Starting phenix.real_space_refine on Sun Feb 8 01:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r9w_53862/02_2026/9r9w_53862.map" } resolution = 3.34 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= 0.060 sd= 0.489 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 360 5.16 5 C 23880 2.51 5 N 6816 2.21 5 O 6912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 384 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: 37968 Number of models: 1 Model: "" Number of chains: 24 Chain: "Aa" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ab" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ac" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ad" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ae" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Af" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ag" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ah" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ai" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Aj" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ak" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Al" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Am" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "An" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ao" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ap" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Aq" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ar" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "As" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "At" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Au" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Av" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Aw" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Chain: "Ax" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1582 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Time building chain proxies: 8.61, per 1000 atoms: 0.23 Number of scatterers: 37968 At special positions: 0 Unit cell: (142.5, 143.45, 188.1, 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 360 16.00 O 6912 8.00 N 6816 7.00 C 23880 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8928 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 48 sheets defined 57.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'Aa' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAa 69 " --> pdb=" O ASNAa 65 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 73 through 77 Processing helix chain 'Aa' and resid 83 through 99 Processing helix chain 'Aa' and resid 101 through 120 Processing helix chain 'Aa' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAa 148 " --> pdb=" O PROAa 144 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 152 through 158 Processing helix chain 'Aa' and resid 160 through 172 Processing helix chain 'Aa' and resid 179 through 184 Processing helix chain 'Aa' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAa 194 " --> pdb=" O SERAa 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALAAa 196 " --> pdb=" O SERAa 193 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAa 218 " --> pdb=" O HISAa 214 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 227 through 231 removed outlier: 3.580A pdb=" N PHEAa 230 " --> pdb=" O THRAa 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAa 231 " --> pdb=" O ARGAa 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 227 through 231' Processing helix chain 'Ab' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAb 69 " --> pdb=" O ASNAb 65 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 73 through 77 Processing helix chain 'Ab' and resid 83 through 99 Processing helix chain 'Ab' and resid 101 through 120 Processing helix chain 'Ab' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAb 148 " --> pdb=" O PROAb 144 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 152 through 158 Processing helix chain 'Ab' and resid 160 through 172 Processing helix chain 'Ab' and resid 179 through 184 Processing helix chain 'Ab' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAb 194 " --> pdb=" O SERAb 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAAb 196 " --> pdb=" O SERAb 193 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAb 218 " --> pdb=" O HISAb 214 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAb 230 " --> pdb=" O THRAb 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAb 231 " --> pdb=" O ARGAb 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 227 through 231' Processing helix chain 'Ac' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAc 69 " --> pdb=" O ASNAc 65 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 73 through 77 Processing helix chain 'Ac' and resid 83 through 99 Processing helix chain 'Ac' and resid 101 through 120 Processing helix chain 'Ac' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAc 148 " --> pdb=" O PROAc 144 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 152 through 158 Processing helix chain 'Ac' and resid 160 through 172 Processing helix chain 'Ac' and resid 179 through 184 Processing helix chain 'Ac' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAc 194 " --> pdb=" O SERAc 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAc 196 " --> pdb=" O SERAc 193 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAc 218 " --> pdb=" O HISAc 214 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAc 230 " --> pdb=" O THRAc 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAc 231 " --> pdb=" O ARGAc 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 227 through 231' Processing helix chain 'Ad' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAd 69 " --> pdb=" O ASNAd 65 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 73 through 77 Processing helix chain 'Ad' and resid 83 through 99 Processing helix chain 'Ad' and resid 101 through 120 Processing helix chain 'Ad' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAd 148 " --> pdb=" O PROAd 144 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 152 through 158 Processing helix chain 'Ad' and resid 160 through 172 Processing helix chain 'Ad' and resid 179 through 184 Processing helix chain 'Ad' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAd 194 " --> pdb=" O SERAd 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAd 196 " --> pdb=" O SERAd 193 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAd 218 " --> pdb=" O HISAd 214 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAd 230 " --> pdb=" O THRAd 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAd 231 " --> pdb=" O ARGAd 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 227 through 231' Processing helix chain 'Ae' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAe 69 " --> pdb=" O ASNAe 65 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 73 through 77 Processing helix chain 'Ae' and resid 83 through 99 Processing helix chain 'Ae' and resid 101 through 120 Processing helix chain 'Ae' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAe 148 " --> pdb=" O PROAe 144 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 152 through 158 Processing helix chain 'Ae' and resid 160 through 172 Processing helix chain 'Ae' and resid 179 through 184 Processing helix chain 'Ae' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAe 194 " --> pdb=" O SERAe 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAe 196 " --> pdb=" O SERAe 193 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAe 218 " --> pdb=" O HISAe 214 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAe 230 " --> pdb=" O THRAe 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAe 231 " --> pdb=" O ARGAe 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 227 through 231' Processing helix chain 'Af' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAf 69 " --> pdb=" O ASNAf 65 " (cutoff:3.500A) Processing helix chain 'Af' and resid 73 through 77 Processing helix chain 'Af' and resid 83 through 99 Processing helix chain 'Af' and resid 101 through 120 Processing helix chain 'Af' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAf 148 " --> pdb=" O PROAf 144 " (cutoff:3.500A) Processing helix chain 'Af' and resid 152 through 158 Processing helix chain 'Af' and resid 160 through 172 Processing helix chain 'Af' and resid 179 through 184 Processing helix chain 'Af' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAf 194 " --> pdb=" O SERAf 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAf 196 " --> pdb=" O SERAf 193 " (cutoff:3.500A) Processing helix chain 'Af' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAf 218 " --> pdb=" O HISAf 214 " (cutoff:3.500A) Processing helix chain 'Af' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAf 230 " --> pdb=" O THRAf 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAf 231 " --> pdb=" O ARGAf 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Af' and resid 227 through 231' Processing helix chain 'Ag' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAg 69 " --> pdb=" O ASNAg 65 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 73 through 77 Processing helix chain 'Ag' and resid 83 through 99 Processing helix chain 'Ag' and resid 101 through 120 Processing helix chain 'Ag' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAg 148 " --> pdb=" O PROAg 144 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 152 through 158 Processing helix chain 'Ag' and resid 160 through 172 Processing helix chain 'Ag' and resid 179 through 184 Processing helix chain 'Ag' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAg 194 " --> pdb=" O SERAg 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAg 196 " --> pdb=" O SERAg 193 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 207 through 224 removed outlier: 3.668A pdb=" N LYSAg 218 " --> pdb=" O HISAg 214 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAg 230 " --> pdb=" O THRAg 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAg 231 " --> pdb=" O ARGAg 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 227 through 231' Processing helix chain 'Ah' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAh 69 " --> pdb=" O ASNAh 65 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 73 through 77 Processing helix chain 'Ah' and resid 83 through 99 Processing helix chain 'Ah' and resid 101 through 120 Processing helix chain 'Ah' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAh 148 " --> pdb=" O PROAh 144 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 152 through 158 Processing helix chain 'Ah' and resid 160 through 172 Processing helix chain 'Ah' and resid 179 through 184 Processing helix chain 'Ah' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAh 194 " --> pdb=" O SERAh 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAh 196 " --> pdb=" O SERAh 193 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAh 218 " --> pdb=" O HISAh 214 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAh 230 " --> pdb=" O THRAh 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAh 231 " --> pdb=" O ARGAh 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 227 through 231' Processing helix chain 'Ai' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAi 69 " --> pdb=" O ASNAi 65 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 73 through 77 Processing helix chain 'Ai' and resid 83 through 99 Processing helix chain 'Ai' and resid 101 through 120 Processing helix chain 'Ai' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAi 148 " --> pdb=" O PROAi 144 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 152 through 158 Processing helix chain 'Ai' and resid 160 through 172 Processing helix chain 'Ai' and resid 179 through 184 Processing helix chain 'Ai' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAi 194 " --> pdb=" O SERAi 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAi 196 " --> pdb=" O SERAi 193 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAi 218 " --> pdb=" O HISAi 214 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 227 through 231 removed outlier: 3.580A pdb=" N PHEAi 230 " --> pdb=" O THRAi 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAi 231 " --> pdb=" O ARGAi 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ai' and resid 227 through 231' Processing helix chain 'Aj' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAj 69 " --> pdb=" O ASNAj 65 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 73 through 77 Processing helix chain 'Aj' and resid 83 through 99 Processing helix chain 'Aj' and resid 101 through 120 Processing helix chain 'Aj' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAj 148 " --> pdb=" O PROAj 144 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 152 through 158 Processing helix chain 'Aj' and resid 160 through 172 Processing helix chain 'Aj' and resid 179 through 184 Processing helix chain 'Aj' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAj 194 " --> pdb=" O SERAj 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAj 196 " --> pdb=" O SERAj 193 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAj 218 " --> pdb=" O HISAj 214 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAj 230 " --> pdb=" O THRAj 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAj 231 " --> pdb=" O ARGAj 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aj' and resid 227 through 231' Processing helix chain 'Ak' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAk 69 " --> pdb=" O ASNAk 65 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 73 through 77 Processing helix chain 'Ak' and resid 83 through 99 Processing helix chain 'Ak' and resid 101 through 120 Processing helix chain 'Ak' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAk 148 " --> pdb=" O PROAk 144 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 152 through 158 Processing helix chain 'Ak' and resid 160 through 172 Processing helix chain 'Ak' and resid 179 through 184 Processing helix chain 'Ak' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAk 194 " --> pdb=" O SERAk 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAk 196 " --> pdb=" O SERAk 193 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAk 218 " --> pdb=" O HISAk 214 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAk 230 " --> pdb=" O THRAk 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAk 231 " --> pdb=" O ARGAk 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 227 through 231' Processing helix chain 'Al' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAl 69 " --> pdb=" O ASNAl 65 " (cutoff:3.500A) Processing helix chain 'Al' and resid 73 through 77 Processing helix chain 'Al' and resid 83 through 99 Processing helix chain 'Al' and resid 101 through 120 Processing helix chain 'Al' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAl 148 " --> pdb=" O PROAl 144 " (cutoff:3.500A) Processing helix chain 'Al' and resid 152 through 158 Processing helix chain 'Al' and resid 160 through 172 Processing helix chain 'Al' and resid 179 through 184 Processing helix chain 'Al' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAl 194 " --> pdb=" O SERAl 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAl 196 " --> pdb=" O SERAl 193 " (cutoff:3.500A) Processing helix chain 'Al' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAl 218 " --> pdb=" O HISAl 214 " (cutoff:3.500A) Processing helix chain 'Al' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAl 230 " --> pdb=" O THRAl 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAl 231 " --> pdb=" O ARGAl 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Al' and resid 227 through 231' Processing helix chain 'Am' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAm 69 " --> pdb=" O ASNAm 65 " (cutoff:3.500A) Processing helix chain 'Am' and resid 73 through 77 Processing helix chain 'Am' and resid 83 through 99 Processing helix chain 'Am' and resid 101 through 120 Processing helix chain 'Am' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAm 148 " --> pdb=" O PROAm 144 " (cutoff:3.500A) Processing helix chain 'Am' and resid 152 through 158 Processing helix chain 'Am' and resid 160 through 172 Processing helix chain 'Am' and resid 179 through 184 Processing helix chain 'Am' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAm 194 " --> pdb=" O SERAm 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALAAm 196 " --> pdb=" O SERAm 193 " (cutoff:3.500A) Processing helix chain 'Am' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAm 218 " --> pdb=" O HISAm 214 " (cutoff:3.500A) Processing helix chain 'Am' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAm 230 " --> pdb=" O THRAm 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAm 231 " --> pdb=" O ARGAm 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Am' and resid 227 through 231' Processing helix chain 'An' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAn 69 " --> pdb=" O ASNAn 65 " (cutoff:3.500A) Processing helix chain 'An' and resid 73 through 77 Processing helix chain 'An' and resid 83 through 99 Processing helix chain 'An' and resid 101 through 120 Processing helix chain 'An' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAn 148 " --> pdb=" O PROAn 144 " (cutoff:3.500A) Processing helix chain 'An' and resid 152 through 158 Processing helix chain 'An' and resid 160 through 172 Processing helix chain 'An' and resid 179 through 184 Processing helix chain 'An' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAn 194 " --> pdb=" O SERAn 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAAn 196 " --> pdb=" O SERAn 193 " (cutoff:3.500A) Processing helix chain 'An' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAn 218 " --> pdb=" O HISAn 214 " (cutoff:3.500A) Processing helix chain 'An' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAn 230 " --> pdb=" O THRAn 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAn 231 " --> pdb=" O ARGAn 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'An' and resid 227 through 231' Processing helix chain 'Ao' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAo 69 " --> pdb=" O ASNAo 65 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 73 through 77 Processing helix chain 'Ao' and resid 83 through 99 Processing helix chain 'Ao' and resid 101 through 120 Processing helix chain 'Ao' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAo 148 " --> pdb=" O PROAo 144 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 152 through 158 Processing helix chain 'Ao' and resid 160 through 172 Processing helix chain 'Ao' and resid 179 through 184 Processing helix chain 'Ao' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAo 194 " --> pdb=" O SERAo 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAo 196 " --> pdb=" O SERAo 193 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAo 218 " --> pdb=" O HISAo 214 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 227 through 231 removed outlier: 3.580A pdb=" N PHEAo 230 " --> pdb=" O THRAo 227 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLYAo 231 " --> pdb=" O ARGAo 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ao' and resid 227 through 231' Processing helix chain 'Ap' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAp 69 " --> pdb=" O ASNAp 65 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 73 through 77 Processing helix chain 'Ap' and resid 83 through 99 Processing helix chain 'Ap' and resid 101 through 120 Processing helix chain 'Ap' and resid 142 through 148 removed outlier: 3.646A pdb=" N ASNAp 148 " --> pdb=" O PROAp 144 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 152 through 158 Processing helix chain 'Ap' and resid 160 through 172 Processing helix chain 'Ap' and resid 179 through 184 Processing helix chain 'Ap' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAp 194 " --> pdb=" O SERAp 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAp 196 " --> pdb=" O SERAp 193 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAp 218 " --> pdb=" O HISAp 214 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAp 230 " --> pdb=" O THRAp 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAp 231 " --> pdb=" O ARGAp 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ap' and resid 227 through 231' Processing helix chain 'Aq' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAq 69 " --> pdb=" O ASNAq 65 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 73 through 77 Processing helix chain 'Aq' and resid 83 through 99 Processing helix chain 'Aq' and resid 101 through 120 Processing helix chain 'Aq' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAq 148 " --> pdb=" O PROAq 144 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 152 through 158 Processing helix chain 'Aq' and resid 160 through 172 Processing helix chain 'Aq' and resid 179 through 184 Processing helix chain 'Aq' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAq 194 " --> pdb=" O SERAq 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAq 196 " --> pdb=" O SERAq 193 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAq 218 " --> pdb=" O HISAq 214 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 227 through 231 removed outlier: 3.580A pdb=" N PHEAq 230 " --> pdb=" O THRAq 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAq 231 " --> pdb=" O ARGAq 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aq' and resid 227 through 231' Processing helix chain 'Ar' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAr 69 " --> pdb=" O ASNAr 65 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 73 through 77 Processing helix chain 'Ar' and resid 83 through 99 Processing helix chain 'Ar' and resid 101 through 120 Processing helix chain 'Ar' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAr 148 " --> pdb=" O PROAr 144 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 152 through 158 Processing helix chain 'Ar' and resid 160 through 172 Processing helix chain 'Ar' and resid 179 through 184 Processing helix chain 'Ar' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAr 194 " --> pdb=" O SERAr 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAAr 196 " --> pdb=" O SERAr 193 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAr 218 " --> pdb=" O HISAr 214 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAr 230 " --> pdb=" O THRAr 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAr 231 " --> pdb=" O ARGAr 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ar' and resid 227 through 231' Processing helix chain 'As' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAs 69 " --> pdb=" O ASNAs 65 " (cutoff:3.500A) Processing helix chain 'As' and resid 73 through 77 Processing helix chain 'As' and resid 83 through 99 Processing helix chain 'As' and resid 101 through 120 Processing helix chain 'As' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAs 148 " --> pdb=" O PROAs 144 " (cutoff:3.500A) Processing helix chain 'As' and resid 152 through 158 Processing helix chain 'As' and resid 160 through 172 Processing helix chain 'As' and resid 179 through 184 Processing helix chain 'As' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAs 194 " --> pdb=" O SERAs 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAs 196 " --> pdb=" O SERAs 193 " (cutoff:3.500A) Processing helix chain 'As' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAs 218 " --> pdb=" O HISAs 214 " (cutoff:3.500A) Processing helix chain 'As' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAs 230 " --> pdb=" O THRAs 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAs 231 " --> pdb=" O ARGAs 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'As' and resid 227 through 231' Processing helix chain 'At' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAt 69 " --> pdb=" O ASNAt 65 " (cutoff:3.500A) Processing helix chain 'At' and resid 73 through 77 Processing helix chain 'At' and resid 83 through 99 Processing helix chain 'At' and resid 101 through 120 Processing helix chain 'At' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAt 148 " --> pdb=" O PROAt 144 " (cutoff:3.500A) Processing helix chain 'At' and resid 152 through 158 Processing helix chain 'At' and resid 160 through 172 Processing helix chain 'At' and resid 179 through 184 Processing helix chain 'At' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAt 194 " --> pdb=" O SERAt 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAt 196 " --> pdb=" O SERAt 193 " (cutoff:3.500A) Processing helix chain 'At' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAt 218 " --> pdb=" O HISAt 214 " (cutoff:3.500A) Processing helix chain 'At' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAt 230 " --> pdb=" O THRAt 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAt 231 " --> pdb=" O ARGAt 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'At' and resid 227 through 231' Processing helix chain 'Au' and resid 63 through 69 removed outlier: 3.985A pdb=" N GLYAu 69 " --> pdb=" O ASNAu 65 " (cutoff:3.500A) Processing helix chain 'Au' and resid 73 through 77 Processing helix chain 'Au' and resid 83 through 99 Processing helix chain 'Au' and resid 101 through 120 Processing helix chain 'Au' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAu 148 " --> pdb=" O PROAu 144 " (cutoff:3.500A) Processing helix chain 'Au' and resid 152 through 158 Processing helix chain 'Au' and resid 160 through 172 Processing helix chain 'Au' and resid 179 through 184 Processing helix chain 'Au' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAu 194 " --> pdb=" O SERAu 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAu 196 " --> pdb=" O SERAu 193 " (cutoff:3.500A) Processing helix chain 'Au' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAu 218 " --> pdb=" O HISAu 214 " (cutoff:3.500A) Processing helix chain 'Au' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAu 230 " --> pdb=" O THRAu 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAu 231 " --> pdb=" O ARGAu 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Au' and resid 227 through 231' Processing helix chain 'Av' and resid 63 through 69 removed outlier: 3.983A pdb=" N GLYAv 69 " --> pdb=" O ASNAv 65 " (cutoff:3.500A) Processing helix chain 'Av' and resid 73 through 77 Processing helix chain 'Av' and resid 83 through 99 Processing helix chain 'Av' and resid 101 through 120 Processing helix chain 'Av' and resid 142 through 148 removed outlier: 3.646A pdb=" N ASNAv 148 " --> pdb=" O PROAv 144 " (cutoff:3.500A) Processing helix chain 'Av' and resid 152 through 158 Processing helix chain 'Av' and resid 160 through 172 Processing helix chain 'Av' and resid 179 through 184 Processing helix chain 'Av' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAv 194 " --> pdb=" O SERAv 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAAv 196 " --> pdb=" O SERAv 193 " (cutoff:3.500A) Processing helix chain 'Av' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAv 218 " --> pdb=" O HISAv 214 " (cutoff:3.500A) Processing helix chain 'Av' and resid 227 through 231 removed outlier: 3.580A pdb=" N PHEAv 230 " --> pdb=" O THRAv 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYAv 231 " --> pdb=" O ARGAv 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Av' and resid 227 through 231' Processing helix chain 'Aw' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAw 69 " --> pdb=" O ASNAw 65 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 73 through 77 Processing helix chain 'Aw' and resid 83 through 99 Processing helix chain 'Aw' and resid 101 through 120 Processing helix chain 'Aw' and resid 142 through 148 removed outlier: 3.644A pdb=" N ASNAw 148 " --> pdb=" O PROAw 144 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 152 through 158 Processing helix chain 'Aw' and resid 160 through 172 Processing helix chain 'Aw' and resid 179 through 184 Processing helix chain 'Aw' and resid 189 through 196 removed outlier: 4.714A pdb=" N ARGAw 194 " --> pdb=" O SERAw 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAAw 196 " --> pdb=" O SERAw 193 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 207 through 224 removed outlier: 3.669A pdb=" N LYSAw 218 " --> pdb=" O HISAw 214 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 227 through 231 removed outlier: 3.581A pdb=" N PHEAw 230 " --> pdb=" O THRAw 227 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLYAw 231 " --> pdb=" O ARGAw 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aw' and resid 227 through 231' Processing helix chain 'Ax' and resid 63 through 69 removed outlier: 3.984A pdb=" N GLYAx 69 " --> pdb=" O ASNAx 65 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 73 through 77 Processing helix chain 'Ax' and resid 83 through 99 Processing helix chain 'Ax' and resid 101 through 120 Processing helix chain 'Ax' and resid 142 through 148 removed outlier: 3.645A pdb=" N ASNAx 148 " --> pdb=" O PROAx 144 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 152 through 158 Processing helix chain 'Ax' and resid 160 through 172 Processing helix chain 'Ax' and resid 179 through 184 Processing helix chain 'Ax' and resid 189 through 196 removed outlier: 4.713A pdb=" N ARGAx 194 " --> pdb=" O SERAx 191 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAx 196 " --> pdb=" O SERAx 193 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 207 through 224 removed outlier: 3.670A pdb=" N LYSAx 218 " --> pdb=" O HISAx 214 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 227 through 231 removed outlier: 3.582A pdb=" N PHEAx 230 " --> pdb=" O THRAx 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYAx 231 " --> pdb=" O ARGAx 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ax' and resid 227 through 231' Processing sheet with id=AA1, first strand: chain 'Aa' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 128 through 133 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 128 through 133 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 128 through 133 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 128 through 133 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 55 through 56 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 128 through 133 Processing sheet with id=AB2, first strand: chain 'Af' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'Af' and resid 128 through 133 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 128 through 133 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 55 through 56 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 128 through 133 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 55 through 56 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 128 through 133 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 128 through 133 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 55 through 56 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 128 through 133 Processing sheet with id=AC5, first strand: chain 'Al' and resid 55 through 56 Processing sheet with id=AC6, first strand: chain 'Al' and resid 128 through 133 Processing sheet with id=AC7, first strand: chain 'Am' and resid 55 through 56 Processing sheet with id=AC8, first strand: chain 'Am' and resid 128 through 133 Processing sheet with id=AC9, first strand: chain 'An' and resid 55 through 56 Processing sheet with id=AD1, first strand: chain 'An' and resid 128 through 133 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 55 through 56 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 128 through 133 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 55 through 56 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 128 through 133 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 128 through 133 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 55 through 56 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 128 through 133 Processing sheet with id=AE1, first strand: chain 'As' and resid 55 through 56 Processing sheet with id=AE2, first strand: chain 'As' and resid 128 through 133 Processing sheet with id=AE3, first strand: chain 'At' and resid 55 through 56 Processing sheet with id=AE4, first strand: chain 'At' and resid 128 through 133 Processing sheet with id=AE5, first strand: chain 'Au' and resid 55 through 56 Processing sheet with id=AE6, first strand: chain 'Au' and resid 128 through 133 Processing sheet with id=AE7, first strand: chain 'Av' and resid 55 through 56 Processing sheet with id=AE8, first strand: chain 'Av' and resid 128 through 133 Processing sheet with id=AE9, first strand: chain 'Aw' and resid 55 through 56 Processing sheet with id=AF1, first strand: chain 'Aw' and resid 128 through 133 Processing sheet with id=AF2, first strand: chain 'Ax' and resid 55 through 56 Processing sheet with id=AF3, first strand: chain 'Ax' and resid 128 through 133 1752 hydrogen bonds defined for protein. 4752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12173 1.34 - 1.45: 5534 1.45 - 1.57: 20429 1.57 - 1.69: 0 1.69 - 1.80: 696 Bond restraints: 38832 Sorted by residual: bond pdb=" N VALAf 100 " pdb=" CA VALAf 100 " ideal model delta sigma weight residual 1.456 1.501 -0.046 1.15e-02 7.56e+03 1.58e+01 bond pdb=" N VALAv 100 " pdb=" CA VALAv 100 " ideal model delta sigma weight residual 1.456 1.501 -0.046 1.15e-02 7.56e+03 1.58e+01 bond pdb=" N VALAp 100 " pdb=" CA VALAp 100 " ideal model delta sigma weight residual 1.456 1.501 -0.046 1.15e-02 7.56e+03 1.57e+01 bond pdb=" N VALAh 100 " pdb=" CA VALAh 100 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.15e-02 7.56e+03 1.55e+01 bond pdb=" N VALAn 100 " pdb=" CA VALAn 100 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.15e-02 7.56e+03 1.55e+01 ... (remaining 38827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 47657 1.56 - 3.13: 4099 3.13 - 4.69: 588 4.69 - 6.25: 144 6.25 - 7.82: 48 Bond angle restraints: 52536 Sorted by residual: angle pdb=" N ASPAi 133 " pdb=" CA ASPAi 133 " pdb=" CB ASPAi 133 " ideal model delta sigma weight residual 110.37 118.19 -7.82 1.65e+00 3.67e-01 2.24e+01 angle pdb=" N ASPAp 133 " pdb=" CA ASPAp 133 " pdb=" CB ASPAp 133 " ideal model delta sigma weight residual 110.37 118.18 -7.81 1.65e+00 3.67e-01 2.24e+01 angle pdb=" N ASPAa 133 " pdb=" CA ASPAa 133 " pdb=" CB ASPAa 133 " ideal model delta sigma weight residual 110.37 118.15 -7.78 1.65e+00 3.67e-01 2.23e+01 angle pdb=" N ASPAl 133 " pdb=" CA ASPAl 133 " pdb=" CB ASPAl 133 " ideal model delta sigma weight residual 110.37 118.15 -7.78 1.65e+00 3.67e-01 2.22e+01 angle pdb=" N ASPAf 133 " pdb=" CA ASPAf 133 " pdb=" CB ASPAf 133 " ideal model delta sigma weight residual 110.37 118.15 -7.78 1.65e+00 3.67e-01 2.22e+01 ... (remaining 52531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 20099 16.38 - 32.75: 2317 32.75 - 49.13: 912 49.13 - 65.50: 216 65.50 - 81.88: 72 Dihedral angle restraints: 23616 sinusoidal: 9792 harmonic: 13824 Sorted by residual: dihedral pdb=" CA ASPAk 162 " pdb=" CB ASPAk 162 " pdb=" CG ASPAk 162 " pdb=" OD1 ASPAk 162 " ideal model delta sinusoidal sigma weight residual -30.00 -88.38 58.38 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASPAx 162 " pdb=" CB ASPAx 162 " pdb=" CG ASPAx 162 " pdb=" OD1 ASPAx 162 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASPAh 162 " pdb=" CB ASPAh 162 " pdb=" CG ASPAh 162 " pdb=" OD1 ASPAh 162 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 23613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4356 0.060 - 0.120: 971 0.120 - 0.180: 193 0.180 - 0.241: 48 0.241 - 0.301: 24 Chirality restraints: 5592 Sorted by residual: chirality pdb=" CA LEUAd 142 " pdb=" N LEUAd 142 " pdb=" C LEUAd 142 " pdb=" CB LEUAd 142 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEUAw 142 " pdb=" N LEUAw 142 " pdb=" C LEUAw 142 " pdb=" CB LEUAw 142 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEUAl 142 " pdb=" N LEUAl 142 " pdb=" C LEUAl 142 " pdb=" CB LEUAl 142 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 5589 not shown) Planarity restraints: 6888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYRAi 70 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C TYRAi 70 " -0.032 2.00e-02 2.50e+03 pdb=" O TYRAi 70 " 0.012 2.00e-02 2.50e+03 pdb=" N LYSAi 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYRAq 70 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C TYRAq 70 " -0.032 2.00e-02 2.50e+03 pdb=" O TYRAq 70 " 0.012 2.00e-02 2.50e+03 pdb=" N LYSAq 71 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYRAa 70 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C TYRAa 70 " -0.032 2.00e-02 2.50e+03 pdb=" O TYRAa 70 " 0.012 2.00e-02 2.50e+03 pdb=" N LYSAa 71 " 0.011 2.00e-02 2.50e+03 ... (remaining 6885 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 14421 2.88 - 3.38: 34850 3.38 - 3.89: 63169 3.89 - 4.39: 70558 4.39 - 4.90: 126314 Nonbonded interactions: 309312 Sorted by model distance: nonbonded pdb=" NE2 GLNAp 74 " pdb=" OE2 GLUAq 118 " model vdw 2.372 3.120 nonbonded pdb=" NE2 GLNAt 74 " pdb=" OE2 GLUAu 118 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLNAd 74 " pdb=" OE2 GLUAe 118 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLNAl 74 " pdb=" OE2 GLUAm 118 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLNAm 74 " pdb=" OE2 GLUAn 118 " model vdw 2.384 3.120 ... (remaining 309307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.440 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.009 0.048 38832 Z= 0.491 Angle : 0.950 7.817 52536 Z= 0.634 Chirality : 0.058 0.301 5592 Planarity : 0.004 0.028 6888 Dihedral : 16.970 81.878 14688 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 27.22 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.10), residues: 4656 helix: -2.28 (0.08), residues: 2184 sheet: -1.85 (0.27), residues: 240 loop : -1.77 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAl 55 TYR 0.013 0.002 TYRAo 195 PHE 0.015 0.003 PHEAv 112 TRP 0.019 0.002 TRPAw 129 HIS 0.006 0.002 HISAn 159 Details of bonding type rmsd covalent geometry : bond 0.00862 (38832) covalent geometry : angle 0.94981 (52536) hydrogen bonds : bond 0.15232 ( 1752) hydrogen bonds : angle 6.57459 ( 4752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 1.442 Fit side-chains REVERT: Ab 57 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: Ac 57 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8155 (mtm-85) REVERT: Ag 132 MET cc_start: 0.8388 (mmm) cc_final: 0.8149 (mmt) REVERT: Ai 57 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8298 (mtm-85) REVERT: Ai 131 MET cc_start: 0.8983 (ttt) cc_final: 0.8774 (ttt) REVERT: Ai 215 MET cc_start: 0.8402 (mtm) cc_final: 0.8141 (mtp) REVERT: Ak 113 MET cc_start: 0.8272 (ttp) cc_final: 0.7913 (ttp) REVERT: Am 57 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: Am 113 MET cc_start: 0.8278 (ttp) cc_final: 0.7928 (ttp) REVERT: Am 157 MET cc_start: 0.8638 (mmt) cc_final: 0.8339 (mmp) REVERT: Ap 132 MET cc_start: 0.8436 (mmm) cc_final: 0.8157 (mmm) REVERT: Ap 195 TYR cc_start: 0.9090 (m-80) cc_final: 0.8872 (m-80) REVERT: Aq 57 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8158 (mtm-85) REVERT: Aq 113 MET cc_start: 0.8280 (ttp) cc_final: 0.7897 (ttp) REVERT: Ar 113 MET cc_start: 0.8255 (ttp) cc_final: 0.7990 (ttp) REVERT: As 57 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: As 113 MET cc_start: 0.8242 (ttp) cc_final: 0.8031 (ttp) REVERT: At 217 MET cc_start: 0.8599 (mtp) cc_final: 0.8395 (mtm) REVERT: Av 95 MET cc_start: 0.8335 (ttm) cc_final: 0.8047 (ttm) REVERT: Aw 57 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: Aw 95 MET cc_start: 0.8412 (ttm) cc_final: 0.8198 (ttm) REVERT: Ax 95 MET cc_start: 0.8291 (ttm) cc_final: 0.8007 (ttm) outliers start: 0 outliers final: 0 residues processed: 717 average time/residue: 0.2537 time to fit residues: 293.4637 Evaluate side-chains 628 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 184 GLN Aa 224 ASN ** Ab 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 184 GLN Ab 224 ASN ** Ac 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 224 ASN ** Ad 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 184 GLN Ad 224 ASN Ae 110 ASN Ae 224 ASN Af 92 GLN Af 110 ASN Af 224 ASN Ag 110 ASN Ag 184 GLN Ag 224 ASN ** Ah 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 224 ASN ** Ai 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 184 GLN Ai 224 ASN Aj 110 ASN Aj 224 ASN Ak 104 GLN ** Ak 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 184 GLN Ak 224 ASN Al 104 GLN Al 110 ASN Al 184 GLN Al 224 ASN Am 104 GLN Am 110 ASN Am 184 GLN Am 224 ASN An 104 GLN An 110 ASN An 224 ASN Ao 104 GLN ** Ao 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 224 ASN Ap 104 GLN Ap 110 ASN Ap 184 GLN Ap 224 ASN Aq 104 GLN Aq 110 ASN Aq 184 GLN Aq 224 ASN Ar 104 GLN ** Ar 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 184 GLN Ar 224 ASN As 104 GLN ** As 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 184 GLN As 224 ASN At 104 GLN At 110 ASN At 224 ASN Au 104 GLN ** Au 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 224 ASN Av 104 GLN Av 110 ASN Av 184 GLN Av 224 ASN Aw 104 GLN Aw 110 ASN Aw 224 ASN Ax 104 GLN Ax 110 ASN Ax 224 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.104452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.085715 restraints weight = 45519.443| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.65 r_work: 0.2633 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38832 Z= 0.127 Angle : 0.543 8.779 52536 Z= 0.277 Chirality : 0.038 0.118 5592 Planarity : 0.004 0.037 6888 Dihedral : 4.111 12.803 5256 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.45 % Allowed : 22.39 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.11), residues: 4656 helix: -0.38 (0.10), residues: 2040 sheet: -2.16 (0.24), residues: 288 loop : -1.35 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAi 55 TYR 0.008 0.001 TYRAo 177 PHE 0.015 0.002 PHEAb 112 TRP 0.014 0.001 TRPAk 129 HIS 0.003 0.001 HISAb 91 Details of bonding type rmsd covalent geometry : bond 0.00294 (38832) covalent geometry : angle 0.54327 (52536) hydrogen bonds : bond 0.04048 ( 1752) hydrogen bonds : angle 4.70786 ( 4752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 646 time to evaluate : 1.450 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: Aa 184 GLN cc_start: 0.8658 (mt0) cc_final: 0.8448 (mt0) REVERT: Ac 43 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: Ad 43 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7841 (mtt-85) REVERT: Af 43 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8278 (mtt-85) REVERT: Af 105 MET cc_start: 0.8520 (tpt) cc_final: 0.8291 (tpt) REVERT: Ah 43 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8123 (mtt-85) REVERT: Ah 57 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8159 (mtm-85) REVERT: Ai 57 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8202 (mtm-85) REVERT: Ai 205 LYS cc_start: 0.8745 (ptmm) cc_final: 0.8369 (pttt) REVERT: Ai 215 MET cc_start: 0.8664 (mtm) cc_final: 0.8281 (mtm) REVERT: Aj 43 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7966 (mtt-85) REVERT: Ak 43 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7933 (mtt-85) REVERT: Ak 113 MET cc_start: 0.8477 (ttp) cc_final: 0.8090 (ttp) REVERT: Am 57 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8314 (mtm-85) REVERT: Am 113 MET cc_start: 0.8479 (ttp) cc_final: 0.8103 (ttp) REVERT: Aq 57 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8364 (mtm-85) REVERT: Aq 113 MET cc_start: 0.8447 (ttp) cc_final: 0.8057 (ttp) REVERT: Aq 145 MET cc_start: 0.9120 (mmm) cc_final: 0.8740 (mmm) REVERT: Aq 155 GLN cc_start: 0.9107 (mt0) cc_final: 0.8861 (mt0) REVERT: Ar 113 MET cc_start: 0.8479 (ttp) cc_final: 0.8207 (ttp) REVERT: As 57 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8343 (mtm-85) REVERT: As 113 MET cc_start: 0.8426 (ttp) cc_final: 0.8226 (ttp) REVERT: As 184 GLN cc_start: 0.8733 (mt0) cc_final: 0.8490 (mt0) REVERT: At 157 MET cc_start: 0.8837 (mmp) cc_final: 0.8614 (mmt) REVERT: Au 155 GLN cc_start: 0.9135 (mt0) cc_final: 0.8815 (mt0) REVERT: Av 57 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: Aw 57 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8234 (mtm-85) outliers start: 140 outliers final: 69 residues processed: 738 average time/residue: 0.2535 time to fit residues: 300.0449 Evaluate side-chains 701 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 625 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 51 LEU Chi-restraints excluded: chain Aa residue 105 MET Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 51 LEU Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 43 ARG Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 139 SER Chi-restraints excluded: chain Ac residue 152 THR Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 43 ARG Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 152 THR Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 51 LEU Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 43 ARG Chi-restraints excluded: chain Af residue 51 LEU Chi-restraints excluded: chain Af residue 96 THR Chi-restraints excluded: chain Af residue 139 SER Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 51 LEU Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 43 ARG Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 139 SER Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 43 ARG Chi-restraints excluded: chain Aj residue 51 LEU Chi-restraints excluded: chain Aj residue 139 SER Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 43 ARG Chi-restraints excluded: chain Ak residue 51 LEU Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 51 LEU Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 51 LEU Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 51 LEU Chi-restraints excluded: chain An residue 139 SER Chi-restraints excluded: chain An residue 190 MET Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 51 LEU Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 139 SER Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 152 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 51 LEU Chi-restraints excluded: chain At residue 95 MET Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 51 LEU Chi-restraints excluded: chain Au residue 56 MET Chi-restraints excluded: chain Au residue 152 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 152 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 51 LEU Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 78 SER Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 198 optimal weight: 0.0070 chunk 92 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 349 optimal weight: 5.9990 chunk 329 optimal weight: 0.6980 chunk 284 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 110 ASN Ac 110 ASN Ac 184 GLN Ad 110 ASN Af 184 GLN Ag 184 GLN Ah 110 ASN Ai 110 ASN Ai 184 GLN Ak 110 ASN Am 184 GLN Ao 110 ASN Aq 184 GLN Ar 110 ASN Ar 184 GLN As 110 ASN Au 110 ASN Au 184 GLN Av 184 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.085882 restraints weight = 45612.013| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.67 r_work: 0.2649 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38832 Z= 0.114 Angle : 0.502 7.644 52536 Z= 0.254 Chirality : 0.037 0.117 5592 Planarity : 0.004 0.041 6888 Dihedral : 3.903 13.329 5256 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.30 % Allowed : 22.76 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4656 helix: 0.29 (0.11), residues: 2040 sheet: -1.51 (0.24), residues: 288 loop : -1.10 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAp 55 TYR 0.007 0.001 TYRAs 177 PHE 0.014 0.002 PHEAl 112 TRP 0.012 0.001 TRPAo 129 HIS 0.003 0.001 HISAi 91 Details of bonding type rmsd covalent geometry : bond 0.00268 (38832) covalent geometry : angle 0.50169 (52536) hydrogen bonds : bond 0.03824 ( 1752) hydrogen bonds : angle 4.54818 ( 4752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 639 time to evaluate : 1.614 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: Ab 215 MET cc_start: 0.8591 (mtp) cc_final: 0.8384 (mtm) REVERT: Ac 43 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7759 (mtt-85) REVERT: Ad 43 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8028 (mtt-85) REVERT: Ad 215 MET cc_start: 0.8637 (mtm) cc_final: 0.8384 (mtm) REVERT: Af 43 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8436 (mpt180) REVERT: Ah 43 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8198 (mtt-85) REVERT: Ai 57 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: Ai 205 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8439 (pttt) REVERT: Ai 215 MET cc_start: 0.8639 (mtm) cc_final: 0.8326 (mtm) REVERT: Aj 43 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7994 (mtt-85) REVERT: Aj 118 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: Ak 43 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7721 (mtt-85) REVERT: Ak 57 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: Ak 113 MET cc_start: 0.8489 (ttp) cc_final: 0.8089 (ttp) REVERT: Ak 215 MET cc_start: 0.8596 (mtp) cc_final: 0.8269 (mtm) REVERT: Am 57 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8346 (mtm-85) REVERT: Am 113 MET cc_start: 0.8510 (ttp) cc_final: 0.8118 (ttp) REVERT: Aq 57 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8441 (mtm-85) REVERT: Aq 113 MET cc_start: 0.8448 (ttp) cc_final: 0.8021 (ttp) REVERT: Aq 145 MET cc_start: 0.9116 (mmm) cc_final: 0.8839 (mmm) REVERT: Aq 155 GLN cc_start: 0.9075 (mt0) cc_final: 0.8805 (mt0) REVERT: Aq 215 MET cc_start: 0.8628 (mtm) cc_final: 0.8391 (mtm) REVERT: Ar 57 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8328 (mtm-85) REVERT: Ar 113 MET cc_start: 0.8516 (ttp) cc_final: 0.8238 (ttp) REVERT: Ar 195 TYR cc_start: 0.9111 (m-80) cc_final: 0.8890 (m-80) REVERT: As 113 MET cc_start: 0.8439 (ttp) cc_final: 0.8215 (ttp) REVERT: At 157 MET cc_start: 0.8781 (mmt) cc_final: 0.8568 (mmt) REVERT: At 205 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8401 (ptpt) REVERT: Aw 57 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: Aw 194 ARG cc_start: 0.8744 (ptm-80) cc_final: 0.8266 (ptm160) REVERT: Ax 178 MET cc_start: 0.8722 (tpt) cc_final: 0.8516 (tpt) outliers start: 134 outliers final: 79 residues processed: 732 average time/residue: 0.2448 time to fit residues: 290.5209 Evaluate side-chains 716 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 629 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 51 LEU Chi-restraints excluded: chain Aa residue 60 VAL Chi-restraints excluded: chain Aa residue 105 MET Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 51 LEU Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 43 ARG Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 105 MET Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 43 ARG Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 152 THR Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 51 LEU Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 43 ARG Chi-restraints excluded: chain Af residue 51 LEU Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 51 LEU Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 43 ARG Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 43 ARG Chi-restraints excluded: chain Aj residue 51 LEU Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 118 GLU Chi-restraints excluded: chain Aj residue 139 SER Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 43 ARG Chi-restraints excluded: chain Ak residue 51 LEU Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 152 THR Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 51 LEU Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 51 LEU Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 51 LEU Chi-restraints excluded: chain An residue 139 SER Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 51 LEU Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 152 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 152 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 51 LEU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 51 LEU Chi-restraints excluded: chain Au residue 56 MET Chi-restraints excluded: chain Au residue 95 MET Chi-restraints excluded: chain Au residue 152 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 152 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 51 LEU Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 78 SER Chi-restraints excluded: chain Ax residue 152 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 115 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 320 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 425 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 184 GLN Ag 184 GLN Ai 184 GLN Ak 184 GLN Au 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.087383 restraints weight = 45302.081| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.61 r_work: 0.2667 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38832 Z= 0.130 Angle : 0.507 6.673 52536 Z= 0.256 Chirality : 0.038 0.118 5592 Planarity : 0.004 0.042 6888 Dihedral : 3.889 14.810 5256 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.46 % Allowed : 20.64 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4656 helix: 0.56 (0.11), residues: 2040 sheet: -1.13 (0.23), residues: 288 loop : -0.95 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAl 55 TYR 0.011 0.001 TYRAw 195 PHE 0.011 0.002 PHEAd 160 TRP 0.012 0.001 TRPAf 129 HIS 0.003 0.001 HISAi 91 Details of bonding type rmsd covalent geometry : bond 0.00309 (38832) covalent geometry : angle 0.50683 (52536) hydrogen bonds : bond 0.03884 ( 1752) hydrogen bonds : angle 4.44868 ( 4752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 638 time to evaluate : 1.170 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7756 (mtt-85) REVERT: Aa 195 TYR cc_start: 0.9168 (m-80) cc_final: 0.8897 (m-80) REVERT: Ab 105 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: Ab 215 MET cc_start: 0.8574 (mtp) cc_final: 0.8353 (mtm) REVERT: Ac 43 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7818 (mtt-85) REVERT: Ad 43 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8148 (mtt-85) REVERT: Ad 215 MET cc_start: 0.8548 (mtm) cc_final: 0.8305 (mtm) REVERT: Af 43 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8503 (mpt180) REVERT: Ah 43 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8254 (mtt-85) REVERT: Ai 57 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8332 (mtm-85) REVERT: Ai 184 GLN cc_start: 0.8787 (mt0) cc_final: 0.8548 (mt0) REVERT: Ai 215 MET cc_start: 0.8592 (mtm) cc_final: 0.8291 (mtm) REVERT: Aj 43 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7934 (mtt-85) REVERT: Ak 43 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8110 (mtt-85) REVERT: Ak 113 MET cc_start: 0.8483 (ttp) cc_final: 0.8065 (ttp) REVERT: Ak 215 MET cc_start: 0.8512 (mtp) cc_final: 0.8200 (mtm) REVERT: Am 113 MET cc_start: 0.8497 (ttp) cc_final: 0.8102 (ttp) REVERT: Am 118 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: An 118 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: Ao 118 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: Ap 215 MET cc_start: 0.8476 (mtp) cc_final: 0.8174 (mtm) REVERT: Aq 113 MET cc_start: 0.8456 (ttp) cc_final: 0.8027 (ttp) REVERT: Aq 118 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: Aq 155 GLN cc_start: 0.9056 (mt0) cc_final: 0.8783 (mt0) REVERT: Ar 113 MET cc_start: 0.8498 (ttp) cc_final: 0.8214 (ttp) REVERT: As 113 MET cc_start: 0.8407 (ttp) cc_final: 0.8192 (ttp) REVERT: As 118 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: At 118 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: At 205 LYS cc_start: 0.8815 (ptmm) cc_final: 0.8403 (ptpt) REVERT: Au 118 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: Au 215 MET cc_start: 0.8525 (mtp) cc_final: 0.8230 (mtm) REVERT: Aw 57 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8164 (mtm-85) REVERT: Ax 118 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: Ax 178 MET cc_start: 0.8714 (tpt) cc_final: 0.8511 (tpt) outliers start: 181 outliers final: 101 residues processed: 773 average time/residue: 0.2332 time to fit residues: 295.9553 Evaluate side-chains 741 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 624 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 44 ILE Chi-restraints excluded: chain Aa residue 51 LEU Chi-restraints excluded: chain Aa residue 60 VAL Chi-restraints excluded: chain Aa residue 105 MET Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 51 LEU Chi-restraints excluded: chain Ab residue 105 MET Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 43 ARG Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 188 THR Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 43 ARG Chi-restraints excluded: chain Ad residue 44 ILE Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 152 THR Chi-restraints excluded: chain Ad residue 188 THR Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 51 LEU Chi-restraints excluded: chain Ae residue 78 SER Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 43 ARG Chi-restraints excluded: chain Af residue 51 LEU Chi-restraints excluded: chain Af residue 56 MET Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 51 LEU Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 43 ARG Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 139 SER Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 43 ARG Chi-restraints excluded: chain Aj residue 44 ILE Chi-restraints excluded: chain Aj residue 51 LEU Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 188 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 43 ARG Chi-restraints excluded: chain Ak residue 44 ILE Chi-restraints excluded: chain Ak residue 51 LEU Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 51 LEU Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 51 LEU Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 118 GLU Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 51 LEU Chi-restraints excluded: chain An residue 118 GLU Chi-restraints excluded: chain An residue 139 SER Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 44 ILE Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 96 THR Chi-restraints excluded: chain Ao residue 118 GLU Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 51 LEU Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 118 GLU Chi-restraints excluded: chain Aq residue 125 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 152 THR Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 118 GLU Chi-restraints excluded: chain As residue 152 THR Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 118 GLU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 51 LEU Chi-restraints excluded: chain Au residue 56 MET Chi-restraints excluded: chain Au residue 95 MET Chi-restraints excluded: chain Au residue 118 GLU Chi-restraints excluded: chain Au residue 152 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 152 THR Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 51 LEU Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 78 SER Chi-restraints excluded: chain Ax residue 118 GLU Chi-restraints excluded: chain Ax residue 152 THR Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 415 optimal weight: 0.0370 chunk 130 optimal weight: 5.9990 chunk 411 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 61 optimal weight: 0.0040 chunk 248 optimal weight: 0.5980 chunk 417 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 212 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ag 184 GLN Am 172 ASN Am 184 GLN Ao 186 ASN Ao 224 ASN Ar 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.094585 restraints weight = 44916.924| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.63 r_work: 0.2728 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38832 Z= 0.088 Angle : 0.468 5.239 52536 Z= 0.237 Chirality : 0.036 0.118 5592 Planarity : 0.004 0.042 6888 Dihedral : 3.642 13.629 5256 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.43 % Allowed : 21.28 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4656 helix: 0.89 (0.11), residues: 2184 sheet: -0.11 (0.25), residues: 240 loop : -0.59 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAh 57 TYR 0.011 0.001 TYRAt 53 PHE 0.017 0.001 PHEAw 112 TRP 0.012 0.001 TRPAk 129 HIS 0.003 0.001 HISAn 91 Details of bonding type rmsd covalent geometry : bond 0.00199 (38832) covalent geometry : angle 0.46751 (52536) hydrogen bonds : bond 0.03216 ( 1752) hydrogen bonds : angle 4.13900 ( 4752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 650 time to evaluate : 1.478 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7763 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: Aa 195 TYR cc_start: 0.9063 (m-80) cc_final: 0.8806 (m-10) REVERT: Ad 105 MET cc_start: 0.8591 (tpt) cc_final: 0.8344 (tpt) REVERT: Ad 215 MET cc_start: 0.8545 (mtm) cc_final: 0.8327 (mtm) REVERT: Ae 57 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8299 (ttm-80) REVERT: Ai 215 MET cc_start: 0.8516 (mtm) cc_final: 0.8281 (mtm) REVERT: Ak 113 MET cc_start: 0.8443 (ttp) cc_final: 0.7999 (ttp) REVERT: Ak 215 MET cc_start: 0.8468 (mtp) cc_final: 0.8171 (mtm) REVERT: Am 113 MET cc_start: 0.8459 (ttp) cc_final: 0.8051 (ttp) REVERT: Aq 113 MET cc_start: 0.8451 (ttp) cc_final: 0.8009 (ttp) REVERT: Aq 155 GLN cc_start: 0.8956 (mt0) cc_final: 0.8668 (mt0) REVERT: Ar 113 MET cc_start: 0.8516 (ttp) cc_final: 0.8221 (ttp) REVERT: Ar 215 MET cc_start: 0.8428 (mtp) cc_final: 0.8164 (mtm) REVERT: As 113 MET cc_start: 0.8444 (ttp) cc_final: 0.8190 (ttp) REVERT: Au 155 GLN cc_start: 0.8967 (mt0) cc_final: 0.8712 (mt0) REVERT: Au 215 MET cc_start: 0.8484 (mtp) cc_final: 0.8182 (mtt) REVERT: Aw 57 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: Ax 51 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 139 outliers final: 73 residues processed: 750 average time/residue: 0.2349 time to fit residues: 288.5386 Evaluate side-chains 697 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 622 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 60 VAL Chi-restraints excluded: chain Aa residue 105 MET Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 105 MET Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 56 MET Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ah residue 217 MET Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 142 LEU Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 142 LEU Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 125 LEU Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 56 MET Chi-restraints excluded: chain Aq residue 125 LEU Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 125 LEU Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Aw residue 204 SER Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 240 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 419 optimal weight: 0.0050 chunk 350 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 432 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 184 GLN Ag 184 GLN Ai 184 GLN Av 184 GLN Av 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.105544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.087071 restraints weight = 45377.478| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.64 r_work: 0.2635 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38832 Z= 0.137 Angle : 0.511 7.392 52536 Z= 0.255 Chirality : 0.038 0.121 5592 Planarity : 0.004 0.042 6888 Dihedral : 3.800 15.068 5256 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.81 % Allowed : 21.01 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 4656 helix: 0.96 (0.11), residues: 2040 sheet: -0.53 (0.24), residues: 288 loop : -0.69 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAc 57 TYR 0.012 0.001 TYRAp 195 PHE 0.012 0.002 PHEAw 199 TRP 0.012 0.001 TRPAb 129 HIS 0.003 0.001 HISAi 91 Details of bonding type rmsd covalent geometry : bond 0.00329 (38832) covalent geometry : angle 0.51125 (52536) hydrogen bonds : bond 0.03772 ( 1752) hydrogen bonds : angle 4.32216 ( 4752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 632 time to evaluate : 1.361 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7844 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8206 (mtm-85) REVERT: Ad 43 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8158 (mtt-85) REVERT: Ad 215 MET cc_start: 0.8528 (mtm) cc_final: 0.8273 (mtm) REVERT: Ae 57 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8344 (ttm-80) REVERT: Ai 215 MET cc_start: 0.8563 (mtm) cc_final: 0.8322 (mtm) REVERT: Ak 113 MET cc_start: 0.8514 (ttp) cc_final: 0.8101 (ttp) REVERT: Ak 215 MET cc_start: 0.8483 (mtp) cc_final: 0.8192 (mtm) REVERT: Al 118 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: Al 217 MET cc_start: 0.8384 (ttm) cc_final: 0.8034 (ttm) REVERT: Am 113 MET cc_start: 0.8504 (ttp) cc_final: 0.8113 (ttp) REVERT: Am 118 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: An 51 LEU cc_start: 0.8610 (tp) cc_final: 0.8370 (tp) REVERT: An 118 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: Ao 118 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: Aq 113 MET cc_start: 0.8490 (ttp) cc_final: 0.8058 (ttp) REVERT: Ar 113 MET cc_start: 0.8531 (ttp) cc_final: 0.8247 (ttp) REVERT: Ar 215 MET cc_start: 0.8402 (mtp) cc_final: 0.8161 (mtm) REVERT: As 113 MET cc_start: 0.8465 (ttp) cc_final: 0.8255 (ttp) REVERT: At 118 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: At 184 GLN cc_start: 0.8947 (mt0) cc_final: 0.8692 (mt0) REVERT: Au 215 MET cc_start: 0.8517 (mtp) cc_final: 0.8215 (mtt) outliers start: 114 outliers final: 75 residues processed: 720 average time/residue: 0.2201 time to fit residues: 261.7266 Evaluate side-chains 695 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 613 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 60 VAL Chi-restraints excluded: chain Aa residue 105 MET Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 43 ARG Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 188 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 105 MET Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 119 ASN Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 142 LEU Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 118 GLU Chi-restraints excluded: chain Al residue 152 THR Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 118 GLU Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 118 GLU Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 118 GLU Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 125 LEU Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 118 GLU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 56 MET Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 78 SER Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 195 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 417 optimal weight: 20.0000 chunk 302 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ag 184 GLN Ao 186 ASN Ao 224 ASN At 104 GLN Av 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.096036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.079798 restraints weight = 46854.371| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.39 r_work: 0.2558 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 38832 Z= 0.341 Angle : 0.674 8.160 52536 Z= 0.339 Chirality : 0.046 0.159 5592 Planarity : 0.005 0.040 6888 Dihedral : 4.453 16.886 5256 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.21 % Allowed : 20.32 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4656 helix: 0.34 (0.11), residues: 1968 sheet: -0.58 (0.25), residues: 288 loop : -0.83 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAc 57 TYR 0.019 0.002 TYRAp 195 PHE 0.015 0.003 PHEAe 199 TRP 0.014 0.002 TRPAe 129 HIS 0.005 0.001 HISAp 91 Details of bonding type rmsd covalent geometry : bond 0.00835 (38832) covalent geometry : angle 0.67395 (52536) hydrogen bonds : bond 0.05201 ( 1752) hydrogen bonds : angle 4.85436 ( 4752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 624 time to evaluate : 1.288 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8032 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: Aa 71 LYS cc_start: 0.9362 (mtmt) cc_final: 0.9135 (mtmm) REVERT: Aa 184 GLN cc_start: 0.8939 (mt0) cc_final: 0.8677 (mt0) REVERT: Ab 145 MET cc_start: 0.9136 (mmt) cc_final: 0.8739 (mmt) REVERT: Ac 118 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: Ae 57 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8387 (ttm-80) REVERT: Ai 215 MET cc_start: 0.8720 (mtm) cc_final: 0.8415 (mtm) REVERT: Ak 113 MET cc_start: 0.8545 (ttp) cc_final: 0.8155 (ttp) REVERT: Al 118 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: Al 184 GLN cc_start: 0.8760 (mt0) cc_final: 0.8471 (mt0) REVERT: Al 217 MET cc_start: 0.8567 (ttm) cc_final: 0.8176 (ttm) REVERT: Am 113 MET cc_start: 0.8550 (ttp) cc_final: 0.8215 (ttp) REVERT: Am 118 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: An 43 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7940 (mtt-85) REVERT: An 118 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: Ao 118 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: Ar 57 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8112 (mtm-85) REVERT: Ar 113 MET cc_start: 0.8582 (ttp) cc_final: 0.8338 (ttp) REVERT: At 118 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7563 (mp0) outliers start: 130 outliers final: 94 residues processed: 724 average time/residue: 0.2283 time to fit residues: 267.5891 Evaluate side-chains 696 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 594 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 119 ASN Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 44 ILE Chi-restraints excluded: chain Ab residue 51 LEU Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 56 MET Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 118 GLU Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 44 ILE Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 152 THR Chi-restraints excluded: chain Ae residue 188 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 44 ILE Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 119 ASN Chi-restraints excluded: chain Ah residue 188 THR Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 188 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 44 ILE Chi-restraints excluded: chain Ak residue 56 MET Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 96 THR Chi-restraints excluded: chain Ak residue 188 THR Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 118 GLU Chi-restraints excluded: chain Al residue 152 THR Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 118 GLU Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 43 ARG Chi-restraints excluded: chain An residue 44 ILE Chi-restraints excluded: chain An residue 118 GLU Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 44 ILE Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 96 THR Chi-restraints excluded: chain Ao residue 118 GLU Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 125 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 44 ILE Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 60 VAL Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 95 MET Chi-restraints excluded: chain At residue 118 GLU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 44 ILE Chi-restraints excluded: chain Au residue 95 MET Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 44 ILE Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 56 MET Chi-restraints excluded: chain Av residue 161 SER Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 96 THR Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 22 optimal weight: 0.6980 chunk 437 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 429 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 184 GLN Ag 184 GLN Ao 184 GLN Ao 216 GLN Ar 184 GLN As 184 GLN At 104 GLN At 184 GLN At 186 ASN At 224 ASN Ax 184 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.101320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.084638 restraints weight = 45607.113| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.46 r_work: 0.2635 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38832 Z= 0.114 Angle : 0.512 8.322 52536 Z= 0.258 Chirality : 0.038 0.118 5592 Planarity : 0.004 0.039 6888 Dihedral : 4.045 15.139 5256 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.51 % Allowed : 20.91 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4656 helix: 0.65 (0.11), residues: 2040 sheet: -0.15 (0.26), residues: 288 loop : -0.63 (0.14), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAd 43 TYR 0.008 0.001 TYRAr 195 PHE 0.019 0.002 PHEAl 112 TRP 0.016 0.001 TRPAk 129 HIS 0.003 0.001 HISAe 91 Details of bonding type rmsd covalent geometry : bond 0.00270 (38832) covalent geometry : angle 0.51160 (52536) hydrogen bonds : bond 0.03831 ( 1752) hydrogen bonds : angle 4.41618 ( 4752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 619 time to evaluate : 1.737 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7811 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: Aa 71 LYS cc_start: 0.9315 (mtmt) cc_final: 0.9111 (mtmm) REVERT: Ab 145 MET cc_start: 0.9101 (mmt) cc_final: 0.8800 (mmt) REVERT: Ad 105 MET cc_start: 0.8585 (tpt) cc_final: 0.8377 (tpt) REVERT: Ad 215 MET cc_start: 0.8624 (mtm) cc_final: 0.8357 (mtm) REVERT: Ai 215 MET cc_start: 0.8541 (mtm) cc_final: 0.8326 (mtm) REVERT: Ak 113 MET cc_start: 0.8475 (ttp) cc_final: 0.8104 (ttp) REVERT: Al 217 MET cc_start: 0.8363 (ttm) cc_final: 0.7953 (ttm) REVERT: Am 43 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8481 (mtt-85) REVERT: Am 113 MET cc_start: 0.8533 (ttp) cc_final: 0.8161 (ttp) REVERT: Ar 57 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8111 (mtm-85) REVERT: Ar 113 MET cc_start: 0.8519 (ttp) cc_final: 0.8263 (ttp) outliers start: 102 outliers final: 82 residues processed: 700 average time/residue: 0.2412 time to fit residues: 275.3797 Evaluate side-chains 691 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 607 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 188 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 56 MET Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 44 ILE Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 188 THR Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 105 MET Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 56 MET Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 188 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 188 THR Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 152 THR Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 43 ARG Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 125 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 60 VAL Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 95 MET Chi-restraints excluded: chain At residue 142 LEU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 95 MET Chi-restraints excluded: chain Au residue 142 LEU Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 56 MET Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 95 MET Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 56 MET Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 152 THR Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 192 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 319 optimal weight: 7.9990 chunk 287 optimal weight: 0.6980 chunk 288 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 381 optimal weight: 0.0770 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ar 186 ASN Ar 224 ASN As 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.107182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.091455 restraints weight = 45630.806| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.39 r_work: 0.2720 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38832 Z= 0.094 Angle : 0.487 7.760 52536 Z= 0.244 Chirality : 0.036 0.117 5592 Planarity : 0.004 0.039 6888 Dihedral : 3.823 15.646 5256 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.27 % Allowed : 21.10 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.12), residues: 4656 helix: 1.08 (0.11), residues: 2040 sheet: 0.16 (0.27), residues: 288 loop : -0.44 (0.14), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAd 43 TYR 0.008 0.001 TYRAa 195 PHE 0.021 0.002 PHEAw 112 TRP 0.013 0.001 TRPAk 129 HIS 0.003 0.001 HISAi 91 Details of bonding type rmsd covalent geometry : bond 0.00217 (38832) covalent geometry : angle 0.48651 (52536) hydrogen bonds : bond 0.03419 ( 1752) hydrogen bonds : angle 4.19240 ( 4752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 632 time to evaluate : 1.361 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7727 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8090 (mtm-85) REVERT: Ab 145 MET cc_start: 0.9044 (mmt) cc_final: 0.8760 (mmt) REVERT: Ac 195 TYR cc_start: 0.9074 (m-80) cc_final: 0.8805 (m-80) REVERT: Ad 215 MET cc_start: 0.8558 (mtm) cc_final: 0.8357 (mtm) REVERT: Aj 145 MET cc_start: 0.8982 (mmt) cc_final: 0.8337 (mmt) REVERT: Ak 113 MET cc_start: 0.8479 (ttp) cc_final: 0.8076 (ttp) REVERT: Al 217 MET cc_start: 0.8441 (ttm) cc_final: 0.8046 (ttm) REVERT: Am 113 MET cc_start: 0.8493 (ttp) cc_final: 0.8122 (ttp) REVERT: Am 145 MET cc_start: 0.8967 (mmt) cc_final: 0.8665 (mmt) REVERT: Ar 57 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8101 (mtm-85) REVERT: Ar 113 MET cc_start: 0.8512 (ttp) cc_final: 0.8256 (ttp) REVERT: Ar 215 MET cc_start: 0.8520 (mtp) cc_final: 0.8295 (mtm) REVERT: As 194 ARG cc_start: 0.8732 (ptm-80) cc_final: 0.8496 (ptm-80) REVERT: Ax 51 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7817 (mt) outliers start: 92 outliers final: 73 residues processed: 705 average time/residue: 0.2302 time to fit residues: 266.8466 Evaluate side-chains 677 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 602 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 105 MET Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 44 ILE Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 105 MET Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 188 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 105 MET Chi-restraints excluded: chain Ak residue 188 THR Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 152 THR Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 125 LEU Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 142 LEU Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 56 MET Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 428 optimal weight: 0.0170 chunk 455 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 239 optimal weight: 0.8980 chunk 293 optimal weight: 0.6980 chunk 395 optimal weight: 8.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Al 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 186 ASN Ao 224 ASN Av 186 ASN Ax 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.105700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.089272 restraints weight = 45505.179| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.48 r_work: 0.2662 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38832 Z= 0.123 Angle : 0.520 8.182 52536 Z= 0.258 Chirality : 0.038 0.118 5592 Planarity : 0.004 0.040 6888 Dihedral : 3.880 21.877 5256 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.07 % Allowed : 22.07 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4656 helix: 1.08 (0.11), residues: 2040 sheet: 0.28 (0.28), residues: 288 loop : -0.38 (0.14), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAw 57 TYR 0.011 0.001 TYRAe 195 PHE 0.014 0.002 PHEAl 112 TRP 0.012 0.001 TRPAf 129 HIS 0.003 0.001 HISAn 91 Details of bonding type rmsd covalent geometry : bond 0.00296 (38832) covalent geometry : angle 0.52010 (52536) hydrogen bonds : bond 0.03698 ( 1752) hydrogen bonds : angle 4.29646 ( 4752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9312 Ramachandran restraints generated. 4656 Oldfield, 0 Emsley, 4656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 621 time to evaluate : 1.473 Fit side-chains REVERT: Aa 43 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7795 (mtt-85) REVERT: Aa 57 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8109 (mtm-85) REVERT: Ab 145 MET cc_start: 0.9073 (mmt) cc_final: 0.8781 (mmt) REVERT: Ad 215 MET cc_start: 0.8553 (mtm) cc_final: 0.8291 (mtm) REVERT: Ak 113 MET cc_start: 0.8504 (ttp) cc_final: 0.8102 (ttp) REVERT: Al 217 MET cc_start: 0.8534 (ttm) cc_final: 0.8139 (ttm) REVERT: Am 113 MET cc_start: 0.8528 (ttp) cc_final: 0.8150 (ttp) REVERT: Ar 57 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8145 (mtm-85) REVERT: Ar 113 MET cc_start: 0.8527 (ttp) cc_final: 0.8273 (ttp) REVERT: Ar 215 MET cc_start: 0.8546 (mtp) cc_final: 0.8302 (mtm) REVERT: Au 215 MET cc_start: 0.8547 (mtp) cc_final: 0.8290 (mtt) REVERT: Av 132 MET cc_start: 0.8690 (mmm) cc_final: 0.8252 (mmt) REVERT: Ax 51 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7885 (mt) outliers start: 84 outliers final: 73 residues processed: 686 average time/residue: 0.2269 time to fit residues: 255.9605 Evaluate side-chains 678 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 603 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 ARG Chi-restraints excluded: chain Aa residue 152 THR Chi-restraints excluded: chain Aa residue 203 THR Chi-restraints excluded: chain Ab residue 152 THR Chi-restraints excluded: chain Ab residue 203 THR Chi-restraints excluded: chain Ac residue 60 VAL Chi-restraints excluded: chain Ac residue 105 MET Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ad residue 44 ILE Chi-restraints excluded: chain Ad residue 51 LEU Chi-restraints excluded: chain Ad residue 60 VAL Chi-restraints excluded: chain Ad residue 203 THR Chi-restraints excluded: chain Ae residue 203 THR Chi-restraints excluded: chain Af residue 60 VAL Chi-restraints excluded: chain Af residue 105 MET Chi-restraints excluded: chain Af residue 188 THR Chi-restraints excluded: chain Af residue 203 THR Chi-restraints excluded: chain Ag residue 188 THR Chi-restraints excluded: chain Ag residue 203 THR Chi-restraints excluded: chain Ah residue 51 LEU Chi-restraints excluded: chain Ah residue 203 THR Chi-restraints excluded: chain Ai residue 51 LEU Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 188 THR Chi-restraints excluded: chain Ai residue 203 THR Chi-restraints excluded: chain Aj residue 60 VAL Chi-restraints excluded: chain Aj residue 152 THR Chi-restraints excluded: chain Aj residue 188 THR Chi-restraints excluded: chain Aj residue 203 THR Chi-restraints excluded: chain Ak residue 60 VAL Chi-restraints excluded: chain Ak residue 188 THR Chi-restraints excluded: chain Ak residue 203 THR Chi-restraints excluded: chain Al residue 60 VAL Chi-restraints excluded: chain Al residue 152 THR Chi-restraints excluded: chain Al residue 188 THR Chi-restraints excluded: chain Al residue 203 THR Chi-restraints excluded: chain Am residue 60 VAL Chi-restraints excluded: chain Am residue 152 THR Chi-restraints excluded: chain Am residue 188 THR Chi-restraints excluded: chain Am residue 203 THR Chi-restraints excluded: chain An residue 188 THR Chi-restraints excluded: chain An residue 203 THR Chi-restraints excluded: chain Ao residue 51 LEU Chi-restraints excluded: chain Ao residue 60 VAL Chi-restraints excluded: chain Ao residue 188 THR Chi-restraints excluded: chain Ao residue 203 THR Chi-restraints excluded: chain Ap residue 188 THR Chi-restraints excluded: chain Ap residue 203 THR Chi-restraints excluded: chain Aq residue 51 LEU Chi-restraints excluded: chain Aq residue 152 THR Chi-restraints excluded: chain Aq residue 188 THR Chi-restraints excluded: chain Aq residue 203 THR Chi-restraints excluded: chain Ar residue 51 LEU Chi-restraints excluded: chain Ar residue 95 MET Chi-restraints excluded: chain Ar residue 125 LEU Chi-restraints excluded: chain Ar residue 188 THR Chi-restraints excluded: chain Ar residue 203 THR Chi-restraints excluded: chain As residue 51 LEU Chi-restraints excluded: chain As residue 188 THR Chi-restraints excluded: chain As residue 203 THR Chi-restraints excluded: chain At residue 95 MET Chi-restraints excluded: chain At residue 152 THR Chi-restraints excluded: chain At residue 188 THR Chi-restraints excluded: chain At residue 203 THR Chi-restraints excluded: chain Au residue 203 THR Chi-restraints excluded: chain Av residue 51 LEU Chi-restraints excluded: chain Av residue 56 MET Chi-restraints excluded: chain Av residue 188 THR Chi-restraints excluded: chain Av residue 203 THR Chi-restraints excluded: chain Aw residue 188 THR Chi-restraints excluded: chain Aw residue 203 THR Chi-restraints excluded: chain Ax residue 51 LEU Chi-restraints excluded: chain Ax residue 60 VAL Chi-restraints excluded: chain Ax residue 188 THR Chi-restraints excluded: chain Ax residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 251 optimal weight: 0.7980 chunk 368 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 362 optimal weight: 0.0070 chunk 258 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Al 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 184 GLN Av 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.103364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.087365 restraints weight = 45758.790| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.39 r_work: 0.2671 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38832 Z= 0.118 Angle : 0.514 7.890 52536 Z= 0.255 Chirality : 0.038 0.118 5592 Planarity : 0.004 0.039 6888 Dihedral : 3.867 21.674 5256 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.10 % Allowed : 22.07 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.12), residues: 4656 helix: 1.10 (0.11), residues: 2040 sheet: 0.44 (0.28), residues: 288 loop : -0.34 (0.14), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAw 57 TYR 0.010 0.001 TYRAe 195 PHE 0.014 0.002 PHEAp 112 TRP 0.012 0.001 TRPAk 129 HIS 0.003 0.001 HISAt 91 Details of bonding type rmsd covalent geometry : bond 0.00284 (38832) covalent geometry : angle 0.51431 (52536) hydrogen bonds : bond 0.03651 ( 1752) hydrogen bonds : angle 4.25815 ( 4752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9105.88 seconds wall clock time: 156 minutes 28.46 seconds (9388.46 seconds total)