545 (t0) cc_final: 0.7838 (t0) REVERT: Aq 128 ASN cc_start: 0.8519 (t0) cc_final: 0.8154 (t0) REVERT: Aq 141 MET cc_start: 0.7342 (tpp) cc_final: 0.6303 (tpp) REVERT: Aq 142 ASP cc_start: 0.8614 (t0) cc_final: 0.8148 (t0) REVERT: Aq 187 MET cc_start: 0.7803 (ttm) cc_final: 0.7230 (ttm) REVERT: Aq 199 MET cc_start: 0.8778 (tpp) cc_final: 0.8317 (tpp) REVERT: Ar 72 ASN cc_start: 0.8821 (t0) cc_final: 0.8554 (t0) REVERT: Ar 83 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8344 (tm-30) REVERT: Ar 98 ASN cc_start: 0.8457 (t0) cc_final: 0.7807 (t0) REVERT: Ar 122 MET cc_start: 0.9441 (ttm) cc_final: 0.9241 (ttp) REVERT: Ar 133 ASN cc_start: 0.8322 (p0) cc_final: 0.8055 (t0) REVERT: Ar 141 MET cc_start: 0.7565 (tpp) cc_final: 0.7263 (tpp) REVERT: Ar 142 ASP cc_start: 0.8792 (t0) cc_final: 0.8266 (t70) REVERT: Ar 166 MET cc_start: 0.8233 (mmp) cc_final: 0.7485 (tpp) REVERT: Ar 199 MET cc_start: 0.8718 (tpp) cc_final: 0.8496 (tpp) REVERT: Ar 207 ASP cc_start: 0.8785 (p0) cc_final: 0.8125 (t0) REVERT: Ar 208 PHE cc_start: 0.8714 (p90) cc_final: 0.8464 (p90) REVERT: As 58 GLU cc_start: 0.8615 (mp0) cc_final: 0.8225 (mp0) REVERT: As 72 ASN cc_start: 0.8865 (t0) cc_final: 0.8534 (t0) REVERT: As 79 TYR cc_start: 0.8153 (t80) cc_final: 0.7807 (t80) REVERT: As 83 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8336 (tm-30) REVERT: As 98 ASN cc_start: 0.8518 (t0) cc_final: 0.8167 (t0) REVERT: As 110 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8906 (mm-40) REVERT: As 111 GLU cc_start: 0.8468 (tp30) cc_final: 0.8209 (tp30) REVERT: As 166 MET cc_start: 0.8003 (tpp) cc_final: 0.7687 (tpp) REVERT: As 187 MET cc_start: 0.8180 (tmm) cc_final: 0.7587 (tmm) REVERT: As 190 TYR cc_start: 0.8819 (t80) cc_final: 0.8563 (t80) REVERT: As 192 LEU cc_start: 0.9504 (mt) cc_final: 0.9097 (mt) REVERT: As 226 MET cc_start: 0.8992 (mtm) cc_final: 0.8691 (mtp) REVERT: At 58 GLU cc_start: 0.8557 (mp0) cc_final: 0.8176 (mp0) REVERT: At 76 LEU cc_start: 0.8324 (tp) cc_final: 0.8096 (tp) REVERT: At 79 TYR cc_start: 0.8062 (t80) cc_final: 0.7763 (t80) REVERT: At 83 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8167 (tm-30) REVERT: At 91 SER cc_start: 0.8882 (m) cc_final: 0.8593 (t) REVERT: At 98 ASN cc_start: 0.8650 (t0) cc_final: 0.8056 (t0) REVERT: At 121 LEU cc_start: 0.9551 (tp) cc_final: 0.9183 (tt) REVERT: At 122 MET cc_start: 0.9472 (ttm) cc_final: 0.8971 (tpp) REVERT: At 159 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8347 (mtmt) REVERT: At 166 MET cc_start: 0.8193 (mmp) cc_final: 0.7777 (tpp) REVERT: At 218 ARG cc_start: 0.9007 (ttt90) cc_final: 0.8780 (ttm170) REVERT: At 226 MET cc_start: 0.8632 (mtp) cc_final: 0.8430 (mtp) REVERT: Au 58 GLU cc_start: 0.8795 (mp0) cc_final: 0.8352 (mp0) REVERT: Au 79 TYR cc_start: 0.8105 (t80) cc_final: 0.7369 (t80) REVERT: Au 83 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8014 (tm-30) REVERT: Au 98 ASN cc_start: 0.8696 (t0) cc_final: 0.8249 (t0) REVERT: Au 111 GLU cc_start: 0.8499 (tp30) cc_final: 0.8060 (tp30) REVERT: Au 133 ASN cc_start: 0.8175 (p0) cc_final: 0.7926 (t0) REVERT: Au 142 ASP cc_start: 0.8775 (t0) cc_final: 0.8315 (t0) REVERT: Au 159 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8284 (mtmm) REVERT: Au 166 MET cc_start: 0.8238 (mmp) cc_final: 0.7731 (tpp) REVERT: Au 190 TYR cc_start: 0.8819 (t80) cc_final: 0.8614 (t80) REVERT: Au 212 THR cc_start: 0.9364 (t) cc_final: 0.8903 (p) REVERT: Au 218 ARG cc_start: 0.9073 (ttt90) cc_final: 0.8707 (ttp-170) REVERT: Au 226 MET cc_start: 0.8984 (mtm) cc_final: 0.8606 (mtm) REVERT: Av 58 GLU cc_start: 0.8745 (mp0) cc_final: 0.8293 (mp0) REVERT: Av 76 LEU cc_start: 0.8447 (tp) cc_final: 0.8201 (tp) REVERT: Av 79 TYR cc_start: 0.8104 (t80) cc_final: 0.7827 (t80) REVERT: Av 91 SER cc_start: 0.8922 (m) cc_final: 0.8683 (t) REVERT: Av 98 ASN cc_start: 0.8526 (t0) cc_final: 0.7845 (t0) REVERT: Av 128 ASN cc_start: 0.8495 (t0) cc_final: 0.8209 (t0) REVERT: Av 166 MET cc_start: 0.8295 (mmp) cc_final: 0.7905 (tpp) REVERT: Av 187 MET cc_start: 0.8265 (tmm) cc_final: 0.8063 (tmm) REVERT: Av 190 TYR cc_start: 0.8790 (t80) cc_final: 0.8471 (t80) REVERT: Av 218 ARG cc_start: 0.8856 (ttt90) cc_final: 0.8615 (ttp-170) REVERT: Av 226 MET cc_start: 0.8999 (mtm) cc_final: 0.8677 (mtp) REVERT: Aw 58 GLU cc_start: 0.8622 (mp0) cc_final: 0.8310 (mp0) REVERT: Aw 83 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8276 (tm-30) REVERT: Aw 95 GLN cc_start: 0.8174 (mt0) cc_final: 0.7955 (mt0) REVERT: Aw 98 ASN cc_start: 0.8587 (t0) cc_final: 0.8358 (t0) REVERT: Aw 110 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8784 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8656 (t0) cc_final: 0.8450 (t0) REVERT: Aw 142 ASP cc_start: 0.8745 (t0) cc_final: 0.8399 (t0) REVERT: Aw 166 MET cc_start: 0.8338 (mmp) cc_final: 0.7398 (tpp) REVERT: Aw 187 MET cc_start: 0.8021 (tmm) cc_final: 0.7482 (tmm) REVERT: Aw 190 TYR cc_start: 0.8759 (t80) cc_final: 0.8494 (t80) REVERT: Aw 196 LEU cc_start: 0.9449 (mt) cc_final: 0.9215 (mt) REVERT: Aw 199 MET cc_start: 0.8704 (tpp) cc_final: 0.8401 (tpp) REVERT: Aw 226 MET cc_start: 0.8993 (mtm) cc_final: 0.8643 (mtp) REVERT: Ax 58 GLU cc_start: 0.8612 (mp0) cc_final: 0.8251 (mp0) REVERT: Ax 76 LEU cc_start: 0.8387 (tp) cc_final: 0.8097 (tp) REVERT: Ax 83 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8384 (tm-30) REVERT: Ax 98 ASN cc_start: 0.8463 (t0) cc_final: 0.7795 (t0) REVERT: Ax 166 MET cc_start: 0.8187 (mmp) cc_final: 0.7929 (tpp) REVERT: Ax 187 MET cc_start: 0.8241 (tmm) cc_final: 0.7212 (tmm) REVERT: Ax 190 TYR cc_start: 0.8399 (t80) cc_final: 0.7731 (t80) REVERT: Ax 218 ARG cc_start: 0.9044 (ttt90) cc_final: 0.8428 (ttm170) REVERT: Ay 58 GLU cc_start: 0.8621 (mp0) cc_final: 0.8217 (mp0) REVERT: Ay 72 ASN cc_start: 0.8658 (t0) cc_final: 0.8425 (t0) REVERT: Ay 76 LEU cc_start: 0.8322 (tp) cc_final: 0.8099 (tp) REVERT: Ay 79 TYR cc_start: 0.8172 (t80) cc_final: 0.7882 (t80) REVERT: Ay 83 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8278 (tm-30) REVERT: Ay 98 ASN cc_start: 0.8541 (t0) cc_final: 0.7856 (t0) REVERT: Ay 122 MET cc_start: 0.9471 (ttm) cc_final: 0.9267 (ttp) REVERT: Ay 141 MET cc_start: 0.7518 (tpt) cc_final: 0.7192 (tpt) REVERT: Ay 166 MET cc_start: 0.8208 (mmp) cc_final: 0.7681 (tpp) REVERT: Ay 190 TYR cc_start: 0.8600 (t80) cc_final: 0.8302 (t80) REVERT: Ay 192 LEU cc_start: 0.9506 (mm) cc_final: 0.9060 (mm) REVERT: Ay 218 ARG cc_start: 0.9105 (ttt90) cc_final: 0.8837 (ttm170) REVERT: Az 58 GLU cc_start: 0.8652 (mp0) cc_final: 0.8358 (mp0) REVERT: Az 79 TYR cc_start: 0.8173 (t80) cc_final: 0.7324 (t80) REVERT: Az 91 SER cc_start: 0.8888 (m) cc_final: 0.8643 (t) REVERT: Az 98 ASN cc_start: 0.8552 (t0) cc_final: 0.7924 (t0) REVERT: Az 141 MET cc_start: 0.7834 (tpp) cc_final: 0.7339 (tpp) REVERT: Az 142 ASP cc_start: 0.8931 (t0) cc_final: 0.8317 (t0) REVERT: Az 146 GLN cc_start: 0.8672 (pt0) cc_final: 0.8120 (pt0) REVERT: Az 166 MET cc_start: 0.8428 (mmp) cc_final: 0.7945 (tpp) REVERT: Az 187 MET cc_start: 0.8038 (ttm) cc_final: 0.7476 (mtp) REVERT: Az 190 TYR cc_start: 0.8874 (t80) cc_final: 0.8603 (t80) REVERT: Az 199 MET cc_start: 0.8637 (tpp) cc_final: 0.8254 (tpp) REVERT: Az 218 ARG cc_start: 0.9002 (ttt90) cc_final: 0.8744 (ttp-170) REVERT: Az 226 MET cc_start: 0.9061 (mtm) cc_final: 0.8715 (mtm) REVERT: Ba 58 GLU cc_start: 0.8802 (mp0) cc_final: 0.8397 (mp0) REVERT: Ba 72 ASN cc_start: 0.8848 (t0) cc_final: 0.8546 (t0) REVERT: Ba 76 LEU cc_start: 0.8528 (tp) cc_final: 0.8300 (tp) REVERT: Ba 79 TYR cc_start: 0.8225 (t80) cc_final: 0.7862 (t80) REVERT: Ba 98 ASN cc_start: 0.8485 (t0) cc_final: 0.7916 (t0) REVERT: Ba 128 ASN cc_start: 0.8616 (t0) cc_final: 0.8344 (t0) REVERT: Ba 166 MET cc_start: 0.8305 (mmp) cc_final: 0.7712 (tpp) REVERT: Ba 190 TYR cc_start: 0.8785 (t80) cc_final: 0.8516 (t80) outliers start: 0 outliers final: 0 residues processed: 2042 average time/residue: 0.2166 time to fit residues: 768.0130 Evaluate side-chains 1546 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1546 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 299 optimal weight: 0.9990 chunk 322 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 418 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 128 ASN Ab 146 GLN Ac 75 HIS Ac 146 GLN Ad 75 HIS Ad 146 GLN Ae 146 GLN Af 75 HIS Af 146 GLN Ag 146 GLN Ah 75 HIS Ah 146 GLN Ai 75 HIS ** Ai 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 146 GLN Aj 88 ASN Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Al 75 HIS Al 146 GLN Am 75 HIS Am 146 GLN An 146 GLN ** Ao 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 88 ASN Ao 128 ASN Ao 146 GLN Ap 75 HIS Ap 146 GLN Aq 75 HIS Aq 146 GLN Ar 128 ASN Ar 146 GLN As 128 ASN As 146 GLN At 88 ASN At 128 ASN At 146 GLN Au 146 GLN Av 146 GLN Aw 146 GLN Ax 128 ASN Ax 146 GLN Ay 88 ASN Ay 98 ASN Ay 146 GLN ** Az 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 146 GLN Ba 75 HIS Ba 146 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103294 restraints weight = 66585.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106307 restraints weight = 44704.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108505 restraints weight = 32901.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110083 restraints weight = 25912.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111367 restraints weight = 21475.652| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41391 Z= 0.164 Angle : 0.615 5.858 55782 Z= 0.328 Chirality : 0.040 0.257 5940 Planarity : 0.005 0.042 7209 Dihedral : 4.404 20.374 5535 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 4941 helix: 0.41 (0.11), residues: 2160 sheet: 0.45 (0.36), residues: 270 loop : -0.97 (0.13), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAp 218 TYR 0.038 0.002 TYRAu 204 PHE 0.017 0.002 PHEAn 208 TRP 0.022 0.003 TRPAi 99 HIS 0.006 0.001 HISAy 168 Details of bonding type rmsd covalent geometry : bond 0.00375 (41391) covalent geometry : angle 0.61475 (55782) hydrogen bonds : bond 0.03549 ( 1574) hydrogen bonds : angle 4.27037 ( 4317) *********************** 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 1820 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1815 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8435 (tm-30) REVERT: Aa 95 GLN cc_start: 0.8377 (mt0) cc_final: 0.8139 (mt0) REVERT: Aa 128 ASN cc_start: 0.8508 (t0) cc_final: 0.8155 (t0) REVERT: Aa 141 MET cc_start: 0.8457 (mmt) cc_final: 0.7881 (tpp) REVERT: Aa 166 MET cc_start: 0.8053 (mmp) cc_final: 0.7406 (tpp) REVERT: Aa 187 MET cc_start: 0.8089 (ttm) cc_final: 0.6912 (mtp) REVERT: Aa 190 TYR cc_start: 0.8780 (t80) cc_final: 0.8219 (t80) REVERT: Aa 199 MET cc_start: 0.8770 (tpp) cc_final: 0.7613 (tpp) REVERT: Ab 76 LEU cc_start: 0.8234 (tp) cc_final: 0.7753 (tp) REVERT: Ab 83 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8377 (tm-30) REVERT: Ab 108 ASP cc_start: 0.8648 (t70) cc_final: 0.8389 (t0) REVERT: Ab 141 MET cc_start: 0.7656 (tpt) cc_final: 0.7402 (tpt) REVERT: Ab 166 MET cc_start: 0.8206 (mmp) cc_final: 0.7685 (tpp) REVERT: Ab 190 TYR cc_start: 0.8507 (t80) cc_final: 0.8144 (t80) REVERT: Ab 196 LEU cc_start: 0.9113 (mt) cc_final: 0.8759 (mt) REVERT: Ac 83 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8292 (tm-30) REVERT: Ac 141 MET cc_start: 0.7677 (tpt) cc_final: 0.7301 (tpt) REVERT: Ac 142 ASP cc_start: 0.8705 (t0) cc_final: 0.8355 (t0) REVERT: Ac 166 MET cc_start: 0.8184 (mmp) cc_final: 0.7571 (tpp) REVERT: Ac 187 MET cc_start: 0.7961 (ttm) cc_final: 0.7008 (mtp) REVERT: Ac 190 TYR cc_start: 0.8579 (t80) cc_final: 0.8148 (t80) REVERT: Ac 199 MET cc_start: 0.8703 (tpp) cc_final: 0.8102 (tpp) REVERT: Ad 72 ASN cc_start: 0.8823 (t0) cc_final: 0.8464 (t0) REVERT: Ad 76 LEU cc_start: 0.8215 (tp) cc_final: 0.7736 (tp) REVERT: Ad 83 GLN cc_start: 0.8628 (pt0) cc_final: 0.8272 (tm-30) REVERT: Ad 118 MET cc_start: 0.8813 (mmm) cc_final: 0.8609 (mmm) REVERT: Ad 128 ASN cc_start: 0.9254 (p0) cc_final: 0.9037 (p0) REVERT: Ad 141 MET cc_start: 0.7724 (tpt) cc_final: 0.7490 (tpt) REVERT: Ad 166 MET cc_start: 0.8222 (mmp) cc_final: 0.7687 (tpp) REVERT: Ad 190 TYR cc_start: 0.8660 (t80) cc_final: 0.7966 (t80) REVERT: Ae 70 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (p) REVERT: Ae 72 ASN cc_start: 0.8823 (t0) cc_final: 0.8546 (t0) REVERT: Ae 76 LEU cc_start: 0.8424 (tp) cc_final: 0.7961 (tp) REVERT: Ae 83 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8172 (tm-30) REVERT: Ae 108 ASP cc_start: 0.8809 (t70) cc_final: 0.8599 (t0) REVERT: Ae 128 ASN cc_start: 0.8660 (t0) cc_final: 0.8397 (t0) REVERT: Ae 166 MET cc_start: 0.8208 (mmp) cc_final: 0.7488 (tpp) REVERT: Ae 187 MET cc_start: 0.8056 (ttm) cc_final: 0.7816 (ttm) REVERT: Ae 190 TYR cc_start: 0.8729 (t80) cc_final: 0.8188 (t80) REVERT: Ae 199 MET cc_start: 0.8717 (tpp) cc_final: 0.8437 (tpp) REVERT: Af 60 MET cc_start: 0.8015 (tpp) cc_final: 0.7741 (tpp) REVERT: Af 76 LEU cc_start: 0.8253 (tp) cc_final: 0.7774 (tp) REVERT: Af 83 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7853 (tm-30) REVERT: Af 95 GLN cc_start: 0.8374 (mt0) cc_final: 0.8107 (mt0) REVERT: Af 98 ASN cc_start: 0.8693 (t0) cc_final: 0.8429 (t0) REVERT: Af 128 ASN cc_start: 0.8495 (t0) cc_final: 0.8202 (t0) REVERT: Af 141 MET cc_start: 0.7749 (tpt) cc_final: 0.7453 (tpt) REVERT: Af 142 ASP cc_start: 0.8681 (t0) cc_final: 0.8378 (t0) REVERT: Af 166 MET cc_start: 0.8249 (mmp) cc_final: 0.7908 (tpp) REVERT: Af 190 TYR cc_start: 0.8662 (t80) cc_final: 0.8360 (t80) REVERT: Af 195 ASN cc_start: 0.9121 (t0) cc_final: 0.8896 (t0) REVERT: Af 212 THR cc_start: 0.9525 (t) cc_final: 0.9046 (p) REVERT: Ag 76 LEU cc_start: 0.8346 (tp) cc_final: 0.8007 (tp) REVERT: Ag 83 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8433 (tm-30) REVERT: Ag 86 ILE cc_start: 0.9269 (mp) cc_final: 0.8926 (pt) REVERT: Ag 98 ASN cc_start: 0.8455 (t0) cc_final: 0.8092 (t0) REVERT: Ag 128 ASN cc_start: 0.9248 (p0) cc_final: 0.9019 (p0) REVERT: Ag 141 MET cc_start: 0.7675 (tpt) cc_final: 0.7411 (tpt) REVERT: Ag 166 MET cc_start: 0.8335 (mmp) cc_final: 0.7787 (tpp) REVERT: Ag 188 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8575 (Cg_endo) REVERT: Ag 190 TYR cc_start: 0.8573 (t80) cc_final: 0.8040 (t80) REVERT: Ag 195 ASN cc_start: 0.9245 (t0) cc_final: 0.9000 (t0) REVERT: Ah 83 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8367 (tm-30) REVERT: Ah 95 GLN cc_start: 0.8429 (mt0) cc_final: 0.8178 (mt0) REVERT: Ah 98 ASN cc_start: 0.8563 (t0) cc_final: 0.7995 (t0) REVERT: Ah 122 MET cc_start: 0.9476 (ttm) cc_final: 0.9274 (ttp) REVERT: Ah 141 MET cc_start: 0.7668 (tpp) cc_final: 0.7160 (tpp) REVERT: Ah 166 MET cc_start: 0.8332 (mmp) cc_final: 0.7664 (tpp) REVERT: Ah 190 TYR cc_start: 0.8510 (t80) cc_final: 0.8203 (t80) REVERT: Ai 95 GLN cc_start: 0.8271 (mt0) cc_final: 0.7980 (mt0) REVERT: Ai 98 ASN cc_start: 0.8494 (t0) cc_final: 0.8230 (t0) REVERT: Ai 112 GLU cc_start: 0.8723 (pp20) cc_final: 0.8479 (tm-30) REVERT: Ai 166 MET cc_start: 0.8337 (mmp) cc_final: 0.7617 (tpp) REVERT: Ai 190 TYR cc_start: 0.8759 (t80) cc_final: 0.8547 (t80) REVERT: Aj 60 MET cc_start: 0.7735 (tpp) cc_final: 0.7501 (tpp) REVERT: Aj 79 TYR cc_start: 0.8039 (t80) cc_final: 0.7769 (t80) REVERT: Aj 98 ASN cc_start: 0.8565 (t0) cc_final: 0.7890 (t0) REVERT: Aj 142 ASP cc_start: 0.8725 (t0) cc_final: 0.8253 (t0) REVERT: Aj 166 MET cc_start: 0.8368 (mmp) cc_final: 0.7665 (tpp) REVERT: Aj 187 MET cc_start: 0.8160 (tmm) cc_final: 0.7695 (tmm) REVERT: Aj 192 LEU cc_start: 0.9494 (mt) cc_final: 0.9291 (mt) REVERT: Aj 207 ASP cc_start: 0.8835 (p0) cc_final: 0.7785 (t0) REVERT: Aj 208 PHE cc_start: 0.8711 (p90) cc_final: 0.8488 (p90) REVERT: Ak 98 ASN cc_start: 0.8607 (t0) cc_final: 0.7865 (t0) REVERT: Ak 166 MET cc_start: 0.8467 (mmp) cc_final: 0.8000 (tpp) REVERT: Ak 187 MET cc_start: 0.8046 (ttm) cc_final: 0.7676 (ttm) REVERT: Ak 199 MET cc_start: 0.8636 (tpp) cc_final: 0.8348 (tpt) REVERT: Al 72 ASN cc_start: 0.8874 (t0) cc_final: 0.8484 (t0) REVERT: Al 83 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8275 (tm-30) REVERT: Al 98 ASN cc_start: 0.8559 (t0) cc_final: 0.8324 (t0) REVERT: Al 166 MET cc_start: 0.8313 (mmp) cc_final: 0.7360 (tpp) REVERT: Al 190 TYR cc_start: 0.8458 (t80) cc_final: 0.8198 (t80) REVERT: Al 192 LEU cc_start: 0.9473 (mm) cc_final: 0.8983 (mm) REVERT: Al 226 MET cc_start: 0.9054 (mtm) cc_final: 0.8771 (mtp) REVERT: Am 83 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8273 (tm-30) REVERT: Am 98 ASN cc_start: 0.8521 (t0) cc_final: 0.8277 (t0) REVERT: Am 112 GLU cc_start: 0.8695 (pp20) cc_final: 0.8467 (pp20) REVERT: Am 166 MET cc_start: 0.8534 (tpp) cc_final: 0.7471 (tpp) REVERT: Am 199 MET cc_start: 0.8839 (tpp) cc_final: 0.8569 (tpp) REVERT: An 72 ASN cc_start: 0.8830 (t0) cc_final: 0.8409 (t0) REVERT: An 83 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8268 (tm-30) REVERT: An 98 ASN cc_start: 0.8579 (t0) cc_final: 0.7866 (t0) REVERT: An 118 MET cc_start: 0.8551 (mmm) cc_final: 0.8255 (mmm) REVERT: An 146 GLN cc_start: 0.8805 (pt0) cc_final: 0.8531 (pt0) REVERT: An 156 GLU cc_start: 0.8660 (pp20) cc_final: 0.8166 (pp20) REVERT: An 166 MET cc_start: 0.8464 (mmp) cc_final: 0.7818 (tpp) REVERT: An 187 MET cc_start: 0.8232 (ttm) cc_final: 0.7342 (mtp) REVERT: An 199 MET cc_start: 0.8657 (tpp) cc_final: 0.8122 (tpp) REVERT: An 226 MET cc_start: 0.9024 (mtm) cc_final: 0.8766 (mtp) REVERT: Ao 72 ASN cc_start: 0.8854 (t0) cc_final: 0.8406 (t0) REVERT: Ao 98 ASN cc_start: 0.8630 (t0) cc_final: 0.7932 (t0) REVERT: Ao 141 MET cc_start: 0.7592 (tpt) cc_final: 0.7376 (tpt) REVERT: Ao 142 ASP cc_start: 0.8732 (t0) cc_final: 0.8369 (t0) REVERT: Ao 156 GLU cc_start: 0.8857 (pp20) cc_final: 0.8384 (pp20) REVERT: Ao 166 MET cc_start: 0.8235 (mmp) cc_final: 0.7951 (tpp) REVERT: Ao 187 MET cc_start: 0.8157 (ttm) cc_final: 0.7794 (ttm) REVERT: Ao 199 MET cc_start: 0.8679 (tpp) cc_final: 0.8331 (tpp) REVERT: Ap 72 ASN cc_start: 0.8749 (t0) cc_final: 0.8384 (t0) REVERT: Ap 79 TYR cc_start: 0.7927 (t80) cc_final: 0.7603 (t80) REVERT: Ap 83 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8224 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8578 (t0) cc_final: 0.7938 (t0) REVERT: Ap 141 MET cc_start: 0.7729 (tpt) cc_final: 0.7362 (tpt) REVERT: Ap 166 MET cc_start: 0.8044 (tpp) cc_final: 0.6289 (tpp) REVERT: Ap 207 ASP cc_start: 0.8755 (p0) cc_final: 0.8044 (t0) REVERT: Ap 208 PHE cc_start: 0.8605 (p90) cc_final: 0.7922 (p90) REVERT: Aq 83 GLN cc_start: 0.8416 (pt0) cc_final: 0.8210 (tm-30) REVERT: Aq 98 ASN cc_start: 0.8631 (t0) cc_final: 0.7869 (t0) REVERT: Aq 128 ASN cc_start: 0.8644 (t0) cc_final: 0.8313 (t0) REVERT: Aq 141 MET cc_start: 0.7414 (tpp) cc_final: 0.6460 (tpp) REVERT: Aq 166 MET cc_start: 0.8485 (tpp) cc_final: 0.7162 (tpp) REVERT: Aq 188 PRO cc_start: 0.8964 (Cg_exo) cc_final: 0.8628 (Cg_endo) REVERT: Aq 208 PHE cc_start: 0.8780 (p90) cc_final: 0.8570 (p90) REVERT: Ar 72 ASN cc_start: 0.8830 (t0) cc_final: 0.8418 (t0) REVERT: Ar 83 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8146 (tm-30) REVERT: Ar 98 ASN cc_start: 0.8561 (t0) cc_final: 0.7842 (t0) REVERT: Ar 166 MET cc_start: 0.8299 (mmp) cc_final: 0.7247 (tpp) REVERT: Ar 207 ASP cc_start: 0.8797 (p0) cc_final: 0.8125 (t0) REVERT: As 58 GLU cc_start: 0.8776 (mp0) cc_final: 0.8344 (mp0) REVERT: As 76 LEU cc_start: 0.8262 (tp) cc_final: 0.7944 (tp) REVERT: As 79 TYR cc_start: 0.8102 (t80) cc_final: 0.7236 (t80) REVERT: As 83 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8100 (tm-30) REVERT: As 98 ASN cc_start: 0.8667 (t0) cc_final: 0.8377 (t0) REVERT: As 166 MET cc_start: 0.7991 (tpp) cc_final: 0.7615 (tpp) REVERT: As 187 MET cc_start: 0.8126 (tmm) cc_final: 0.7820 (tmm) REVERT: As 190 TYR cc_start: 0.8800 (t80) cc_final: 0.7857 (t80) REVERT: As 192 LEU cc_start: 0.9553 (mt) cc_final: 0.9326 (mt) REVERT: As 207 ASP cc_start: 0.8631 (p0) cc_final: 0.7875 (t70) REVERT: At 58 GLU cc_start: 0.8770 (mp0) cc_final: 0.8349 (mp0) REVERT: At 76 LEU cc_start: 0.8175 (tp) cc_final: 0.7911 (tp) REVERT: At 79 TYR cc_start: 0.7929 (t80) cc_final: 0.7070 (t80) REVERT: At 83 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8119 (tm-30) REVERT: At 98 ASN cc_start: 0.8713 (t0) cc_final: 0.8165 (t0) REVERT: At 121 LEU cc_start: 0.9507 (tp) cc_final: 0.9191 (tt) REVERT: At 122 MET cc_start: 0.9515 (ttm) cc_final: 0.8931 (tpp) REVERT: At 166 MET cc_start: 0.8197 (mmp) cc_final: 0.7667 (tpp) REVERT: At 187 MET cc_start: 0.8022 (tmm) cc_final: 0.7471 (tmm) REVERT: At 192 LEU cc_start: 0.9416 (mm) cc_final: 0.8051 (mm) REVERT: At 208 PHE cc_start: 0.8762 (p90) cc_final: 0.8516 (p90) REVERT: At 218 ARG cc_start: 0.9100 (ttt90) cc_final: 0.8741 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8934 (mp0) cc_final: 0.8448 (mp0) REVERT: Au 76 LEU cc_start: 0.8417 (tp) cc_final: 0.8077 (tp) REVERT: Au 79 TYR cc_start: 0.8051 (t80) cc_final: 0.7537 (t80) REVERT: Au 83 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8239 (tm-30) REVERT: Au 159 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8475 (mmmm) REVERT: Au 166 MET cc_start: 0.8472 (mmp) cc_final: 0.7767 (tpp) REVERT: Au 195 ASN cc_start: 0.9332 (t0) cc_final: 0.9061 (t0) REVERT: Au 212 THR cc_start: 0.9225 (t) cc_final: 0.8777 (p) REVERT: Au 218 ARG cc_start: 0.9121 (ttt90) cc_final: 0.8372 (ttp-170) REVERT: Au 226 MET cc_start: 0.9018 (mtm) cc_final: 0.8753 (mtp) REVERT: Av 60 MET cc_start: 0.8081 (tpp) cc_final: 0.7877 (tpp) REVERT: Av 76 LEU cc_start: 0.8330 (tp) cc_final: 0.7998 (tp) REVERT: Av 128 ASN cc_start: 0.8553 (t0) cc_final: 0.8280 (t0) REVERT: Av 166 MET cc_start: 0.8353 (mmp) cc_final: 0.7745 (tpp) REVERT: Av 187 MET cc_start: 0.8243 (tmm) cc_final: 0.7963 (tmm) REVERT: Av 190 TYR cc_start: 0.8725 (t80) cc_final: 0.8372 (t80) REVERT: Av 218 ARG cc_start: 0.9059 (ttt90) cc_final: 0.8621 (ttp-170) REVERT: Av 226 MET cc_start: 0.9010 (mtm) cc_final: 0.8654 (mtp) REVERT: Aw 58 GLU cc_start: 0.8824 (mp0) cc_final: 0.8500 (mp0) REVERT: Aw 98 ASN cc_start: 0.8712 (t0) cc_final: 0.8457 (t0) REVERT: Aw 110 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8734 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8672 (t0) cc_final: 0.8450 (t0) REVERT: Aw 141 MET cc_start: 0.7681 (tpt) cc_final: 0.7298 (tpt) REVERT: Aw 142 ASP cc_start: 0.8755 (t0) cc_final: 0.8331 (t70) REVERT: Aw 156 GLU cc_start: 0.8883 (pp20) cc_final: 0.8470 (pp20) REVERT: Aw 166 MET cc_start: 0.8332 (mmp) cc_final: 0.7755 (tpp) REVERT: Aw 187 MET cc_start: 0.7986 (tmm) cc_final: 0.7442 (tmm) REVERT: Aw 190 TYR cc_start: 0.8667 (t80) cc_final: 0.8277 (t80) REVERT: Aw 199 MET cc_start: 0.8692 (tpp) cc_final: 0.8325 (tpp) REVERT: Aw 218 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7433 (ttp-170) REVERT: Aw 226 MET cc_start: 0.8946 (mtm) cc_final: 0.8529 (mtp) REVERT: Ax 58 GLU cc_start: 0.8829 (mp0) cc_final: 0.8391 (mp0) REVERT: Ax 83 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8408 (tm-30) REVERT: Ax 86 ILE cc_start: 0.9302 (mp) cc_final: 0.9085 (pt) REVERT: Ax 98 ASN cc_start: 0.8517 (t0) cc_final: 0.7870 (t0) REVERT: Ax 166 MET cc_start: 0.8287 (mmp) cc_final: 0.7831 (tpp) REVERT: Ax 187 MET cc_start: 0.7807 (tmm) cc_final: 0.7550 (tmm) REVERT: Ax 192 LEU cc_start: 0.9415 (mm) cc_final: 0.8956 (mm) REVERT: Ax 218 ARG cc_start: 0.9031 (ttt90) cc_final: 0.8756 (ttm170) REVERT: Ay 58 GLU cc_start: 0.8778 (mp0) cc_final: 0.8363 (mp0) REVERT: Ay 72 ASN cc_start: 0.8708 (t0) cc_final: 0.8363 (t0) REVERT: Ay 76 LEU cc_start: 0.8299 (tp) cc_final: 0.7896 (tp) REVERT: Ay 79 TYR cc_start: 0.8024 (t80) cc_final: 0.7687 (t80) REVERT: Ay 83 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8329 (tm-30) REVERT: Ay 122 MET cc_start: 0.9561 (ttm) cc_final: 0.9204 (ttp) REVERT: Ay 141 MET cc_start: 0.7680 (tpt) cc_final: 0.7346 (tpt) REVERT: Ay 166 MET cc_start: 0.8360 (mmp) cc_final: 0.7568 (tpp) REVERT: Ay 176 TYR cc_start: 0.8297 (t80) cc_final: 0.8038 (t80) REVERT: Ay 187 MET cc_start: 0.8079 (tmm) cc_final: 0.7661 (tmm) REVERT: Ay 192 LEU cc_start: 0.9426 (mm) cc_final: 0.8586 (mm) REVERT: Ay 218 ARG cc_start: 0.9136 (ttt90) cc_final: 0.8479 (ttm170) REVERT: Az 58 GLU cc_start: 0.8749 (mp0) cc_final: 0.8393 (mp0) REVERT: Az 76 LEU cc_start: 0.8750 (tp) cc_final: 0.8462 (tp) REVERT: Az 79 TYR cc_start: 0.8129 (t80) cc_final: 0.7218 (t80) REVERT: Az 98 ASN cc_start: 0.8557 (t0) cc_final: 0.7932 (t0) REVERT: Az 142 ASP cc_start: 0.8781 (t0) cc_final: 0.8482 (t0) REVERT: Az 166 MET cc_start: 0.8392 (mmp) cc_final: 0.7877 (tpp) REVERT: Az 187 MET cc_start: 0.8021 (ttm) cc_final: 0.7622 (mtp) REVERT: Az 199 MET cc_start: 0.8671 (tpp) cc_final: 0.8257 (tpp) REVERT: Az 218 ARG cc_start: 0.9095 (ttt90) cc_final: 0.8763 (ttp-170) REVERT: Ba 72 ASN cc_start: 0.8811 (t0) cc_final: 0.8382 (t0) REVERT: Ba 83 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8387 (tm-30) REVERT: Ba 98 ASN cc_start: 0.8644 (t0) cc_final: 0.8115 (t0) REVERT: Ba 128 ASN cc_start: 0.8642 (t0) cc_final: 0.8335 (t0) REVERT: Ba 159 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8520 (mmmt) REVERT: Ba 166 MET cc_start: 0.8456 (mmp) cc_final: 0.7603 (tpp) REVERT: Ba 187 MET cc_start: 0.7843 (tmm) cc_final: 0.7461 (tmm) REVERT: Ba 190 TYR cc_start: 0.8639 (t80) cc_final: 0.8332 (t80) outliers start: 5 outliers final: 0 residues processed: 1818 average time/residue: 0.2063 time to fit residues: 658.5061 Evaluate side-chains 1463 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1462 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 422 optimal weight: 0.0470 chunk 52 optimal weight: 9.9990 chunk 474 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 328 optimal weight: 0.9980 chunk 478 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 371 optimal weight: 0.0980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 146 GLN Ab 75 HIS Ab 88 ASN Ab 146 GLN ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 75 HIS Ac 95 GLN Ac 146 GLN ** Ad 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 146 GLN Ae 75 HIS Ae 146 GLN Af 146 GLN Ag 146 GLN Ah 128 ASN Ah 146 GLN Ai 146 GLN Aj 128 ASN Aj 146 GLN Ak 146 GLN ** Al 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 146 GLN Am 128 ASN Am 146 GLN ** An 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 146 GLN Ao 146 GLN ** Ap 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 146 GLN Aq 146 GLN Ar 128 ASN Ar 146 GLN As 146 GLN At 88 ASN ** At 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 146 GLN Au 75 HIS ** Au 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 128 ASN Au 146 GLN Av 146 GLN ** Aw 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 ASN Ay 146 GLN Az 75 HIS ** Az 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113722 restraints weight = 63723.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116941 restraints weight = 41750.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119308 restraints weight = 30134.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121064 restraints weight = 23258.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122429 restraints weight = 18833.980| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 41391 Z= 0.107 Angle : 0.564 5.265 55782 Z= 0.296 Chirality : 0.038 0.197 5940 Planarity : 0.004 0.043 7209 Dihedral : 4.092 16.705 5535 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.00 (0.12), residues: 4941 helix: 0.93 (0.11), residues: 2160 sheet: 1.07 (0.35), residues: 270 loop : -0.95 (0.13), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAk 90 TYR 0.031 0.002 TYRAz 190 PHE 0.018 0.001 PHEAl 208 TRP 0.020 0.002 TRPAf 99 HIS 0.006 0.002 HISBa 168 Details of bonding type rmsd covalent geometry : bond 0.00238 (41391) covalent geometry : angle 0.56387 (55782) hydrogen bonds : bond 0.02700 ( 1574) hydrogen bonds : angle 3.72872 ( 4317) *********************** 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 1856 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1853 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8398 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8387 (t0) cc_final: 0.8008 (t0) REVERT: Aa 141 MET cc_start: 0.7771 (mmm) cc_final: 0.7499 (mmt) REVERT: Aa 142 ASP cc_start: 0.8698 (t0) cc_final: 0.8275 (t0) REVERT: Aa 157 ASN cc_start: 0.8392 (m110) cc_final: 0.7891 (m110) REVERT: Aa 166 MET cc_start: 0.8026 (mmp) cc_final: 0.7167 (tpp) REVERT: Aa 187 MET cc_start: 0.7837 (ttm) cc_final: 0.6983 (mtp) REVERT: Aa 190 TYR cc_start: 0.8474 (t80) cc_final: 0.8011 (t80) REVERT: Aa 199 MET cc_start: 0.8738 (tpp) cc_final: 0.7820 (tpp) REVERT: Aa 207 ASP cc_start: 0.8567 (t70) cc_final: 0.8317 (t70) REVERT: Ab 60 MET cc_start: 0.8065 (tpp) cc_final: 0.7672 (tpp) REVERT: Ab 83 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8437 (tm-30) REVERT: Ab 108 ASP cc_start: 0.8671 (t70) cc_final: 0.8444 (t0) REVERT: Ab 166 MET cc_start: 0.8203 (mmp) cc_final: 0.7588 (tpp) REVERT: Ab 187 MET cc_start: 0.7940 (ttm) cc_final: 0.7554 (ttp) REVERT: Ac 83 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8255 (tm-30) REVERT: Ac 110 GLN cc_start: 0.9028 (mm110) cc_final: 0.8813 (mm110) REVERT: Ac 141 MET cc_start: 0.7529 (tpt) cc_final: 0.7287 (tpt) REVERT: Ac 142 ASP cc_start: 0.8671 (t0) cc_final: 0.8300 (t0) REVERT: Ac 166 MET cc_start: 0.8142 (mmp) cc_final: 0.7548 (tpp) REVERT: Ac 176 TYR cc_start: 0.8295 (t80) cc_final: 0.8093 (t80) REVERT: Ac 187 MET cc_start: 0.7784 (ttm) cc_final: 0.7009 (mtp) REVERT: Ac 199 MET cc_start: 0.8669 (tpp) cc_final: 0.8239 (tpp) REVERT: Ad 72 ASN cc_start: 0.8811 (t0) cc_final: 0.8400 (t0) REVERT: Ad 83 GLN cc_start: 0.8773 (pt0) cc_final: 0.8281 (tm-30) REVERT: Ad 166 MET cc_start: 0.8001 (mmp) cc_final: 0.7567 (tpp) REVERT: Ad 190 TYR cc_start: 0.8437 (t80) cc_final: 0.7782 (t80) REVERT: Ae 60 MET cc_start: 0.8003 (tpp) cc_final: 0.7705 (tpp) REVERT: Ae 72 ASN cc_start: 0.8762 (t0) cc_final: 0.8544 (t0) REVERT: Ae 83 GLN cc_start: 0.8701 (tm-30) cc_final: 0.7921 (tm-30) REVERT: Ae 122 MET cc_start: 0.9246 (ttm) cc_final: 0.8897 (tpp) REVERT: Ae 166 MET cc_start: 0.8081 (mmp) cc_final: 0.7017 (tpp) REVERT: Ae 190 TYR cc_start: 0.8424 (t80) cc_final: 0.7942 (t80) REVERT: Ae 208 PHE cc_start: 0.8713 (p90) cc_final: 0.8311 (p90) REVERT: Af 58 GLU cc_start: 0.8757 (mp0) cc_final: 0.8540 (mp0) REVERT: Af 83 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7763 (tm-30) REVERT: Af 95 GLN cc_start: 0.8249 (mt0) cc_final: 0.8018 (mt0) REVERT: Af 128 ASN cc_start: 0.8419 (t0) cc_final: 0.8154 (t0) REVERT: Af 142 ASP cc_start: 0.8696 (t0) cc_final: 0.8447 (t0) REVERT: Af 166 MET cc_start: 0.8082 (mmp) cc_final: 0.7492 (tpp) REVERT: Af 190 TYR cc_start: 0.8593 (t80) cc_final: 0.8195 (t80) REVERT: Af 195 ASN cc_start: 0.9043 (t0) cc_final: 0.8841 (t0) REVERT: Af 212 THR cc_start: 0.9523 (t) cc_final: 0.8907 (p) REVERT: Ag 83 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8300 (tm-30) REVERT: Ag 86 ILE cc_start: 0.9190 (mp) cc_final: 0.8734 (pt) REVERT: Ag 98 ASN cc_start: 0.8398 (t0) cc_final: 0.8078 (t0) REVERT: Ag 166 MET cc_start: 0.8155 (mmp) cc_final: 0.7349 (tpp) REVERT: Ag 190 TYR cc_start: 0.8400 (t80) cc_final: 0.7776 (t80) REVERT: Ag 195 ASN cc_start: 0.9198 (t0) cc_final: 0.8946 (t0) REVERT: Ah 83 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8416 (t0) cc_final: 0.7896 (t0) REVERT: Ah 141 MET cc_start: 0.7334 (tpp) cc_final: 0.7112 (tpp) REVERT: Ah 142 ASP cc_start: 0.8844 (t0) cc_final: 0.8453 (t0) REVERT: Ah 166 MET cc_start: 0.8205 (mmp) cc_final: 0.7545 (tpp) REVERT: Ah 176 TYR cc_start: 0.8170 (t80) cc_final: 0.7822 (t80) REVERT: Ai 98 ASN cc_start: 0.8338 (t0) cc_final: 0.7984 (t0) REVERT: Ai 141 MET cc_start: 0.7741 (tpt) cc_final: 0.7526 (tpt) REVERT: Ai 166 MET cc_start: 0.8167 (mmp) cc_final: 0.7425 (tpp) REVERT: Ai 187 MET cc_start: 0.8127 (ttp) cc_final: 0.7828 (ttt) REVERT: Aj 79 TYR cc_start: 0.7854 (t80) cc_final: 0.7403 (t80) REVERT: Aj 83 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8254 (tm-30) REVERT: Aj 98 ASN cc_start: 0.8498 (t0) cc_final: 0.7858 (t0) REVERT: Aj 141 MET cc_start: 0.7854 (tpt) cc_final: 0.7633 (tpt) REVERT: Aj 142 ASP cc_start: 0.8785 (t0) cc_final: 0.8150 (t0) REVERT: Aj 166 MET cc_start: 0.8289 (mmp) cc_final: 0.7582 (tpp) REVERT: Aj 187 MET cc_start: 0.8202 (tmm) cc_final: 0.7806 (tmm) REVERT: Ak 98 ASN cc_start: 0.8524 (t0) cc_final: 0.7719 (t0) REVERT: Ak 140 MET cc_start: 0.8030 (tmm) cc_final: 0.7724 (tmm) REVERT: Ak 146 GLN cc_start: 0.8676 (pt0) cc_final: 0.8037 (pt0) REVERT: Ak 166 MET cc_start: 0.8353 (mmp) cc_final: 0.7768 (tpp) REVERT: Ak 187 MET cc_start: 0.7977 (ttm) cc_final: 0.7744 (ttm) REVERT: Ak 199 MET cc_start: 0.8542 (tpp) cc_final: 0.8321 (tpp) REVERT: Al 72 ASN cc_start: 0.8704 (t0) cc_final: 0.8277 (t0) REVERT: Al 83 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8268 (tm-30) REVERT: Al 90 ARG cc_start: 0.8372 (ttm170) cc_final: 0.7992 (ttm170) REVERT: Al 98 ASN cc_start: 0.8539 (t0) cc_final: 0.8289 (t0) REVERT: Al 141 MET cc_start: 0.7413 (tpp) cc_final: 0.6665 (tpp) REVERT: Al 166 MET cc_start: 0.8128 (mmp) cc_final: 0.6752 (tpp) REVERT: Al 187 MET cc_start: 0.7905 (tmm) cc_final: 0.7522 (tmm) REVERT: Al 188 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8331 (Cg_exo) REVERT: Al 190 TYR cc_start: 0.8260 (t80) cc_final: 0.8038 (t80) REVERT: Al 192 LEU cc_start: 0.9421 (mm) cc_final: 0.8909 (mm) REVERT: Al 226 MET cc_start: 0.8987 (mtm) cc_final: 0.8705 (mtp) REVERT: Am 83 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8239 (tm-30) REVERT: Am 166 MET cc_start: 0.8472 (tpp) cc_final: 0.7265 (tpp) REVERT: Am 187 MET cc_start: 0.8296 (tpp) cc_final: 0.7948 (tmm) REVERT: Am 192 LEU cc_start: 0.9495 (mm) cc_final: 0.9271 (mm) REVERT: Am 208 PHE cc_start: 0.8800 (p90) cc_final: 0.8487 (p90) REVERT: An 72 ASN cc_start: 0.8755 (t0) cc_final: 0.8231 (t0) REVERT: An 83 GLN cc_start: 0.8684 (tm-30) cc_final: 0.7965 (tm-30) REVERT: An 92 THR cc_start: 0.8857 (p) cc_final: 0.8375 (p) REVERT: An 98 ASN cc_start: 0.8554 (t0) cc_final: 0.7833 (t0) REVERT: An 146 GLN cc_start: 0.8646 (pt0) cc_final: 0.7780 (pt0) REVERT: An 156 GLU cc_start: 0.8572 (pp20) cc_final: 0.8233 (pp20) REVERT: An 166 MET cc_start: 0.8295 (mmp) cc_final: 0.7317 (tpp) REVERT: Ao 72 ASN cc_start: 0.8741 (t0) cc_final: 0.8299 (t0) REVERT: Ao 83 GLN cc_start: 0.8534 (pt0) cc_final: 0.7894 (tm-30) REVERT: Ao 98 ASN cc_start: 0.8637 (t0) cc_final: 0.7865 (t0) REVERT: Ao 111 GLU cc_start: 0.8509 (tp30) cc_final: 0.8287 (tp30) REVERT: Ao 122 MET cc_start: 0.9495 (ttp) cc_final: 0.9280 (ttp) REVERT: Ao 142 ASP cc_start: 0.8763 (t0) cc_final: 0.8311 (t0) REVERT: Ao 156 GLU cc_start: 0.8759 (pp20) cc_final: 0.8491 (pp20) REVERT: Ao 166 MET cc_start: 0.8227 (mmp) cc_final: 0.7531 (tpp) REVERT: Ao 187 MET cc_start: 0.8049 (ttm) cc_final: 0.7754 (ttm) REVERT: Ao 199 MET cc_start: 0.8576 (tpp) cc_final: 0.8294 (tpp) REVERT: Ap 72 ASN cc_start: 0.8670 (t0) cc_final: 0.8282 (t0) REVERT: Ap 79 TYR cc_start: 0.7833 (t80) cc_final: 0.7502 (t80) REVERT: Ap 83 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8181 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8515 (t0) cc_final: 0.7977 (t0) REVERT: Ap 141 MET cc_start: 0.7393 (tpt) cc_final: 0.7043 (tpt) REVERT: Ap 166 MET cc_start: 0.8024 (tpp) cc_final: 0.6281 (tpp) REVERT: Ap 188 PRO cc_start: 0.8668 (Cg_exo) cc_final: 0.8355 (Cg_endo) REVERT: Ap 208 PHE cc_start: 0.8432 (p90) cc_final: 0.8165 (p90) REVERT: Aq 79 TYR cc_start: 0.7711 (t80) cc_final: 0.7257 (t80) REVERT: Aq 83 GLN cc_start: 0.8479 (pt0) cc_final: 0.8104 (tm-30) REVERT: Aq 98 ASN cc_start: 0.8709 (t0) cc_final: 0.7784 (t0) REVERT: Aq 122 MET cc_start: 0.9390 (ttm) cc_final: 0.9145 (ttp) REVERT: Aq 128 ASN cc_start: 0.8490 (t0) cc_final: 0.8155 (t0) REVERT: Aq 141 MET cc_start: 0.7169 (tpp) cc_final: 0.6782 (tpp) REVERT: Aq 166 MET cc_start: 0.8358 (tpp) cc_final: 0.7297 (tpp) REVERT: Aq 188 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8580 (Cg_endo) REVERT: Aq 199 MET cc_start: 0.8848 (tpp) cc_final: 0.8493 (tpp) REVERT: Ar 72 ASN cc_start: 0.8833 (t0) cc_final: 0.8435 (t0) REVERT: Ar 79 TYR cc_start: 0.7663 (t80) cc_final: 0.7443 (t80) REVERT: Ar 83 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8048 (tm-30) REVERT: Ar 98 ASN cc_start: 0.8537 (t0) cc_final: 0.7784 (t0) REVERT: Ar 166 MET cc_start: 0.8147 (mmp) cc_final: 0.7207 (tpp) REVERT: Ar 187 MET cc_start: 0.8061 (tmm) cc_final: 0.7795 (tmm) REVERT: Ar 208 PHE cc_start: 0.8615 (p90) cc_final: 0.8364 (p90) REVERT: As 58 GLU cc_start: 0.8753 (mp0) cc_final: 0.8375 (mp0) REVERT: As 60 MET cc_start: 0.8001 (tpp) cc_final: 0.7773 (tpp) REVERT: As 83 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8020 (tm-30) REVERT: As 98 ASN cc_start: 0.8648 (t0) cc_final: 0.8236 (t0) REVERT: As 166 MET cc_start: 0.8007 (tpp) cc_final: 0.6414 (tpp) REVERT: As 176 TYR cc_start: 0.8144 (t80) cc_final: 0.7913 (t80) REVERT: As 187 MET cc_start: 0.8133 (tmm) cc_final: 0.7885 (tmm) REVERT: At 58 GLU cc_start: 0.8750 (mp0) cc_final: 0.8321 (mp0) REVERT: At 79 TYR cc_start: 0.7738 (t80) cc_final: 0.7330 (t80) REVERT: At 83 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8115 (tm-30) REVERT: At 98 ASN cc_start: 0.8660 (t0) cc_final: 0.8049 (t0) REVERT: At 122 MET cc_start: 0.9152 (ttm) cc_final: 0.8716 (tpp) REVERT: At 156 GLU cc_start: 0.8776 (pp20) cc_final: 0.8342 (pp20) REVERT: At 166 MET cc_start: 0.8182 (mmp) cc_final: 0.7177 (tpp) REVERT: At 187 MET cc_start: 0.7987 (tmm) cc_final: 0.7712 (tmm) REVERT: At 192 LEU cc_start: 0.9412 (mm) cc_final: 0.9036 (mm) REVERT: At 208 PHE cc_start: 0.8609 (p90) cc_final: 0.8280 (p90) REVERT: At 218 ARG cc_start: 0.9002 (ttt90) cc_final: 0.8426 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8878 (mp0) cc_final: 0.8461 (mp0) REVERT: Au 60 MET cc_start: 0.7887 (tpp) cc_final: 0.7685 (tpp) REVERT: Au 79 TYR cc_start: 0.7789 (t80) cc_final: 0.7552 (t80) REVERT: Au 83 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8221 (tm-30) REVERT: Au 159 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8390 (mmmm) REVERT: Au 166 MET cc_start: 0.8260 (mmp) cc_final: 0.7070 (tpp) REVERT: Au 195 ASN cc_start: 0.9306 (t0) cc_final: 0.9023 (t0) REVERT: Au 208 PHE cc_start: 0.8450 (p90) cc_final: 0.8205 (p90) REVERT: Au 212 THR cc_start: 0.9226 (t) cc_final: 0.8765 (p) REVERT: Au 218 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8600 (ttp-170) REVERT: Au 226 MET cc_start: 0.8933 (mtm) cc_final: 0.8462 (mtp) REVERT: Av 60 MET cc_start: 0.8005 (tpp) cc_final: 0.7717 (tpp) REVERT: Av 79 TYR cc_start: 0.7899 (t80) cc_final: 0.7619 (t80) REVERT: Av 92 THR cc_start: 0.8523 (p) cc_final: 0.8247 (p) REVERT: Av 98 ASN cc_start: 0.8461 (t0) cc_final: 0.7684 (t0) REVERT: Av 166 MET cc_start: 0.8241 (mmp) cc_final: 0.7095 (tpp) REVERT: Av 190 TYR cc_start: 0.8665 (t80) cc_final: 0.8245 (t80) REVERT: Av 218 ARG cc_start: 0.9048 (ttt90) cc_final: 0.8631 (ttp-170) REVERT: Av 226 MET cc_start: 0.8889 (mtm) cc_final: 0.8626 (mtp) REVERT: Aw 98 ASN cc_start: 0.8674 (t0) cc_final: 0.8399 (t0) REVERT: Aw 110 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8559 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8486 (t0) cc_final: 0.8182 (t0) REVERT: Aw 142 ASP cc_start: 0.8793 (t0) cc_final: 0.8549 (t0) REVERT: Aw 156 GLU cc_start: 0.8693 (pp20) cc_final: 0.8316 (pp20) REVERT: Aw 166 MET cc_start: 0.8274 (mmp) cc_final: 0.7484 (tpp) REVERT: Aw 187 MET cc_start: 0.7759 (tmm) cc_final: 0.6958 (tmm) REVERT: Aw 190 TYR cc_start: 0.8501 (t80) cc_final: 0.7975 (t80) REVERT: Aw 192 LEU cc_start: 0.9458 (mt) cc_final: 0.8574 (mt) REVERT: Aw 199 MET cc_start: 0.8581 (tpp) cc_final: 0.8236 (tpp) REVERT: Aw 226 MET cc_start: 0.8906 (mtm) cc_final: 0.8558 (mtp) REVERT: Ax 58 GLU cc_start: 0.8866 (mp0) cc_final: 0.8433 (mp0) REVERT: Ax 86 ILE cc_start: 0.9112 (mp) cc_final: 0.8688 (pt) REVERT: Ax 98 ASN cc_start: 0.8405 (t0) cc_final: 0.7687 (t0) REVERT: Ax 156 GLU cc_start: 0.8797 (pp20) cc_final: 0.8127 (pp20) REVERT: Ax 166 MET cc_start: 0.8255 (mmp) cc_final: 0.7811 (tpp) REVERT: Ax 192 LEU cc_start: 0.9414 (mm) cc_final: 0.9051 (mm) REVERT: Ax 218 ARG cc_start: 0.8987 (ttt90) cc_final: 0.8783 (ttp-170) REVERT: Ay 58 GLU cc_start: 0.8738 (mp0) cc_final: 0.8372 (mp0) REVERT: Ay 72 ASN cc_start: 0.8607 (t0) cc_final: 0.8254 (t0) REVERT: Ay 83 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8213 (tm-30) REVERT: Ay 98 ASN cc_start: 0.8189 (t160) cc_final: 0.7918 (t0) REVERT: Ay 112 GLU cc_start: 0.8627 (pp20) cc_final: 0.8420 (pp20) REVERT: Ay 118 MET cc_start: 0.8757 (mmm) cc_final: 0.8326 (mmm) REVERT: Ay 166 MET cc_start: 0.8282 (mmp) cc_final: 0.6875 (tpp) REVERT: Ay 208 PHE cc_start: 0.8626 (p90) cc_final: 0.8054 (p90) REVERT: Ay 218 ARG cc_start: 0.9037 (ttt90) cc_final: 0.8754 (ttm170) REVERT: Az 58 GLU cc_start: 0.8676 (mp0) cc_final: 0.8449 (mp0) REVERT: Az 60 MET cc_start: 0.7860 (tpp) cc_final: 0.7555 (tpp) REVERT: Az 72 ASN cc_start: 0.8972 (t0) cc_final: 0.8542 (t0) REVERT: Az 79 TYR cc_start: 0.7997 (t80) cc_final: 0.7138 (t80) REVERT: Az 98 ASN cc_start: 0.8507 (t0) cc_final: 0.7934 (t0) REVERT: Az 142 ASP cc_start: 0.8652 (t0) cc_final: 0.8338 (t0) REVERT: Az 156 GLU cc_start: 0.8667 (pp20) cc_final: 0.8444 (pp20) REVERT: Az 166 MET cc_start: 0.8200 (mmp) cc_final: 0.7552 (tpp) REVERT: Az 218 ARG cc_start: 0.9076 (ttt90) cc_final: 0.8333 (ttp-170) REVERT: Ba 72 ASN cc_start: 0.8704 (t0) cc_final: 0.8260 (t0) REVERT: Ba 83 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8396 (tm-30) REVERT: Ba 84 VAL cc_start: 0.8848 (m) cc_final: 0.8573 (m) REVERT: Ba 98 ASN cc_start: 0.8545 (t0) cc_final: 0.7966 (t0) REVERT: Ba 128 ASN cc_start: 0.8551 (t0) cc_final: 0.8216 (t0) REVERT: Ba 166 MET cc_start: 0.8273 (mmp) cc_final: 0.6863 (tpp) REVERT: Ba 176 TYR cc_start: 0.8091 (t80) cc_final: 0.7871 (t80) REVERT: Ba 187 MET cc_start: 0.7770 (tmm) cc_final: 0.7519 (tmm) REVERT: Ba 190 TYR cc_start: 0.8496 (t80) cc_final: 0.8219 (t80) outliers start: 3 outliers final: 0 residues processed: 1856 average time/residue: 0.1974 time to fit residues: 642.9439 Evaluate side-chains 1477 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1477 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 171 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 357 optimal weight: 5.9990 chunk 261 optimal weight: 0.0070 chunk 471 optimal weight: 5.9990 chunk 419 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 485 optimal weight: 10.0000 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 88 ASN Ab 146 GLN ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 75 HIS Ac 95 GLN Ac 146 GLN ** Ad 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 75 HIS Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 146 GLN Ag 75 HIS Ag 146 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN ** Ai 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 146 GLN Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 75 HIS Ak 146 GLN ** Ak 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 146 GLN Am 146 GLN ** Am 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 75 HIS An 146 GLN ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 146 GLN Ap 146 GLN ** Ap 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 146 GLN ** Ar 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 128 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 146 GLN ** At 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 128 ASN At 146 GLN ** Au 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 75 HIS Au 146 GLN Av 146 GLN ** Aw 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN Ax 128 ASN ** Ax 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 75 HIS Ay 88 ASN Ay 98 ASN Ay 146 GLN ** Ay 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 65 GLN ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110088 restraints weight = 64541.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113352 restraints weight = 42152.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115749 restraints weight = 30475.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117539 restraints weight = 23631.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118895 restraints weight = 19236.729| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41391 Z= 0.167 Angle : 0.624 7.215 55782 Z= 0.329 Chirality : 0.039 0.229 5940 Planarity : 0.004 0.043 7209 Dihedral : 4.198 19.176 5535 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.05 (0.12), residues: 4941 helix: 0.98 (0.11), residues: 2133 sheet: 0.95 (0.32), residues: 270 loop : -1.04 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAl 189 TYR 0.033 0.002 TYRAh 204 PHE 0.019 0.002 PHEAd 208 TRP 0.018 0.002 TRPAr 99 HIS 0.007 0.002 HISAw 168 Details of bonding type rmsd covalent geometry : bond 0.00390 (41391) covalent geometry : angle 0.62426 (55782) hydrogen bonds : bond 0.03417 ( 1574) hydrogen bonds : angle 3.96995 ( 4317) *********************** 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 1727 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1725 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8045 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8369 (t0) cc_final: 0.7950 (t0) REVERT: Aa 142 ASP cc_start: 0.8507 (t0) cc_final: 0.8080 (t70) REVERT: Aa 157 ASN cc_start: 0.8551 (m110) cc_final: 0.7794 (m110) REVERT: Aa 166 MET cc_start: 0.8075 (mmp) cc_final: 0.7597 (tpp) REVERT: Aa 190 TYR cc_start: 0.8465 (t80) cc_final: 0.7981 (t80) REVERT: Aa 199 MET cc_start: 0.8693 (tpp) cc_final: 0.8359 (tmm) REVERT: Ab 60 MET cc_start: 0.8115 (tpp) cc_final: 0.7752 (tpp) REVERT: Ab 83 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8364 (tm-30) REVERT: Ab 166 MET cc_start: 0.8074 (mmp) cc_final: 0.7669 (tpp) REVERT: Ab 187 MET cc_start: 0.8081 (ttm) cc_final: 0.7747 (ttp) REVERT: Ab 199 MET cc_start: 0.8694 (tpt) cc_final: 0.8029 (tpp) REVERT: Ac 83 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8071 (tm-30) REVERT: Ac 140 MET cc_start: 0.6952 (tmm) cc_final: 0.6668 (tmm) REVERT: Ac 141 MET cc_start: 0.7848 (tpt) cc_final: 0.7343 (tpp) REVERT: Ac 142 ASP cc_start: 0.8700 (t0) cc_final: 0.8338 (t0) REVERT: Ac 166 MET cc_start: 0.7921 (mmp) cc_final: 0.7290 (tpp) REVERT: Ac 187 MET cc_start: 0.8002 (ttm) cc_final: 0.7092 (mtp) REVERT: Ac 199 MET cc_start: 0.8576 (tpp) cc_final: 0.8281 (tpp) REVERT: Ad 72 ASN cc_start: 0.8794 (t0) cc_final: 0.8426 (t0) REVERT: Ad 76 LEU cc_start: 0.8001 (tp) cc_final: 0.7746 (tp) REVERT: Ad 79 TYR cc_start: 0.7773 (t80) cc_final: 0.6795 (t80) REVERT: Ad 83 GLN cc_start: 0.8692 (pt0) cc_final: 0.8276 (tm-30) REVERT: Ad 85 ASP cc_start: 0.8386 (m-30) cc_final: 0.7935 (m-30) REVERT: Ad 166 MET cc_start: 0.8043 (mmp) cc_final: 0.7753 (tpp) REVERT: Ae 60 MET cc_start: 0.7960 (tpp) cc_final: 0.7610 (tpp) REVERT: Ae 83 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8116 (tm-30) REVERT: Ae 122 MET cc_start: 0.9330 (ttm) cc_final: 0.8803 (tpp) REVERT: Ae 141 MET cc_start: 0.7472 (tpp) cc_final: 0.7066 (tpp) REVERT: Ae 166 MET cc_start: 0.8143 (mmp) cc_final: 0.7548 (tpp) REVERT: Ae 187 MET cc_start: 0.7810 (tmm) cc_final: 0.7330 (tmm) REVERT: Ae 207 ASP cc_start: 0.8609 (p0) cc_final: 0.8098 (t0) REVERT: Af 76 LEU cc_start: 0.8130 (tp) cc_final: 0.7791 (tp) REVERT: Af 83 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7835 (tm-30) REVERT: Af 95 GLN cc_start: 0.8340 (mt0) cc_final: 0.8139 (mt0) REVERT: Af 142 ASP cc_start: 0.8756 (t0) cc_final: 0.8517 (t0) REVERT: Af 190 TYR cc_start: 0.8600 (t80) cc_final: 0.8180 (t80) REVERT: Ag 83 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8134 (tm-30) REVERT: Ag 98 ASN cc_start: 0.8258 (t0) cc_final: 0.7882 (t0) REVERT: Ag 105 LYS cc_start: 0.9053 (tppp) cc_final: 0.8715 (tppt) REVERT: Ag 166 MET cc_start: 0.8126 (mmp) cc_final: 0.7712 (tpp) REVERT: Ag 190 TYR cc_start: 0.8359 (t80) cc_final: 0.7848 (t80) REVERT: Ag 195 ASN cc_start: 0.9128 (t0) cc_final: 0.8910 (t0) REVERT: Ah 83 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8173 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8382 (t0) cc_final: 0.7728 (t0) REVERT: Ah 141 MET cc_start: 0.7571 (tpp) cc_final: 0.7303 (tpp) REVERT: Ah 166 MET cc_start: 0.8119 (mmp) cc_final: 0.7680 (tpp) REVERT: Ai 141 MET cc_start: 0.7738 (tpt) cc_final: 0.7492 (tpt) REVERT: Ai 166 MET cc_start: 0.8280 (mmp) cc_final: 0.7639 (tpp) REVERT: Aj 83 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Aj 98 ASN cc_start: 0.8433 (t0) cc_final: 0.7793 (t0) REVERT: Aj 141 MET cc_start: 0.8183 (tpt) cc_final: 0.7673 (tpt) REVERT: Aj 142 ASP cc_start: 0.8701 (t0) cc_final: 0.8242 (t0) REVERT: Aj 166 MET cc_start: 0.8263 (mmp) cc_final: 0.7750 (tpp) REVERT: Aj 187 MET cc_start: 0.8477 (tmm) cc_final: 0.7857 (tmm) REVERT: Aj 192 LEU cc_start: 0.9499 (mt) cc_final: 0.9236 (mt) REVERT: Ak 98 ASN cc_start: 0.8491 (t0) cc_final: 0.7741 (t0) REVERT: Ak 140 MET cc_start: 0.7942 (tmm) cc_final: 0.7694 (tmm) REVERT: Ak 166 MET cc_start: 0.8495 (mmp) cc_final: 0.7680 (tpp) REVERT: Ak 187 MET cc_start: 0.7983 (ttm) cc_final: 0.7382 (mtp) REVERT: Ak 199 MET cc_start: 0.8513 (tpp) cc_final: 0.8187 (tpp) REVERT: Al 72 ASN cc_start: 0.8701 (t0) cc_final: 0.8244 (t0) REVERT: Al 79 TYR cc_start: 0.7807 (t80) cc_final: 0.7526 (t80) REVERT: Al 83 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8074 (tm-30) REVERT: Al 166 MET cc_start: 0.8244 (mmp) cc_final: 0.7506 (tpp) REVERT: Al 187 MET cc_start: 0.8124 (tmm) cc_final: 0.7703 (tmm) REVERT: Al 192 LEU cc_start: 0.9472 (mm) cc_final: 0.9058 (mm) REVERT: Al 226 MET cc_start: 0.8997 (mtm) cc_final: 0.8692 (mtp) REVERT: Am 83 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8171 (tm-30) REVERT: Am 140 MET cc_start: 0.6631 (tmm) cc_final: 0.6371 (tmm) REVERT: Am 166 MET cc_start: 0.8308 (tpp) cc_final: 0.7501 (tpp) REVERT: Am 187 MET cc_start: 0.8483 (tpp) cc_final: 0.8054 (tmm) REVERT: Am 192 LEU cc_start: 0.9500 (mm) cc_final: 0.9196 (mm) REVERT: An 72 ASN cc_start: 0.8715 (t0) cc_final: 0.8396 (t0) REVERT: An 79 TYR cc_start: 0.7499 (t80) cc_final: 0.6485 (t80) REVERT: An 83 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8156 (tm-30) REVERT: An 142 ASP cc_start: 0.8877 (t0) cc_final: 0.7983 (t0) REVERT: An 166 MET cc_start: 0.8323 (mmp) cc_final: 0.7550 (tpp) REVERT: An 188 PRO cc_start: 0.8707 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: Ao 72 ASN cc_start: 0.8715 (t0) cc_final: 0.8272 (t0) REVERT: Ao 83 GLN cc_start: 0.8684 (pt0) cc_final: 0.7995 (tm-30) REVERT: Ao 85 ASP cc_start: 0.8374 (m-30) cc_final: 0.7967 (m-30) REVERT: Ao 98 ASN cc_start: 0.8660 (t0) cc_final: 0.7845 (t0) REVERT: Ao 111 GLU cc_start: 0.8481 (tp30) cc_final: 0.8280 (tp30) REVERT: Ao 142 ASP cc_start: 0.8696 (t0) cc_final: 0.8491 (t0) REVERT: Ao 156 GLU cc_start: 0.8833 (pp20) cc_final: 0.8274 (pp20) REVERT: Ao 166 MET cc_start: 0.8128 (mmp) cc_final: 0.7576 (tpp) REVERT: Ao 187 MET cc_start: 0.8223 (ttm) cc_final: 0.7903 (ttm) REVERT: Ap 72 ASN cc_start: 0.8692 (t0) cc_final: 0.8269 (t0) REVERT: Ap 83 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8047 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8560 (t0) cc_final: 0.7724 (t0) REVERT: Ap 166 MET cc_start: 0.8139 (tpp) cc_final: 0.6626 (tpp) REVERT: Ap 188 PRO cc_start: 0.8849 (Cg_exo) cc_final: 0.8617 (Cg_endo) REVERT: Ap 196 LEU cc_start: 0.8984 (mt) cc_final: 0.8723 (mt) REVERT: Ap 208 PHE cc_start: 0.8670 (p90) cc_final: 0.8055 (p90) REVERT: Aq 98 ASN cc_start: 0.8720 (t0) cc_final: 0.7776 (t0) REVERT: Aq 128 ASN cc_start: 0.8507 (t0) cc_final: 0.8097 (t0) REVERT: Aq 141 MET cc_start: 0.7618 (tpp) cc_final: 0.6894 (tpp) REVERT: Aq 156 GLU cc_start: 0.8891 (pp20) cc_final: 0.8668 (pp20) REVERT: Aq 166 MET cc_start: 0.8351 (tpp) cc_final: 0.7340 (tpp) REVERT: Aq 187 MET cc_start: 0.8208 (ttm) cc_final: 0.7821 (ttm) REVERT: Aq 188 PRO cc_start: 0.9085 (Cg_exo) cc_final: 0.8811 (Cg_endo) REVERT: Ar 72 ASN cc_start: 0.8800 (t0) cc_final: 0.8308 (t0) REVERT: Ar 79 TYR cc_start: 0.7744 (t80) cc_final: 0.7524 (t80) REVERT: Ar 83 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8050 (tm-30) REVERT: Ar 166 MET cc_start: 0.8267 (mmp) cc_final: 0.6806 (tpp) REVERT: Ar 208 PHE cc_start: 0.8864 (p90) cc_final: 0.8337 (p90) REVERT: As 58 GLU cc_start: 0.8674 (mp0) cc_final: 0.8326 (mp0) REVERT: As 76 LEU cc_start: 0.8288 (tp) cc_final: 0.8058 (tp) REVERT: As 79 TYR cc_start: 0.7754 (t80) cc_final: 0.7008 (t80) REVERT: As 83 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7960 (tm-30) REVERT: As 98 ASN cc_start: 0.8584 (t0) cc_final: 0.8220 (t0) REVERT: As 142 ASP cc_start: 0.8619 (t0) cc_final: 0.8135 (t0) REVERT: As 166 MET cc_start: 0.7875 (tpp) cc_final: 0.6613 (tpp) REVERT: As 187 MET cc_start: 0.8315 (tmm) cc_final: 0.7870 (tmm) REVERT: As 192 LEU cc_start: 0.9512 (mt) cc_final: 0.9158 (mt) REVERT: At 58 GLU cc_start: 0.8711 (mp0) cc_final: 0.8340 (mp0) REVERT: At 83 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8322 (tm-30) REVERT: At 98 ASN cc_start: 0.8507 (t0) cc_final: 0.7844 (t0) REVERT: At 141 MET cc_start: 0.7967 (tpp) cc_final: 0.7605 (tpp) REVERT: At 146 GLN cc_start: 0.8568 (pt0) cc_final: 0.8307 (pt0) REVERT: At 166 MET cc_start: 0.8037 (mmp) cc_final: 0.7623 (tpp) REVERT: At 187 MET cc_start: 0.8042 (tmm) cc_final: 0.7818 (tmm) REVERT: At 190 TYR cc_start: 0.8240 (t80) cc_final: 0.7974 (t80) REVERT: At 192 LEU cc_start: 0.9465 (mm) cc_final: 0.9071 (mm) REVERT: At 218 ARG cc_start: 0.8938 (ttt90) cc_final: 0.8611 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8854 (mp0) cc_final: 0.8427 (mp0) REVERT: Au 76 LEU cc_start: 0.8537 (tp) cc_final: 0.8189 (tp) REVERT: Au 79 TYR cc_start: 0.8170 (t80) cc_final: 0.7551 (t80) REVERT: Au 83 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8177 (tm-30) REVERT: Au 128 ASN cc_start: 0.8807 (t0) cc_final: 0.8436 (t0) REVERT: Au 140 MET cc_start: 0.6583 (tmm) cc_final: 0.6234 (tmm) REVERT: Au 166 MET cc_start: 0.8298 (mmp) cc_final: 0.7674 (tpp) REVERT: Au 195 ASN cc_start: 0.9272 (t0) cc_final: 0.8986 (t0) REVERT: Au 201 LEU cc_start: 0.9467 (mm) cc_final: 0.9256 (mm) REVERT: Au 218 ARG cc_start: 0.8981 (ttt90) cc_final: 0.8638 (ttp-170) REVERT: Au 226 MET cc_start: 0.8967 (mtm) cc_final: 0.8728 (mtp) REVERT: Av 79 TYR cc_start: 0.8251 (t80) cc_final: 0.7873 (t80) REVERT: Av 128 ASN cc_start: 0.8938 (t0) cc_final: 0.8595 (t0) REVERT: Av 166 MET cc_start: 0.8198 (mmp) cc_final: 0.7634 (tpp) REVERT: Av 187 MET cc_start: 0.8186 (tmm) cc_final: 0.7730 (tmm) REVERT: Av 190 TYR cc_start: 0.8688 (t80) cc_final: 0.8233 (t80) REVERT: Av 192 LEU cc_start: 0.9490 (mt) cc_final: 0.8758 (mt) REVERT: Av 218 ARG cc_start: 0.9067 (ttt90) cc_final: 0.8675 (ttp-170) REVERT: Av 226 MET cc_start: 0.8967 (mtm) cc_final: 0.8575 (mtp) REVERT: Aw 79 TYR cc_start: 0.8053 (t80) cc_final: 0.7818 (t80) REVERT: Aw 98 ASN cc_start: 0.8643 (t0) cc_final: 0.8426 (t0) REVERT: Aw 110 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8701 (mm-40) REVERT: Aw 122 MET cc_start: 0.9540 (ttm) cc_final: 0.9300 (ttp) REVERT: Aw 128 ASN cc_start: 0.8587 (t0) cc_final: 0.8223 (t0) REVERT: Aw 142 ASP cc_start: 0.8889 (t0) cc_final: 0.8573 (t0) REVERT: Aw 166 MET cc_start: 0.8237 (mmp) cc_final: 0.7611 (tpp) REVERT: Aw 187 MET cc_start: 0.8019 (tmm) cc_final: 0.7396 (tmm) REVERT: Aw 188 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.7808 (Cg_exo) REVERT: Aw 190 TYR cc_start: 0.8494 (t80) cc_final: 0.7362 (t80) REVERT: Aw 192 LEU cc_start: 0.9507 (mt) cc_final: 0.8646 (mt) REVERT: Aw 207 ASP cc_start: 0.8709 (p0) cc_final: 0.7584 (t0) REVERT: Ax 58 GLU cc_start: 0.8801 (mp0) cc_final: 0.8390 (mp0) REVERT: Ax 166 MET cc_start: 0.8151 (mmp) cc_final: 0.7812 (tpp) REVERT: Ax 187 MET cc_start: 0.8053 (tmm) cc_final: 0.7573 (tmm) REVERT: Ax 192 LEU cc_start: 0.9439 (mm) cc_final: 0.8474 (mm) REVERT: Ax 218 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8727 (ttp-170) REVERT: Ay 58 GLU cc_start: 0.8753 (mp0) cc_final: 0.8375 (mp0) REVERT: Ay 72 ASN cc_start: 0.8576 (t0) cc_final: 0.8373 (t0) REVERT: Ay 83 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8235 (tm-30) REVERT: Ay 121 LEU cc_start: 0.9283 (tp) cc_final: 0.8979 (tt) REVERT: Ay 166 MET cc_start: 0.8318 (mmp) cc_final: 0.7425 (tpp) REVERT: Ay 190 TYR cc_start: 0.8197 (t80) cc_final: 0.7964 (t80) REVERT: Ay 192 LEU cc_start: 0.9434 (mm) cc_final: 0.8873 (mm) REVERT: Ay 218 ARG cc_start: 0.9041 (ttt90) cc_final: 0.8804 (ttm170) REVERT: Az 58 GLU cc_start: 0.8673 (mp0) cc_final: 0.8457 (mp0) REVERT: Az 98 ASN cc_start: 0.8623 (t0) cc_final: 0.7956 (t0) REVERT: Az 140 MET cc_start: 0.6420 (tmm) cc_final: 0.6134 (tmm) REVERT: Az 142 ASP cc_start: 0.8834 (t0) cc_final: 0.7948 (t0) REVERT: Az 166 MET cc_start: 0.8443 (mmp) cc_final: 0.7937 (tpp) REVERT: Az 218 ARG cc_start: 0.8998 (ttt90) cc_final: 0.8604 (ttp-170) REVERT: Ba 72 ASN cc_start: 0.8769 (t0) cc_final: 0.8310 (t0) REVERT: Ba 83 GLN cc_start: 0.8608 (tm-30) cc_final: 0.7861 (tm-30) REVERT: Ba 128 ASN cc_start: 0.8598 (t0) cc_final: 0.8286 (t0) REVERT: Ba 166 MET cc_start: 0.8220 (mmp) cc_final: 0.7458 (tpp) REVERT: Ba 187 MET cc_start: 0.8079 (tmm) cc_final: 0.7399 (tmm) REVERT: Ba 190 TYR cc_start: 0.8450 (t80) cc_final: 0.8121 (t80) REVERT: Ba 192 LEU cc_start: 0.9505 (mt) cc_final: 0.8877 (mt) outliers start: 2 outliers final: 0 residues processed: 1727 average time/residue: 0.1913 time to fit residues: 579.4469 Evaluate side-chains 1415 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1415 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 235 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 320 optimal weight: 0.5980 chunk 453 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 146 GLN ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN Ac 146 GLN ** Ad 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 146 GLN Ag 146 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN ** Ai 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 146 GLN Aj 75 HIS Aj 128 ASN Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Al 146 GLN ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 146 GLN ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 128 ASN Ao 146 GLN Ap 146 GLN Aq 83 GLN Aq 146 GLN Ar 128 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 146 GLN At 88 ASN At 146 GLN ** Au 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 75 HIS Au 88 ASN Au 146 GLN Av 146 GLN Aw 133 ASN Aw 146 GLN ** Aw 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 ASN ** Ay 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 146 GLN ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108836 restraints weight = 66161.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112096 restraints weight = 43447.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114483 restraints weight = 31495.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116266 restraints weight = 24492.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117544 restraints weight = 20016.154| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41391 Z= 0.140 Angle : 0.614 7.514 55782 Z= 0.319 Chirality : 0.038 0.174 5940 Planarity : 0.004 0.046 7209 Dihedral : 4.139 18.213 5535 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.05 (0.12), residues: 4941 helix: 1.02 (0.11), residues: 2133 sheet: 0.92 (0.28), residues: 270 loop : -1.07 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 189 TYR 0.032 0.002 TYRAl 190 PHE 0.018 0.002 PHEAy 206 TRP 0.019 0.002 TRPAs 99 HIS 0.007 0.002 HISAz 168 Details of bonding type rmsd covalent geometry : bond 0.00329 (41391) covalent geometry : angle 0.61392 (55782) hydrogen bonds : bond 0.03066 ( 1574) hydrogen bonds : angle 3.78971 ( 4317) *********************** 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 1721 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1719 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8064 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8467 (t0) cc_final: 0.8024 (t0) REVERT: Aa 142 ASP cc_start: 0.8739 (t0) cc_final: 0.8158 (t0) REVERT: Aa 166 MET cc_start: 0.8015 (mmp) cc_final: 0.7653 (tpp) REVERT: Ab 60 MET cc_start: 0.8073 (tpp) cc_final: 0.7823 (tpp) REVERT: Ab 83 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8426 (tm-30) REVERT: Ab 166 MET cc_start: 0.8090 (mmp) cc_final: 0.7584 (tpp) REVERT: Ab 187 MET cc_start: 0.7998 (ttm) cc_final: 0.7758 (ttp) REVERT: Ab 190 TYR cc_start: 0.8390 (t80) cc_final: 0.8150 (t80) REVERT: Ac 83 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Ac 141 MET cc_start: 0.7758 (tpt) cc_final: 0.7323 (tpp) REVERT: Ac 142 ASP cc_start: 0.8759 (t0) cc_final: 0.8361 (t0) REVERT: Ac 166 MET cc_start: 0.7970 (mmp) cc_final: 0.7329 (tpp) REVERT: Ac 190 TYR cc_start: 0.8130 (t80) cc_final: 0.7329 (t80) REVERT: Ac 192 LEU cc_start: 0.9529 (mt) cc_final: 0.9088 (mt) REVERT: Ac 226 MET cc_start: 0.9015 (mtm) cc_final: 0.8713 (mtp) REVERT: Ad 72 ASN cc_start: 0.8859 (t0) cc_final: 0.8463 (t0) REVERT: Ad 166 MET cc_start: 0.7971 (mmp) cc_final: 0.7734 (tpp) REVERT: Ad 187 MET cc_start: 0.8223 (ttp) cc_final: 0.7907 (tmm) REVERT: Ad 190 TYR cc_start: 0.8188 (t80) cc_final: 0.7495 (t80) REVERT: Ad 192 LEU cc_start: 0.9496 (mt) cc_final: 0.9034 (mt) REVERT: Ae 83 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8200 (tm-30) REVERT: Ae 122 MET cc_start: 0.9123 (ttm) cc_final: 0.8888 (tpp) REVERT: Ae 166 MET cc_start: 0.8083 (mmp) cc_final: 0.7146 (tpp) REVERT: Ae 208 PHE cc_start: 0.8847 (p90) cc_final: 0.8483 (p90) REVERT: Af 76 LEU cc_start: 0.7994 (tp) cc_final: 0.7656 (tp) REVERT: Af 83 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7907 (tm-30) REVERT: Af 95 GLN cc_start: 0.8357 (mt0) cc_final: 0.8085 (mt0) REVERT: Af 118 MET cc_start: 0.8598 (mmm) cc_final: 0.8392 (mmm) REVERT: Af 126 ILE cc_start: 0.9412 (tp) cc_final: 0.9207 (tp) REVERT: Af 127 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7558 (mm-30) REVERT: Af 142 ASP cc_start: 0.8777 (t0) cc_final: 0.8532 (t0) REVERT: Af 166 MET cc_start: 0.8030 (tpp) cc_final: 0.7609 (tpp) REVERT: Af 190 TYR cc_start: 0.8628 (t80) cc_final: 0.7842 (t80) REVERT: Ag 72 ASN cc_start: 0.8720 (t0) cc_final: 0.8477 (t0) REVERT: Ag 83 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8244 (tm-30) REVERT: Ag 98 ASN cc_start: 0.8247 (t0) cc_final: 0.8039 (t0) REVERT: Ag 105 LYS cc_start: 0.9045 (tppp) cc_final: 0.8729 (tppt) REVERT: Ag 166 MET cc_start: 0.8137 (mmp) cc_final: 0.7756 (tpp) REVERT: Ag 195 ASN cc_start: 0.9150 (t0) cc_final: 0.8941 (t0) REVERT: Ah 83 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8258 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8196 (t0) cc_final: 0.7444 (t0) REVERT: Ah 166 MET cc_start: 0.8151 (mmp) cc_final: 0.7626 (tpp) REVERT: Ai 141 MET cc_start: 0.7662 (tpt) cc_final: 0.7446 (tpt) REVERT: Ai 166 MET cc_start: 0.8208 (mmp) cc_final: 0.7628 (tpp) REVERT: Ai 190 TYR cc_start: 0.8438 (t80) cc_final: 0.7822 (t80) REVERT: Ai 192 LEU cc_start: 0.9434 (mm) cc_final: 0.8939 (mm) REVERT: Ai 199 MET cc_start: 0.8697 (tpp) cc_final: 0.8454 (tpp) REVERT: Aj 79 TYR cc_start: 0.7684 (t80) cc_final: 0.7334 (t80) REVERT: Aj 83 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8093 (tm-30) REVERT: Aj 98 ASN cc_start: 0.8386 (t0) cc_final: 0.7726 (t0) REVERT: Aj 141 MET cc_start: 0.7938 (tpt) cc_final: 0.7486 (tpt) REVERT: Aj 142 ASP cc_start: 0.8691 (t0) cc_final: 0.8372 (t0) REVERT: Aj 146 GLN cc_start: 0.8846 (pt0) cc_final: 0.8542 (pt0) REVERT: Aj 166 MET cc_start: 0.8366 (mmp) cc_final: 0.7772 (tpp) REVERT: Aj 187 MET cc_start: 0.8544 (tmm) cc_final: 0.7868 (tmm) REVERT: Aj 192 LEU cc_start: 0.9548 (mt) cc_final: 0.9286 (mt) REVERT: Ak 98 ASN cc_start: 0.8482 (t0) cc_final: 0.7666 (t0) REVERT: Ak 112 GLU cc_start: 0.8330 (pp20) cc_final: 0.8097 (tm-30) REVERT: Ak 166 MET cc_start: 0.8487 (mmp) cc_final: 0.7681 (tpp) REVERT: Ak 190 TYR cc_start: 0.8138 (t80) cc_final: 0.7497 (t80) REVERT: Ak 207 ASP cc_start: 0.8634 (p0) cc_final: 0.7567 (t70) REVERT: Al 72 ASN cc_start: 0.8676 (t0) cc_final: 0.8149 (t0) REVERT: Al 83 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7974 (tm-30) REVERT: Al 98 ASN cc_start: 0.8458 (t0) cc_final: 0.8178 (t0) REVERT: Al 166 MET cc_start: 0.8099 (mmp) cc_final: 0.7891 (tpp) REVERT: Al 187 MET cc_start: 0.8157 (tmm) cc_final: 0.7782 (tmm) REVERT: Al 188 PRO cc_start: 0.8859 (Cg_endo) cc_final: 0.8494 (Cg_exo) REVERT: Al 192 LEU cc_start: 0.9498 (mm) cc_final: 0.9095 (mm) REVERT: Al 226 MET cc_start: 0.8917 (mtm) cc_final: 0.8623 (mtp) REVERT: Am 58 GLU cc_start: 0.8659 (mp0) cc_final: 0.8329 (mp0) REVERT: Am 83 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7910 (tm-30) REVERT: Am 112 GLU cc_start: 0.8603 (pp20) cc_final: 0.8390 (pp20) REVERT: Am 140 MET cc_start: 0.6547 (tmm) cc_final: 0.6163 (tmm) REVERT: Am 187 MET cc_start: 0.8503 (tpp) cc_final: 0.8127 (tmm) REVERT: Am 192 LEU cc_start: 0.9519 (mm) cc_final: 0.9207 (mm) REVERT: An 72 ASN cc_start: 0.8610 (t0) cc_final: 0.8302 (t0) REVERT: An 79 TYR cc_start: 0.7595 (t80) cc_final: 0.6357 (t80) REVERT: An 83 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8154 (tm-30) REVERT: An 142 ASP cc_start: 0.8576 (t0) cc_final: 0.8163 (t0) REVERT: An 166 MET cc_start: 0.8407 (mmp) cc_final: 0.7495 (tpp) REVERT: An 187 MET cc_start: 0.8731 (tpp) cc_final: 0.7862 (mmm) REVERT: An 188 PRO cc_start: 0.8789 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: Ao 72 ASN cc_start: 0.8684 (t0) cc_final: 0.8197 (t0) REVERT: Ao 156 GLU cc_start: 0.8814 (pp20) cc_final: 0.8234 (pp20) REVERT: Ao 166 MET cc_start: 0.8121 (mmp) cc_final: 0.7683 (tpp) REVERT: Ao 187 MET cc_start: 0.8222 (ttm) cc_final: 0.7801 (ttm) REVERT: Ao 199 MET cc_start: 0.8646 (tpp) cc_final: 0.8323 (tpp) REVERT: Ap 72 ASN cc_start: 0.8726 (t0) cc_final: 0.8322 (t0) REVERT: Ap 83 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8473 (t0) cc_final: 0.7708 (t0) REVERT: Ap 112 GLU cc_start: 0.8669 (pp20) cc_final: 0.8469 (pp20) REVERT: Ap 142 ASP cc_start: 0.8301 (t0) cc_final: 0.7902 (t0) REVERT: Ap 166 MET cc_start: 0.8153 (tpp) cc_final: 0.7192 (tpp) REVERT: Ap 188 PRO cc_start: 0.8862 (Cg_exo) cc_final: 0.8422 (Cg_endo) REVERT: Aq 83 GLN cc_start: 0.8440 (pt0) cc_final: 0.8121 (tm-30) REVERT: Aq 84 VAL cc_start: 0.9087 (m) cc_final: 0.8777 (m) REVERT: Aq 98 ASN cc_start: 0.8670 (t0) cc_final: 0.7733 (t0) REVERT: Aq 128 ASN cc_start: 0.8502 (t0) cc_final: 0.8100 (t0) REVERT: Aq 141 MET cc_start: 0.7407 (tpp) cc_final: 0.6782 (tpp) REVERT: Aq 166 MET cc_start: 0.8353 (tpp) cc_final: 0.7298 (tpp) REVERT: Aq 187 MET cc_start: 0.8307 (ttm) cc_final: 0.6511 (mtp) REVERT: Aq 188 PRO cc_start: 0.8953 (Cg_exo) cc_final: 0.8619 (Cg_endo) REVERT: Aq 199 MET cc_start: 0.8662 (tpp) cc_final: 0.7795 (tpp) REVERT: Ar 72 ASN cc_start: 0.8718 (t0) cc_final: 0.8188 (t0) REVERT: Ar 83 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8217 (tm-30) REVERT: Ar 95 GLN cc_start: 0.7320 (mt0) cc_final: 0.7057 (mt0) REVERT: Ar 141 MET cc_start: 0.8033 (mmt) cc_final: 0.7551 (tpp) REVERT: Ar 166 MET cc_start: 0.8147 (mmp) cc_final: 0.7149 (tpp) REVERT: Ar 187 MET cc_start: 0.8294 (tmm) cc_final: 0.8023 (tmm) REVERT: As 58 GLU cc_start: 0.8704 (mp0) cc_final: 0.8331 (mp0) REVERT: As 79 TYR cc_start: 0.7868 (t80) cc_final: 0.7500 (t80) REVERT: As 83 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8147 (tm-30) REVERT: As 92 THR cc_start: 0.8771 (p) cc_final: 0.8283 (p) REVERT: As 98 ASN cc_start: 0.8569 (t0) cc_final: 0.8182 (t0) REVERT: As 140 MET cc_start: 0.8237 (tmm) cc_final: 0.7768 (tmm) REVERT: As 142 ASP cc_start: 0.8653 (t0) cc_final: 0.8218 (t0) REVERT: As 156 GLU cc_start: 0.8764 (pp20) cc_final: 0.8308 (pp20) REVERT: As 166 MET cc_start: 0.8179 (tpp) cc_final: 0.7881 (tpp) REVERT: As 187 MET cc_start: 0.8353 (tmm) cc_final: 0.8013 (tmm) REVERT: As 192 LEU cc_start: 0.9507 (mt) cc_final: 0.9277 (mt) REVERT: At 58 GLU cc_start: 0.8726 (mp0) cc_final: 0.8377 (mp0) REVERT: At 83 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8176 (tm-30) REVERT: At 98 ASN cc_start: 0.8478 (t0) cc_final: 0.7895 (t0) REVERT: At 140 MET cc_start: 0.7499 (tmm) cc_final: 0.7109 (tmm) REVERT: At 146 GLN cc_start: 0.8802 (pt0) cc_final: 0.8378 (pt0) REVERT: At 166 MET cc_start: 0.8061 (mmp) cc_final: 0.7550 (tpp) REVERT: At 218 ARG cc_start: 0.8949 (ttt90) cc_final: 0.8612 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8905 (mp0) cc_final: 0.8462 (mp0) REVERT: Au 76 LEU cc_start: 0.8576 (tp) cc_final: 0.8344 (tp) REVERT: Au 79 TYR cc_start: 0.8093 (t80) cc_final: 0.7635 (t80) REVERT: Au 83 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8013 (tm-30) REVERT: Au 128 ASN cc_start: 0.8681 (t0) cc_final: 0.8265 (t0) REVERT: Au 140 MET cc_start: 0.6377 (tmm) cc_final: 0.6023 (tmm) REVERT: Au 166 MET cc_start: 0.8194 (mmp) cc_final: 0.7354 (tpp) REVERT: Au 190 TYR cc_start: 0.8628 (t80) cc_final: 0.8136 (t80) REVERT: Au 195 ASN cc_start: 0.9280 (t0) cc_final: 0.8983 (t0) REVERT: Au 218 ARG cc_start: 0.8995 (ttt90) cc_final: 0.8637 (ttp-170) REVERT: Av 58 GLU cc_start: 0.8830 (mp0) cc_final: 0.8419 (mp0) REVERT: Av 79 TYR cc_start: 0.8080 (t80) cc_final: 0.7355 (t80) REVERT: Av 98 ASN cc_start: 0.8439 (t0) cc_final: 0.7608 (t0) REVERT: Av 111 GLU cc_start: 0.8412 (tp30) cc_final: 0.8171 (tp30) REVERT: Av 128 ASN cc_start: 0.8847 (t0) cc_final: 0.8504 (t0) REVERT: Av 166 MET cc_start: 0.8083 (mmp) cc_final: 0.7419 (tpp) REVERT: Av 187 MET cc_start: 0.8326 (tmm) cc_final: 0.8068 (tmm) REVERT: Av 190 TYR cc_start: 0.8612 (t80) cc_final: 0.7999 (t80) REVERT: Av 195 ASN cc_start: 0.9335 (t0) cc_final: 0.9123 (t0) REVERT: Av 218 ARG cc_start: 0.9078 (ttt90) cc_final: 0.8683 (ttp-170) REVERT: Av 226 MET cc_start: 0.8988 (mtm) cc_final: 0.8635 (mtp) REVERT: Aw 98 ASN cc_start: 0.8606 (t0) cc_final: 0.8369 (t0) REVERT: Aw 110 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8771 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8590 (t0) cc_final: 0.8216 (t0) REVERT: Aw 140 MET cc_start: 0.7850 (ppp) cc_final: 0.7569 (ppp) REVERT: Aw 166 MET cc_start: 0.8250 (mmp) cc_final: 0.7522 (tpp) REVERT: Aw 187 MET cc_start: 0.8110 (tmm) cc_final: 0.7790 (tmm) REVERT: Aw 188 PRO cc_start: 0.8719 (Cg_endo) cc_final: 0.8350 (Cg_exo) REVERT: Aw 190 TYR cc_start: 0.8412 (t80) cc_final: 0.8117 (t80) REVERT: Ax 85 ASP cc_start: 0.8075 (m-30) cc_final: 0.7847 (m-30) REVERT: Ax 98 ASN cc_start: 0.8413 (t0) cc_final: 0.7708 (t0) REVERT: Ax 141 MET cc_start: 0.7829 (mmt) cc_final: 0.7570 (tpp) REVERT: Ax 166 MET cc_start: 0.8163 (mmp) cc_final: 0.7688 (tpp) REVERT: Ax 192 LEU cc_start: 0.9429 (mm) cc_final: 0.9060 (mm) REVERT: Ax 218 ARG cc_start: 0.9025 (ttt90) cc_final: 0.8791 (ttm170) REVERT: Ay 58 GLU cc_start: 0.8862 (mp0) cc_final: 0.8448 (mp0) REVERT: Ay 83 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8191 (tm-30) REVERT: Ay 166 MET cc_start: 0.8281 (mmp) cc_final: 0.7555 (tpp) REVERT: Ay 187 MET cc_start: 0.8200 (tmm) cc_final: 0.7868 (tmm) REVERT: Ay 192 LEU cc_start: 0.9460 (mm) cc_final: 0.8732 (mm) REVERT: Ay 208 PHE cc_start: 0.8793 (p90) cc_final: 0.8492 (p90) REVERT: Ay 218 ARG cc_start: 0.9071 (ttt90) cc_final: 0.8776 (ttm170) REVERT: Az 58 GLU cc_start: 0.8704 (mp0) cc_final: 0.8474 (mp0) REVERT: Az 60 MET cc_start: 0.7808 (tpp) cc_final: 0.7580 (tpp) REVERT: Az 79 TYR cc_start: 0.7756 (t80) cc_final: 0.6624 (t80) REVERT: Az 98 ASN cc_start: 0.8547 (t0) cc_final: 0.7948 (t0) REVERT: Az 112 GLU cc_start: 0.8605 (pp20) cc_final: 0.8378 (tm-30) REVERT: Az 140 MET cc_start: 0.6348 (tmm) cc_final: 0.6144 (tmm) REVERT: Az 141 MET cc_start: 0.8243 (mmt) cc_final: 0.7870 (tpp) REVERT: Az 142 ASP cc_start: 0.8896 (t0) cc_final: 0.7952 (t0) REVERT: Az 166 MET cc_start: 0.8292 (mmp) cc_final: 0.7767 (tpp) REVERT: Az 218 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8659 (ttp-170) REVERT: Ba 72 ASN cc_start: 0.8677 (t0) cc_final: 0.8308 (t0) REVERT: Ba 79 TYR cc_start: 0.7667 (t80) cc_final: 0.7393 (t80) REVERT: Ba 83 GLN cc_start: 0.8612 (tm-30) cc_final: 0.7946 (tm-30) REVERT: Ba 128 ASN cc_start: 0.8644 (t0) cc_final: 0.8323 (t0) REVERT: Ba 166 MET cc_start: 0.8043 (mmp) cc_final: 0.7207 (tpp) REVERT: Ba 187 MET cc_start: 0.8125 (tmm) cc_final: 0.7704 (tmm) REVERT: Ba 190 TYR cc_start: 0.8321 (t80) cc_final: 0.7990 (t80) REVERT: Ba 192 LEU cc_start: 0.9522 (mt) cc_final: 0.8939 (mt) outliers start: 2 outliers final: 0 residues processed: 1721 average time/residue: 0.1907 time to fit residues: 575.6345 Evaluate side-chains 1425 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1425 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 266 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 402 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 456 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 75 HIS ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 225 GLN ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN Ac 146 GLN ** Ad 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 75 HIS Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 146 GLN Ag 146 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN Ai 146 GLN Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Al 146 GLN ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 75 HIS ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 146 GLN ** Ar 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 128 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 146 GLN ** Au 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 75 HIS ** Au 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 146 GLN ** Av 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN ** Aw 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 128 ASN ** Ax 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 ASN ** Ay 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 146 GLN ** Ay 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101774 restraints weight = 67880.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104807 restraints weight = 45312.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107042 restraints weight = 33448.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108695 restraints weight = 26435.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109917 restraints weight = 21935.764| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 41391 Z= 0.243 Angle : 0.720 8.628 55782 Z= 0.383 Chirality : 0.042 0.161 5940 Planarity : 0.005 0.054 7209 Dihedral : 4.644 22.375 5535 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.31 (0.12), residues: 4941 helix: 0.75 (0.11), residues: 2133 sheet: 0.70 (0.27), residues: 270 loop : -1.16 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAx 189 TYR 0.038 0.002 TYRAp 204 PHE 0.026 0.002 PHEAk 206 TRP 0.020 0.002 TRPAl 99 HIS 0.010 0.002 HISAj 168 Details of bonding type rmsd covalent geometry : bond 0.00564 (41391) covalent geometry : angle 0.71995 (55782) hydrogen bonds : bond 0.03994 ( 1574) hydrogen bonds : angle 4.35937 ( 4317) *********************** 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 1692 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1690 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8235 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8529 (t0) cc_final: 0.7963 (t0) REVERT: Aa 142 ASP cc_start: 0.8435 (t0) cc_final: 0.8026 (t0) REVERT: Aa 166 MET cc_start: 0.8092 (mmp) cc_final: 0.7785 (tpp) REVERT: Ab 166 MET cc_start: 0.8112 (mmp) cc_final: 0.7775 (tpp) REVERT: Ab 187 MET cc_start: 0.8229 (ttm) cc_final: 0.7924 (ttt) REVERT: Ab 190 TYR cc_start: 0.8655 (t80) cc_final: 0.8278 (t80) REVERT: Ab 196 LEU cc_start: 0.8987 (mt) cc_final: 0.8292 (mt) REVERT: Ac 83 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8405 (tm-30) REVERT: Ac 141 MET cc_start: 0.7919 (tpt) cc_final: 0.7667 (tpp) REVERT: Ac 142 ASP cc_start: 0.8756 (t0) cc_final: 0.8481 (t0) REVERT: Ac 166 MET cc_start: 0.7989 (mmp) cc_final: 0.7447 (tpp) REVERT: Ac 190 TYR cc_start: 0.8249 (t80) cc_final: 0.7618 (t80) REVERT: Ad 72 ASN cc_start: 0.8809 (t0) cc_final: 0.8427 (t0) REVERT: Ad 85 ASP cc_start: 0.8364 (m-30) cc_final: 0.8021 (m-30) REVERT: Ad 187 MET cc_start: 0.8332 (ttp) cc_final: 0.7909 (tmm) REVERT: Ad 190 TYR cc_start: 0.8317 (t80) cc_final: 0.8057 (t80) REVERT: Ae 60 MET cc_start: 0.7858 (tpp) cc_final: 0.7622 (tpp) REVERT: Ae 83 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8329 (tm-30) REVERT: Ae 122 MET cc_start: 0.9358 (ttm) cc_final: 0.9097 (ttp) REVERT: Ae 166 MET cc_start: 0.8135 (mmp) cc_final: 0.7583 (tpp) REVERT: Ae 187 MET cc_start: 0.8002 (tmm) cc_final: 0.7416 (tmm) REVERT: Af 83 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8007 (tm-30) REVERT: Af 126 ILE cc_start: 0.9514 (tp) cc_final: 0.9314 (tp) REVERT: Af 142 ASP cc_start: 0.8827 (t0) cc_final: 0.8550 (t0) REVERT: Af 166 MET cc_start: 0.8185 (tpp) cc_final: 0.7595 (tpp) REVERT: Af 190 TYR cc_start: 0.8648 (t80) cc_final: 0.8038 (t80) REVERT: Ag 83 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8429 (tm-30) REVERT: Ag 98 ASN cc_start: 0.8366 (t0) cc_final: 0.8141 (t0) REVERT: Ag 105 LYS cc_start: 0.9106 (tppp) cc_final: 0.8767 (tppt) REVERT: Ag 112 GLU cc_start: 0.8418 (pp20) cc_final: 0.8202 (tm-30) REVERT: Ag 140 MET cc_start: 0.7688 (tmm) cc_final: 0.7280 (tmm) REVERT: Ag 166 MET cc_start: 0.8172 (mmp) cc_final: 0.7804 (tpp) REVERT: Ag 195 ASN cc_start: 0.9181 (t0) cc_final: 0.8953 (t0) REVERT: Ah 83 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8402 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8274 (t0) cc_final: 0.7544 (t0) REVERT: Ah 166 MET cc_start: 0.8146 (mmp) cc_final: 0.7720 (tpp) REVERT: Ah 176 TYR cc_start: 0.8425 (t80) cc_final: 0.8178 (t80) REVERT: Ai 146 GLN cc_start: 0.8790 (pt0) cc_final: 0.8549 (pt0) REVERT: Ai 166 MET cc_start: 0.8440 (mmp) cc_final: 0.7502 (tpp) REVERT: Ai 187 MET cc_start: 0.8382 (tmm) cc_final: 0.8116 (tmm) REVERT: Ai 190 TYR cc_start: 0.8450 (t80) cc_final: 0.8019 (t80) REVERT: Ai 192 LEU cc_start: 0.9404 (mm) cc_final: 0.9005 (mm) REVERT: Aj 95 GLN cc_start: 0.7895 (mt0) cc_final: 0.7682 (mt0) REVERT: Aj 98 ASN cc_start: 0.8570 (t0) cc_final: 0.7901 (t0) REVERT: Aj 141 MET cc_start: 0.8242 (tpt) cc_final: 0.7638 (tpt) REVERT: Aj 142 ASP cc_start: 0.8942 (t0) cc_final: 0.8453 (t0) REVERT: Aj 166 MET cc_start: 0.8215 (mmp) cc_final: 0.7881 (tpp) REVERT: Aj 187 MET cc_start: 0.8506 (tmm) cc_final: 0.8015 (tmm) REVERT: Aj 192 LEU cc_start: 0.9634 (mt) cc_final: 0.9353 (mt) REVERT: Ak 98 ASN cc_start: 0.8608 (t0) cc_final: 0.7826 (t0) REVERT: Ak 111 GLU cc_start: 0.8480 (tp30) cc_final: 0.8236 (tp30) REVERT: Ak 121 LEU cc_start: 0.9330 (tt) cc_final: 0.8997 (tp) REVERT: Ak 188 PRO cc_start: 0.8995 (Cg_exo) cc_final: 0.8782 (Cg_endo) REVERT: Al 72 ASN cc_start: 0.8753 (t0) cc_final: 0.8193 (t0) REVERT: Al 83 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8098 (tm-30) REVERT: Al 95 GLN cc_start: 0.7845 (mt0) cc_final: 0.7347 (mt0) REVERT: Al 141 MET cc_start: 0.7647 (tpp) cc_final: 0.7172 (tpp) REVERT: Al 165 ILE cc_start: 0.9032 (tt) cc_final: 0.8678 (tp) REVERT: Al 187 MET cc_start: 0.8254 (tmm) cc_final: 0.7792 (tmm) REVERT: Al 192 LEU cc_start: 0.9537 (mm) cc_final: 0.8919 (mm) REVERT: Al 226 MET cc_start: 0.8996 (mtm) cc_final: 0.8711 (mtp) REVERT: Am 58 GLU cc_start: 0.8679 (mp0) cc_final: 0.8343 (mp0) REVERT: Am 83 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8206 (tm-30) REVERT: Am 112 GLU cc_start: 0.8651 (pp20) cc_final: 0.8408 (pp20) REVERT: Am 140 MET cc_start: 0.7216 (tmm) cc_final: 0.6708 (tmm) REVERT: An 72 ASN cc_start: 0.8663 (t0) cc_final: 0.8362 (t0) REVERT: An 79 TYR cc_start: 0.7680 (t80) cc_final: 0.6335 (t80) REVERT: An 83 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8215 (tm-30) REVERT: An 141 MET cc_start: 0.8190 (mmm) cc_final: 0.7929 (tpt) REVERT: An 142 ASP cc_start: 0.8433 (t0) cc_final: 0.7970 (t0) REVERT: An 166 MET cc_start: 0.8427 (mmp) cc_final: 0.7654 (tpp) REVERT: An 188 PRO cc_start: 0.9010 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: Ao 72 ASN cc_start: 0.8721 (t0) cc_final: 0.8170 (t0) REVERT: Ao 83 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Ao 166 MET cc_start: 0.8253 (mmp) cc_final: 0.7729 (tpp) REVERT: Ao 187 MET cc_start: 0.8359 (ttm) cc_final: 0.8139 (ttm) REVERT: Ao 199 MET cc_start: 0.8622 (tpp) cc_final: 0.8385 (tpp) REVERT: Ap 72 ASN cc_start: 0.8796 (t0) cc_final: 0.8379 (t0) REVERT: Ap 83 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8318 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8603 (t0) cc_final: 0.7761 (t0) REVERT: Ap 112 GLU cc_start: 0.8709 (pp20) cc_final: 0.8497 (pp20) REVERT: Ap 140 MET cc_start: 0.8668 (ppp) cc_final: 0.8454 (ppp) REVERT: Ap 141 MET cc_start: 0.7762 (tpp) cc_final: 0.7246 (tpt) REVERT: Ap 142 ASP cc_start: 0.8503 (t0) cc_final: 0.7827 (t0) REVERT: Ap 166 MET cc_start: 0.8374 (tpp) cc_final: 0.7469 (tpp) REVERT: Ap 187 MET cc_start: 0.8724 (tpp) cc_final: 0.8129 (tmm) REVERT: Ap 188 PRO cc_start: 0.9104 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: Ap 192 LEU cc_start: 0.9489 (mm) cc_final: 0.8984 (mm) REVERT: Aq 98 ASN cc_start: 0.8759 (t0) cc_final: 0.7879 (t0) REVERT: Aq 128 ASN cc_start: 0.8595 (t0) cc_final: 0.8200 (t0) REVERT: Aq 141 MET cc_start: 0.7705 (tpp) cc_final: 0.7052 (tpp) REVERT: Aq 166 MET cc_start: 0.8344 (tpp) cc_final: 0.7516 (tpp) REVERT: Aq 187 MET cc_start: 0.8369 (ttm) cc_final: 0.6679 (mtp) REVERT: Aq 188 PRO cc_start: 0.9046 (Cg_exo) cc_final: 0.8742 (Cg_endo) REVERT: Aq 199 MET cc_start: 0.8690 (tpp) cc_final: 0.8058 (tpp) REVERT: Ar 72 ASN cc_start: 0.8737 (t0) cc_final: 0.8272 (t0) REVERT: Ar 83 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8447 (tm-30) REVERT: Ar 95 GLN cc_start: 0.7686 (mt0) cc_final: 0.7413 (mt0) REVERT: Ar 166 MET cc_start: 0.8150 (mmp) cc_final: 0.7816 (tpp) REVERT: As 58 GLU cc_start: 0.8751 (mp0) cc_final: 0.8330 (mp0) REVERT: As 79 TYR cc_start: 0.8193 (t80) cc_final: 0.7767 (t80) REVERT: As 83 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8073 (tm-30) REVERT: As 140 MET cc_start: 0.8339 (tmm) cc_final: 0.8067 (tmm) REVERT: As 141 MET cc_start: 0.7574 (mmt) cc_final: 0.7344 (mmt) REVERT: As 142 ASP cc_start: 0.8596 (t0) cc_final: 0.8053 (t0) REVERT: As 166 MET cc_start: 0.8240 (tpp) cc_final: 0.7934 (tpp) REVERT: As 187 MET cc_start: 0.8300 (tmm) cc_final: 0.7831 (tmm) REVERT: As 190 TYR cc_start: 0.8713 (t80) cc_final: 0.8391 (t80) REVERT: As 192 LEU cc_start: 0.9607 (mt) cc_final: 0.9191 (mt) REVERT: At 58 GLU cc_start: 0.8804 (mp0) cc_final: 0.8394 (mp0) REVERT: At 60 MET cc_start: 0.8060 (tpp) cc_final: 0.7843 (tpp) REVERT: At 76 LEU cc_start: 0.8413 (tp) cc_final: 0.8137 (tp) REVERT: At 83 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8173 (tm-30) REVERT: At 98 ASN cc_start: 0.8518 (t0) cc_final: 0.7875 (t0) REVERT: At 140 MET cc_start: 0.8016 (tmm) cc_final: 0.7802 (tmm) REVERT: At 141 MET cc_start: 0.7839 (mtt) cc_final: 0.7412 (mtt) REVERT: At 166 MET cc_start: 0.8115 (mmp) cc_final: 0.7628 (tpp) REVERT: At 188 PRO cc_start: 0.9003 (Cg_exo) cc_final: 0.8706 (Cg_endo) REVERT: At 190 TYR cc_start: 0.8367 (t80) cc_final: 0.7875 (t80) REVERT: At 218 ARG cc_start: 0.8979 (ttt90) cc_final: 0.8693 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8945 (mp0) cc_final: 0.8437 (mp0) REVERT: Au 76 LEU cc_start: 0.8720 (tp) cc_final: 0.8335 (tp) REVERT: Au 79 TYR cc_start: 0.8130 (t80) cc_final: 0.7397 (t80) REVERT: Au 83 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8279 (tm-30) REVERT: Au 109 LEU cc_start: 0.9010 (mt) cc_final: 0.8776 (mt) REVERT: Au 128 ASN cc_start: 0.8815 (t0) cc_final: 0.8386 (t0) REVERT: Au 166 MET cc_start: 0.8319 (mmp) cc_final: 0.7789 (tpp) REVERT: Au 195 ASN cc_start: 0.9283 (t0) cc_final: 0.9034 (t0) REVERT: Au 218 ARG cc_start: 0.9051 (ttt90) cc_final: 0.8753 (ttp-170) REVERT: Av 58 GLU cc_start: 0.8864 (mp0) cc_final: 0.8417 (mp0) REVERT: Av 76 LEU cc_start: 0.8445 (tp) cc_final: 0.8139 (tp) REVERT: Av 128 ASN cc_start: 0.8948 (t0) cc_final: 0.8691 (t0) REVERT: Av 166 MET cc_start: 0.8313 (mmp) cc_final: 0.7697 (tpp) REVERT: Av 187 MET cc_start: 0.8487 (tmm) cc_final: 0.8168 (tmm) REVERT: Av 190 TYR cc_start: 0.8712 (t80) cc_final: 0.8404 (t80) REVERT: Av 218 ARG cc_start: 0.9046 (ttt90) cc_final: 0.8729 (ttp-170) REVERT: Av 226 MET cc_start: 0.9073 (mtm) cc_final: 0.8856 (mtp) REVERT: Aw 58 GLU cc_start: 0.8879 (mp0) cc_final: 0.8571 (mp0) REVERT: Aw 79 TYR cc_start: 0.7791 (t80) cc_final: 0.7403 (t80) REVERT: Aw 98 ASN cc_start: 0.8659 (t0) cc_final: 0.8406 (t0) REVERT: Aw 110 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8942 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8727 (t0) cc_final: 0.8466 (t0) REVERT: Aw 166 MET cc_start: 0.8348 (mmp) cc_final: 0.7766 (tpp) REVERT: Aw 187 MET cc_start: 0.8252 (tmm) cc_final: 0.7601 (tmm) REVERT: Aw 188 PRO cc_start: 0.8805 (Cg_endo) cc_final: 0.7863 (Cg_exo) REVERT: Aw 190 TYR cc_start: 0.8594 (t80) cc_final: 0.7748 (t80) REVERT: Aw 192 LEU cc_start: 0.9556 (mt) cc_final: 0.8667 (mt) REVERT: Aw 207 ASP cc_start: 0.8803 (p0) cc_final: 0.7788 (t70) REVERT: Ax 58 GLU cc_start: 0.8845 (mp0) cc_final: 0.8477 (mp0) REVERT: Ax 141 MET cc_start: 0.7951 (mmt) cc_final: 0.7471 (tpp) REVERT: Ax 166 MET cc_start: 0.8304 (mmp) cc_final: 0.7869 (tpp) REVERT: Ax 192 LEU cc_start: 0.9457 (mm) cc_final: 0.9164 (mm) REVERT: Ax 218 ARG cc_start: 0.9099 (ttt90) cc_final: 0.8782 (ttm170) REVERT: Ay 58 GLU cc_start: 0.8778 (mp0) cc_final: 0.8363 (mp0) REVERT: Ay 76 LEU cc_start: 0.8290 (tp) cc_final: 0.7896 (tp) REVERT: Ay 83 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8164 (tm-30) REVERT: Ay 98 ASN cc_start: 0.8249 (t160) cc_final: 0.8008 (t0) REVERT: Ay 121 LEU cc_start: 0.9357 (tp) cc_final: 0.9057 (tt) REVERT: Ay 142 ASP cc_start: 0.8780 (t0) cc_final: 0.8547 (t70) REVERT: Ay 166 MET cc_start: 0.8285 (mmp) cc_final: 0.7502 (tpp) REVERT: Ay 187 MET cc_start: 0.8290 (tmm) cc_final: 0.7844 (tmm) REVERT: Ay 192 LEU cc_start: 0.9420 (mm) cc_final: 0.8525 (mm) REVERT: Ay 218 ARG cc_start: 0.9133 (ttt90) cc_final: 0.8769 (ttm170) REVERT: Az 58 GLU cc_start: 0.8836 (mp0) cc_final: 0.8509 (mp0) REVERT: Az 79 TYR cc_start: 0.7925 (t80) cc_final: 0.6965 (t80) REVERT: Az 140 MET cc_start: 0.6883 (tmm) cc_final: 0.6324 (tmm) REVERT: Az 141 MET cc_start: 0.8346 (mmt) cc_final: 0.7345 (tpp) REVERT: Az 142 ASP cc_start: 0.8714 (t0) cc_final: 0.8169 (t0) REVERT: Az 166 MET cc_start: 0.8393 (mmp) cc_final: 0.7770 (tpp) REVERT: Az 218 ARG cc_start: 0.9097 (ttt90) cc_final: 0.8683 (ttp-170) REVERT: Ba 76 LEU cc_start: 0.8424 (tp) cc_final: 0.8142 (tp) REVERT: Ba 83 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8216 (tm-30) REVERT: Ba 166 MET cc_start: 0.8289 (mmp) cc_final: 0.7691 (tpp) REVERT: Ba 190 TYR cc_start: 0.8457 (t80) cc_final: 0.8226 (t80) outliers start: 2 outliers final: 0 residues processed: 1692 average time/residue: 0.2060 time to fit residues: 612.5752 Evaluate side-chains 1383 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1383 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 326 optimal weight: 6.9990 chunk 412 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 319 optimal weight: 0.0870 chunk 372 optimal weight: 0.9990 chunk 407 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN Ac 146 GLN Ac 225 GLN Ad 88 ASN Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 146 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN ** Ah 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 128 ASN Aj 146 GLN ** Aj 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN ** Ak 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 146 GLN ** Am 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 146 GLN ** Ar 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 128 ASN At 128 ASN At 146 GLN ** Au 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 146 GLN ** Av 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN Ax 75 HIS ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 146 GLN Ay 88 ASN Ay 98 ASN ** Ay 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 146 GLN ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN ** Ba 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110463 restraints weight = 65227.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113749 restraints weight = 42865.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116177 restraints weight = 31172.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117983 restraints weight = 24270.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119312 restraints weight = 19856.990| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41391 Z= 0.133 Angle : 0.639 7.362 55782 Z= 0.332 Chirality : 0.039 0.202 5940 Planarity : 0.005 0.056 7209 Dihedral : 4.340 19.882 5535 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.11 (0.12), residues: 4941 helix: 1.01 (0.11), residues: 2133 sheet: 0.95 (0.27), residues: 270 loop : -1.16 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAt 189 TYR 0.028 0.002 TYRAq 204 PHE 0.028 0.002 PHEAx 206 TRP 0.021 0.002 TRPAu 99 HIS 0.009 0.002 HISAa 168 Details of bonding type rmsd covalent geometry : bond 0.00317 (41391) covalent geometry : angle 0.63911 (55782) hydrogen bonds : bond 0.02998 ( 1574) hydrogen bonds : angle 3.84296 ( 4317) *********************** 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 1722 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1720 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8215 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8527 (t0) cc_final: 0.8096 (t0) REVERT: Aa 142 ASP cc_start: 0.8361 (t0) cc_final: 0.8090 (t0) REVERT: Aa 166 MET cc_start: 0.7914 (mmp) cc_final: 0.7695 (tpp) REVERT: Ab 60 MET cc_start: 0.7977 (tpp) cc_final: 0.7648 (tpp) REVERT: Ab 83 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8425 (tm-30) REVERT: Ab 166 MET cc_start: 0.8082 (mmp) cc_final: 0.7589 (tpp) REVERT: Ab 190 TYR cc_start: 0.8448 (t80) cc_final: 0.8059 (t80) REVERT: Ac 83 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8415 (tm-30) REVERT: Ac 141 MET cc_start: 0.7755 (tpt) cc_final: 0.7408 (tpp) REVERT: Ac 166 MET cc_start: 0.8001 (mmp) cc_final: 0.7013 (tpp) REVERT: Ac 192 LEU cc_start: 0.9533 (mt) cc_final: 0.9157 (mt) REVERT: Ac 208 PHE cc_start: 0.8903 (p90) cc_final: 0.8628 (p90) REVERT: Ad 72 ASN cc_start: 0.8725 (t0) cc_final: 0.8310 (t0) REVERT: Ad 83 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8436 (tm-30) REVERT: Ad 166 MET cc_start: 0.8182 (tpp) cc_final: 0.7189 (tpp) REVERT: Ad 187 MET cc_start: 0.8269 (ttp) cc_final: 0.7727 (tmm) REVERT: Ae 83 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8187 (tm-30) REVERT: Ae 122 MET cc_start: 0.9265 (ttm) cc_final: 0.8831 (tpp) REVERT: Ae 141 MET cc_start: 0.7393 (tpp) cc_final: 0.7154 (tpt) REVERT: Ae 148 GLU cc_start: 0.7555 (pm20) cc_final: 0.7273 (pt0) REVERT: Ae 166 MET cc_start: 0.8014 (mmp) cc_final: 0.7370 (tpp) REVERT: Ae 187 MET cc_start: 0.7993 (tmm) cc_final: 0.7293 (tmm) REVERT: Ae 207 ASP cc_start: 0.8509 (p0) cc_final: 0.7860 (t70) REVERT: Af 128 ASN cc_start: 0.8846 (t0) cc_final: 0.8572 (t0) REVERT: Af 146 GLN cc_start: 0.8666 (mt0) cc_final: 0.8359 (mt0) REVERT: Af 166 MET cc_start: 0.8101 (tpp) cc_final: 0.7340 (tpp) REVERT: Af 195 ASN cc_start: 0.9028 (t0) cc_final: 0.8807 (t0) REVERT: Ag 72 ASN cc_start: 0.8710 (t0) cc_final: 0.8463 (t0) REVERT: Ag 83 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8142 (tm-30) REVERT: Ag 140 MET cc_start: 0.7488 (tmm) cc_final: 0.7105 (tmm) REVERT: Ag 166 MET cc_start: 0.8138 (mmp) cc_final: 0.7600 (tpp) REVERT: Ag 189 ARG cc_start: 0.9041 (mtp-110) cc_final: 0.8787 (mtp-110) REVERT: Ag 192 LEU cc_start: 0.9381 (mm) cc_final: 0.8504 (mm) REVERT: Ag 195 ASN cc_start: 0.9100 (t0) cc_final: 0.8891 (t0) REVERT: Ag 221 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8371 (tt0) REVERT: Ah 83 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8093 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8140 (t0) cc_final: 0.7850 (t0) REVERT: Ah 166 MET cc_start: 0.8003 (mmp) cc_final: 0.7562 (tpp) REVERT: Ah 176 TYR cc_start: 0.8327 (t80) cc_final: 0.8071 (t80) REVERT: Ai 60 MET cc_start: 0.7712 (tpp) cc_final: 0.7433 (tpp) REVERT: Ai 114 MET cc_start: 0.7636 (ttm) cc_final: 0.7367 (ttp) REVERT: Ai 122 MET cc_start: 0.9135 (ttp) cc_final: 0.8432 (tpp) REVERT: Ai 166 MET cc_start: 0.8354 (mmp) cc_final: 0.7789 (tpp) REVERT: Ai 187 MET cc_start: 0.8331 (tmm) cc_final: 0.8071 (tmm) REVERT: Ai 192 LEU cc_start: 0.9456 (mm) cc_final: 0.9047 (mm) REVERT: Aj 95 GLN cc_start: 0.7798 (mt0) cc_final: 0.7505 (mt0) REVERT: Aj 98 ASN cc_start: 0.8486 (t0) cc_final: 0.7829 (t0) REVERT: Aj 128 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8570 (p0) REVERT: Aj 141 MET cc_start: 0.7958 (tpt) cc_final: 0.7361 (tpt) REVERT: Aj 142 ASP cc_start: 0.8915 (t0) cc_final: 0.8523 (t0) REVERT: Aj 166 MET cc_start: 0.8085 (mmp) cc_final: 0.7651 (tpp) REVERT: Aj 187 MET cc_start: 0.8383 (tmm) cc_final: 0.7831 (tmm) REVERT: Aj 192 LEU cc_start: 0.9546 (mt) cc_final: 0.9272 (mt) REVERT: Ak 98 ASN cc_start: 0.8482 (t0) cc_final: 0.7680 (t0) REVERT: Ak 141 MET cc_start: 0.7600 (tpp) cc_final: 0.7386 (tpp) REVERT: Ak 166 MET cc_start: 0.8505 (tpp) cc_final: 0.7835 (tpp) REVERT: Ak 188 PRO cc_start: 0.8878 (Cg_exo) cc_final: 0.8617 (Cg_endo) REVERT: Al 72 ASN cc_start: 0.8790 (t0) cc_final: 0.8252 (t0) REVERT: Al 83 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7803 (tm-30) REVERT: Al 98 ASN cc_start: 0.8468 (t0) cc_final: 0.8132 (t0) REVERT: Al 141 MET cc_start: 0.7484 (tpp) cc_final: 0.7166 (tpp) REVERT: Al 166 MET cc_start: 0.8426 (tpp) cc_final: 0.7457 (tpp) REVERT: Al 187 MET cc_start: 0.8218 (tmm) cc_final: 0.7752 (tmm) REVERT: Al 188 PRO cc_start: 0.8844 (Cg_endo) cc_final: 0.8403 (Cg_exo) REVERT: Al 192 LEU cc_start: 0.9538 (mm) cc_final: 0.9006 (mm) REVERT: Al 208 PHE cc_start: 0.8946 (p90) cc_final: 0.8669 (p90) REVERT: Al 226 MET cc_start: 0.9001 (mtm) cc_final: 0.8776 (mtp) REVERT: Am 83 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7990 (tm-30) REVERT: Am 112 GLU cc_start: 0.8657 (pp20) cc_final: 0.8401 (pp20) REVERT: Am 140 MET cc_start: 0.6774 (tmm) cc_final: 0.6365 (tmm) REVERT: Am 142 ASP cc_start: 0.8912 (t0) cc_final: 0.8626 (t0) REVERT: Am 166 MET cc_start: 0.8253 (tpp) cc_final: 0.7728 (tpp) REVERT: Am 187 MET cc_start: 0.8539 (tpp) cc_final: 0.8069 (tmm) REVERT: Am 192 LEU cc_start: 0.9533 (mm) cc_final: 0.9069 (mm) REVERT: An 72 ASN cc_start: 0.8606 (t0) cc_final: 0.8302 (t0) REVERT: An 83 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8162 (tm-30) REVERT: An 84 VAL cc_start: 0.8935 (m) cc_final: 0.8733 (m) REVERT: An 98 ASN cc_start: 0.8522 (t0) cc_final: 0.7812 (t0) REVERT: An 141 MET cc_start: 0.7884 (mmm) cc_final: 0.7374 (tpp) REVERT: An 142 ASP cc_start: 0.8444 (t0) cc_final: 0.7828 (t0) REVERT: An 166 MET cc_start: 0.8243 (mmp) cc_final: 0.7248 (tpp) REVERT: An 188 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8455 (Cg_endo) REVERT: Ao 72 ASN cc_start: 0.8610 (t0) cc_final: 0.8011 (t0) REVERT: Ao 83 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8236 (tm-30) REVERT: Ao 98 ASN cc_start: 0.8614 (t0) cc_final: 0.7885 (t0) REVERT: Ao 141 MET cc_start: 0.8045 (mmt) cc_final: 0.7592 (tpp) REVERT: Ao 166 MET cc_start: 0.8122 (mmp) cc_final: 0.7351 (tpp) REVERT: Ap 72 ASN cc_start: 0.8773 (t0) cc_final: 0.8297 (t0) REVERT: Ap 83 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8046 (tm-30) REVERT: Ap 98 ASN cc_start: 0.8510 (t0) cc_final: 0.7712 (t0) REVERT: Ap 112 GLU cc_start: 0.8692 (pp20) cc_final: 0.8458 (pp20) REVERT: Ap 141 MET cc_start: 0.7536 (tpp) cc_final: 0.7112 (tpt) REVERT: Ap 142 ASP cc_start: 0.8546 (t0) cc_final: 0.7842 (t0) REVERT: Ap 166 MET cc_start: 0.8264 (tpp) cc_final: 0.6991 (tpp) REVERT: Ap 187 MET cc_start: 0.8567 (tpp) cc_final: 0.8179 (tmm) REVERT: Ap 188 PRO cc_start: 0.8877 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: Ap 192 LEU cc_start: 0.9411 (mm) cc_final: 0.9094 (mm) REVERT: Aq 98 ASN cc_start: 0.8686 (t0) cc_final: 0.7756 (t0) REVERT: Aq 128 ASN cc_start: 0.8501 (t0) cc_final: 0.8067 (t0) REVERT: Aq 166 MET cc_start: 0.8248 (tpp) cc_final: 0.7266 (tpp) REVERT: Aq 187 MET cc_start: 0.8389 (ttm) cc_final: 0.6642 (mtp) REVERT: Aq 188 PRO cc_start: 0.8980 (Cg_exo) cc_final: 0.8642 (Cg_endo) REVERT: Aq 190 TYR cc_start: 0.8369 (t80) cc_final: 0.7971 (t80) REVERT: Aq 199 MET cc_start: 0.8627 (tpp) cc_final: 0.8070 (tpp) REVERT: Aq 207 ASP cc_start: 0.8394 (p0) cc_final: 0.7141 (t0) REVERT: Ar 72 ASN cc_start: 0.8588 (t0) cc_final: 0.8358 (t0) REVERT: Ar 83 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8452 (tm-30) REVERT: Ar 95 GLN cc_start: 0.7630 (mt0) cc_final: 0.7226 (mt0) REVERT: Ar 166 MET cc_start: 0.8059 (mmp) cc_final: 0.7610 (tpp) REVERT: Ar 187 MET cc_start: 0.8254 (tmm) cc_final: 0.7986 (tmm) REVERT: Ar 190 TYR cc_start: 0.8132 (t80) cc_final: 0.7491 (t80) REVERT: Ar 207 ASP cc_start: 0.8565 (p0) cc_final: 0.7314 (t0) REVERT: As 58 GLU cc_start: 0.8759 (mp0) cc_final: 0.8327 (mp0) REVERT: As 79 TYR cc_start: 0.7979 (t80) cc_final: 0.7681 (t80) REVERT: As 83 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8096 (tm-30) REVERT: As 84 VAL cc_start: 0.8716 (m) cc_final: 0.8475 (m) REVERT: As 140 MET cc_start: 0.8190 (tmm) cc_final: 0.7850 (tmm) REVERT: As 142 ASP cc_start: 0.8469 (t0) cc_final: 0.7964 (t0) REVERT: As 166 MET cc_start: 0.7990 (tpp) cc_final: 0.6576 (tpp) REVERT: As 187 MET cc_start: 0.8222 (tmm) cc_final: 0.7667 (tmm) REVERT: As 190 TYR cc_start: 0.8563 (t80) cc_final: 0.8286 (t80) REVERT: As 192 LEU cc_start: 0.9581 (mt) cc_final: 0.9267 (mt) REVERT: As 208 PHE cc_start: 0.8763 (p90) cc_final: 0.8512 (p90) REVERT: At 58 GLU cc_start: 0.8790 (mp0) cc_final: 0.8367 (mp0) REVERT: At 76 LEU cc_start: 0.7942 (tp) cc_final: 0.7687 (tp) REVERT: At 79 TYR cc_start: 0.7594 (t80) cc_final: 0.6262 (t80) REVERT: At 83 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8165 (tm-30) REVERT: At 98 ASN cc_start: 0.8449 (t0) cc_final: 0.7808 (t0) REVERT: At 121 LEU cc_start: 0.9140 (tt) cc_final: 0.8901 (tt) REVERT: At 166 MET cc_start: 0.8029 (mmp) cc_final: 0.7471 (tpp) REVERT: At 188 PRO cc_start: 0.8762 (Cg_exo) cc_final: 0.8476 (Cg_endo) REVERT: At 196 LEU cc_start: 0.9266 (mt) cc_final: 0.8977 (mt) REVERT: At 218 ARG cc_start: 0.8958 (ttt90) cc_final: 0.8690 (ttp-170) REVERT: At 226 MET cc_start: 0.9037 (ttm) cc_final: 0.8808 (mtp) REVERT: Au 58 GLU cc_start: 0.8868 (mp0) cc_final: 0.8452 (mp0) REVERT: Au 76 LEU cc_start: 0.8543 (tp) cc_final: 0.8127 (tp) REVERT: Au 79 TYR cc_start: 0.7862 (t80) cc_final: 0.7465 (t80) REVERT: Au 92 THR cc_start: 0.8542 (p) cc_final: 0.8060 (p) REVERT: Au 121 LEU cc_start: 0.9142 (tt) cc_final: 0.8912 (tp) REVERT: Au 128 ASN cc_start: 0.8700 (t0) cc_final: 0.8287 (t0) REVERT: Au 166 MET cc_start: 0.8250 (mmp) cc_final: 0.7640 (tpp) REVERT: Au 195 ASN cc_start: 0.9244 (t0) cc_final: 0.9011 (t0) REVERT: Au 212 THR cc_start: 0.9026 (t) cc_final: 0.8723 (p) REVERT: Au 218 ARG cc_start: 0.8945 (ttt90) cc_final: 0.8601 (ttp-170) REVERT: Av 58 GLU cc_start: 0.8880 (mp0) cc_final: 0.8465 (mp0) REVERT: Av 79 TYR cc_start: 0.8024 (t80) cc_final: 0.7653 (t80) REVERT: Av 98 ASN cc_start: 0.8458 (t0) cc_final: 0.7624 (t0) REVERT: Av 128 ASN cc_start: 0.8777 (t0) cc_final: 0.8463 (t0) REVERT: Av 166 MET cc_start: 0.8070 (mmp) cc_final: 0.7403 (tpp) REVERT: Av 187 MET cc_start: 0.8266 (tmm) cc_final: 0.7917 (tmm) REVERT: Av 190 TYR cc_start: 0.8518 (t80) cc_final: 0.8089 (t80) REVERT: Av 192 LEU cc_start: 0.9530 (mt) cc_final: 0.8874 (mt) REVERT: Av 218 ARG cc_start: 0.8983 (ttt90) cc_final: 0.8704 (ttp-170) REVERT: Av 226 MET cc_start: 0.9016 (mtm) cc_final: 0.8687 (mtp) REVERT: Aw 58 GLU cc_start: 0.8850 (mp0) cc_final: 0.8523 (mp0) REVERT: Aw 98 ASN cc_start: 0.8534 (t0) cc_final: 0.8241 (t0) REVERT: Aw 110 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8871 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8638 (t0) cc_final: 0.8380 (t0) REVERT: Aw 157 ASN cc_start: 0.9017 (m-40) cc_final: 0.8411 (m110) REVERT: Aw 166 MET cc_start: 0.8247 (mmp) cc_final: 0.7481 (tpp) REVERT: Aw 187 MET cc_start: 0.8226 (tmm) cc_final: 0.7960 (tmm) REVERT: Aw 188 PRO cc_start: 0.8853 (Cg_endo) cc_final: 0.8434 (Cg_exo) REVERT: Aw 190 TYR cc_start: 0.8207 (t80) cc_final: 0.7925 (t80) REVERT: Aw 192 LEU cc_start: 0.9544 (mt) cc_final: 0.9328 (mt) REVERT: Ax 58 GLU cc_start: 0.8846 (mp0) cc_final: 0.8495 (mp0) REVERT: Ax 98 ASN cc_start: 0.8386 (t0) cc_final: 0.7609 (t0) REVERT: Ax 140 MET cc_start: 0.8084 (tmm) cc_final: 0.7866 (tmm) REVERT: Ax 141 MET cc_start: 0.7771 (mmt) cc_final: 0.7494 (mmt) REVERT: Ax 166 MET cc_start: 0.8155 (mmp) cc_final: 0.7720 (tpp) REVERT: Ax 192 LEU cc_start: 0.9407 (mm) cc_final: 0.9094 (mm) REVERT: Ax 218 ARG cc_start: 0.9019 (ttt90) cc_final: 0.8780 (ttm170) REVERT: Ay 58 GLU cc_start: 0.8802 (mp0) cc_final: 0.8457 (mp0) REVERT: Ay 83 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8213 (tm-30) REVERT: Ay 98 ASN cc_start: 0.8170 (t160) cc_final: 0.7966 (t0) REVERT: Ay 122 MET cc_start: 0.9246 (ttp) cc_final: 0.8578 (tpp) REVERT: Ay 142 ASP cc_start: 0.8653 (t0) cc_final: 0.8450 (t0) REVERT: Ay 166 MET cc_start: 0.8236 (mmp) cc_final: 0.7515 (tpp) REVERT: Ay 187 MET cc_start: 0.8255 (tmm) cc_final: 0.7779 (tmm) REVERT: Ay 192 LEU cc_start: 0.9451 (mm) cc_final: 0.8492 (mm) REVERT: Ay 218 ARG cc_start: 0.9086 (ttt90) cc_final: 0.8716 (ttp-170) REVERT: Az 58 GLU cc_start: 0.8716 (mp0) cc_final: 0.8432 (mp0) REVERT: Az 79 TYR cc_start: 0.7518 (t80) cc_final: 0.7214 (t80) REVERT: Az 98 ASN cc_start: 0.8555 (t0) cc_final: 0.7957 (t0) REVERT: Az 140 MET cc_start: 0.6513 (tmm) cc_final: 0.6134 (tmm) REVERT: Az 141 MET cc_start: 0.8220 (mmt) cc_final: 0.7871 (tpp) REVERT: Az 218 ARG cc_start: 0.9010 (ttt90) cc_final: 0.8634 (ttp-170) REVERT: Ba 83 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8150 (tm-30) REVERT: Ba 140 MET cc_start: 0.7379 (tmm) cc_final: 0.6971 (tmm) REVERT: Ba 166 MET cc_start: 0.8057 (mmp) cc_final: 0.7278 (tpp) REVERT: Ba 187 MET cc_start: 0.8061 (tmm) cc_final: 0.7536 (tmm) REVERT: Ba 188 PRO cc_start: 0.8682 (Cg_endo) cc_final: 0.8010 (Cg_exo) REVERT: Ba 190 TYR cc_start: 0.8334 (t80) cc_final: 0.8067 (t80) REVERT: Ba 192 LEU cc_start: 0.9432 (mt) cc_final: 0.8844 (mt) outliers start: 2 outliers final: 0 residues processed: 1722 average time/residue: 0.2071 time to fit residues: 627.3542 Evaluate side-chains 1411 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1410 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 420 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN ** Ac 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 146 GLN Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 88 ASN ** Ae 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 146 GLN ** Ah 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN ** Ai 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Al 146 GLN ** Am 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 146 GLN ** Ap 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 146 GLN ** Ar 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 128 ASN At 146 GLN ** Au 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 146 GLN Aw 95 GLN ** Aw 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 146 GLN ** Ax 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 95 GLN Ay 98 ASN ** Ay 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 146 GLN ** Ay 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109812 restraints weight = 66052.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113100 restraints weight = 43514.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115529 restraints weight = 31605.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117316 restraints weight = 24556.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118707 restraints weight = 20080.422| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41391 Z= 0.138 Angle : 0.655 7.700 55782 Z= 0.340 Chirality : 0.039 0.174 5940 Planarity : 0.005 0.057 7209 Dihedral : 4.326 19.195 5535 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.02 % Allowed : 0.78 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.10 (0.12), residues: 4941 helix: 1.03 (0.11), residues: 2133 sheet: 0.86 (0.27), residues: 270 loop : -1.16 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAw 189 TYR 0.033 0.002 TYRAv 204 PHE 0.023 0.002 PHEAx 206 TRP 0.020 0.002 TRPAl 99 HIS 0.010 0.002 HISAa 168 Details of bonding type rmsd covalent geometry : bond 0.00327 (41391) covalent geometry : angle 0.65544 (55782) hydrogen bonds : bond 0.03040 ( 1574) hydrogen bonds : angle 3.80446 ( 4317) *********************** 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 1718 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1717 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8117 (tm-30) REVERT: Aa 128 ASN cc_start: 0.8532 (t0) cc_final: 0.8126 (t0) REVERT: Aa 142 ASP cc_start: 0.8422 (t0) cc_final: 0.8116 (t0) REVERT: Aa 166 MET cc_start: 0.7899 (mmp) cc_final: 0.7369 (tpp) REVERT: Aa 190 TYR cc_start: 0.8110 (t80) cc_final: 0.7751 (t80) REVERT: Ab 76 LEU cc_start: 0.8052 (tp) cc_final: 0.7777 (tp) REVERT: Ab 142 ASP cc_start: 0.8826 (t0) cc_final: 0.8318 (t0) REVERT: Ab 166 MET cc_start: 0.8044 (mmp) cc_final: 0.7678 (tpp) REVERT: Ab 190 TYR cc_start: 0.8449 (t80) cc_final: 0.8056 (t80) REVERT: Ac 83 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8196 (tm-30) REVERT: Ac 166 MET cc_start: 0.8061 (mmp) cc_final: 0.7249 (tpp) REVERT: Ac 192 LEU cc_start: 0.9529 (mt) cc_final: 0.9143 (mt) REVERT: Ad 72 ASN cc_start: 0.8703 (t0) cc_final: 0.8285 (t0) REVERT: Ad 76 LEU cc_start: 0.7833 (tp) cc_final: 0.7624 (tp) REVERT: Ad 84 VAL cc_start: 0.9068 (m) cc_final: 0.8837 (m) REVERT: Ad 85 ASP cc_start: 0.8250 (m-30) cc_final: 0.7950 (m-30) REVERT: Ad 142 ASP cc_start: 0.8903 (t0) cc_final: 0.8697 (t0) REVERT: Ad 166 MET cc_start: 0.8125 (tpp) cc_final: 0.7072 (tpp) REVERT: Ad 187 MET cc_start: 0.8256 (ttp) cc_final: 0.7836 (tmm) REVERT: Ad 190 TYR cc_start: 0.8060 (t80) cc_final: 0.7719 (t80) REVERT: Ad 208 PHE cc_start: 0.8836 (p90) cc_final: 0.8580 (p90) REVERT: Ae 83 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8152 (tm-30) REVERT: Ae 122 MET cc_start: 0.9141 (ttm) cc_final: 0.8539 (tpp) REVERT: Ae 128 ASN cc_start: 0.8870 (t0) cc_final: 0.8648 (t0) REVERT: Ae 140 MET cc_start: 0.7023 (tmm) cc_final: 0.6784 (tmm) REVERT: Ae 141 MET cc_start: 0.7385 (tpp) cc_final: 0.7171 (tpp) REVERT: Ae 166 MET cc_start: 0.8000 (mmp) cc_final: 0.6952 (tpp) REVERT: Ae 187 MET cc_start: 0.8026 (tmm) cc_final: 0.7599 (tmm) REVERT: Ae 190 TYR cc_start: 0.7797 (t80) cc_final: 0.7192 (t80) REVERT: Ae 207 ASP cc_start: 0.8454 (p0) cc_final: 0.7812 (t0) REVERT: Ae 208 PHE cc_start: 0.8846 (p90) cc_final: 0.8131 (p90) REVERT: Af 76 LEU cc_start: 0.8120 (tp) cc_final: 0.7890 (tp) REVERT: Af 128 ASN cc_start: 0.8672 (t0) cc_final: 0.8385 (t0) REVERT: Af 141 MET cc_start: 0.7384 (mmt) cc_final: 0.6565 (mmt) REVERT: Af 142 ASP cc_start: 0.8519 (t0) cc_final: 0.7983 (t0) REVERT: Af 166 MET cc_start: 0.8017 (tpp) cc_final: 0.7414 (tpp) REVERT: Ag 83 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8133 (tm-30) REVERT: Ag 140 MET cc_start: 0.7325 (tmm) cc_final: 0.7084 (tmm) REVERT: Ag 166 MET cc_start: 0.8104 (mmp) cc_final: 0.7331 (tpp) REVERT: Ag 208 PHE cc_start: 0.8930 (p90) cc_final: 0.8324 (p90) REVERT: Ag 221 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8388 (tt0) REVERT: Ah 83 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8109 (tm-30) REVERT: Ah 98 ASN cc_start: 0.8070 (t0) cc_final: 0.7808 (t0) REVERT: Ah 112 GLU cc_start: 0.8541 (pp20) cc_final: 0.8328 (pp20) REVERT: Ah 142 ASP cc_start: 0.8897 (t0) cc_final: 0.8585 (t0) REVERT: Ah 166 MET cc_start: 0.7971 (mmp) cc_final: 0.7569 (tpp) REVERT: Ah 190 TYR cc_start: 0.8268 (t80) cc_final: 0.8050 (t80) REVERT: Ah 207 ASP cc_start: 0.8402 (t70) cc_final: 0.8172 (t0) REVERT: Ai 60 MET cc_start: 0.7750 (tpp) cc_final: 0.7479 (tpp) REVERT: Ai 114 MET cc_start: 0.7721 (ttm) cc_final: 0.7448 (ttp) REVERT: Ai 122 MET cc_start: 0.9046 (ttp) cc_final: 0.8424 (tpp) REVERT: Ai 166 MET cc_start: 0.8124 (mmp) cc_final: 0.7619 (tpp) REVERT: Ai 187 MET cc_start: 0.8361 (tmm) cc_final: 0.8101 (tmm) REVERT: Ai 192 LEU cc_start: 0.9409 (mm) cc_final: 0.8985 (mm) REVERT: Aj 95 GLN cc_start: 0.7715 (mt0) cc_final: 0.7419 (mt0) REVERT: Aj 141 MET cc_start: 0.8003 (tpt) cc_final: 0.7485 (tpt) REVERT: Aj 142 ASP cc_start: 0.8924 (t0) cc_final: 0.8432 (t0) REVERT: Aj 166 MET cc_start: 0.7964 (mmp) cc_final: 0.7443 (tpp) REVERT: Aj 187 MET cc_start: 0.8515 (tmm) cc_final: 0.7933 (tmm) REVERT: Aj 192 LEU cc_start: 0.9533 (mt) cc_final: 0.9312 (mt) REVERT: Ak 72 ASN cc_start: 0.8440 (t0) cc_final: 0.8090 (t0) REVERT: Ak 98 ASN cc_start: 0.8437 (t0) cc_final: 0.7562 (t0) REVERT: Ak 140 MET cc_start: 0.7879 (tmm) cc_final: 0.7594 (tmm) REVERT: Ak 166 MET cc_start: 0.8405 (tpp) cc_final: 0.7945 (tpp) REVERT: Al 72 ASN cc_start: 0.8805 (t0) cc_final: 0.8349 (t0) REVERT: Al 83 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7830 (tm-30) REVERT: Al 98 ASN cc_start: 0.8394 (t0) cc_final: 0.8115 (t0) REVERT: Al 141 MET cc_start: 0.7472 (tpp) cc_final: 0.7055 (tpp) REVERT: Al 145 GLU cc_start: 0.7406 (pm20) cc_final: 0.7202 (pm20) REVERT: Al 165 ILE cc_start: 0.8941 (pt) cc_final: 0.8507 (pt) REVERT: Al 166 MET cc_start: 0.8444 (tpp) cc_final: 0.7334 (tpp) REVERT: Al 187 MET cc_start: 0.8170 (tmm) cc_final: 0.7740 (tmm) REVERT: Al 188 PRO cc_start: 0.8882 (Cg_endo) cc_final: 0.8502 (Cg_exo) REVERT: Al 192 LEU cc_start: 0.9527 (mm) cc_final: 0.8985 (mm) REVERT: Al 208 PHE cc_start: 0.8915 (p90) cc_final: 0.8555 (p90) REVERT: Al 226 MET cc_start: 0.8962 (mtm) cc_final: 0.8758 (mtp) REVERT: Am 58 GLU cc_start: 0.8576 (mp0) cc_final: 0.8292 (mp0) REVERT: Am 83 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8069 (tm-30) REVERT: Am 112 GLU cc_start: 0.8665 (pp20) cc_final: 0.8423 (pp20) REVERT: Am 140 MET cc_start: 0.6092 (tmm) cc_final: 0.5881 (tmm) REVERT: Am 142 ASP cc_start: 0.8799 (t0) cc_final: 0.8506 (t0) REVERT: Am 166 MET cc_start: 0.8190 (tpp) cc_final: 0.6799 (tpp) REVERT: Am 187 MET cc_start: 0.8598 (tpp) cc_final: 0.8264 (tmm) REVERT: Am 192 LEU cc_start: 0.9536 (mm) cc_final: 0.9162 (mm) REVERT: An 72 ASN cc_start: 0.8522 (t0) cc_final: 0.8227 (t0) REVERT: An 79 TYR cc_start: 0.7508 (t80) cc_final: 0.6521 (t80) REVERT: An 83 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8123 (tm-30) REVERT: An 141 MET cc_start: 0.7938 (mmm) cc_final: 0.7361 (tpp) REVERT: An 142 ASP cc_start: 0.8405 (t0) cc_final: 0.7702 (t0) REVERT: An 166 MET cc_start: 0.8147 (mmp) cc_final: 0.7274 (tpp) REVERT: An 188 PRO cc_start: 0.8746 (Cg_exo) cc_final: 0.8496 (Cg_endo) REVERT: Ao 72 ASN cc_start: 0.8563 (t0) cc_final: 0.8003 (t0) REVERT: Ao 98 ASN cc_start: 0.8578 (t0) cc_final: 0.7780 (t0) REVERT: Ao 142 ASP cc_start: 0.8652 (t0) cc_final: 0.8362 (t0) REVERT: Ao 166 MET cc_start: 0.8059 (mmp) cc_final: 0.7340 (tpp) REVERT: Ao 196 LEU cc_start: 0.8972 (mt) cc_final: 0.8668 (mt) REVERT: Ap 72 ASN cc_start: 0.8794 (t0) cc_final: 0.8345 (t0) REVERT: Ap 83 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8085 (tm-30) REVERT: Ap 141 MET cc_start: 0.7523 (tpp) cc_final: 0.6595 (tpp) REVERT: Ap 142 ASP cc_start: 0.8504 (t0) cc_final: 0.7840 (t0) REVERT: Ap 166 MET cc_start: 0.8179 (tpp) cc_final: 0.7002 (tpp) REVERT: Ap 192 LEU cc_start: 0.9364 (mm) cc_final: 0.9089 (mm) REVERT: Aq 92 THR cc_start: 0.8729 (p) cc_final: 0.8255 (p) REVERT: Aq 98 ASN cc_start: 0.8662 (t0) cc_final: 0.7683 (t0) REVERT: Aq 128 ASN cc_start: 0.8480 (t0) cc_final: 0.8028 (t0) REVERT: Aq 166 MET cc_start: 0.8138 (tpp) cc_final: 0.6991 (tpp) REVERT: Aq 188 PRO cc_start: 0.8930 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: Aq 190 TYR cc_start: 0.8309 (t80) cc_final: 0.7771 (t80) REVERT: Aq 207 ASP cc_start: 0.8407 (p0) cc_final: 0.7164 (t70) REVERT: Ar 72 ASN cc_start: 0.8502 (t0) cc_final: 0.8292 (t0) REVERT: Ar 83 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8513 (tm-30) REVERT: Ar 95 GLN cc_start: 0.7454 (mt0) cc_final: 0.7217 (mt0) REVERT: Ar 166 MET cc_start: 0.7985 (mmp) cc_final: 0.7468 (tpp) REVERT: Ar 187 MET cc_start: 0.8269 (tmm) cc_final: 0.8045 (tmm) REVERT: As 58 GLU cc_start: 0.8789 (mp0) cc_final: 0.8369 (mp0) REVERT: As 79 TYR cc_start: 0.7869 (t80) cc_final: 0.7616 (t80) REVERT: As 83 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8181 (tm-30) REVERT: As 135 SER cc_start: 0.8909 (m) cc_final: 0.8448 (t) REVERT: As 142 ASP cc_start: 0.8837 (t0) cc_final: 0.8037 (t0) REVERT: As 166 MET cc_start: 0.7955 (tpp) cc_final: 0.6544 (tpp) REVERT: As 187 MET cc_start: 0.8238 (tmm) cc_final: 0.7680 (tmm) REVERT: As 190 TYR cc_start: 0.8489 (t80) cc_final: 0.8249 (t80) REVERT: As 192 LEU cc_start: 0.9572 (mt) cc_final: 0.9253 (mt) REVERT: As 208 PHE cc_start: 0.8779 (p90) cc_final: 0.8422 (p90) REVERT: At 58 GLU cc_start: 0.8765 (mp0) cc_final: 0.8379 (mp0) REVERT: At 76 LEU cc_start: 0.7895 (tp) cc_final: 0.7694 (tp) REVERT: At 79 TYR cc_start: 0.7642 (t80) cc_final: 0.6403 (t80) REVERT: At 83 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8162 (tm-30) REVERT: At 98 ASN cc_start: 0.8381 (t0) cc_final: 0.7711 (t0) REVERT: At 122 MET cc_start: 0.8893 (ttt) cc_final: 0.8571 (tpp) REVERT: At 141 MET cc_start: 0.7462 (mtt) cc_final: 0.7094 (mtt) REVERT: At 166 MET cc_start: 0.7999 (mmp) cc_final: 0.7500 (tpp) REVERT: At 187 MET cc_start: 0.7966 (tmm) cc_final: 0.7492 (tmm) REVERT: At 188 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.7819 (Cg_endo) REVERT: At 218 ARG cc_start: 0.8858 (ttt90) cc_final: 0.8548 (ttp-170) REVERT: Au 58 GLU cc_start: 0.8914 (mp0) cc_final: 0.8464 (mp0) REVERT: Au 76 LEU cc_start: 0.8428 (tp) cc_final: 0.8026 (tp) REVERT: Au 79 TYR cc_start: 0.7917 (t80) cc_final: 0.7471 (t80) REVERT: Au 92 THR cc_start: 0.8629 (p) cc_final: 0.8253 (p) REVERT: Au 128 ASN cc_start: 0.8684 (t0) cc_final: 0.8283 (t0) REVERT: Au 135 SER cc_start: 0.9073 (m) cc_final: 0.8685 (t) REVERT: Au 141 MET cc_start: 0.7886 (mmt) cc_final: 0.7590 (mmt) REVERT: Au 166 MET cc_start: 0.8175 (mmp) cc_final: 0.7414 (tpp) REVERT: Au 187 MET cc_start: 0.8088 (tmm) cc_final: 0.7782 (tmm) REVERT: Au 195 ASN cc_start: 0.9141 (t0) cc_final: 0.8922 (t0) REVERT: Au 212 THR cc_start: 0.9142 (t) cc_final: 0.8775 (p) REVERT: Au 218 ARG cc_start: 0.8904 (ttt90) cc_final: 0.8619 (ttp-170) REVERT: Av 58 GLU cc_start: 0.8865 (mp0) cc_final: 0.8449 (mp0) REVERT: Av 128 ASN cc_start: 0.8774 (t0) cc_final: 0.8501 (t0) REVERT: Av 141 MET cc_start: 0.7236 (tpp) cc_final: 0.6351 (tpp) REVERT: Av 166 MET cc_start: 0.8033 (mmp) cc_final: 0.7411 (tpp) REVERT: Av 187 MET cc_start: 0.8456 (tmm) cc_final: 0.7845 (tmm) REVERT: Av 192 LEU cc_start: 0.9529 (mt) cc_final: 0.8790 (mt) REVERT: Av 218 ARG cc_start: 0.8936 (ttt90) cc_final: 0.8707 (ttp-170) REVERT: Aw 58 GLU cc_start: 0.8841 (mp0) cc_final: 0.8487 (mp0) REVERT: Aw 110 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8821 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8597 (t0) cc_final: 0.8339 (t0) REVERT: Aw 166 MET cc_start: 0.8187 (mmp) cc_final: 0.7512 (tpp) REVERT: Aw 187 MET cc_start: 0.8198 (tmm) cc_final: 0.7527 (tmm) REVERT: Aw 188 PRO cc_start: 0.8874 (Cg_endo) cc_final: 0.7972 (Cg_exo) REVERT: Aw 190 TYR cc_start: 0.8230 (t80) cc_final: 0.7728 (t80) REVERT: Aw 192 LEU cc_start: 0.9520 (mt) cc_final: 0.8672 (mt) REVERT: Ax 58 GLU cc_start: 0.8847 (mp0) cc_final: 0.8493 (mp0) REVERT: Ax 98 ASN cc_start: 0.8333 (t0) cc_final: 0.7606 (t0) REVERT: Ax 141 MET cc_start: 0.7887 (mmt) cc_final: 0.7534 (tpp) REVERT: Ax 166 MET cc_start: 0.8172 (mmp) cc_final: 0.7775 (tpp) REVERT: Ax 192 LEU cc_start: 0.9407 (mm) cc_final: 0.9111 (mm) REVERT: Ay 58 GLU cc_start: 0.8856 (mp0) cc_final: 0.8489 (mp0) REVERT: Ay 83 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Ay 142 ASP cc_start: 0.8697 (t0) cc_final: 0.8458 (t0) REVERT: Ay 166 MET cc_start: 0.8164 (mmp) cc_final: 0.7347 (tpp) REVERT: Ay 187 MET cc_start: 0.8269 (tmm) cc_final: 0.7661 (tmm) REVERT: Ay 218 ARG cc_start: 0.9035 (ttt90) cc_final: 0.8769 (ttp-170) REVERT: Az 58 GLU cc_start: 0.8725 (mp0) cc_final: 0.8447 (mp0) REVERT: Az 140 MET cc_start: 0.6376 (tmm) cc_final: 0.5953 (tmm) REVERT: Az 141 MET cc_start: 0.8251 (mmt) cc_final: 0.7940 (tpp) REVERT: Az 142 ASP cc_start: 0.8727 (t0) cc_final: 0.8282 (t0) REVERT: Az 166 MET cc_start: 0.7926 (mmp) cc_final: 0.7661 (tpp) REVERT: Az 218 ARG cc_start: 0.9015 (ttt90) cc_final: 0.8628 (ttp-170) REVERT: Ba 58 GLU cc_start: 0.8836 (mp0) cc_final: 0.8385 (mp0) REVERT: Ba 83 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8148 (tm-30) REVERT: Ba 140 MET cc_start: 0.7193 (tmm) cc_final: 0.6959 (tmm) REVERT: Ba 166 MET cc_start: 0.7972 (mmp) cc_final: 0.7244 (tpp) REVERT: Ba 187 MET cc_start: 0.8114 (tmm) cc_final: 0.7650 (tmm) REVERT: Ba 188 PRO cc_start: 0.8676 (Cg_endo) cc_final: 0.8144 (Cg_exo) REVERT: Ba 190 TYR cc_start: 0.8252 (t80) cc_final: 0.8045 (t80) REVERT: Ba 192 LEU cc_start: 0.9479 (mt) cc_final: 0.8910 (mt) outliers start: 1 outliers final: 0 residues processed: 1718 average time/residue: 0.2115 time to fit residues: 638.5730 Evaluate side-chains 1392 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1392 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 137 optimal weight: 0.9990 chunk 152 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 464 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 409 optimal weight: 0.0670 chunk 282 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN ** Ac 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 146 GLN Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 146 GLN ** Ag 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 65 GLN ** Ah 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 146 GLN ** Ah 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 95 GLN ** Aj 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 146 GLN ** Aj 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Ak 168 HIS Al 146 GLN ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 146 GLN ** Aq 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 75 HIS Ar 95 GLN ** Ar 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 128 ASN ** At 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 146 GLN ** Au 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 98 ASN Av 146 GLN ** Aw 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN ** Ax 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 146 GLN Ay 98 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 98 ASN ** Ba 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 146 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113168 restraints weight = 64908.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116354 restraints weight = 43612.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118706 restraints weight = 31971.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120463 restraints weight = 24929.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121768 restraints weight = 20378.430| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41391 Z= 0.120 Angle : 0.647 7.777 55782 Z= 0.335 Chirality : 0.038 0.200 5940 Planarity : 0.005 0.055 7209 Dihedral : 4.272 24.322 5535 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.64 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.01 (0.12), residues: 4941 helix: 1.15 (0.12), residues: 2133 sheet: 0.92 (0.27), residues: 270 loop : -1.16 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAv 189 TYR 0.026 0.002 TYRAv 204 PHE 0.020 0.002 PHEAj 208 TRP 0.022 0.002 TRPBa 99 HIS 0.008 0.001 HISAa 168 Details of bonding type rmsd covalent geometry : bond 0.00281 (41391) covalent geometry : angle 0.64650 (55782) hydrogen bonds : bond 0.02599 ( 1574) hydrogen bonds : angle 3.67146 ( 4317) ********************** 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 1751 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1749 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 83 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7918 (tm-30) REVERT: Aa 84 VAL cc_start: 0.8691 (m) cc_final: 0.8469 (m) REVERT: Aa 128 ASN cc_start: 0.8416 (t0) cc_final: 0.8031 (t0) REVERT: Aa 142 ASP cc_start: 0.8325 (t0) cc_final: 0.7994 (t0) REVERT: Aa 166 MET cc_start: 0.7845 (mmp) cc_final: 0.7382 (tpp) REVERT: Aa 190 TYR cc_start: 0.7961 (t80) cc_final: 0.7643 (t80) REVERT: Ab 142 ASP cc_start: 0.8524 (t0) cc_final: 0.8143 (t0) REVERT: Ab 166 MET cc_start: 0.7908 (mmp) cc_final: 0.7601 (tpp) REVERT: Ab 190 TYR cc_start: 0.8195 (t80) cc_final: 0.7945 (t80) REVERT: Ac 83 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8094 (tm-30) REVERT: Ac 141 MET cc_start: 0.7738 (tpt) cc_final: 0.7082 (tpt) REVERT: Ac 166 MET cc_start: 0.7890 (mmp) cc_final: 0.6577 (tpp) REVERT: Ac 192 LEU cc_start: 0.9508 (mt) cc_final: 0.9180 (mt) REVERT: Ad 72 ASN cc_start: 0.8609 (t0) cc_final: 0.8359 (t0) REVERT: Ad 85 ASP cc_start: 0.8083 (m-30) cc_final: 0.7852 (m-30) REVERT: Ad 92 THR cc_start: 0.8652 (p) cc_final: 0.8317 (p) REVERT: Ad 122 MET cc_start: 0.8814 (ttp) cc_final: 0.8137 (tpp) REVERT: Ad 142 ASP cc_start: 0.8438 (t0) cc_final: 0.8214 (t0) REVERT: Ad 166 MET cc_start: 0.8109 (tpp) cc_final: 0.7069 (tpp) REVERT: Ad 187 MET cc_start: 0.8128 (ttp) cc_final: 0.7611 (tmm) REVERT: Ad 190 TYR cc_start: 0.7941 (t80) cc_final: 0.7682 (t80) REVERT: Ae 83 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8120 (tm-30) REVERT: Ae 122 MET cc_start: 0.8905 (ttm) cc_final: 0.8455 (tpp) REVERT: Ae 166 MET cc_start: 0.7898 (mmp) cc_final: 0.6802 (tpp) REVERT: Ae 187 MET cc_start: 0.8030 (tmm) cc_final: 0.7424 (tmm) REVERT: Ae 190 TYR cc_start: 0.7499 (t80) cc_final: 0.7107 (t80) REVERT: Ae 207 ASP cc_start: 0.8394 (p0) cc_final: 0.7698 (t0) REVERT: Ae 208 PHE cc_start: 0.8716 (p90) cc_final: 0.8169 (p90) REVERT: Af 122 MET cc_start: 0.9013 (ttp) cc_final: 0.8788 (tpp) REVERT: Af 142 ASP cc_start: 0.8162 (t0) cc_final: 0.7787 (t0) REVERT: Af 166 MET cc_start: 0.7842 (tpp) cc_final: 0.7511 (tpp) REVERT: Ag 83 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8017 (tm-30) REVERT: Ag 166 MET cc_start: 0.7980 (mmp) cc_final: 0.7451 (tpp) REVERT: Ag 190 TYR cc_start: 0.7701 (t80) cc_final: 0.7405 (t80) REVERT: Ag 208 PHE cc_start: 0.8788 (p90) cc_final: 0.8247 (p90) REVERT: Ah 83 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8073 (tm-30) REVERT: Ah 112 GLU cc_start: 0.8405 (pp20) cc_final: 0.8145 (pp20) REVERT: Ah 142 ASP cc_start: 0.8563 (t0) cc_final: 0.8204 (t0) REVERT: Ah 166 MET cc_start: 0.7738 (mmp) cc_final: 0.7485 (tpp) REVERT: Ah 190 TYR cc_start: 0.8037 (t80) cc_final: 0.7719 (t80) REVERT: Ah 207 ASP cc_start: 0.8368 (t70) cc_final: 0.8071 (t0) REVERT: Ai 114 MET cc_start: 0.7655 (ttm) cc_final: 0.7354 (ttp) REVERT: Ai 122 MET cc_start: 0.8930 (ttp) cc_final: 0.8489 (tpp) REVERT: Ai 141 MET cc_start: 0.7907 (tpp) cc_final: 0.6769 (tpp) REVERT: Ai 166 MET cc_start: 0.8007 (mmp) cc_final: 0.7503 (tpp) REVERT: Ai 187 MET cc_start: 0.8341 (tmm) cc_final: 0.8088 (tmm) REVERT: Ai 190 TYR cc_start: 0.8142 (t80) cc_final: 0.7604 (t80) REVERT: Ai 192 LEU cc_start: 0.9405 (mm) cc_final: 0.8971 (mm) REVERT: Aj 141 MET cc_start: 0.7960 (tpt) cc_final: 0.7386 (tpt) REVERT: Aj 142 ASP cc_start: 0.8944 (t0) cc_final: 0.8479 (t0) REVERT: Aj 166 MET cc_start: 0.7879 (mmp) cc_final: 0.7464 (tpp) REVERT: Aj 187 MET cc_start: 0.8417 (tmm) cc_final: 0.7953 (tmm) REVERT: Aj 199 MET cc_start: 0.8399 (tpp) cc_final: 0.8178 (tpp) REVERT: Ak 98 ASN cc_start: 0.8353 (t0) cc_final: 0.7506 (t0) REVERT: Ak 166 MET cc_start: 0.8231 (tpp) cc_final: 0.7579 (tpp) REVERT: Ak 187 MET cc_start: 0.8125 (ttm) cc_final: 0.7383 (mtt) REVERT: Al 72 ASN cc_start: 0.8651 (t0) cc_final: 0.8168 (t0) REVERT: Al 83 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7752 (tm-30) REVERT: Al 98 ASN cc_start: 0.8363 (t0) cc_final: 0.8057 (t0) REVERT: Al 141 MET cc_start: 0.7374 (tpp) cc_final: 0.6583 (tpp) REVERT: Al 166 MET cc_start: 0.8272 (tpp) cc_final: 0.7052 (tpp) REVERT: Al 187 MET cc_start: 0.8150 (tmm) cc_final: 0.7751 (tmm) REVERT: Al 188 PRO cc_start: 0.8849 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: Al 192 LEU cc_start: 0.9470 (mm) cc_final: 0.8962 (mm) REVERT: Al 208 PHE cc_start: 0.8736 (p90) cc_final: 0.8473 (p90) REVERT: Am 58 GLU cc_start: 0.8483 (mp0) cc_final: 0.8233 (mp0) REVERT: Am 83 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7984 (tm-30) REVERT: Am 141 MET cc_start: 0.8059 (mmt) cc_final: 0.7833 (mmt) REVERT: Am 142 ASP cc_start: 0.8711 (t0) cc_final: 0.8500 (t0) REVERT: Am 166 MET cc_start: 0.8118 (tpp) cc_final: 0.6705 (tpp) REVERT: Am 187 MET cc_start: 0.8525 (tpp) cc_final: 0.7962 (tmm) REVERT: Am 192 LEU cc_start: 0.9444 (mm) cc_final: 0.9193 (mm) REVERT: Am 208 PHE cc_start: 0.8965 (p90) cc_final: 0.8583 (p90) REVERT: An 83 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7988 (tm-30) REVERT: An 98 ASN cc_start: 0.8401 (t0) cc_final: 0.7771 (t0) REVERT: An 141 MET cc_start: 0.7611 (mmm) cc_final: 0.7097 (tpp) REVERT: An 142 ASP cc_start: 0.8194 (t0) cc_final: 0.7475 (t0) REVERT: An 166 MET cc_start: 0.7971 (mmp) cc_final: 0.7260 (tpp) REVERT: Ao 72 ASN cc_start: 0.8465 (t0) cc_final: 0.8189 (t0) REVERT: Ao 91 SER cc_start: 0.8802 (m) cc_final: 0.8480 (m) REVERT: Ao 98 ASN cc_start: 0.8426 (t0) cc_final: 0.7725 (t0) REVERT: Ao 141 MET cc_start: 0.7947 (mmt) cc_final: 0.7596 (mmt) REVERT: Ao 166 MET cc_start: 0.7934 (mmp) cc_final: 0.7330 (tpp) REVERT: Ap 72 ASN cc_start: 0.8754 (t0) cc_final: 0.8280 (t0) REVERT: Ap 83 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7993 (tm-30) REVERT: Ap 112 GLU cc_start: 0.8528 (pp20) cc_final: 0.8296 (pp20) REVERT: Ap 142 ASP cc_start: 0.8502 (t0) cc_final: 0.8033 (t0) REVERT: Ap 166 MET cc_start: 0.8137 (tpp) cc_final: 0.6437 (tpp) REVERT: Ap 190 TYR cc_start: 0.7889 (t80) cc_final: 0.7682 (t80) REVERT: Ap 192 LEU cc_start: 0.9321 (mm) cc_final: 0.8930 (mm) REVERT: Ap 208 PHE cc_start: 0.8865 (p90) cc_final: 0.8208 (p90) REVERT: Aq 92 THR cc_start: 0.8638 (p) cc_final: 0.8161 (p) REVERT: Aq 98 ASN cc_start: 0.8537 (t0) cc_final: 0.7563 (t0) REVERT: Aq 128 ASN cc_start: 0.8382 (t0) cc_final: 0.7937 (t0) REVERT: Aq 166 MET cc_start: 0.8054 (tpp) cc_final: 0.6922 (tpp) REVERT: Aq 187 MET cc_start: 0.7964 (tmm) cc_final: 0.7763 (tmm) REVERT: Aq 190 TYR cc_start: 0.7974 (t80) cc_final: 0.7531 (t80) REVERT: Aq 207 ASP cc_start: 0.8357 (p0) cc_final: 0.6927 (t70) REVERT: Ar 72 ASN cc_start: 0.8372 (t0) cc_final: 0.7978 (t0) REVERT: Ar 142 ASP cc_start: 0.8355 (t0) cc_final: 0.8114 (t0) REVERT: Ar 166 MET cc_start: 0.7841 (mmp) cc_final: 0.6943 (tpp) REVERT: Ar 187 MET cc_start: 0.8224 (tmm) cc_final: 0.7966 (tmm) REVERT: As 58 GLU cc_start: 0.8715 (mp0) cc_final: 0.8357 (mp0) REVERT: As 83 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8068 (tm-30) REVERT: As 135 SER cc_start: 0.8835 (m) cc_final: 0.8494 (t) REVERT: As 140 MET cc_start: 0.7955 (tmm) cc_final: 0.7664 (tmm) REVERT: As 142 ASP cc_start: 0.8393 (t0) cc_final: 0.7790 (t0) REVERT: As 166 MET cc_start: 0.7820 (tpp) cc_final: 0.6623 (tpp) REVERT: As 187 MET cc_start: 0.8135 (tmm) cc_final: 0.7672 (tmm) REVERT: As 192 LEU cc_start: 0.9510 (mt) cc_final: 0.9283 (mt) REVERT: At 58 GLU cc_start: 0.8675 (mp0) cc_final: 0.8321 (mp0) REVERT: At 79 TYR cc_start: 0.7615 (t80) cc_final: 0.6573 (t80) REVERT: At 83 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7993 (tm-30) REVERT: At 92 THR cc_start: 0.8404 (p) cc_final: 0.8000 (p) REVERT: At 98 ASN cc_start: 0.8310 (t0) cc_final: 0.7613 (t0) REVERT: At 122 MET cc_start: 0.8745 (ttt) cc_final: 0.8538 (tpp) REVERT: At 142 ASP cc_start: 0.8307 (t0) cc_final: 0.8058 (p0) REVERT: At 166 MET cc_start: 0.7934 (mmp) cc_final: 0.7388 (tpp) REVERT: At 188 PRO cc_start: 0.8612 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: Au 58 GLU cc_start: 0.8787 (mp0) cc_final: 0.8396 (mp0) REVERT: Au 92 THR cc_start: 0.8339 (p) cc_final: 0.7924 (p) REVERT: Au 128 ASN cc_start: 0.8668 (t0) cc_final: 0.8302 (t0) REVERT: Au 135 SER cc_start: 0.9163 (m) cc_final: 0.8875 (t) REVERT: Au 141 MET cc_start: 0.7795 (mmt) cc_final: 0.7578 (mmt) REVERT: Au 166 MET cc_start: 0.8080 (mmp) cc_final: 0.6846 (tpp) REVERT: Au 195 ASN cc_start: 0.9171 (t0) cc_final: 0.8968 (t0) REVERT: Au 201 LEU cc_start: 0.9379 (mm) cc_final: 0.9154 (mm) REVERT: Au 212 THR cc_start: 0.8978 (t) cc_final: 0.8770 (p) REVERT: Au 218 ARG cc_start: 0.8940 (ttt90) cc_final: 0.8662 (ttp-170) REVERT: Av 58 GLU cc_start: 0.8770 (mp0) cc_final: 0.8416 (mp0) REVERT: Av 98 ASN cc_start: 0.8358 (t0) cc_final: 0.7647 (t0) REVERT: Av 128 ASN cc_start: 0.8754 (t0) cc_final: 0.8477 (t0) REVERT: Av 166 MET cc_start: 0.7857 (mmp) cc_final: 0.7265 (tpp) REVERT: Av 187 MET cc_start: 0.8339 (tmm) cc_final: 0.7847 (tmm) REVERT: Av 192 LEU cc_start: 0.9522 (mt) cc_final: 0.8915 (mt) REVERT: Aw 58 GLU cc_start: 0.8759 (mp0) cc_final: 0.8443 (mp0) REVERT: Aw 110 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8775 (mm-40) REVERT: Aw 128 ASN cc_start: 0.8482 (t0) cc_final: 0.8220 (t0) REVERT: Aw 166 MET cc_start: 0.8034 (mmp) cc_final: 0.7521 (tpp) REVERT: Aw 187 MET cc_start: 0.7985 (tmm) cc_final: 0.7579 (tmm) REVERT: Aw 188 PRO cc_start: 0.8728 (Cg_endo) cc_final: 0.8379 (Cg_exo) REVERT: Aw 192 LEU cc_start: 0.9413 (mt) cc_final: 0.8969 (mt) REVERT: Ax 58 GLU cc_start: 0.8785 (mp0) cc_final: 0.8429 (mp0) REVERT: Ax 98 ASN cc_start: 0.8293 (t0) cc_final: 0.7572 (t0) REVERT: Ax 141 MET cc_start: 0.7566 (mmt) cc_final: 0.7209 (tpp) REVERT: Ax 166 MET cc_start: 0.8015 (mmp) cc_final: 0.7708 (tpp) REVERT: Ax 187 MET cc_start: 0.8285 (tmm) cc_final: 0.7527 (tmm) REVERT: Ax 190 TYR cc_start: 0.8181 (t80) cc_final: 0.7955 (t80) REVERT: Ax 192 LEU cc_start: 0.9406 (mm) cc_final: 0.7756 (mm) REVERT: Ay 58 GLU cc_start: 0.8810 (mp0) cc_final: 0.8454 (mp0) REVERT: Ay 72 ASN cc_start: 0.8377 (t0) cc_final: 0.8077 (t0) REVERT: Ay 83 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Ay 141 MET cc_start: 0.7342 (tpp) cc_final: 0.6921 (mmt) REVERT: Ay 142 ASP cc_start: 0.8625 (t0) cc_final: 0.8281 (t0) REVERT: Ay 166 MET cc_start: 0.8027 (mmp) cc_final: 0.7307 (tpp) REVERT: Ay 187 MET cc_start: 0.8309 (tmm) cc_final: 0.7694 (tmm) REVERT: Ay 218 ARG cc_start: 0.8954 (ttt90) cc_final: 0.8570 (ttp-170) REVERT: Az 58 GLU cc_start: 0.8618 (mp0) cc_final: 0.8375 (mp0) REVERT: Az 72 ASN cc_start: 0.8508 (t0) cc_final: 0.8160 (t0) REVERT: Az 98 ASN cc_start: 0.8416 (t0) cc_final: 0.7768 (t0) REVERT: Az 140 MET cc_start: 0.6223 (tmm) cc_final: 0.6011 (tmm) REVERT: Az 141 MET cc_start: 0.8102 (mmt) cc_final: 0.7809 (tpp) REVERT: Az 142 ASP cc_start: 0.8766 (t0) cc_final: 0.8343 (t0) REVERT: Az 166 MET cc_start: 0.7635 (mmp) cc_final: 0.7116 (tpp) REVERT: Az 218 ARG cc_start: 0.8923 (ttt90) cc_final: 0.8678 (ttp-170) REVERT: Ba 58 GLU cc_start: 0.8715 (mp0) cc_final: 0.8301 (mp0) REVERT: Ba 83 GLN cc_start: 0.8517 (tm-30) cc_final: 0.7969 (tm-30) REVERT: Ba 84 VAL cc_start: 0.8566 (m) cc_final: 0.8281 (m) REVERT: Ba 98 ASN cc_start: 0.8374 (t0) cc_final: 0.7834 (t0) REVERT: Ba 166 MET cc_start: 0.7825 (mmp) cc_final: 0.7116 (tpp) REVERT: Ba 187 MET cc_start: 0.8004 (tmm) cc_final: 0.7497 (tmm) REVERT: Ba 188 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8024 (Cg_exo) REVERT: Ba 190 TYR cc_start: 0.8062 (t80) cc_final: 0.7831 (t80) REVERT: Ba 192 LEU cc_start: 0.9458 (mt) cc_final: 0.8870 (mt) outliers start: 2 outliers final: 0 residues processed: 1751 average time/residue: 0.2156 time to fit residues: 666.9888 Evaluate side-chains 1409 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1409 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 7 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 385 optimal weight: 6.9990 chunk 286 optimal weight: 0.2980 chunk 369 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 95 GLN Ac 146 GLN Ad 146 GLN ** Ae 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN ** Af 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 146 GLN Ah 146 GLN ** Ah 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 128 ASN Aj 146 GLN ** Ak 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 146 GLN Al 95 GLN Al 128 ASN Al 146 GLN Am 95 GLN ** Am 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 146 GLN ** Ap 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 75 HIS As 95 GLN As 128 ASN ** As 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 75 HIS ** At 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 75 HIS Av 98 ASN Av 146 GLN ** Av 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 225 GLN Aw 95 GLN ** Aw 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 146 GLN ** Ax 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 ASN ** Ay 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 98 ASN Ba 146 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111289 restraints weight = 65541.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114435 restraints weight = 43934.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116748 restraints weight = 32322.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118376 restraints weight = 25334.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119747 restraints weight = 20978.282| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41391 Z= 0.158 Angle : 0.684 8.338 55782 Z= 0.358 Chirality : 0.039 0.184 5940 Planarity : 0.005 0.055 7209 Dihedral : 4.368 18.906 5535 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4941 helix: 1.00 (0.11), residues: 2133 sheet: 0.85 (0.26), residues: 270 loop : -1.18 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAp 189 TYR 0.025 0.002 TYRAn 204 PHE 0.022 0.002 PHEAx 206 TRP 0.021 0.002 TRPAx 99 HIS 0.011 0.002 HISAk 168 Details of bonding type rmsd covalent geometry : bond 0.00375 (41391) covalent geometry : angle 0.68356 (55782) hydrogen bonds : bond 0.03226 ( 1574) hydrogen bonds : angle 3.92179 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10131.64 seconds wall clock time: 174 minutes 52.16 seconds (10492.16 seconds total)