Starting phenix.real_space_refine on Mon Jul 6 22:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.map" model { file = "/net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ydx_72840/07_2026/9ydx_72840.cif" } resolution = 3.75 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= 0.001 sd= 0.022 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 34 5.16 5 C 23868 2.51 5 N 6834 2.21 5 O 7820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38556 Number of models: 1 Model: "" Number of chains: 34 Chain: "Aa" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ab" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ac" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ad" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ae" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Af" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ag" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ah" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ai" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Aj" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ak" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Al" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Am" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "An" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ao" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ap" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Aq" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ar" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "As" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "At" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Au" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Av" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Aw" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ax" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ay" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Az" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Ba" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bb" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bc" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bd" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Be" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bf" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bg" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Chain: "Bh" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 2 Time building chain proxies: 7.18, per 1000 atoms: 0.19 Number of scatterers: 38556 At special positions: 0 Unit cell: (241.67, 241.67, 98.67, 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 34 16.00 O 7820 8.00 N 6834 7.00 C 23868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9316 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 65 sheets defined 30.9% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'Aa' and resid 259 through 283 removed outlier: 4.012A pdb=" N GLUAa 263 " --> pdb=" O ALAAa 259 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLNAa 264 " --> pdb=" O ARGAa 260 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VALAa 281 " --> pdb=" O LYSAa 277 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 420 through 436 removed outlier: 3.672A pdb=" N GLYAa 433 " --> pdb=" O GLNAa 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VALAa 435 " --> pdb=" O LEUAa 431 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 256 through 260 removed outlier: 3.544A pdb=" N ALAAb 259 " --> pdb=" O VALAb 256 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARGAb 260 " --> pdb=" O SERAb 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 256 through 260' Processing helix chain 'Ab' and resid 261 through 286 removed outlier: 3.921A pdb=" N GLUAb 265 " --> pdb=" O ARGAb 261 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLUAb 267 " --> pdb=" O GLUAb 263 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALAb 281 " --> pdb=" O LYSAb 277 " (cutoff:3.500A) Proline residue: Ab 284 - end of helix Processing helix chain 'Ab' and resid 420 through 436 Processing helix chain 'Ac' and resid 258 through 286 removed outlier: 3.554A pdb=" N GLUAc 263 " --> pdb=" O ALAAc 259 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLNAc 264 " --> pdb=" O ARGAc 260 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILEAc 283 " --> pdb=" O ASPAc 279 " (cutoff:3.500A) Proline residue: Ac 284 - end of helix Processing helix chain 'Ac' and resid 420 through 436 removed outlier: 3.680A pdb=" N GLYAc 433 " --> pdb=" O GLNAc 429 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THRAc 434 " --> pdb=" O VALAc 430 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 258 through 286 removed outlier: 3.673A pdb=" N LYSAd 262 " --> pdb=" O ALAAd 258 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALAd 281 " --> pdb=" O LYSAd 277 " (cutoff:3.500A) Proline residue: Ad 284 - end of helix Processing helix chain 'Ad' and resid 420 through 436 Processing helix chain 'Ae' and resid 258 through 283 removed outlier: 4.135A pdb=" N LYSAe 262 " --> pdb=" O ALAAe 258 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLNAe 264 " --> pdb=" O ARGAe 260 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUAe 265 " --> pdb=" O ARGAe 261 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLUAe 267 " --> pdb=" O GLUAe 263 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSAe 268 " --> pdb=" O GLNAe 264 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALAe 281 " --> pdb=" O LYSAe 277 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 420 through 436 Processing helix chain 'Af' and resid 258 through 286 removed outlier: 3.555A pdb=" N LYSAf 262 " --> pdb=" O ALAAf 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLNAf 264 " --> pdb=" O ARGAf 260 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALAf 281 " --> pdb=" O LYSAf 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEAf 283 " --> pdb=" O ASPAf 279 " (cutoff:3.500A) Proline residue: Af 284 - end of helix Processing helix chain 'Af' and resid 420 through 436 Processing helix chain 'Ag' and resid 259 through 283 removed outlier: 3.998A pdb=" N GLNAg 264 " --> pdb=" O ARGAg 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLUAg 267 " --> pdb=" O GLUAg 263 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VALAg 281 " --> pdb=" O LYSAg 277 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 420 through 436 Processing helix chain 'Ah' and resid 258 through 279 removed outlier: 3.557A pdb=" N GLNAh 264 " --> pdb=" O ARGAh 260 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 420 through 436 removed outlier: 3.501A pdb=" N GLYAh 433 " --> pdb=" O GLNAh 429 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 258 through 287 removed outlier: 3.506A pdb=" N LYSAi 277 " --> pdb=" O ALAAi 273 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILEAi 278 " --> pdb=" O LEUAi 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALAi 281 " --> pdb=" O LYSAi 277 " (cutoff:3.500A) Proline residue: Ai 284 - end of helix Processing helix chain 'Ai' and resid 420 through 436 removed outlier: 3.553A pdb=" N GLYAi 433 " --> pdb=" O GLNAi 429 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 258 through 282 removed outlier: 3.761A pdb=" N LYSAj 262 " --> pdb=" O ALAAj 258 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLUAj 263 " --> pdb=" O ALAAj 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLNAj 264 " --> pdb=" O ARGAj 260 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 420 through 436 Processing helix chain 'Ak' and resid 259 through 286 removed outlier: 3.865A pdb=" N GLNAk 264 " --> pdb=" O ARGAk 260 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLUAk 267 " --> pdb=" O GLUAk 263 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALAk 281 " --> pdb=" O LYSAk 277 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILEAk 283 " --> pdb=" O ASPAk 279 " (cutoff:3.500A) Proline residue: Ak 284 - end of helix Processing helix chain 'Ak' and resid 420 through 436 Processing helix chain 'Al' and resid 259 through 286 removed outlier: 3.872A pdb=" N GLNAl 264 " --> pdb=" O ARGAl 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLUAl 267 " --> pdb=" O GLUAl 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALAl 281 " --> pdb=" O LYSAl 277 " (cutoff:3.500A) Proline residue: Al 284 - end of helix Processing helix chain 'Al' and resid 420 through 436 Processing helix chain 'Am' and resid 258 through 286 removed outlier: 3.591A pdb=" N LYSAm 277 " --> pdb=" O ALAAm 273 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEAm 278 " --> pdb=" O LEUAm 274 " (cutoff:3.500A) Proline residue: Am 284 - end of helix Processing helix chain 'Am' and resid 420 through 436 removed outlier: 3.562A pdb=" N GLYAm 433 " --> pdb=" O GLNAm 429 " (cutoff:3.500A) Processing helix chain 'An' and resid 258 through 286 removed outlier: 3.786A pdb=" N LYSAn 262 " --> pdb=" O ALAAn 258 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VALAn 281 " --> pdb=" O LYSAn 277 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILEAn 283 " --> pdb=" O ASPAn 279 " (cutoff:3.500A) Proline residue: An 284 - end of helix Processing helix chain 'An' and resid 420 through 436 Processing helix chain 'Ao' and resid 257 through 283 removed outlier: 4.283A pdb=" N ARGAo 261 " --> pdb=" O SERAo 257 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLNAo 264 " --> pdb=" O ARGAo 260 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLUAo 267 " --> pdb=" O GLUAo 263 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYSAo 268 " --> pdb=" O GLNAo 264 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VALAo 281 " --> pdb=" O LYSAo 277 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 420 through 436 Processing helix chain 'Ap' and resid 257 through 283 removed outlier: 4.942A pdb=" N GLNAp 264 " --> pdb=" O ARGAp 260 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLUAp 265 " --> pdb=" O ARGAp 261 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VALAp 281 " --> pdb=" O LYSAp 277 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 420 through 436 Processing helix chain 'Aq' and resid 258 through 286 removed outlier: 3.919A pdb=" N GLNAq 264 " --> pdb=" O ARGAq 260 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEUAq 266 " --> pdb=" O LYSAq 262 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLUAq 267 " --> pdb=" O GLUAq 263 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYSAq 268 " --> pdb=" O GLNAq 264 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VALAq 281 " --> pdb=" O LYSAq 277 " (cutoff:3.500A) Proline residue: Aq 284 - end of helix Processing helix chain 'Aq' and resid 420 through 436 Processing helix chain 'Ar' and resid 259 through 280 removed outlier: 4.277A pdb=" N GLUAr 263 " --> pdb=" O ALAAr 259 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLNAr 264 " --> pdb=" O ARGAr 260 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 420 through 436 removed outlier: 3.570A pdb=" N GLYAr 433 " --> pdb=" O GLNAr 429 " (cutoff:3.500A) Processing helix chain 'As' and resid 258 through 286 removed outlier: 3.901A pdb=" N LYSAs 262 " --> pdb=" O ALAAs 258 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VALAs 281 " --> pdb=" O LYSAs 277 " (cutoff:3.500A) Proline residue: As 284 - end of helix Processing helix chain 'As' and resid 420 through 436 Processing helix chain 'At' and resid 258 through 286 removed outlier: 4.437A pdb=" N LYSAt 262 " --> pdb=" O ALAAt 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLUAt 263 " --> pdb=" O ALAAt 259 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLNAt 264 " --> pdb=" O ARGAt 260 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLUAt 267 " --> pdb=" O GLUAt 263 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYSAt 268 " --> pdb=" O GLNAt 264 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALAt 281 " --> pdb=" O LYSAt 277 " (cutoff:3.500A) Proline residue: At 284 - end of helix Processing helix chain 'At' and resid 420 through 436 Processing helix chain 'Au' and resid 256 through 258 No H-bonds generated for 'chain 'Au' and resid 256 through 258' Processing helix chain 'Au' and resid 259 through 286 removed outlier: 4.001A pdb=" N GLUAu 263 " --> pdb=" O ALAAu 259 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLNAu 264 " --> pdb=" O ARGAu 260 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VALAu 281 " --> pdb=" O LYSAu 277 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILEAu 283 " --> pdb=" O ASPAu 279 " (cutoff:3.500A) Proline residue: Au 284 - end of helix Processing helix chain 'Au' and resid 420 through 436 Processing helix chain 'Av' and resid 258 through 280 removed outlier: 3.861A pdb=" N LYSAv 262 " --> pdb=" O ALAAv 258 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLUAv 263 " --> pdb=" O ALAAv 259 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLNAv 264 " --> pdb=" O ARGAv 260 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLUAv 267 " --> pdb=" O GLUAv 263 " (cutoff:3.500A) Processing helix chain 'Av' and resid 281 through 286 removed outlier: 3.565A pdb=" N ILEAv 285 " --> pdb=" O VALAv 281 " (cutoff:3.500A) Processing helix chain 'Av' and resid 420 through 436 Processing helix chain 'Aw' and resid 258 through 279 removed outlier: 4.006A pdb=" N LYSAw 262 " --> pdb=" O ALAAw 258 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLNAw 264 " --> pdb=" O ARGAw 260 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 420 through 436 Processing helix chain 'Ax' and resid 257 through 283 removed outlier: 4.216A pdb=" N ARGAx 261 " --> pdb=" O SERAx 257 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLNAx 264 " --> pdb=" O ARGAx 260 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VALAx 281 " --> pdb=" O LYSAx 277 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 420 through 436 Processing helix chain 'Ay' and resid 258 through 286 removed outlier: 3.548A pdb=" N LYSAy 262 " --> pdb=" O ALAAy 258 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLNAy 264 " --> pdb=" O ARGAy 260 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VALAy 281 " --> pdb=" O LYSAy 277 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILEAy 283 " --> pdb=" O ASPAy 279 " (cutoff:3.500A) Proline residue: Ay 284 - end of helix Processing helix chain 'Ay' and resid 420 through 436 Processing helix chain 'Az' and resid 261 through 286 removed outlier: 6.033A pdb=" N GLUAz 267 " --> pdb=" O GLUAz 263 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYSAz 268 " --> pdb=" O GLNAz 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYSAz 277 " --> pdb=" O ALAAz 273 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VALAz 281 " --> pdb=" O LYSAz 277 " (cutoff:3.500A) Proline residue: Az 284 - end of helix Processing helix chain 'Az' and resid 420 through 436 Processing helix chain 'Ba' and resid 264 through 280 removed outlier: 3.857A pdb=" N LYSBa 268 " --> pdb=" O GLNBa 264 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 420 through 436 Processing helix chain 'Bb' and resid 258 through 286 removed outlier: 3.502A pdb=" N LYSBb 262 " --> pdb=" O ALABb 258 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLNBb 264 " --> pdb=" O ARGBb 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYBb 276 " --> pdb=" O GLUBb 272 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSBb 277 " --> pdb=" O ALABb 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VALBb 281 " --> pdb=" O LYSBb 277 " (cutoff:3.500A) Proline residue: Bb 284 - end of helix Processing helix chain 'Bb' and resid 420 through 436 Processing helix chain 'Bc' and resid 256 through 258 No H-bonds generated for 'chain 'Bc' and resid 256 through 258' Processing helix chain 'Bc' and resid 259 through 283 removed outlier: 3.797A pdb=" N GLNBc 264 " --> pdb=" O ARGBc 260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VALBc 281 " --> pdb=" O LYSBc 277 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 420 through 436 Processing helix chain 'Bd' and resid 258 through 286 removed outlier: 4.137A pdb=" N LYSBd 262 " --> pdb=" O ALABd 258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALBd 281 " --> pdb=" O LYSBd 277 " (cutoff:3.500A) Proline residue: Bd 284 - end of helix Processing helix chain 'Bd' and resid 420 through 436 Processing helix chain 'Be' and resid 256 through 258 No H-bonds generated for 'chain 'Be' and resid 256 through 258' Processing helix chain 'Be' and resid 259 through 286 removed outlier: 3.788A pdb=" N GLUBe 263 " --> pdb=" O ALABe 259 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLNBe 264 " --> pdb=" O ARGBe 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLYBe 276 " --> pdb=" O GLUBe 272 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYSBe 277 " --> pdb=" O ALABe 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILEBe 278 " --> pdb=" O LEUBe 274 " (cutoff:3.500A) Proline residue: Be 284 - end of helix Processing helix chain 'Be' and resid 420 through 436 Processing helix chain 'Bf' and resid 258 through 286 removed outlier: 3.693A pdb=" N LYSBf 262 " --> pdb=" O ALABf 258 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLNBf 264 " --> pdb=" O ARGBf 260 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VALBf 281 " --> pdb=" O LYSBf 277 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILEBf 283 " --> pdb=" O ASPBf 279 " (cutoff:3.500A) Proline residue: Bf 284 - end of helix Processing helix chain 'Bf' and resid 420 through 436 Processing helix chain 'Bg' and resid 258 through 286 removed outlier: 3.826A pdb=" N LYSBg 262 " --> pdb=" O ALABg 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLNBg 264 " --> pdb=" O ARGBg 260 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VALBg 281 " --> pdb=" O LYSBg 277 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILEBg 283 " --> pdb=" O ASPBg 279 " (cutoff:3.500A) Proline residue: Bg 284 - end of helix Processing helix chain 'Bg' and resid 420 through 436 Processing helix chain 'Bh' and resid 258 through 287 removed outlier: 3.755A pdb=" N LYSBh 262 " --> pdb=" O ALABh 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLNBh 264 " --> pdb=" O ARGBh 260 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUBh 267 " --> pdb=" O GLUBh 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALBh 281 " --> pdb=" O LYSBh 277 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILEBh 283 " --> pdb=" O ASPBh 279 " (cutoff:3.500A) Proline residue: Bh 284 - end of helix Processing helix chain 'Bh' and resid 420 through 436 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 292 through 300 removed outlier: 3.566A pdb=" N GLNAa 294 " --> pdb=" O ALAAa 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THRAa 396 " --> pdb=" O ASPAa 296 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARGAa 394 " --> pdb=" O GLUAa 298 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASPAa 300 " --> pdb=" O ILEAa 392 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILEAa 392 " --> pdb=" O ASPAa 300 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LEUAa 444 " --> pdb=" O ASNAa 393 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLNAa 395 " --> pdb=" O LEUAa 444 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASNAa 446 " --> pdb=" O GLNAa 395 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VALAa 397 " --> pdb=" O ASNAa 446 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEUAa 448 " --> pdb=" O VALAa 397 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VALAa 399 " --> pdb=" O LEUAa 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Aa' and resid 305 through 311 removed outlier: 4.178A pdb=" N THRAa 380 " --> pdb=" O LYSAb 309 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALAAc 303 " --> pdb=" O ARGAb 386 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILEAd 382 " --> pdb=" O THRAe 307 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARGAe 308 " --> pdb=" O SERAe 383 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THRAe 380 " --> pdb=" O LYSAf 309 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THRAg 380 " --> pdb=" O LYSAh 309 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THRAh 380 " --> pdb=" O LYSAi 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ak' and resid 305 through 306 current: chain 'Ak' and resid 380 through 386 removed outlier: 4.072A pdb=" N THRAm 380 " --> pdb=" O LYSAn 309 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEAn 382 " --> pdb=" O THRAo 307 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HISAn 384 " --> pdb=" O GLUAo 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ap' and resid 382 through 386 current: chain 'Aq' and resid 380 through 386 removed outlier: 3.624A pdb=" N THRAq 380 " --> pdb=" O LYSAr 309 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VALAr 304 " --> pdb=" O LYSAr 387 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THRAr 380 " --> pdb=" O LYSAs 309 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VALAs 310 " --> pdb=" O THRAs 381 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'At' and resid 303 through 306 current: chain 'At' and resid 380 through 386 removed outlier: 3.509A pdb=" N THRAt 380 " --> pdb=" O LYSAu 309 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THRAu 380 " --> pdb=" O LYSAv 309 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALAAy 303 " --> pdb=" O ARGAx 386 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILEAz 382 " --> pdb=" O THRBa 307 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THRBb 380 " --> pdb=" O LYSBc 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILEBc 382 " --> pdb=" O THRBd 307 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THRBd 380 " --> pdb=" O LYSBe 309 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THRBg 380 " --> pdb=" O LYSBh 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Aa' and resid 317 through 320 removed outlier: 3.690A pdb=" N ALAAa 317 " --> pdb=" O GLUAa 377 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASNAa 375 " --> pdb=" O ARGAa 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Aa' and resid 369 through 372 Processing sheet with id=AA5, first strand: chain 'Ab' and resid 293 through 300 removed outlier: 6.953A pdb=" N GLNAb 294 " --> pdb=" O VALAb 397 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VALAb 397 " --> pdb=" O GLNAb 294 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASPAb 296 " --> pdb=" O GLNAb 395 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLNAb 395 " --> pdb=" O ASPAb 296 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLUAb 298 " --> pdb=" O ASNAb 393 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N LEUAb 444 " --> pdb=" O ASNAb 393 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLNAb 395 " --> pdb=" O LEUAb 444 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASNAb 446 " --> pdb=" O GLNAb 395 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VALAb 397 " --> pdb=" O ASNAb 446 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEUAb 448 " --> pdb=" O VALAb 397 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VALAb 399 " --> pdb=" O LEUAb 448 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N METAb 450 " --> pdb=" O VALAb 399 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VALAb 401 " --> pdb=" O METAb 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Ab' and resid 317 through 320 removed outlier: 3.789A pdb=" N ALAAb 317 " --> pdb=" O GLUAb 377 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASNAb 375 " --> pdb=" O ARGAb 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ab' and resid 369 through 372 removed outlier: 3.519A pdb=" N SERAe 320 " --> pdb=" O ASNAe 375 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLUAe 377 " --> pdb=" O THRAe 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THRAe 318 " --> pdb=" O GLUAe 377 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARGAe 319 " --> pdb=" O TYRAf 376 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASNAf 375 " --> pdb=" O ARGAf 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ac' and resid 293 through 299 removed outlier: 3.594A pdb=" N ARGAc 394 " --> pdb=" O GLUAc 298 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N LEUAc 444 " --> pdb=" O ASNAc 393 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLNAc 395 " --> pdb=" O LEUAc 444 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASNAc 446 " --> pdb=" O GLNAc 395 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VALAc 397 " --> pdb=" O ASNAc 446 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEUAc 448 " --> pdb=" O VALAc 397 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VALAc 399 " --> pdb=" O LEUAc 448 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N METAc 450 " --> pdb=" O VALAc 399 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VALAc 401 " --> pdb=" O METAc 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ac' and resid 317 through 320 removed outlier: 6.577A pdb=" N ASNAc 375 " --> pdb=" O ARGAc 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ad' and resid 291 through 300 removed outlier: 3.867A pdb=" N ARGAd 394 " --> pdb=" O GLUAd 298 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASPAd 300 " --> pdb=" O ILEAd 392 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILEAd 392 " --> pdb=" O ASPAd 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ad' and resid 317 through 320 removed outlier: 5.170A pdb=" N THRAd 318 " --> pdb=" O GLUAd 377 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLUAd 377 " --> pdb=" O THRAd 318 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ae' and resid 292 through 300 removed outlier: 3.643A pdb=" N GLNAe 294 " --> pdb=" O ALAAe 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARGAe 394 " --> pdb=" O GLUAe 298 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASPAe 300 " --> pdb=" O ILEAe 392 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILEAe 392 " --> pdb=" O ASPAe 300 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N LEUAe 444 " --> pdb=" O ASNAe 393 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLNAe 395 " --> pdb=" O LEUAe 444 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ASNAe 446 " --> pdb=" O GLNAe 395 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VALAe 397 " --> pdb=" O ASNAe 446 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEUAe 448 " --> pdb=" O VALAe 397 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VALAe 399 " --> pdb=" O LEUAe 448 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N METAe 450 " --> pdb=" O VALAe 399 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VALAe 401 " --> pdb=" O METAe 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Af' and resid 292 through 299 removed outlier: 7.012A pdb=" N THRAf 292 " --> pdb=" O VALAf 399 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VALAf 399 " --> pdb=" O THRAf 292 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLNAf 294 " --> pdb=" O VALAf 397 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VALAf 397 " --> pdb=" O GLNAf 294 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASPAf 296 " --> pdb=" O GLNAf 395 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLNAf 395 " --> pdb=" O ASPAf 296 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLUAf 298 " --> pdb=" O ASNAf 393 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N LEUAf 444 " --> pdb=" O ASNAf 393 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLNAf 395 " --> pdb=" O LEUAf 444 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASNAf 446 " --> pdb=" O GLNAf 395 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VALAf 397 " --> pdb=" O ASNAf 446 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEUAf 448 " --> pdb=" O VALAf 397 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VALAf 399 " --> pdb=" O LEUAf 448 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N METAf 450 " --> pdb=" O VALAf 399 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VALAf 401 " --> pdb=" O METAf 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Af' and resid 323 through 326 removed outlier: 6.379A pdb=" N HISAk 369 " --> pdb=" O GLUAk 325 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLUAk 325 " --> pdb=" O HISAk 369 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLUAk 371 " --> pdb=" O THRAk 323 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THRAk 323 " --> pdb=" O GLUAk 371 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THRAk 373 " --> pdb=" O GLUAk 321 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLUAk 321 " --> pdb=" O THRAk 373 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASNAk 375 " --> pdb=" O ARGAk 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ag' and resid 293 through 300 removed outlier: 3.552A pdb=" N GLNAg 294 " --> pdb=" O ALAAg 398 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARGAg 394 " --> pdb=" O GLUAg 298 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASPAg 300 " --> pdb=" O ILEAg 392 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILEAg 392 " --> pdb=" O ASPAg 300 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LEUAg 444 " --> pdb=" O ASNAg 393 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLNAg 395 " --> pdb=" O LEUAg 444 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASNAg 446 " --> pdb=" O GLNAg 395 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VALAg 397 " --> pdb=" O ASNAg 446 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEUAg 448 " --> pdb=" O VALAg 397 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VALAg 399 " --> pdb=" O LEUAg 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ag' and resid 317 through 320 removed outlier: 3.595A pdb=" N ALAAg 317 " --> pdb=" O GLUAg 377 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASNAg 375 " --> pdb=" O ARGAg 319 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ah' and resid 293 through 300 removed outlier: 4.224A pdb=" N ARGAh 394 " --> pdb=" O GLUAh 298 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASPAh 300 " --> pdb=" O ILEAh 392 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILEAh 392 " --> pdb=" O ASPAh 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ah' and resid 317 through 320 removed outlier: 3.785A pdb=" N ALAAh 317 " --> pdb=" O GLUAh 377 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASNAh 375 " --> pdb=" O ARGAh 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ai' and resid 293 through 299 removed outlier: 3.836A pdb=" N ARGAi 394 " --> pdb=" O GLUAi 298 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEUAi 444 " --> pdb=" O ASNAi 393 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLNAi 395 " --> pdb=" O LEUAi 444 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASNAi 446 " --> pdb=" O GLNAi 395 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VALAi 397 " --> pdb=" O ASNAi 446 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEUAi 448 " --> pdb=" O VALAi 397 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VALAi 399 " --> pdb=" O LEUAi 448 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N METAi 450 " --> pdb=" O VALAi 399 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VALAi 401 " --> pdb=" O METAi 450 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ai' and resid 318 through 320 removed outlier: 6.695A pdb=" N ASNAi 375 " --> pdb=" O ARGAi 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Aj' and resid 291 through 299 removed outlier: 3.552A pdb=" N THRAj 292 " --> pdb=" O ALAAj 400 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARGAj 394 " --> pdb=" O GLUAj 298 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N LEUAj 444 " --> pdb=" O ASNAj 393 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLNAj 395 " --> pdb=" O LEUAj 444 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASNAj 446 " --> pdb=" O GLNAj 395 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VALAj 397 " --> pdb=" O ASNAj 446 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEUAj 448 " --> pdb=" O VALAj 397 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VALAj 399 " --> pdb=" O LEUAj 448 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N METAj 450 " --> pdb=" O VALAj 399 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VALAj 401 " --> pdb=" O METAj 450 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Aj' and resid 317 through 320 removed outlier: 3.628A pdb=" N ALAAj 317 " --> pdb=" O GLUAj 377 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASNAj 375 " --> pdb=" O ARGAj 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Ak' and resid 293 through 300 removed outlier: 3.963A pdb=" N ARGAk 394 " --> pdb=" O GLUAk 298 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASPAk 300 " --> pdb=" O ILEAk 392 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILEAk 392 " --> pdb=" O ASPAk 300 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LEUAk 444 " --> pdb=" O ASNAk 393 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLNAk 395 " --> pdb=" O LEUAk 444 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASNAk 446 " --> pdb=" O GLNAk 395 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VALAk 397 " --> pdb=" O ASNAk 446 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEUAk 448 " --> pdb=" O VALAk 397 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VALAk 399 " --> pdb=" O LEUAk 448 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N METAk 450 " --> pdb=" O VALAk 399 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VALAk 401 " --> pdb=" O METAk 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Al' and resid 293 through 299 removed outlier: 6.981A pdb=" N GLNAl 294 " --> pdb=" O VALAl 397 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VALAl 397 " --> pdb=" O GLNAl 294 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASPAl 296 " --> pdb=" O GLNAl 395 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLNAl 395 " --> pdb=" O ASPAl 296 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLUAl 298 " --> pdb=" O ASNAl 393 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEUAl 444 " --> pdb=" O ASNAl 393 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLNAl 395 " --> pdb=" O LEUAl 444 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASNAl 446 " --> pdb=" O GLNAl 395 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VALAl 397 " --> pdb=" O ASNAl 446 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEUAl 448 " --> pdb=" O VALAl 397 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VALAl 399 " --> pdb=" O LEUAl 448 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N METAl 450 " --> pdb=" O VALAl 399 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VALAl 401 " --> pdb=" O METAl 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Al' and resid 317 through 320 removed outlier: 3.598A pdb=" N ALAAl 317 " --> pdb=" O GLUAl 377 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASNAl 375 " --> pdb=" O ARGAl 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Am' and resid 293 through 299 removed outlier: 7.061A pdb=" N GLNAm 294 " --> pdb=" O VALAm 397 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VALAm 397 " --> pdb=" O GLNAm 294 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASPAm 296 " --> pdb=" O GLNAm 395 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLNAm 395 " --> pdb=" O ASPAm 296 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLUAm 298 " --> pdb=" O ASNAm 393 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASNAm 446 " --> pdb=" O GLNAm 395 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VALAm 397 " --> pdb=" O ASNAm 446 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEUAm 448 " --> pdb=" O VALAm 397 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VALAm 399 " --> pdb=" O LEUAm 448 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N METAm 450 " --> pdb=" O VALAm 399 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VALAm 401 " --> pdb=" O METAm 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Am' and resid 317 through 320 removed outlier: 3.968A pdb=" N ALAAm 317 " --> pdb=" O GLUAm 377 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASNAm 375 " --> pdb=" O ARGAm 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Am' and resid 323 through 326 WARNING: can't find start of bonding for strands! previous: chain 'Am' and resid 323 through 326 current: chain 'An' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'An' and resid 369 through 372 current: chain 'Ao' and resid 369 through 377 WARNING: can't find start of bonding for strands! previous: chain 'Ao' and resid 369 through 377 current: chain 'Ap' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'Ap' and resid 369 through 372 current: chain 'Aq' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'Aq' and resid 369 through 372 current: chain 'Ar' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'Ar' and resid 369 through 372 current: chain 'As' and resid 369 through 372 WARNING: can't find start of bonding for strands! previous: chain 'As' and resid 369 through 372 current: chain 'At' and resid 369 through 372 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'An' and resid 292 through 300 removed outlier: 3.725A pdb=" N THRAn 292 " --> pdb=" O ALAAn 400 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLNAn 294 " --> pdb=" O ALAAn 398 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARGAn 394 " --> pdb=" O GLUAn 298 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASPAn 300 " --> pdb=" O ILEAn 392 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILEAn 392 " --> pdb=" O ASPAn 300 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LEUAn 444 " --> pdb=" O ASNAn 393 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLNAn 395 " --> pdb=" O LEUAn 444 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASNAn 446 " --> pdb=" O GLNAn 395 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VALAn 397 " --> pdb=" O ASNAn 446 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEUAn 448 " --> pdb=" O VALAn 397 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VALAn 399 " --> pdb=" O LEUAn 448 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N METAn 450 " --> pdb=" O VALAn 399 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VALAn 401 " --> pdb=" O METAn 450 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Ao' and resid 293 through 297 removed outlier: 3.794A pdb=" N GLNAo 294 " --> pdb=" O ALAAo 398 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLNAo 395 " --> pdb=" O LEUAo 444 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASNAo 446 " --> pdb=" O GLNAo 395 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VALAo 397 " --> pdb=" O ASNAo 446 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEUAo 448 " --> pdb=" O VALAo 397 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VALAo 399 " --> pdb=" O LEUAo 448 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N METAo 450 " --> pdb=" O VALAo 399 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VALAo 401 " --> pdb=" O METAo 450 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Ap' and resid 291 through 300 removed outlier: 3.596A pdb=" N THRAp 292 " --> pdb=" O ALAAp 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLNAp 294 " --> pdb=" O ALAAp 398 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARGAp 394 " --> pdb=" O GLUAp 298 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASPAp 300 " --> pdb=" O ILEAp 392 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILEAp 392 " --> pdb=" O ASPAp 300 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEUAp 444 " --> pdb=" O ASNAp 393 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLNAp 395 " --> pdb=" O LEUAp 444 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASNAp 446 " --> pdb=" O GLNAp 395 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VALAp 397 " --> pdb=" O ASNAp 446 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEUAp 448 " --> pdb=" O VALAp 397 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VALAp 399 " --> pdb=" O LEUAp 448 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N METAp 450 " --> pdb=" O VALAp 399 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VALAp 401 " --> pdb=" O METAp 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Ap' and resid 317 through 320 removed outlier: 6.743A pdb=" N ASNAp 375 " --> pdb=" O ARGAp 319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Aq' and resid 293 through 300 removed outlier: 6.981A pdb=" N GLNAq 294 " --> pdb=" O VALAq 397 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VALAq 397 " --> pdb=" O GLNAq 294 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASPAq 296 " --> pdb=" O GLNAq 395 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLNAq 395 " --> pdb=" O ASPAq 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLUAq 298 " --> pdb=" O ASNAq 393 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALAq 391 " --> pdb=" O ASPAq 300 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEUAq 444 " --> pdb=" O ASNAq 393 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLNAq 395 " --> pdb=" O LEUAq 444 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASNAq 446 " --> pdb=" O GLNAq 395 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VALAq 397 " --> pdb=" O ASNAq 446 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEUAq 448 " --> pdb=" O VALAq 397 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VALAq 399 " --> pdb=" O LEUAq 448 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N METAq 450 " --> pdb=" O VALAq 399 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VALAq 401 " --> pdb=" O METAq 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Aq' and resid 317 through 320 removed outlier: 3.630A pdb=" N ALAAq 317 " --> pdb=" O GLUAq 377 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASNAq 375 " --> pdb=" O ARGAq 319 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Ar' and resid 293 through 300 removed outlier: 3.623A pdb=" N ARGAr 394 " --> pdb=" O GLUAr 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASPAr 300 " --> pdb=" O ILEAr 392 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILEAr 392 " --> pdb=" O ASPAr 300 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASNAr 446 " --> pdb=" O GLNAr 395 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VALAr 397 " --> pdb=" O ASNAr 446 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEUAr 448 " --> pdb=" O VALAr 397 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VALAr 399 " --> pdb=" O LEUAr 448 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N METAr 450 " --> pdb=" O VALAr 399 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VALAr 401 " --> pdb=" O METAr 450 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Ar' and resid 317 through 320 removed outlier: 6.913A pdb=" N ASNAr 375 " --> pdb=" O ARGAr 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'As' and resid 293 through 300 removed outlier: 7.009A pdb=" N GLNAs 294 " --> pdb=" O VALAs 397 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VALAs 397 " --> pdb=" O GLNAs 294 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASPAs 296 " --> pdb=" O GLNAs 395 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLNAs 395 " --> pdb=" O ASPAs 296 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLUAs 298 " --> pdb=" O ASNAs 393 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASNAs 393 " --> pdb=" O GLUAs 298 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEUAs 444 " --> pdb=" O ASNAs 393 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLNAs 395 " --> pdb=" O LEUAs 444 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASNAs 446 " --> pdb=" O GLNAs 395 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VALAs 397 " --> pdb=" O ASNAs 446 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEUAs 448 " --> pdb=" O VALAs 397 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VALAs 399 " --> pdb=" O LEUAs 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'As' and resid 317 through 320 removed outlier: 6.604A pdb=" N ASNAs 375 " --> pdb=" O ARGAs 319 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'At' and resid 292 through 299 removed outlier: 7.177A pdb=" N THRAt 292 " --> pdb=" O VALAt 399 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VALAt 399 " --> pdb=" O THRAt 292 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLNAt 294 " --> pdb=" O VALAt 397 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VALAt 397 " --> pdb=" O GLNAt 294 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASPAt 296 " --> pdb=" O GLNAt 395 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLNAt 395 " --> pdb=" O ASPAt 296 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLUAt 298 " --> pdb=" O ASNAt 393 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N LEUAt 444 " --> pdb=" O ASNAt 393 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLNAt 395 " --> pdb=" O LEUAt 444 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASNAt 446 " --> pdb=" O GLNAt 395 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VALAt 397 " --> pdb=" O ASNAt 446 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEUAt 448 " --> pdb=" O VALAt 397 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VALAt 399 " --> pdb=" O LEUAt 448 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'At' and resid 317 through 320 removed outlier: 6.521A pdb=" N ASNAt 375 " --> pdb=" O ARGAt 319 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Au' and resid 293 through 300 removed outlier: 3.872A pdb=" N ARGAu 394 " --> pdb=" O GLUAu 298 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASPAu 300 " --> pdb=" O ILEAu 392 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILEAu 392 " --> pdb=" O ASPAu 300 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Au' and resid 317 through 320 removed outlier: 6.810A pdb=" N ASNAu 375 " --> pdb=" O ARGAu 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Au' and resid 323 through 326 removed outlier: 6.406A pdb=" N HISAv 369 " --> pdb=" O GLUAv 325 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLUAv 325 " --> pdb=" O HISAv 369 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLUAv 371 " --> pdb=" O THRAv 323 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRAv 323 " --> pdb=" O GLUAv 371 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THRAv 373 " --> pdb=" O GLUAv 321 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAv 321 " --> pdb=" O THRAv 373 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASNAv 375 " --> pdb=" O ARGAv 319 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ARGAv 319 " --> pdb=" O TYRAw 376 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLUAw 377 " --> pdb=" O THRAw 318 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THRAw 318 " --> pdb=" O GLUAw 377 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARGAw 319 " --> pdb=" O TYRAx 376 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARGAx 319 " --> pdb=" O TYRAy 376 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLUAy 377 " --> pdb=" O THRAy 318 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THRAy 318 " --> pdb=" O GLUAy 377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Av' and resid 291 through 300 removed outlier: 3.510A pdb=" N GLNAv 294 " --> pdb=" O ALAAv 398 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARGAv 394 " --> pdb=" O GLUAv 298 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASPAv 300 " --> pdb=" O ILEAv 392 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILEAv 392 " --> pdb=" O ASPAv 300 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEUAv 444 " --> pdb=" O GLNAv 395 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Aw' and resid 293 through 299 removed outlier: 7.093A pdb=" N GLNAw 294 " --> pdb=" O VALAw 397 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VALAw 397 " --> pdb=" O GLNAw 294 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASPAw 296 " --> pdb=" O GLNAw 395 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLNAw 395 " --> pdb=" O ASPAw 296 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLUAw 298 " --> pdb=" O ASNAw 393 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEUAw 444 " --> pdb=" O ASNAw 393 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLNAw 395 " --> pdb=" O LEUAw 444 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASNAw 446 " --> pdb=" O GLNAw 395 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VALAw 397 " --> pdb=" O ASNAw 446 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEUAw 448 " --> pdb=" O VALAw 397 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VALAw 399 " --> pdb=" O LEUAw 448 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N METAw 450 " --> pdb=" O VALAw 399 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VALAw 401 " --> pdb=" O METAw 450 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Ax' and resid 291 through 300 removed outlier: 3.756A pdb=" N GLUAx 298 " --> pdb=" O ARGAx 394 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARGAx 394 " --> pdb=" O GLUAx 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASPAx 300 " --> pdb=" O ILEAx 392 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILEAx 392 " --> pdb=" O ASPAx 300 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEUAx 444 " --> pdb=" O ASNAx 393 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLNAx 395 " --> pdb=" O LEUAx 444 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASNAx 446 " --> pdb=" O GLNAx 395 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VALAx 397 " --> pdb=" O ASNAx 446 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEUAx 448 " --> pdb=" O VALAx 397 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VALAx 399 " --> pdb=" O LEUAx 448 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Ay' and resid 292 through 300 removed outlier: 3.645A pdb=" N GLNAy 294 " --> pdb=" O ALAAy 398 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARGAy 394 " --> pdb=" O GLUAy 298 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASPAy 300 " --> pdb=" O ILEAy 392 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILEAy 392 " --> pdb=" O ASPAy 300 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LEUAy 444 " --> pdb=" O ASNAy 393 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLNAy 395 " --> pdb=" O LEUAy 444 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASNAy 446 " --> pdb=" O GLNAy 395 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VALAy 397 " --> pdb=" O ASNAy 446 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEUAy 448 " --> pdb=" O VALAy 397 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VALAy 399 " --> pdb=" O LEUAy 448 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N METAy 450 " --> pdb=" O VALAy 399 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VALAy 401 " --> pdb=" O METAy 450 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Az' and resid 293 through 300 removed outlier: 3.535A pdb=" N GLNAz 294 " --> pdb=" O ALAAz 398 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARGAz 394 " --> pdb=" O GLUAz 298 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASPAz 300 " --> pdb=" O ILEAz 392 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILEAz 392 " --> pdb=" O ASPAz 300 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEUAz 444 " --> pdb=" O ASNAz 393 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLNAz 395 " --> pdb=" O LEUAz 444 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASNAz 446 " --> pdb=" O GLNAz 395 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VALAz 397 " --> pdb=" O ASNAz 446 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEUAz 448 " --> pdb=" O VALAz 397 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VALAz 399 " --> pdb=" O LEUAz 448 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N METAz 450 " --> pdb=" O VALAz 399 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VALAz 401 " --> pdb=" O METAz 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Az' and resid 317 through 320 removed outlier: 3.547A pdb=" N ALAAz 317 " --> pdb=" O GLUAz 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASNAz 375 " --> pdb=" O ARGAz 319 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Ba' and resid 292 through 300 removed outlier: 4.212A pdb=" N ARGBa 394 " --> pdb=" O GLUBa 298 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASPBa 300 " --> pdb=" O ILEBa 392 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILEBa 392 " --> pdb=" O ASPBa 300 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LEUBa 444 " --> pdb=" O ASNBa 393 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLNBa 395 " --> pdb=" O LEUBa 444 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASNBa 446 " --> pdb=" O GLNBa 395 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VALBa 397 " --> pdb=" O ASNBa 446 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEUBa 448 " --> pdb=" O VALBa 397 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VALBa 399 " --> pdb=" O LEUBa 448 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Ba' and resid 317 through 320 removed outlier: 3.769A pdb=" N ALABa 317 " --> pdb=" O GLUBa 377 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASNBa 375 " --> pdb=" O ARGBa 319 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Bb' and resid 293 through 300 removed outlier: 3.816A pdb=" N ARGBb 394 " --> pdb=" O GLUBb 298 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASPBb 300 " --> pdb=" O ILEBb 392 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILEBb 392 " --> pdb=" O ASPBb 300 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUBb 444 " --> pdb=" O GLNBb 395 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Bb' and resid 318 through 320 removed outlier: 6.697A pdb=" N ASNBb 375 " --> pdb=" O ARGBb 319 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Bc' and resid 293 through 299 removed outlier: 6.939A pdb=" N GLNBc 294 " --> pdb=" O VALBc 397 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VALBc 397 " --> pdb=" O GLNBc 294 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASPBc 296 " --> pdb=" O GLNBc 395 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLNBc 395 " --> pdb=" O ASPBc 296 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLUBc 298 " --> pdb=" O ASNBc 393 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEUBc 444 " --> pdb=" O ASNBc 393 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLNBc 395 " --> pdb=" O LEUBc 444 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASNBc 446 " --> pdb=" O GLNBc 395 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VALBc 397 " --> pdb=" O ASNBc 446 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEUBc 448 " --> pdb=" O VALBc 397 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VALBc 399 " --> pdb=" O LEUBc 448 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N METBc 450 " --> pdb=" O VALBc 399 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VALBc 401 " --> pdb=" O METBc 450 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Bc' and resid 317 through 320 removed outlier: 3.662A pdb=" N ALABc 317 " --> pdb=" O GLUBc 377 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASNBc 375 " --> pdb=" O ARGBc 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Bd' and resid 293 through 300 removed outlier: 4.032A pdb=" N ARGBd 394 " --> pdb=" O GLUBd 298 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASPBd 300 " --> pdb=" O ILEBd 392 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILEBd 392 " --> pdb=" O ASPBd 300 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASNBd 446 " --> pdb=" O GLNBd 395 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VALBd 397 " --> pdb=" O ASNBd 446 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEUBd 448 " --> pdb=" O VALBd 397 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VALBd 399 " --> pdb=" O LEUBd 448 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Bd' and resid 317 through 320 removed outlier: 6.612A pdb=" N ASNBd 375 " --> pdb=" O ARGBd 319 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Be' and resid 292 through 300 removed outlier: 6.994A pdb=" N THRBe 292 " --> pdb=" O VALBe 399 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VALBe 399 " --> pdb=" O THRBe 292 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLNBe 294 " --> pdb=" O VALBe 397 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VALBe 397 " --> pdb=" O GLNBe 294 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASPBe 296 " --> pdb=" O GLNBe 395 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLNBe 395 " --> pdb=" O ASPBe 296 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLUBe 298 " --> pdb=" O ASNBe 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALBe 391 " --> pdb=" O ASPBe 300 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEUBe 444 " --> pdb=" O ASNBe 393 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLNBe 395 " --> pdb=" O LEUBe 444 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASNBe 446 " --> pdb=" O GLNBe 395 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VALBe 397 " --> pdb=" O ASNBe 446 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEUBe 448 " --> pdb=" O VALBe 397 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VALBe 399 " --> pdb=" O LEUBe 448 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N METBe 450 " --> pdb=" O VALBe 399 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VALBe 401 " --> pdb=" O METBe 450 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Be' and resid 318 through 320 removed outlier: 6.580A pdb=" N ASNBe 375 " --> pdb=" O ARGBe 319 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Bf' and resid 293 through 300 removed outlier: 3.998A pdb=" N ARGBf 394 " --> pdb=" O GLUBf 298 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASPBf 300 " --> pdb=" O ILEBf 392 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILEBf 392 " --> pdb=" O ASPBf 300 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASNBf 446 " --> pdb=" O GLNBf 395 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VALBf 397 " --> pdb=" O ASNBf 446 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEUBf 448 " --> pdb=" O VALBf 397 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VALBf 399 " --> pdb=" O LEUBf 448 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Bf' and resid 317 through 320 removed outlier: 6.581A pdb=" N ASNBf 375 " --> pdb=" O ARGBf 319 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Bg' and resid 293 through 299 removed outlier: 7.010A pdb=" N GLNBg 294 " --> pdb=" O VALBg 397 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VALBg 397 " --> pdb=" O GLNBg 294 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASPBg 296 " --> pdb=" O GLNBg 395 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLNBg 395 " --> pdb=" O ASPBg 296 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLUBg 298 " --> pdb=" O ASNBg 393 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N LEUBg 444 " --> pdb=" O ASNBg 393 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLNBg 395 " --> pdb=" O LEUBg 444 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASNBg 446 " --> pdb=" O GLNBg 395 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VALBg 397 " --> pdb=" O ASNBg 446 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEUBg 448 " --> pdb=" O VALBg 397 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VALBg 399 " --> pdb=" O LEUBg 448 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Bg' and resid 317 through 320 removed outlier: 6.521A pdb=" N ASNBg 375 " --> pdb=" O ARGBg 319 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Bh' and resid 292 through 300 removed outlier: 7.070A pdb=" N THRBh 292 " --> pdb=" O VALBh 399 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VALBh 399 " --> pdb=" O THRBh 292 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLNBh 294 " --> pdb=" O VALBh 397 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VALBh 397 " --> pdb=" O GLNBh 294 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASPBh 296 " --> pdb=" O GLNBh 395 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLNBh 395 " --> pdb=" O ASPBh 296 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLUBh 298 " --> pdb=" O ASNBh 393 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VALBh 391 " --> pdb=" O ASPBh 300 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEUBh 444 " --> pdb=" O ASNBh 393 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLNBh 395 " --> pdb=" O LEUBh 444 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASNBh 446 " --> pdb=" O GLNBh 395 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VALBh 397 " --> pdb=" O ASNBh 446 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEUBh 448 " --> pdb=" O VALBh 397 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VALBh 399 " --> pdb=" O LEUBh 448 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N METBh 450 " --> pdb=" O VALBh 399 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VALBh 401 " --> pdb=" O METBh 450 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Bh' and resid 317 through 320 removed outlier: 6.611A pdb=" N ASNBh 375 " --> pdb=" O ARGBh 319 " (cutoff:3.500A) 1783 hydrogen bonds defined for protein. 5061 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: 3.16 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: 13363 1.34 - 1.46: 4323 1.46 - 1.57: 21176 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 38930 Sorted by residual: bond pdb=" C ILEBd 283 " pdb=" N PROBd 284 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.77e+00 bond pdb=" CA TYRAk 291 " pdb=" CB TYRAk 291 " ideal model delta sigma weight residual 1.528 1.556 -0.028 1.47e-02 4.63e+03 3.68e+00 bond pdb=" CA TYRAl 291 " pdb=" CB TYRAl 291 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.47e-02 4.63e+03 3.45e+00 bond pdb=" CA TYRAo 291 " pdb=" CB TYRAo 291 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.47e-02 4.63e+03 2.79e+00 bond pdb=" CA ILEAq 283 " pdb=" CB ILEAq 283 " ideal model delta sigma weight residual 1.534 1.545 -0.010 6.80e-03 2.16e+04 2.35e+00 ... (remaining 38925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 51337 1.69 - 3.38: 1110 3.38 - 5.08: 79 5.08 - 6.77: 10 6.77 - 8.46: 28 Bond angle restraints: 52564 Sorted by residual: angle pdb=" N VALAu 281 " pdb=" CA VALAu 281 " pdb=" C VALAu 281 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 angle pdb=" N VALAw 281 " pdb=" CA VALAw 281 " pdb=" C VALAw 281 " ideal model delta sigma weight residual 113.47 108.44 5.03 1.01e+00 9.80e-01 2.48e+01 angle pdb=" N VALAg 281 " pdb=" CA VALAg 281 " pdb=" C VALAg 281 " ideal model delta sigma weight residual 113.20 108.67 4.53 9.60e-01 1.09e+00 2.23e+01 angle pdb=" N VALBa 281 " pdb=" CA VALBa 281 " pdb=" C VALBa 281 " ideal model delta sigma weight residual 113.71 109.39 4.32 9.50e-01 1.11e+00 2.07e+01 angle pdb=" N VALAx 281 " pdb=" CA VALAx 281 " pdb=" C VALAx 281 " ideal model delta sigma weight residual 113.47 109.52 3.95 1.01e+00 9.80e-01 1.53e+01 ... (remaining 52559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 21935 17.37 - 34.74: 1695 34.74 - 52.11: 393 52.11 - 69.48: 68 69.48 - 86.84: 15 Dihedral angle restraints: 24106 sinusoidal: 9826 harmonic: 14280 Sorted by residual: dihedral pdb=" CA LEUAr 282 " pdb=" C LEUAr 282 " pdb=" N ILEAr 283 " pdb=" CA ILEAr 283 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLUAe 377 " pdb=" C GLUAe 377 " pdb=" N LEUAe 378 " pdb=" CA LEUAe 378 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA GLUAi 377 " pdb=" C GLUAi 377 " pdb=" N LEUAi 378 " pdb=" CA LEUAi 378 " ideal model delta harmonic sigma weight residual 180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 24103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3729 0.029 - 0.059: 1647 0.059 - 0.088: 478 0.088 - 0.117: 256 0.117 - 0.146: 78 Chirality restraints: 6188 Sorted by residual: chirality pdb=" CA VALBh 397 " pdb=" N VALBh 397 " pdb=" C VALBh 397 " pdb=" CB VALBh 397 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA VALAk 397 " pdb=" N VALAk 397 " pdb=" C VALAk 397 " pdb=" CB VALAk 397 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA VALAm 397 " pdb=" N VALAm 397 " pdb=" C VALAm 397 " pdb=" CB VALAm 397 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 6185 not shown) Planarity restraints: 6902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILEAn 283 " -0.030 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PROAn 284 " 0.077 5.00e-02 4.00e+02 pdb=" CA PROAn 284 " -0.021 5.00e-02 4.00e+02 pdb=" CD PROAn 284 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEAu 283 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PROAu 284 " 0.068 5.00e-02 4.00e+02 pdb=" CA PROAu 284 " -0.019 5.00e-02 4.00e+02 pdb=" CD PROAu 284 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEAq 283 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PROAq 284 " 0.068 5.00e-02 4.00e+02 pdb=" CA PROAq 284 " -0.019 5.00e-02 4.00e+02 pdb=" CD PROAq 284 " -0.022 5.00e-02 4.00e+02 ... (remaining 6899 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 18572 3.01 - 3.48: 37994 3.48 - 3.96: 59711 3.96 - 4.43: 66653 4.43 - 4.90: 113648 Nonbonded interactions: 296578 Sorted by model distance: nonbonded pdb=" N THRBf 396 " pdb=" OG1 THRBf 396 " model vdw 2.538 2.496 nonbonded pdb=" N THRAx 396 " pdb=" OG1 THRAx 396 " model vdw 2.546 2.496 nonbonded pdb=" N THRAp 396 " pdb=" OG1 THRAp 396 " model vdw 2.552 2.496 nonbonded pdb=" N THRBd 396 " pdb=" OG1 THRBd 396 " model vdw 2.560 2.496 nonbonded pdb=" C THRAj 380 " pdb=" OG1 THRAj 380 " model vdw 2.576 2.616 ... (remaining 296573 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: 0.01 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bh' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 31.230 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 : 0.004 0.045 38930 Z= 0.179 Angle : 0.625 8.459 52564 Z= 0.368 Chirality : 0.041 0.146 6188 Planarity : 0.003 0.044 6902 Dihedral : 13.217 86.844 14790 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.18 % Allowed : 8.47 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.36 (0.11), residues: 4692 helix: -0.68 (0.13), residues: 1294 sheet: -1.67 (0.15), residues: 1324 loop : -3.69 (0.10), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBa 441 TYR 0.016 0.002 TYRAl 437 PHE 0.010 0.002 PHEAn 311 HIS 0.006 0.001 HISBg 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (38930) covalent geometry : angle 0.62456 / 0.37 (52564) hydrogen bonds : bond 0.22528 / 15.11 ( 1783) hydrogen bonds : angle 9.34598 / 6.48 ( 5061) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 1367 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 429 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7293 (mm-40) REVERT: Ab 305 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7246 (tt0) REVERT: Ab 425 ASN cc_start: 0.8337 (p0) cc_final: 0.8077 (p0) REVERT: Ab 446 ASN cc_start: 0.8421 (m110) cc_final: 0.7689 (m110) REVERT: Ac 296 ASP cc_start: 0.7737 (t0) cc_final: 0.7238 (t0) REVERT: Ac 425 ASN cc_start: 0.7865 (p0) cc_final: 0.7641 (p0) REVERT: Ac 443 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: Ad 320 SER cc_start: 0.8136 (t) cc_final: 0.7920 (t) REVERT: Ad 379 ASP cc_start: 0.8449 (m-30) cc_final: 0.7699 (t0) REVERT: Ad 425 ASN cc_start: 0.8347 (p0) cc_final: 0.8125 (p0) REVERT: Ae 296 ASP cc_start: 0.7933 (t70) cc_final: 0.7619 (t0) REVERT: Ae 300 ASP cc_start: 0.8412 (p0) cc_final: 0.8185 (p0) REVERT: Ae 378 LEU cc_start: 0.8165 (mt) cc_final: 0.7915 (mt) REVERT: Ae 381 THR cc_start: 0.8828 (m) cc_final: 0.8435 (p) REVERT: Ae 424 LEU cc_start: 0.8940 (mt) cc_final: 0.8708 (mt) REVERT: Af 299 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8339 (mt) REVERT: Af 378 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7595 (mt) REVERT: Af 429 GLN cc_start: 0.7673 (mm110) cc_final: 0.7251 (mp10) REVERT: Af 444 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7598 (tt) REVERT: Af 450 MET cc_start: 0.6309 (mtp) cc_final: 0.6030 (mtp) REVERT: Ag 300 ASP cc_start: 0.8806 (p0) cc_final: 0.8559 (p0) REVERT: Ag 301 PHE cc_start: 0.9088 (m-80) cc_final: 0.8568 (m-80) REVERT: Ag 424 LEU cc_start: 0.9039 (tp) cc_final: 0.8643 (tp) REVERT: Ag 426 SER cc_start: 0.8512 (m) cc_final: 0.7891 (p) REVERT: Ag 445 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8000 (tt) REVERT: Ah 282 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7394 (mm) REVERT: Ah 319 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7276 (ttm170) REVERT: Ah 377 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7541 (tm-30) REVERT: Ah 450 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6664 (ttp) REVERT: Ai 309 LYS cc_start: 0.8495 (tttt) cc_final: 0.7836 (mttp) REVERT: Ai 425 ASN cc_start: 0.8329 (p0) cc_final: 0.8031 (p0) REVERT: Aj 282 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7195 (mm) REVERT: Aj 301 PHE cc_start: 0.8950 (m-80) cc_final: 0.8724 (m-80) REVERT: Aj 376 TYR cc_start: 0.7973 (m-10) cc_final: 0.7667 (m-10) REVERT: Aj 423 ASP cc_start: 0.8219 (t0) cc_final: 0.7962 (t0) REVERT: Ak 266 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8938 (tm) REVERT: Ak 272 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8018 (mm-30) REVERT: Ak 296 ASP cc_start: 0.7950 (t70) cc_final: 0.7638 (t0) REVERT: Ak 388 GLN cc_start: 0.8575 (pt0) cc_final: 0.8337 (pt0) REVERT: Ak 423 ASP cc_start: 0.8086 (t0) cc_final: 0.7836 (t0) REVERT: Ak 430 VAL cc_start: 0.7129 (t) cc_final: 0.6691 (t) REVERT: Ak 432 ILE cc_start: 0.7892 (mm) cc_final: 0.7572 (mt) REVERT: Al 296 ASP cc_start: 0.8088 (t70) cc_final: 0.7805 (t0) REVERT: Al 321 GLU cc_start: 0.6996 (tt0) cc_final: 0.6751 (tt0) REVERT: Al 378 LEU cc_start: 0.8214 (mt) cc_final: 0.7555 (mt) REVERT: Al 385 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7727 (tm-30) REVERT: Al 446 ASN cc_start: 0.8841 (m110) cc_final: 0.8638 (m110) REVERT: Am 272 GLU cc_start: 0.8685 (tp30) cc_final: 0.8355 (tp30) REVERT: Am 296 ASP cc_start: 0.8341 (t0) cc_final: 0.7877 (t0) REVERT: Am 312 ASP cc_start: 0.8119 (t0) cc_final: 0.7864 (t0) REVERT: Am 376 TYR cc_start: 0.8479 (m-80) cc_final: 0.8238 (m-80) REVERT: Am 424 LEU cc_start: 0.8757 (mm) cc_final: 0.8409 (mm) REVERT: Am 431 LEU cc_start: 0.7940 (mt) cc_final: 0.7715 (mm) REVERT: An 376 TYR cc_start: 0.8126 (m-80) cc_final: 0.7606 (m-80) REVERT: An 432 ILE cc_start: 0.8070 (mt) cc_final: 0.7853 (mt) REVERT: An 434 THR cc_start: 0.8348 (m) cc_final: 0.8006 (t) REVERT: An 445 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7458 (tt) REVERT: Ap 432 ILE cc_start: 0.8024 (mm) cc_final: 0.7722 (mt) REVERT: Ap 438 SER cc_start: 0.6905 (p) cc_final: 0.6616 (p) REVERT: Ap 445 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (tt) REVERT: Aq 299 LEU cc_start: 0.8767 (mp) cc_final: 0.8536 (mt) REVERT: Aq 301 PHE cc_start: 0.8814 (m-80) cc_final: 0.8581 (m-80) REVERT: Aq 385 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7466 (tm-30) REVERT: Ar 266 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8611 (tm) REVERT: Ar 270 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: Ar 272 GLU cc_start: 0.8513 (tp30) cc_final: 0.8136 (tp30) REVERT: Ar 376 TYR cc_start: 0.7879 (m-80) cc_final: 0.7055 (m-80) REVERT: Ar 429 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7753 (mm-40) REVERT: As 272 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7767 (mm-30) REVERT: As 305 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6905 (tt0) REVERT: As 321 GLU cc_start: 0.7293 (tt0) cc_final: 0.6967 (tt0) REVERT: As 376 TYR cc_start: 0.8050 (m-10) cc_final: 0.7809 (m-80) REVERT: As 395 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: As 425 ASN cc_start: 0.8159 (p0) cc_final: 0.7912 (p0) REVERT: As 430 VAL cc_start: 0.6594 (t) cc_final: 0.6214 (t) REVERT: At 266 LEU cc_start: 0.9188 (tp) cc_final: 0.8921 (tt) REVERT: At 282 LEU cc_start: 0.7863 (mt) cc_final: 0.7611 (mt) REVERT: At 296 ASP cc_start: 0.7932 (t0) cc_final: 0.7508 (t0) REVERT: At 396 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7930 (m) REVERT: At 429 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7003 (mm-40) REVERT: At 430 VAL cc_start: 0.6568 (t) cc_final: 0.6077 (t) REVERT: At 446 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7049 (p0) REVERT: Au 282 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7078 (mm) REVERT: Au 450 MET cc_start: 0.7954 (pmm) cc_final: 0.7171 (pmm) REVERT: Av 296 ASP cc_start: 0.8172 (t70) cc_final: 0.7834 (t0) REVERT: Av 376 TYR cc_start: 0.7843 (m-80) cc_final: 0.6667 (m-80) REVERT: Av 393 ASN cc_start: 0.7874 (t0) cc_final: 0.7672 (t0) REVERT: Av 401 VAL cc_start: 0.8873 (t) cc_final: 0.8655 (t) REVERT: Av 432 ILE cc_start: 0.8525 (mm) cc_final: 0.8265 (mt) REVERT: Aw 270 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8330 (mm-40) REVERT: Aw 296 ASP cc_start: 0.7917 (t70) cc_final: 0.7705 (t70) REVERT: Aw 375 ASN cc_start: 0.7834 (t0) cc_final: 0.7520 (t0) REVERT: Aw 394 ARG cc_start: 0.8133 (ttt90) cc_final: 0.7728 (ttm-80) REVERT: Aw 428 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7933 (ttm-80) REVERT: Aw 432 ILE cc_start: 0.7976 (mm) cc_final: 0.7625 (mt) REVERT: Ax 296 ASP cc_start: 0.7270 (t70) cc_final: 0.6803 (t0) REVERT: Ax 309 LYS cc_start: 0.8515 (tttt) cc_final: 0.8002 (mttp) REVERT: Ax 393 ASN cc_start: 0.8262 (t0) cc_final: 0.8035 (t0) REVERT: Ax 396 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7859 (m) REVERT: Ay 295 VAL cc_start: 0.8513 (m) cc_final: 0.8294 (t) REVERT: Ay 378 LEU cc_start: 0.8024 (mt) cc_final: 0.7672 (mt) REVERT: Ay 385 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: Ay 423 ASP cc_start: 0.7862 (t0) cc_final: 0.7563 (t0) REVERT: Ay 432 ILE cc_start: 0.7883 (mt) cc_final: 0.7650 (mt) REVERT: Az 376 TYR cc_start: 0.8046 (m-10) cc_final: 0.7827 (m-10) REVERT: Az 378 LEU cc_start: 0.8288 (mt) cc_final: 0.8010 (mt) REVERT: Az 445 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (tp) REVERT: Ba 296 ASP cc_start: 0.7592 (t70) cc_final: 0.7345 (t70) REVERT: Bb 272 GLU cc_start: 0.8543 (tp30) cc_final: 0.7682 (tp30) REVERT: Bb 423 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8134 (t0) REVERT: Bb 428 ARG cc_start: 0.7192 (ttm110) cc_final: 0.6857 (ttm-80) REVERT: Bb 429 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: Bb 432 ILE cc_start: 0.8023 (mt) cc_final: 0.7495 (mt) REVERT: Bb 445 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7411 (tt) REVERT: Bb 446 ASN cc_start: 0.8722 (m110) cc_final: 0.8511 (m-40) REVERT: Bc 296 ASP cc_start: 0.7605 (t70) cc_final: 0.7319 (t0) REVERT: Bc 425 ASN cc_start: 0.7921 (p0) cc_final: 0.7656 (p0) REVERT: Bc 429 GLN cc_start: 0.7626 (mm110) cc_final: 0.7420 (mp10) REVERT: Bd 296 ASP cc_start: 0.7594 (t70) cc_final: 0.7391 (t0) REVERT: Bd 300 ASP cc_start: 0.8913 (p0) cc_final: 0.8501 (p0) REVERT: Bd 450 MET cc_start: 0.8624 (pmm) cc_final: 0.7875 (pmm) REVERT: Be 272 GLU cc_start: 0.8587 (tp30) cc_final: 0.8359 (tp30) REVERT: Be 299 LEU cc_start: 0.8675 (mt) cc_final: 0.8386 (mt) REVERT: Be 385 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: Be 387 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8630 (mmtp) REVERT: Be 428 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7167 (ttm-80) REVERT: Be 432 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7711 (mt) REVERT: Be 446 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.6662 (p0) REVERT: Bf 266 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9095 (tt) REVERT: Bf 279 ASP cc_start: 0.6666 (m-30) cc_final: 0.6235 (m-30) REVERT: Bf 283 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8214 (mp) REVERT: Bf 309 LYS cc_start: 0.8343 (tttt) cc_final: 0.8023 (ttmm) REVERT: Bg 375 ASN cc_start: 0.8573 (t0) cc_final: 0.8096 (t0) REVERT: Bg 394 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7598 (tpt170) REVERT: Bg 432 ILE cc_start: 0.7694 (mm) cc_final: 0.7406 (mt) REVERT: Bh 299 LEU cc_start: 0.8789 (mt) cc_final: 0.8563 (mt) REVERT: Bh 312 ASP cc_start: 0.8519 (t0) cc_final: 0.8277 (t0) REVERT: Bh 425 ASN cc_start: 0.7801 (p0) cc_final: 0.7137 (p0) outliers start: 179 outliers final: 49 residues processed: 1450 average time/residue: 0.2284 time to fit residues: 547.3684 Evaluate side-chains 1322 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1241 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 445 LEU Chi-restraints excluded: chain Ac residue 443 ASP Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Af residue 299 LEU Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 445 LEU Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 282 LEU Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 263 GLU Chi-restraints excluded: chain Aj residue 282 LEU Chi-restraints excluded: chain Aj residue 283 ILE Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain Ap residue 396 THR Chi-restraints excluded: chain Ap residue 445 LEU Chi-restraints excluded: chain Aq residue 266 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 396 THR Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 270 GLN Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 395 GLN Chi-restraints excluded: chain As residue 445 LEU Chi-restraints excluded: chain At residue 396 THR Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 270 GLN Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 396 THR Chi-restraints excluded: chain Ay residue 310 VAL Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Az residue 419 LEU Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 299 LEU Chi-restraints excluded: chain Bb residue 380 THR Chi-restraints excluded: chain Bb residue 423 ASP Chi-restraints excluded: chain Bb residue 429 GLN Chi-restraints excluded: chain Bb residue 445 LEU Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 432 ILE Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 266 LEU Chi-restraints excluded: chain Bf residue 283 ILE Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 377 GLU Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 470 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 294 GLN ** Aa 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 294 GLN Ab 395 GLN Ad 294 GLN Ae 429 GLN Af 395 GLN Af 429 GLN Ag 395 GLN Ah 294 GLN Ah 395 GLN Aj 294 GLN ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 384 HIS Al 395 GLN Al 446 ASN Am 294 GLN An 395 GLN Ao 393 ASN Ao 425 ASN Ar 270 GLN As 393 ASN Av 294 GLN Av 395 GLN Av 425 ASN Av 429 GLN Aw 270 GLN Ax 294 GLN Ay 294 GLN ** Az 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 294 GLN ** Ba 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 429 GLN Bd 369 HIS ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 446 ASN Bg 294 GLN Bg 395 GLN Bh 395 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.253596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 171)---------------| | r_work = 0.4246 r_free = 0.4246 target = 0.182929 restraints weight = 30630.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.188258 restraints weight = 16844.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191018 restraints weight = 11333.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.192096 restraints weight = 10200.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.191953 restraints weight = 8638.734| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38930 Z= 0.167 Angle : 0.553 9.376 52564 Z= 0.288 Chirality : 0.041 0.249 6188 Planarity : 0.003 0.040 6902 Dihedral : 6.643 59.554 5460 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.88 % Allowed : 14.12 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.12), residues: 4692 helix: 1.22 (0.14), residues: 1293 sheet: -1.76 (0.14), residues: 1322 loop : -3.59 (0.10), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAt 261 TYR 0.024 0.002 TYRAo 291 PHE 0.018 0.002 PHEAz 311 HIS 0.005 0.001 HISAp 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (38930) covalent geometry : angle 0.55345 / 0.29 (52564) hydrogen bonds : bond 0.04216 / 2.80 ( 1783) hydrogen bonds : angle 6.09398 / 4.24 ( 5061) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1240 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 261 ARG cc_start: 0.7952 (tmm160) cc_final: 0.7277 (tmm160) REVERT: Aa 324 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8062 (tt) REVERT: Aa 429 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7684 (mm-40) REVERT: Ab 283 ILE cc_start: 0.9032 (mm) cc_final: 0.8634 (mt) REVERT: Ab 385 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7053 (tm-30) REVERT: Ab 429 GLN cc_start: 0.7446 (mp10) cc_final: 0.7217 (mp10) REVERT: Ac 296 ASP cc_start: 0.8174 (t0) cc_final: 0.7597 (t0) REVERT: Ad 379 ASP cc_start: 0.8490 (m-30) cc_final: 0.7464 (t0) REVERT: Ad 425 ASN cc_start: 0.8362 (p0) cc_final: 0.7941 (p0) REVERT: Ae 298 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7641 (mt-10) REVERT: Ae 299 LEU cc_start: 0.8604 (mt) cc_final: 0.8284 (mt) REVERT: Ae 379 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6949 (t0) REVERT: Af 298 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7219 (mt-10) REVERT: Af 378 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7531 (mt) REVERT: Af 394 ARG cc_start: 0.8706 (ttt90) cc_final: 0.8286 (ttm-80) REVERT: Af 425 ASN cc_start: 0.8224 (p0) cc_final: 0.7885 (p0) REVERT: Af 429 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7524 (mp10) REVERT: Ag 300 ASP cc_start: 0.8818 (p0) cc_final: 0.8592 (p0) REVERT: Ag 432 ILE cc_start: 0.8511 (mm) cc_final: 0.8201 (mt) REVERT: Ah 279 ASP cc_start: 0.6711 (m-30) cc_final: 0.6219 (m-30) REVERT: Ah 298 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7205 (mt-10) REVERT: Ah 319 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7549 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7502 (tp30) REVERT: Ai 309 LYS cc_start: 0.8327 (tttt) cc_final: 0.7577 (mttp) REVERT: Ai 376 TYR cc_start: 0.7914 (m-80) cc_final: 0.7583 (m-80) REVERT: Ai 385 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7029 (tm-30) REVERT: Ai 425 ASN cc_start: 0.8549 (p0) cc_final: 0.8307 (p0) REVERT: Aj 266 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9155 (mp) REVERT: Aj 298 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6867 (mt-10) REVERT: Aj 376 TYR cc_start: 0.7872 (m-10) cc_final: 0.7667 (m-10) REVERT: Ak 305 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.7015 (tp30) REVERT: Ak 432 ILE cc_start: 0.8055 (mm) cc_final: 0.7769 (mt) REVERT: Al 296 ASP cc_start: 0.8065 (t70) cc_final: 0.7662 (t0) REVERT: Al 298 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7033 (mt-10) REVERT: Al 385 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7206 (tm-30) REVERT: Am 296 ASP cc_start: 0.8623 (t0) cc_final: 0.8098 (t0) REVERT: Am 312 ASP cc_start: 0.8103 (t0) cc_final: 0.7872 (t0) REVERT: Am 424 LEU cc_start: 0.8830 (mm) cc_final: 0.8596 (mm) REVERT: An 301 PHE cc_start: 0.9499 (m-80) cc_final: 0.9278 (m-80) REVERT: Ao 426 SER cc_start: 0.8668 (m) cc_final: 0.8230 (p) REVERT: Ao 431 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6766 (mm) REVERT: Ap 396 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7923 (m) REVERT: Aq 299 LEU cc_start: 0.8994 (mp) cc_final: 0.8548 (mt) REVERT: Aq 301 PHE cc_start: 0.9122 (m-80) cc_final: 0.8866 (m-80) REVERT: Aq 385 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7245 (tm-30) REVERT: Aq 387 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8169 (mmtp) REVERT: Ar 266 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8979 (tm) REVERT: Ar 272 GLU cc_start: 0.8463 (tp30) cc_final: 0.8254 (tp30) REVERT: Ar 376 TYR cc_start: 0.7820 (m-80) cc_final: 0.6969 (m-80) REVERT: Ar 429 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7649 (mm-40) REVERT: As 378 LEU cc_start: 0.7680 (mt) cc_final: 0.7371 (mt) REVERT: As 430 VAL cc_start: 0.6017 (t) cc_final: 0.5801 (t) REVERT: At 274 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8105 (tm) REVERT: At 296 ASP cc_start: 0.8078 (t0) cc_final: 0.7682 (t0) REVERT: At 393 ASN cc_start: 0.8545 (t0) cc_final: 0.7720 (m-40) REVERT: At 396 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (m) REVERT: At 429 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7157 (mm-40) REVERT: At 430 VAL cc_start: 0.6318 (t) cc_final: 0.6071 (t) REVERT: Au 282 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.6977 (mm) REVERT: Au 305 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6533 (tp30) REVERT: Au 376 TYR cc_start: 0.8093 (m-80) cc_final: 0.7819 (m-80) REVERT: Au 450 MET cc_start: 0.8071 (pmm) cc_final: 0.7162 (pmm) REVERT: Av 266 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8824 (tm) REVERT: Av 272 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8036 (tp30) REVERT: Av 296 ASP cc_start: 0.8356 (t70) cc_final: 0.7906 (t0) REVERT: Av 376 TYR cc_start: 0.7790 (m-80) cc_final: 0.6705 (m-80) REVERT: Aw 387 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8116 (mmtp) REVERT: Aw 428 ARG cc_start: 0.8513 (tpt90) cc_final: 0.8181 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8039 (mm) cc_final: 0.7658 (mt) REVERT: Ax 296 ASP cc_start: 0.7547 (t70) cc_final: 0.7072 (t0) REVERT: Ax 309 LYS cc_start: 0.8900 (tttt) cc_final: 0.8196 (mttp) REVERT: Ax 393 ASN cc_start: 0.8547 (t0) cc_final: 0.8264 (t0) REVERT: Ax 425 ASN cc_start: 0.8421 (p0) cc_final: 0.7593 (p0) REVERT: Ax 429 GLN cc_start: 0.6829 (mp10) cc_final: 0.6439 (mp10) REVERT: Ay 385 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: Az 265 GLU cc_start: 0.8826 (tp30) cc_final: 0.8621 (tp30) REVERT: Az 296 ASP cc_start: 0.7634 (t70) cc_final: 0.7352 (t0) REVERT: Az 378 LEU cc_start: 0.8226 (mt) cc_final: 0.7972 (mt) REVERT: Az 429 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7377 (tp-100) REVERT: Az 431 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7100 (mm) REVERT: Az 432 ILE cc_start: 0.7942 (mm) cc_final: 0.7548 (mt) REVERT: Ba 430 VAL cc_start: 0.6719 (t) cc_final: 0.6518 (t) REVERT: Bb 272 GLU cc_start: 0.8596 (tp30) cc_final: 0.7839 (tp30) REVERT: Bb 423 ASP cc_start: 0.8357 (m-30) cc_final: 0.8037 (t0) REVERT: Bb 428 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7163 (ttm-80) REVERT: Bb 432 ILE cc_start: 0.7816 (mt) cc_final: 0.7431 (mt) REVERT: Bb 445 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7683 (tt) REVERT: Bc 296 ASP cc_start: 0.7773 (t70) cc_final: 0.7403 (t0) REVERT: Bc 425 ASN cc_start: 0.8361 (p0) cc_final: 0.8099 (p0) REVERT: Bd 300 ASP cc_start: 0.9104 (p0) cc_final: 0.8801 (p0) REVERT: Bd 426 SER cc_start: 0.8434 (m) cc_final: 0.7951 (p) REVERT: Bd 450 MET cc_start: 0.8935 (pmm) cc_final: 0.8116 (pmm) REVERT: Be 296 ASP cc_start: 0.7797 (t70) cc_final: 0.7419 (t0) REVERT: Be 299 LEU cc_start: 0.9137 (mt) cc_final: 0.8815 (mt) REVERT: Be 426 SER cc_start: 0.8436 (m) cc_final: 0.7764 (p) REVERT: Be 446 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.6783 (p0) REVERT: Bf 425 ASN cc_start: 0.8141 (p0) cc_final: 0.7852 (p0) REVERT: Bg 296 ASP cc_start: 0.7803 (t0) cc_final: 0.7588 (t0) REVERT: Bg 305 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6497 (tm-30) REVERT: Bg 309 LYS cc_start: 0.8489 (tttt) cc_final: 0.7540 (mttm) REVERT: Bg 324 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7449 (tt) REVERT: Bg 432 ILE cc_start: 0.7969 (mm) cc_final: 0.7644 (mt) REVERT: Bh 299 LEU cc_start: 0.8905 (mt) cc_final: 0.8703 (mt) REVERT: Bh 309 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7940 (ttpt) REVERT: Bh 425 ASN cc_start: 0.8195 (p0) cc_final: 0.7496 (p0) outliers start: 209 outliers final: 112 residues processed: 1346 average time/residue: 0.2284 time to fit residues: 510.6063 Evaluate side-chains 1313 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1179 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 299 LEU Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 324 LEU Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 445 LEU Chi-restraints excluded: chain Ab residue 448 LEU Chi-restraints excluded: chain Ac residue 310 VAL Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 430 VAL Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 420 SER Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Ae residue 438 SER Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 266 LEU Chi-restraints excluded: chain Aj residue 283 ILE Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 305 GLU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Ak residue 448 LEU Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 424 LEU Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 267 GLU Chi-restraints excluded: chain Ap residue 389 SER Chi-restraints excluded: chain Ap residue 396 THR Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Aq residue 266 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 396 THR Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain At residue 274 LEU Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 396 THR Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 438 SER Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 387 LYS Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 280 SER Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 438 SER Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 430 VAL Chi-restraints excluded: chain Az residue 286 LEU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 431 LEU Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 278 ILE Chi-restraints excluded: chain Bb residue 380 THR Chi-restraints excluded: chain Bb residue 427 ILE Chi-restraints excluded: chain Bb residue 445 LEU Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 430 VAL Chi-restraints excluded: chain Bc residue 443 ASP Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 286 LEU Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 377 GLU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 427 ILE Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 278 ILE Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 423 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 214 optimal weight: 0.8980 chunk 390 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 473 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 460 optimal weight: 0.0570 chunk 341 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ae 429 GLN Ai 294 GLN Aj 429 GLN ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 395 GLN Bd 294 GLN Be 425 ASN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.250800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 178)---------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180428 restraints weight = 30793.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.185193 restraints weight = 17512.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187181 restraints weight = 11857.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187605 restraints weight = 10383.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188083 restraints weight = 9631.124| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38930 Z= 0.151 Angle : 0.521 7.116 52564 Z= 0.271 Chirality : 0.041 0.172 6188 Planarity : 0.003 0.043 6902 Dihedral : 5.915 59.578 5399 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.30 % Allowed : 16.39 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 4692 helix: 1.77 (0.14), residues: 1294 sheet: -2.38 (0.11), residues: 2190 loop : -3.11 (0.14), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAt 261 TYR 0.038 0.002 TYRBg 322 PHE 0.014 0.001 PHEAm 301 HIS 0.005 0.001 HISAp 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (38930) covalent geometry : angle 0.52072 / 0.27 (52564) hydrogen bonds : bond 0.03482 / 2.33 ( 1783) hydrogen bonds : angle 5.61962 / 3.90 ( 5061) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1219 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 429 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7727 (mm-40) REVERT: Ab 283 ILE cc_start: 0.9044 (mm) cc_final: 0.8667 (mt) REVERT: Ab 385 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6885 (tm-30) REVERT: Ab 429 GLN cc_start: 0.7567 (mp10) cc_final: 0.7217 (mp10) REVERT: Ac 262 LYS cc_start: 0.9079 (tptm) cc_final: 0.8568 (tttt) REVERT: Ac 296 ASP cc_start: 0.7835 (t0) cc_final: 0.7426 (t0) REVERT: Ad 443 ASP cc_start: 0.7671 (m-30) cc_final: 0.7235 (m-30) REVERT: Ae 299 LEU cc_start: 0.8779 (mt) cc_final: 0.8517 (mt) REVERT: Ae 448 LEU cc_start: 0.8990 (mp) cc_final: 0.8730 (mt) REVERT: Af 298 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6947 (mt-10) REVERT: Af 321 GLU cc_start: 0.8235 (tp30) cc_final: 0.7439 (tt0) REVERT: Af 378 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7968 (mt) REVERT: Af 394 ARG cc_start: 0.8688 (ttt90) cc_final: 0.8289 (ttm-80) REVERT: Af 450 MET cc_start: 0.6414 (mtp) cc_final: 0.6115 (mtp) REVERT: Ag 296 ASP cc_start: 0.7939 (t70) cc_final: 0.7542 (t0) REVERT: Ag 300 ASP cc_start: 0.8747 (p0) cc_final: 0.8534 (p0) REVERT: Ag 425 ASN cc_start: 0.8583 (p0) cc_final: 0.8333 (p0) REVERT: Ah 262 LYS cc_start: 0.8467 (tttt) cc_final: 0.8242 (tptm) REVERT: Ah 312 ASP cc_start: 0.8311 (t70) cc_final: 0.8033 (t0) REVERT: Ah 319 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7590 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7243 (tp30) REVERT: Ai 296 ASP cc_start: 0.7961 (t70) cc_final: 0.7584 (t0) REVERT: Ai 309 LYS cc_start: 0.8322 (tttt) cc_final: 0.7545 (mttp) REVERT: Ai 376 TYR cc_start: 0.7892 (m-80) cc_final: 0.7580 (m-80) REVERT: Ai 385 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7085 (tm-30) REVERT: Ai 425 ASN cc_start: 0.8613 (p0) cc_final: 0.8325 (p0) REVERT: Aj 266 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9207 (mp) REVERT: Aj 298 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6903 (mt-10) REVERT: Aj 376 TYR cc_start: 0.7780 (m-10) cc_final: 0.7474 (m-10) REVERT: Ak 432 ILE cc_start: 0.8169 (mm) cc_final: 0.7881 (mt) REVERT: Al 266 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8970 (tm) REVERT: Al 296 ASP cc_start: 0.8132 (t70) cc_final: 0.7663 (t0) REVERT: Al 298 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6904 (mt-10) REVERT: Al 299 LEU cc_start: 0.8996 (mt) cc_final: 0.8690 (mt) REVERT: Al 385 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6807 (tm-30) REVERT: Al 397 VAL cc_start: 0.8453 (t) cc_final: 0.8215 (t) REVERT: Am 268 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8181 (tptp) REVERT: Am 296 ASP cc_start: 0.8579 (t0) cc_final: 0.8130 (t0) REVERT: Am 305 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7118 (tp30) REVERT: Am 312 ASP cc_start: 0.8243 (t0) cc_final: 0.7955 (t0) REVERT: Am 385 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6710 (tm-30) REVERT: Am 424 LEU cc_start: 0.8799 (mm) cc_final: 0.8540 (mm) REVERT: Am 431 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6857 (mm) REVERT: Am 441 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.7319 (tmm-80) REVERT: An 301 PHE cc_start: 0.9447 (m-80) cc_final: 0.9207 (m-80) REVERT: An 387 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7916 (mmtp) REVERT: Ao 426 SER cc_start: 0.8551 (m) cc_final: 0.7666 (p) REVERT: Ao 431 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6819 (mm) REVERT: Ao 437 TYR cc_start: 0.7905 (t80) cc_final: 0.7679 (t80) REVERT: Ap 272 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7830 (tp30) REVERT: Ap 396 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8140 (m) REVERT: Ap 426 SER cc_start: 0.8616 (m) cc_final: 0.8091 (p) REVERT: Ap 450 MET cc_start: 0.6152 (mtp) cc_final: 0.5925 (mtt) REVERT: Aq 298 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6950 (mt-10) REVERT: Aq 299 LEU cc_start: 0.9020 (mp) cc_final: 0.8612 (mt) REVERT: Aq 301 PHE cc_start: 0.9104 (m-80) cc_final: 0.8733 (m-80) REVERT: Aq 385 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7323 (tm-30) REVERT: Ar 272 GLU cc_start: 0.8479 (tp30) cc_final: 0.8264 (tp30) REVERT: Ar 376 TYR cc_start: 0.7720 (m-80) cc_final: 0.6898 (m-80) REVERT: Ar 429 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: As 309 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8442 (tttt) REVERT: As 378 LEU cc_start: 0.7892 (mt) cc_final: 0.7556 (mt) REVERT: As 430 VAL cc_start: 0.6675 (t) cc_final: 0.6464 (t) REVERT: At 274 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (tm) REVERT: At 393 ASN cc_start: 0.8440 (t0) cc_final: 0.7658 (m-40) REVERT: At 396 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (m) REVERT: At 429 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7075 (mm-40) REVERT: At 446 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7603 (p0) REVERT: Au 282 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7096 (mm) REVERT: Au 298 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7252 (mt-10) REVERT: Au 376 TYR cc_start: 0.7983 (m-80) cc_final: 0.7613 (m-80) REVERT: Au 450 MET cc_start: 0.8149 (pmm) cc_final: 0.7161 (pmm) REVERT: Av 266 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8730 (tm) REVERT: Av 272 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8112 (tp30) REVERT: Av 296 ASP cc_start: 0.8255 (t70) cc_final: 0.7836 (t0) REVERT: Av 376 TYR cc_start: 0.7880 (m-80) cc_final: 0.6704 (m-80) REVERT: Av 397 VAL cc_start: 0.8606 (t) cc_final: 0.8382 (t) REVERT: Aw 428 ARG cc_start: 0.8469 (tpt90) cc_final: 0.8014 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8184 (mm) cc_final: 0.7710 (mp) REVERT: Ax 266 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9237 (tt) REVERT: Ax 309 LYS cc_start: 0.8945 (tttt) cc_final: 0.8191 (mttp) REVERT: Ax 393 ASN cc_start: 0.8567 (t0) cc_final: 0.8295 (t0) REVERT: Ax 425 ASN cc_start: 0.8443 (p0) cc_final: 0.7613 (p0) REVERT: Ax 429 GLN cc_start: 0.6874 (mp10) cc_final: 0.6459 (mp10) REVERT: Ax 431 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7307 (mm) REVERT: Ay 377 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7893 (tm-30) REVERT: Ay 385 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: Az 305 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: Az 429 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7390 (tp-100) REVERT: Az 431 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6892 (mm) REVERT: Az 432 ILE cc_start: 0.8002 (mm) cc_final: 0.7723 (mt) REVERT: Ba 425 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7845 (p0) REVERT: Bb 272 GLU cc_start: 0.8571 (tp30) cc_final: 0.7795 (tp30) REVERT: Bb 373 THR cc_start: 0.8440 (m) cc_final: 0.7920 (p) REVERT: Bb 428 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7143 (ttm-80) REVERT: Bb 429 GLN cc_start: 0.7015 (mp10) cc_final: 0.6655 (mp10) REVERT: Bb 432 ILE cc_start: 0.7770 (mt) cc_final: 0.7235 (mp) REVERT: Bc 286 LEU cc_start: 0.7338 (mt) cc_final: 0.7092 (mt) REVERT: Bc 296 ASP cc_start: 0.7877 (t70) cc_final: 0.7541 (t0) REVERT: Bc 425 ASN cc_start: 0.8370 (p0) cc_final: 0.8017 (p0) REVERT: Bd 263 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8532 (mt-10) REVERT: Bd 296 ASP cc_start: 0.8105 (t0) cc_final: 0.7898 (t0) REVERT: Bd 450 MET cc_start: 0.8975 (pmm) cc_final: 0.8202 (pmm) REVERT: Be 296 ASP cc_start: 0.7842 (t70) cc_final: 0.7512 (t0) REVERT: Be 299 LEU cc_start: 0.9106 (mt) cc_final: 0.8683 (mt) REVERT: Be 385 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: Be 387 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8441 (mmtp) REVERT: Be 426 SER cc_start: 0.8332 (m) cc_final: 0.7948 (p) REVERT: Be 446 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.6614 (p0) REVERT: Bg 268 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8173 (tptt) REVERT: Bg 305 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: Bg 309 LYS cc_start: 0.8467 (tttt) cc_final: 0.7476 (mttm) REVERT: Bg 322 TYR cc_start: 0.7939 (t80) cc_final: 0.7726 (t80) REVERT: Bg 324 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7155 (tt) REVERT: Bg 379 ASP cc_start: 0.8031 (p0) cc_final: 0.7792 (p0) REVERT: Bg 429 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6977 (mm110) REVERT: Bg 432 ILE cc_start: 0.7801 (mm) cc_final: 0.7418 (mp) REVERT: Bh 309 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7929 (ttpt) REVERT: Bh 425 ASN cc_start: 0.7940 (p0) cc_final: 0.7396 (p0) outliers start: 227 outliers final: 143 residues processed: 1338 average time/residue: 0.2239 time to fit residues: 494.1689 Evaluate side-chains 1353 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1183 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 299 LEU Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 448 LEU Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 310 VAL Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 430 VAL Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 420 SER Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 324 LEU Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 286 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 424 LEU Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Aj residue 263 GLU Chi-restraints excluded: chain Aj residue 266 LEU Chi-restraints excluded: chain Aj residue 286 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 429 GLN Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 378 LEU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 424 LEU Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 391 VAL Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ap residue 396 THR Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 396 THR Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain At residue 274 LEU Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 396 THR Chi-restraints excluded: chain At residue 424 LEU Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 438 SER Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 387 LYS Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 266 LEU Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 378 LEU Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 431 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 419 LEU Chi-restraints excluded: chain Az residue 424 LEU Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 431 LEU Chi-restraints excluded: chain Ba residue 266 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 449 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 380 THR Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 430 VAL Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 286 LEU Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 391 VAL Chi-restraints excluded: chain Bd residue 420 SER Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 420 SER Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 377 GLU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 427 ILE Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 153 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 306 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 450 optimal weight: 0.8980 chunk 187 optimal weight: 0.0970 chunk 359 optimal weight: 7.9990 chunk 368 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 chunk 438 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 294 GLN Ao 429 GLN Ax 384 HIS Az 270 GLN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.250689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.187238 restraints weight = 30709.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 101)---------------| | r_work = 0.4275 r_free = 0.4275 target = 0.183612 restraints weight = 20826.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.187491 restraints weight = 13721.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.188883 restraints weight = 10255.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.188636 restraints weight = 9453.116| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38930 Z= 0.127 Angle : 0.500 7.202 52564 Z= 0.259 Chirality : 0.041 0.254 6188 Planarity : 0.003 0.047 6902 Dihedral : 5.553 59.503 5384 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.95 % Allowed : 18.07 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.12), residues: 4692 helix: 2.03 (0.14), residues: 1294 sheet: -2.29 (0.11), residues: 2190 loop : -3.06 (0.14), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 260 TYR 0.024 0.001 TYRBg 322 PHE 0.014 0.001 PHEAb 311 HIS 0.004 0.001 HISAp 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (38930) covalent geometry : angle 0.50024 / 0.26 (52564) hydrogen bonds : bond 0.03097 / 2.07 ( 1783) hydrogen bonds : angle 5.32823 / 3.71 ( 5061) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1203 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 261 ARG cc_start: 0.7933 (tmm160) cc_final: 0.7352 (tmm160) REVERT: Aa 429 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7757 (mm-40) REVERT: Ab 283 ILE cc_start: 0.9038 (mm) cc_final: 0.8710 (mt) REVERT: Ab 385 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6986 (tm-30) REVERT: Ac 262 LYS cc_start: 0.9072 (tptm) cc_final: 0.8559 (tttt) REVERT: Ac 296 ASP cc_start: 0.7784 (t0) cc_final: 0.7434 (t0) REVERT: Ac 428 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7158 (ttm-80) REVERT: Ad 305 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7357 (t0) REVERT: Ad 443 ASP cc_start: 0.7654 (m-30) cc_final: 0.7242 (m-30) REVERT: Ad 450 MET cc_start: 0.6016 (mtp) cc_final: 0.5768 (mtp) REVERT: Ae 299 LEU cc_start: 0.8744 (mt) cc_final: 0.8487 (mt) REVERT: Ae 379 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7048 (t0) REVERT: Ae 448 LEU cc_start: 0.9040 (mp) cc_final: 0.8757 (mt) REVERT: Af 298 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7040 (mt-10) REVERT: Af 321 GLU cc_start: 0.8191 (tp30) cc_final: 0.7394 (tt0) REVERT: Af 377 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8115 (tm-30) REVERT: Af 378 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7564 (mt) REVERT: Af 394 ARG cc_start: 0.8668 (ttt90) cc_final: 0.8445 (ttt-90) REVERT: Af 429 GLN cc_start: 0.7446 (mp10) cc_final: 0.7206 (mp10) REVERT: Af 444 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7120 (tt) REVERT: Af 450 MET cc_start: 0.6579 (mtp) cc_final: 0.6286 (mtp) REVERT: Ag 266 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8910 (tt) REVERT: Ag 296 ASP cc_start: 0.7888 (t70) cc_final: 0.7517 (t0) REVERT: Ag 425 ASN cc_start: 0.8597 (p0) cc_final: 0.8331 (p0) REVERT: Ah 312 ASP cc_start: 0.8356 (t70) cc_final: 0.8051 (t0) REVERT: Ah 319 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7563 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7308 (tp30) REVERT: Ai 296 ASP cc_start: 0.7834 (t70) cc_final: 0.7472 (t0) REVERT: Ai 309 LYS cc_start: 0.8319 (tttt) cc_final: 0.7553 (mttp) REVERT: Ai 376 TYR cc_start: 0.7849 (m-80) cc_final: 0.7481 (m-80) REVERT: Ai 385 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7059 (tm-30) REVERT: Ai 425 ASN cc_start: 0.8463 (p0) cc_final: 0.8177 (p0) REVERT: Aj 266 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9203 (mp) REVERT: Aj 298 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6868 (mt-10) REVERT: Aj 376 TYR cc_start: 0.7618 (m-10) cc_final: 0.7338 (m-10) REVERT: Aj 429 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: Ak 266 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8746 (tm) REVERT: Ak 432 ILE cc_start: 0.8098 (mm) cc_final: 0.7754 (mt) REVERT: Al 266 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8746 (tm) REVERT: Al 283 ILE cc_start: 0.8735 (mt) cc_final: 0.8512 (mp) REVERT: Al 296 ASP cc_start: 0.8166 (t70) cc_final: 0.7752 (t0) REVERT: Al 298 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6916 (mt-10) REVERT: Al 305 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: Al 385 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7111 (tm-30) REVERT: Al 397 VAL cc_start: 0.8381 (t) cc_final: 0.8154 (t) REVERT: Am 268 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8082 (tptp) REVERT: Am 283 ILE cc_start: 0.8960 (mm) cc_final: 0.8730 (mt) REVERT: Am 296 ASP cc_start: 0.8679 (t0) cc_final: 0.8259 (t0) REVERT: Am 312 ASP cc_start: 0.8220 (t0) cc_final: 0.7932 (t0) REVERT: Am 424 LEU cc_start: 0.8764 (mm) cc_final: 0.8507 (mm) REVERT: Am 431 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6810 (mm) REVERT: Am 441 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.7947 (ttp80) REVERT: An 301 PHE cc_start: 0.9407 (m-80) cc_final: 0.9174 (m-80) REVERT: Ao 378 LEU cc_start: 0.8218 (mt) cc_final: 0.7975 (mt) REVERT: Ao 426 SER cc_start: 0.8608 (m) cc_final: 0.8029 (p) REVERT: Ao 431 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6937 (mm) REVERT: Ap 426 SER cc_start: 0.8622 (m) cc_final: 0.8173 (p) REVERT: Ap 429 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7368 (mm-40) REVERT: Aq 298 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6718 (mt-10) REVERT: Aq 299 LEU cc_start: 0.9017 (mp) cc_final: 0.8608 (mt) REVERT: Aq 301 PHE cc_start: 0.9107 (m-80) cc_final: 0.8707 (m-80) REVERT: Aq 385 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7215 (tm-30) REVERT: Ar 376 TYR cc_start: 0.7748 (m-80) cc_final: 0.6963 (m-80) REVERT: Ar 429 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7831 (mm-40) REVERT: As 309 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8355 (tttt) REVERT: As 378 LEU cc_start: 0.7985 (mt) cc_final: 0.7497 (mt) REVERT: As 385 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7390 (tm-30) REVERT: As 429 GLN cc_start: 0.7379 (mp10) cc_final: 0.7163 (mp10) REVERT: As 430 VAL cc_start: 0.6546 (t) cc_final: 0.6265 (t) REVERT: As 431 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7170 (mm) REVERT: At 274 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8215 (tm) REVERT: At 296 ASP cc_start: 0.7709 (t0) cc_final: 0.7301 (t0) REVERT: At 396 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8334 (m) REVERT: At 429 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7086 (mm-40) REVERT: At 446 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7511 (p0) REVERT: Au 282 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7011 (mm) REVERT: Au 305 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: Au 376 TYR cc_start: 0.7936 (m-80) cc_final: 0.7574 (m-80) REVERT: Au 450 MET cc_start: 0.8150 (pmm) cc_final: 0.7136 (pmm) REVERT: Av 266 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8665 (tm) REVERT: Av 272 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8060 (tp30) REVERT: Av 295 VAL cc_start: 0.9001 (m) cc_final: 0.8783 (t) REVERT: Av 387 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7595 (mmtp) REVERT: Av 397 VAL cc_start: 0.8568 (t) cc_final: 0.8183 (t) REVERT: Av 446 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6263 (p0) REVERT: Aw 263 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: Aw 387 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8120 (mmtp) REVERT: Aw 394 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.7949 (tpt-90) REVERT: Aw 428 ARG cc_start: 0.8499 (tpt90) cc_final: 0.8022 (ttm-80) REVERT: Aw 432 ILE cc_start: 0.8225 (mm) cc_final: 0.7758 (mp) REVERT: Ax 266 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9323 (tt) REVERT: Ax 309 LYS cc_start: 0.8810 (tttt) cc_final: 0.8096 (mttp) REVERT: Ax 393 ASN cc_start: 0.8567 (t0) cc_final: 0.8285 (t0) REVERT: Ax 425 ASN cc_start: 0.8477 (p0) cc_final: 0.7579 (p0) REVERT: Ax 429 GLN cc_start: 0.6881 (mp10) cc_final: 0.6419 (mp10) REVERT: Ay 377 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7565 (tm-30) REVERT: Ay 385 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: Az 429 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7273 (tp-100) REVERT: Az 432 ILE cc_start: 0.8003 (mm) cc_final: 0.7770 (mt) REVERT: Ba 425 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7821 (p0) REVERT: Bb 428 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7145 (ttm-80) REVERT: Bb 429 GLN cc_start: 0.7265 (mp10) cc_final: 0.6874 (mp10) REVERT: Bb 432 ILE cc_start: 0.7711 (mt) cc_final: 0.7326 (mt) REVERT: Bc 296 ASP cc_start: 0.7802 (t70) cc_final: 0.7435 (t0) REVERT: Bc 298 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7065 (mt-10) REVERT: Bc 425 ASN cc_start: 0.8398 (p0) cc_final: 0.8021 (p0) REVERT: Bd 296 ASP cc_start: 0.8063 (t0) cc_final: 0.7854 (t0) REVERT: Bd 379 ASP cc_start: 0.7792 (m-30) cc_final: 0.7123 (t0) REVERT: Bd 450 MET cc_start: 0.9007 (pmm) cc_final: 0.8280 (pmm) REVERT: Be 299 LEU cc_start: 0.9088 (mt) cc_final: 0.8669 (mt) REVERT: Be 387 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8408 (mmtp) REVERT: Be 426 SER cc_start: 0.8444 (m) cc_final: 0.7814 (p) REVERT: Be 446 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.6517 (p0) REVERT: Bg 268 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8161 (tptt) REVERT: Bg 309 LYS cc_start: 0.8534 (tttt) cc_final: 0.7350 (mttm) REVERT: Bg 322 TYR cc_start: 0.7987 (t80) cc_final: 0.7738 (t80) REVERT: Bg 324 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7441 (tt) REVERT: Bg 376 TYR cc_start: 0.7842 (m-10) cc_final: 0.7111 (m-10) REVERT: Bg 379 ASP cc_start: 0.8016 (p0) cc_final: 0.7765 (p0) REVERT: Bg 432 ILE cc_start: 0.7793 (mm) cc_final: 0.7552 (mt) REVERT: Bh 425 ASN cc_start: 0.7951 (p0) cc_final: 0.7382 (p0) outliers start: 212 outliers final: 127 residues processed: 1316 average time/residue: 0.2153 time to fit residues: 467.6634 Evaluate side-chains 1323 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1162 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 448 LEU Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 310 VAL Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 424 LEU Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 427 ILE Chi-restraints excluded: chain Ai residue 450 MET Chi-restraints excluded: chain Aj residue 266 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 429 GLN Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 378 LEU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 305 GLU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 396 THR Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain As residue 431 LEU Chi-restraints excluded: chain At residue 274 LEU Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 396 THR Chi-restraints excluded: chain At residue 424 LEU Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 387 LYS Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 266 LEU Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 378 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Ay residue 438 SER Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 266 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 266 LEU Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 380 THR Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 391 VAL Chi-restraints excluded: chain Bc residue 430 VAL Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 286 LEU Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 427 ILE Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 352 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 449 optimal weight: 0.7980 chunk 182 optimal weight: 0.0040 chunk 257 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 265 optimal weight: 4.9990 chunk 389 optimal weight: 0.9990 chunk 308 optimal weight: 0.4980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 306 GLN Ae 429 GLN ** Ai 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 395 GLN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 429 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.250248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.4291 r_free = 0.4291 target = 0.185800 restraints weight = 30671.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184788 restraints weight = 23616.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184610 restraints weight = 17140.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.186650 restraints weight = 13157.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.186607 restraints weight = 10850.307| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38930 Z= 0.125 Angle : 0.501 7.225 52564 Z= 0.260 Chirality : 0.041 0.261 6188 Planarity : 0.003 0.045 6902 Dihedral : 5.414 59.566 5380 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.42 % Allowed : 18.93 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.12), residues: 4692 helix: 2.18 (0.14), residues: 1293 sheet: -2.25 (0.11), residues: 2190 loop : -3.03 (0.14), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa 374 TYR 0.019 0.001 TYRBg 322 PHE 0.018 0.001 PHEAs 301 HIS 0.003 0.001 HISAr 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (38930) covalent geometry : angle 0.50120 / 0.26 (52564) hydrogen bonds : bond 0.03011 / 2.02 ( 1783) hydrogen bonds : angle 5.19435 / 3.62 ( 5061) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1184 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 283 ILE cc_start: 0.9027 (mm) cc_final: 0.8695 (mt) REVERT: Ab 385 GLU cc_start: 0.7477 (tm-30) cc_final: 0.6967 (tm-30) REVERT: Ab 429 GLN cc_start: 0.7497 (mp10) cc_final: 0.7227 (mp10) REVERT: Ac 262 LYS cc_start: 0.9047 (tptm) cc_final: 0.8567 (tttt) REVERT: Ac 296 ASP cc_start: 0.7695 (t0) cc_final: 0.7355 (t0) REVERT: Ac 428 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.7171 (ttm-80) REVERT: Ad 305 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7342 (t0) REVERT: Ad 443 ASP cc_start: 0.7603 (m-30) cc_final: 0.7181 (m-30) REVERT: Ae 272 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8186 (mm-30) REVERT: Ae 299 LEU cc_start: 0.8765 (mt) cc_final: 0.8505 (mt) REVERT: Ae 379 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.6997 (t0) REVERT: Ae 448 LEU cc_start: 0.9037 (mp) cc_final: 0.8745 (mt) REVERT: Af 377 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8050 (tm-30) REVERT: Af 378 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7523 (mt) REVERT: Af 444 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7140 (tt) REVERT: Af 450 MET cc_start: 0.6685 (mtp) cc_final: 0.6445 (mtp) REVERT: Ag 266 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8911 (tt) REVERT: Ag 296 ASP cc_start: 0.7904 (t70) cc_final: 0.7507 (t0) REVERT: Ag 425 ASN cc_start: 0.8629 (p0) cc_final: 0.7785 (p0) REVERT: Ag 429 GLN cc_start: 0.7307 (mp10) cc_final: 0.6988 (mp10) REVERT: Ah 309 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7681 (mttm) REVERT: Ah 312 ASP cc_start: 0.8305 (t70) cc_final: 0.7912 (t0) REVERT: Ah 319 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7495 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7341 (tp30) REVERT: Ai 296 ASP cc_start: 0.7810 (t70) cc_final: 0.7465 (t0) REVERT: Ai 309 LYS cc_start: 0.8403 (tttt) cc_final: 0.7681 (mttp) REVERT: Ai 376 TYR cc_start: 0.7538 (m-80) cc_final: 0.7121 (m-80) REVERT: Ai 385 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6977 (tm-30) REVERT: Ai 425 ASN cc_start: 0.8477 (p0) cc_final: 0.8184 (p0) REVERT: Aj 266 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9215 (mp) REVERT: Aj 376 TYR cc_start: 0.7621 (m-10) cc_final: 0.7337 (m-10) REVERT: Aj 429 GLN cc_start: 0.7743 (mp10) cc_final: 0.7521 (mp10) REVERT: Ak 266 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8757 (tm) REVERT: Ak 432 ILE cc_start: 0.7904 (mm) cc_final: 0.7652 (mt) REVERT: Al 266 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8707 (tm) REVERT: Al 283 ILE cc_start: 0.8728 (mt) cc_final: 0.8508 (mp) REVERT: Al 296 ASP cc_start: 0.8182 (t70) cc_final: 0.7660 (t0) REVERT: Al 298 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6985 (mt-10) REVERT: Al 397 VAL cc_start: 0.8438 (t) cc_final: 0.8213 (t) REVERT: Am 268 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8036 (tptp) REVERT: Am 296 ASP cc_start: 0.8697 (t0) cc_final: 0.8370 (t70) REVERT: Am 312 ASP cc_start: 0.8315 (t0) cc_final: 0.7987 (t0) REVERT: Am 385 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6735 (tm-30) REVERT: Am 387 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7735 (mmtp) REVERT: Am 424 LEU cc_start: 0.8748 (mm) cc_final: 0.8462 (mm) REVERT: Am 431 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6828 (mm) REVERT: Am 441 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8087 (ttp80) REVERT: An 301 PHE cc_start: 0.9415 (m-80) cc_final: 0.9131 (m-80) REVERT: An 305 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6097 (tm-30) REVERT: An 376 TYR cc_start: 0.8013 (m-80) cc_final: 0.7803 (m-80) REVERT: An 377 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7603 (tp30) REVERT: Ao 431 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6951 (mm) REVERT: Ap 426 SER cc_start: 0.8641 (m) cc_final: 0.8108 (p) REVERT: Ap 429 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7464 (mm-40) REVERT: Ap 445 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7966 (tt) REVERT: Aq 299 LEU cc_start: 0.8979 (mp) cc_final: 0.8588 (mt) REVERT: Aq 301 PHE cc_start: 0.9063 (m-80) cc_final: 0.8591 (m-80) REVERT: Aq 385 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7094 (tm-30) REVERT: Ar 376 TYR cc_start: 0.7746 (m-80) cc_final: 0.6871 (m-80) REVERT: Ar 386 ARG cc_start: 0.7447 (ttm110) cc_final: 0.7193 (ttm-80) REVERT: Ar 429 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: As 309 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8298 (tttt) REVERT: As 378 LEU cc_start: 0.7739 (mt) cc_final: 0.7494 (mt) REVERT: As 385 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7399 (tm-30) REVERT: As 430 VAL cc_start: 0.6554 (t) cc_final: 0.6335 (t) REVERT: At 396 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8381 (m) REVERT: At 429 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7071 (mm-40) REVERT: At 438 SER cc_start: 0.8495 (p) cc_final: 0.8215 (p) REVERT: At 446 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7474 (p0) REVERT: Au 282 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7055 (mm) REVERT: Au 305 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: Au 376 TYR cc_start: 0.7951 (m-80) cc_final: 0.7572 (m-80) REVERT: Au 450 MET cc_start: 0.8163 (pmm) cc_final: 0.7144 (pmm) REVERT: Av 266 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8688 (tm) REVERT: Av 397 VAL cc_start: 0.8585 (t) cc_final: 0.8187 (t) REVERT: Av 446 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6337 (p0) REVERT: Aw 263 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: Aw 428 ARG cc_start: 0.8433 (tpt90) cc_final: 0.8058 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8233 (mm) cc_final: 0.7790 (mt) REVERT: Aw 446 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7231 (p0) REVERT: Ax 309 LYS cc_start: 0.8874 (tttt) cc_final: 0.8113 (mttp) REVERT: Ax 393 ASN cc_start: 0.8587 (t0) cc_final: 0.8266 (t0) REVERT: Ax 425 ASN cc_start: 0.8491 (p0) cc_final: 0.7610 (p0) REVERT: Ax 429 GLN cc_start: 0.6842 (mp10) cc_final: 0.6349 (mp10) REVERT: Az 305 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: Az 429 GLN cc_start: 0.7821 (tp-100) cc_final: 0.7295 (tp-100) REVERT: Az 432 ILE cc_start: 0.8017 (mm) cc_final: 0.7575 (mt) REVERT: Ba 376 TYR cc_start: 0.7397 (m-10) cc_final: 0.6996 (m-10) REVERT: Ba 425 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7911 (p0) REVERT: Bb 428 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7200 (ttm-80) REVERT: Bb 432 ILE cc_start: 0.7747 (mt) cc_final: 0.7384 (mt) REVERT: Bc 296 ASP cc_start: 0.7771 (t70) cc_final: 0.7412 (t0) REVERT: Bc 298 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7184 (mt-10) REVERT: Bc 425 ASN cc_start: 0.8509 (p0) cc_final: 0.8108 (p0) REVERT: Bc 432 ILE cc_start: 0.7674 (mt) cc_final: 0.7439 (mp) REVERT: Bd 296 ASP cc_start: 0.8065 (t0) cc_final: 0.7842 (t0) REVERT: Bd 379 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7172 (t0) REVERT: Bd 450 MET cc_start: 0.9012 (pmm) cc_final: 0.8312 (pmm) REVERT: Be 299 LEU cc_start: 0.9051 (mt) cc_final: 0.8618 (mt) REVERT: Be 385 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: Be 387 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8421 (mmtm) REVERT: Be 426 SER cc_start: 0.8359 (m) cc_final: 0.7806 (p) REVERT: Be 446 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.6483 (p0) REVERT: Bg 268 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8164 (tptt) REVERT: Bg 300 ASP cc_start: 0.8764 (p0) cc_final: 0.8484 (p0) REVERT: Bg 305 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: Bg 309 LYS cc_start: 0.8506 (tttt) cc_final: 0.7327 (mttm) REVERT: Bg 322 TYR cc_start: 0.8023 (t80) cc_final: 0.7769 (t80) REVERT: Bg 324 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7409 (tt) REVERT: Bg 376 TYR cc_start: 0.7837 (m-10) cc_final: 0.7124 (m-10) REVERT: Bg 379 ASP cc_start: 0.8039 (p0) cc_final: 0.7639 (p0) REVERT: Bg 393 ASN cc_start: 0.8603 (p0) cc_final: 0.8344 (p0) REVERT: Bg 432 ILE cc_start: 0.7772 (mm) cc_final: 0.7538 (mt) REVERT: Bh 280 SER cc_start: 0.8029 (t) cc_final: 0.7512 (p) REVERT: Bh 309 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7427 (mttp) REVERT: Bh 312 ASP cc_start: 0.8291 (t0) cc_final: 0.8010 (t0) REVERT: Bh 425 ASN cc_start: 0.8586 (p0) cc_final: 0.7595 (p0) REVERT: Bh 429 GLN cc_start: 0.6509 (mp10) cc_final: 0.6278 (mp10) outliers start: 232 outliers final: 154 residues processed: 1302 average time/residue: 0.2179 time to fit residues: 468.7401 Evaluate side-chains 1348 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1159 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 448 LEU Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 310 VAL Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 391 VAL Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 430 VAL Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 309 LYS Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 424 LEU Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 280 SER Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 450 MET Chi-restraints excluded: chain Aj residue 266 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 424 LEU Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 389 SER Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Ap residue 445 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 396 THR Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 396 THR Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 378 LEU Chi-restraints excluded: chain Ax residue 387 LYS Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Ay residue 438 SER Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 266 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 266 LEU Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 281 VAL Chi-restraints excluded: chain Bc residue 391 VAL Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 420 SER Chi-restraints excluded: chain Be residue 321 GLU Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Chi-restraints excluded: chain Bh residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 159 optimal weight: 1.9990 chunk 379 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 182 optimal weight: 0.3980 chunk 463 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 209 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 400 optimal weight: 2.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 328 ASN Ax 369 HIS Bc 395 GLN Be 425 ASN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.243862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.175850 restraints weight = 30547.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.176968 restraints weight = 21624.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175790 restraints weight = 15558.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.177021 restraints weight = 13186.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177833 restraints weight = 11227.376| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38930 Z= 0.123 Angle : 0.500 7.437 52564 Z= 0.260 Chirality : 0.041 0.281 6188 Planarity : 0.003 0.031 6902 Dihedral : 5.310 59.667 5375 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.23 % Allowed : 19.68 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.13), residues: 4692 helix: 2.27 (0.14), residues: 1293 sheet: -2.17 (0.11), residues: 2221 loop : -2.93 (0.14), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa 374 TYR 0.026 0.001 TYRAs 291 PHE 0.014 0.001 PHEAc 301 HIS 0.003 0.001 HISAr 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (38930) covalent geometry : angle 0.49994 / 0.26 (52564) hydrogen bonds : bond 0.02924 / 1.96 ( 1783) hydrogen bonds : angle 5.09542 / 3.55 ( 5061) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1198 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 283 ILE cc_start: 0.8996 (mm) cc_final: 0.8680 (mt) REVERT: Ab 385 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6851 (tm-30) REVERT: Ab 429 GLN cc_start: 0.7759 (mp10) cc_final: 0.7397 (mp10) REVERT: Ac 262 LYS cc_start: 0.9070 (tptm) cc_final: 0.8728 (tttt) REVERT: Ac 296 ASP cc_start: 0.7654 (t0) cc_final: 0.7297 (t0) REVERT: Ac 428 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7203 (ttm-80) REVERT: Ad 305 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7191 (t0) REVERT: Ad 428 ARG cc_start: 0.7284 (ttt180) cc_final: 0.7078 (ttm-80) REVERT: Ad 443 ASP cc_start: 0.7619 (m-30) cc_final: 0.7227 (m-30) REVERT: Ae 272 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8238 (mm-30) REVERT: Ae 299 LEU cc_start: 0.8748 (mt) cc_final: 0.8466 (mt) REVERT: Ae 379 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6824 (t0) REVERT: Ae 448 LEU cc_start: 0.9039 (mp) cc_final: 0.8741 (mt) REVERT: Af 266 LEU cc_start: 0.9412 (tp) cc_final: 0.9193 (tt) REVERT: Af 321 GLU cc_start: 0.8264 (tp30) cc_final: 0.7524 (tt0) REVERT: Af 377 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7955 (tm-30) REVERT: Af 378 LEU cc_start: 0.8066 (mt) cc_final: 0.7461 (mt) REVERT: Af 429 GLN cc_start: 0.7445 (mp10) cc_final: 0.7233 (mp10) REVERT: Af 444 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7035 (tt) REVERT: Af 450 MET cc_start: 0.6772 (mtp) cc_final: 0.6444 (mtp) REVERT: Ag 266 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8850 (tt) REVERT: Ag 296 ASP cc_start: 0.7876 (t70) cc_final: 0.7479 (t0) REVERT: Ag 425 ASN cc_start: 0.8701 (p0) cc_final: 0.8445 (p0) REVERT: Ah 309 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7536 (mttm) REVERT: Ah 312 ASP cc_start: 0.8325 (t70) cc_final: 0.7880 (t0) REVERT: Ah 377 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7374 (tp30) REVERT: Ai 296 ASP cc_start: 0.7769 (t70) cc_final: 0.7387 (t0) REVERT: Ai 309 LYS cc_start: 0.8314 (tttt) cc_final: 0.7558 (mttp) REVERT: Ai 376 TYR cc_start: 0.7621 (m-80) cc_final: 0.7223 (m-80) REVERT: Ai 425 ASN cc_start: 0.8500 (p0) cc_final: 0.8199 (p0) REVERT: Aj 299 LEU cc_start: 0.8510 (mt) cc_final: 0.8234 (mt) REVERT: Aj 328 ASN cc_start: 0.7477 (m-40) cc_final: 0.6980 (m-40) REVERT: Aj 376 TYR cc_start: 0.7736 (m-10) cc_final: 0.7444 (m-10) REVERT: Aj 429 GLN cc_start: 0.7858 (mp10) cc_final: 0.7566 (mp10) REVERT: Ak 266 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8746 (tm) REVERT: Al 266 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8814 (tm) REVERT: Al 272 GLU cc_start: 0.8552 (tp30) cc_final: 0.8269 (tp30) REVERT: Al 283 ILE cc_start: 0.8951 (mt) cc_final: 0.8714 (mp) REVERT: Al 296 ASP cc_start: 0.8143 (t70) cc_final: 0.7580 (t0) REVERT: Al 298 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7077 (mt-10) REVERT: Al 397 VAL cc_start: 0.8334 (t) cc_final: 0.8119 (t) REVERT: Am 268 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7935 (tptp) REVERT: Am 296 ASP cc_start: 0.8706 (t0) cc_final: 0.8229 (t0) REVERT: Am 312 ASP cc_start: 0.8324 (t0) cc_final: 0.7955 (t0) REVERT: Am 385 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6593 (tm-30) REVERT: Am 387 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7756 (mmtm) REVERT: Am 424 LEU cc_start: 0.8746 (mm) cc_final: 0.8468 (mm) REVERT: Am 431 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6591 (mm) REVERT: Am 441 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8200 (tmm-80) REVERT: An 301 PHE cc_start: 0.9417 (m-80) cc_final: 0.9142 (m-80) REVERT: An 377 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7632 (tp30) REVERT: An 385 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: An 387 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7522 (mmtp) REVERT: An 426 SER cc_start: 0.7869 (m) cc_final: 0.7531 (p) REVERT: Ao 305 GLU cc_start: 0.7626 (mt-10) cc_final: 0.6668 (tt0) REVERT: Ao 385 GLU cc_start: 0.8005 (tm-30) cc_final: 0.6899 (tm-30) REVERT: Ao 387 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7494 (mmtp) REVERT: Ao 431 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6752 (mm) REVERT: Ap 272 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7648 (tp30) REVERT: Ap 426 SER cc_start: 0.8582 (m) cc_final: 0.8057 (p) REVERT: Ap 429 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7565 (mm-40) REVERT: Ap 445 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (tt) REVERT: Aq 296 ASP cc_start: 0.7820 (t70) cc_final: 0.7494 (t0) REVERT: Aq 299 LEU cc_start: 0.8973 (mp) cc_final: 0.8556 (mt) REVERT: Aq 301 PHE cc_start: 0.9065 (m-80) cc_final: 0.8766 (m-80) REVERT: Aq 385 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7053 (tm-30) REVERT: Ar 266 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9074 (tm) REVERT: Ar 376 TYR cc_start: 0.7824 (m-80) cc_final: 0.6792 (m-80) REVERT: Ar 379 ASP cc_start: 0.7994 (p0) cc_final: 0.7663 (p0) REVERT: Ar 386 ARG cc_start: 0.7426 (ttm110) cc_final: 0.7207 (ttm-80) REVERT: Ar 429 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: As 309 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8096 (tttt) REVERT: As 378 LEU cc_start: 0.7723 (mt) cc_final: 0.7445 (mt) REVERT: As 385 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7353 (tm-30) REVERT: As 425 ASN cc_start: 0.8409 (p0) cc_final: 0.8189 (p0) REVERT: As 429 GLN cc_start: 0.7439 (mp10) cc_final: 0.7191 (mp10) REVERT: As 430 VAL cc_start: 0.6433 (t) cc_final: 0.6205 (t) REVERT: As 431 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6978 (mm) REVERT: At 296 ASP cc_start: 0.7736 (t0) cc_final: 0.7355 (t0) REVERT: At 429 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7310 (mm-40) REVERT: At 446 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7325 (p0) REVERT: Au 282 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6844 (mm) REVERT: Au 305 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6596 (tp30) REVERT: Au 376 TYR cc_start: 0.7945 (m-80) cc_final: 0.7551 (m-80) REVERT: Au 450 MET cc_start: 0.8225 (pmm) cc_final: 0.7197 (pmm) REVERT: Av 266 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8693 (tm) REVERT: Av 272 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7964 (tp30) REVERT: Av 295 VAL cc_start: 0.9014 (m) cc_final: 0.8797 (t) REVERT: Av 296 ASP cc_start: 0.8224 (t70) cc_final: 0.7995 (t70) REVERT: Av 397 VAL cc_start: 0.8497 (t) cc_final: 0.8140 (t) REVERT: Av 439 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6333 (pp20) REVERT: Av 446 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6158 (p0) REVERT: Aw 387 LYS cc_start: 0.8417 (mmtp) cc_final: 0.8122 (mmtp) REVERT: Aw 428 ARG cc_start: 0.8409 (tpt90) cc_final: 0.8059 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8216 (mm) cc_final: 0.7779 (mt) REVERT: Aw 446 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7172 (p0) REVERT: Ax 309 LYS cc_start: 0.8836 (tttt) cc_final: 0.8033 (mttp) REVERT: Ax 393 ASN cc_start: 0.8616 (t0) cc_final: 0.8246 (t0) REVERT: Ax 425 ASN cc_start: 0.8547 (p0) cc_final: 0.8270 (p0) REVERT: Ax 431 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7202 (mm) REVERT: Ay 385 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: Az 429 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7430 (tp-100) REVERT: Az 432 ILE cc_start: 0.7787 (mm) cc_final: 0.7481 (mt) REVERT: Ba 376 TYR cc_start: 0.7442 (m-10) cc_final: 0.7050 (m-10) REVERT: Ba 425 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.7945 (p0) REVERT: Bb 272 GLU cc_start: 0.8512 (tp30) cc_final: 0.8175 (tp30) REVERT: Bb 428 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7314 (ttm-80) REVERT: Bb 432 ILE cc_start: 0.7664 (mt) cc_final: 0.7298 (mt) REVERT: Bc 296 ASP cc_start: 0.7730 (t70) cc_final: 0.7375 (t0) REVERT: Bc 298 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7212 (mt-10) REVERT: Bc 425 ASN cc_start: 0.8521 (p0) cc_final: 0.8054 (p0) REVERT: Bc 432 ILE cc_start: 0.7615 (mt) cc_final: 0.7379 (mp) REVERT: Bd 296 ASP cc_start: 0.8042 (t0) cc_final: 0.7797 (t0) REVERT: Bd 379 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7044 (t0) REVERT: Bd 450 MET cc_start: 0.9067 (pmm) cc_final: 0.8359 (pmm) REVERT: Be 299 LEU cc_start: 0.9037 (mt) cc_final: 0.8565 (mt) REVERT: Be 385 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: Be 387 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8360 (mmtm) REVERT: Be 426 SER cc_start: 0.8185 (m) cc_final: 0.7766 (p) REVERT: Be 446 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.6466 (p0) REVERT: Bf 429 GLN cc_start: 0.7557 (mp10) cc_final: 0.7265 (mp10) REVERT: Bg 268 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8003 (tptp) REVERT: Bg 305 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: Bg 309 LYS cc_start: 0.8476 (tttt) cc_final: 0.7187 (mttm) REVERT: Bg 376 TYR cc_start: 0.7907 (m-10) cc_final: 0.7168 (m-10) REVERT: Bg 379 ASP cc_start: 0.7972 (p0) cc_final: 0.7586 (p0) REVERT: Bg 432 ILE cc_start: 0.7754 (mm) cc_final: 0.7510 (mt) REVERT: Bh 312 ASP cc_start: 0.8328 (t0) cc_final: 0.7989 (t0) REVERT: Bh 425 ASN cc_start: 0.8635 (p0) cc_final: 0.7850 (p0) outliers start: 224 outliers final: 158 residues processed: 1321 average time/residue: 0.2194 time to fit residues: 480.4922 Evaluate side-chains 1350 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1158 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 391 VAL Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 282 LEU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 391 VAL Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ag residue 450 MET Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 309 LYS Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 424 LEU Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 280 SER Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Ai residue 450 MET Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Aj residue 445 LEU Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Ak residue 448 LEU Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 280 SER Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 449 SER Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 385 GLU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 389 SER Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Ap residue 445 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain As residue 431 LEU Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 439 GLU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 369 HIS Chi-restraints excluded: chain Ax residue 378 LEU Chi-restraints excluded: chain Ax residue 380 THR Chi-restraints excluded: chain Ax residue 431 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Ay residue 438 SER Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 266 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 378 LEU Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 281 VAL Chi-restraints excluded: chain Bc residue 430 VAL Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 420 SER Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 321 GLU Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 310 VAL Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Chi-restraints excluded: chain Bh residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 107 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 384 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 344 optimal weight: 4.9990 chunk 406 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ah 369 HIS ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 369 HIS Az 270 GLN Bc 395 GLN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 429 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.240504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.4080 r_free = 0.4080 target = 0.165833 restraints weight = 30806.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.172250 restraints weight = 16750.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.174423 restraints weight = 11003.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.174653 restraints weight = 9617.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.175402 restraints weight = 8986.321| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38930 Z= 0.156 Angle : 0.532 7.609 52564 Z= 0.277 Chirality : 0.041 0.292 6188 Planarity : 0.003 0.032 6902 Dihedral : 5.320 59.535 5367 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.84 % Allowed : 19.77 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.13), residues: 4692 helix: 2.29 (0.14), residues: 1293 sheet: -2.27 (0.11), residues: 2221 loop : -2.91 (0.14), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 374 TYR 0.028 0.001 TYRAv 291 PHE 0.011 0.001 PHEAb 311 HIS 0.022 0.001 HISAx 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (38930) covalent geometry : angle 0.53242 / 0.28 (52564) hydrogen bonds : bond 0.02995 / 2.01 ( 1783) hydrogen bonds : angle 5.11002 / 3.56 ( 5061) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1218 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 384 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7322 (t-90) REVERT: Ab 283 ILE cc_start: 0.9090 (mm) cc_final: 0.8817 (mt) REVERT: Ab 385 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6886 (tm-30) REVERT: Ac 262 LYS cc_start: 0.9099 (tptm) cc_final: 0.8751 (tttt) REVERT: Ac 296 ASP cc_start: 0.7723 (t0) cc_final: 0.7344 (t0) REVERT: Ad 305 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: Ad 379 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7476 (t0) REVERT: Ad 443 ASP cc_start: 0.7651 (m-30) cc_final: 0.7255 (m-30) REVERT: Ae 272 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8269 (mm-30) REVERT: Ae 379 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.6836 (t0) REVERT: Ae 448 LEU cc_start: 0.9048 (mp) cc_final: 0.8747 (mt) REVERT: Af 266 LEU cc_start: 0.9418 (tp) cc_final: 0.9176 (tt) REVERT: Af 321 GLU cc_start: 0.8281 (tp30) cc_final: 0.7500 (tt0) REVERT: Af 377 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7992 (tm-30) REVERT: Af 378 LEU cc_start: 0.8098 (mt) cc_final: 0.7484 (mt) REVERT: Af 385 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7161 (tm-30) REVERT: Af 429 GLN cc_start: 0.7374 (mp10) cc_final: 0.7124 (mp10) REVERT: Af 444 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7108 (tt) REVERT: Ag 266 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8907 (tt) REVERT: Ag 296 ASP cc_start: 0.7930 (t70) cc_final: 0.7563 (t0) REVERT: Ag 369 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8166 (t-90) REVERT: Ag 425 ASN cc_start: 0.8676 (p0) cc_final: 0.7925 (p0) REVERT: Ag 429 GLN cc_start: 0.7440 (mp10) cc_final: 0.7066 (mp10) REVERT: Ah 309 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7704 (mttm) REVERT: Ah 312 ASP cc_start: 0.8323 (t70) cc_final: 0.7927 (t0) REVERT: Ah 319 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7531 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7341 (tp30) REVERT: Ai 309 LYS cc_start: 0.8391 (tttt) cc_final: 0.7668 (mttp) REVERT: Ai 376 TYR cc_start: 0.7718 (m-80) cc_final: 0.7326 (m-10) REVERT: Ai 425 ASN cc_start: 0.8487 (p0) cc_final: 0.8195 (p0) REVERT: Aj 299 LEU cc_start: 0.8472 (mt) cc_final: 0.8167 (mt) REVERT: Aj 328 ASN cc_start: 0.7518 (m-40) cc_final: 0.7028 (m-40) REVERT: Aj 376 TYR cc_start: 0.7780 (m-10) cc_final: 0.7463 (m-10) REVERT: Aj 429 GLN cc_start: 0.7754 (mp10) cc_final: 0.7419 (mp10) REVERT: Ak 266 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8770 (tm) REVERT: Ak 309 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8367 (pttt) REVERT: Al 266 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8845 (tm) REVERT: Al 272 GLU cc_start: 0.8572 (tp30) cc_final: 0.8288 (tp30) REVERT: Al 283 ILE cc_start: 0.8962 (mt) cc_final: 0.8718 (mp) REVERT: Al 296 ASP cc_start: 0.8153 (t70) cc_final: 0.7695 (t0) REVERT: Al 298 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7137 (mt-10) REVERT: Al 305 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: Al 385 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6747 (tm-30) REVERT: Am 268 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7938 (tptp) REVERT: Am 296 ASP cc_start: 0.8690 (t0) cc_final: 0.8160 (t0) REVERT: Am 424 LEU cc_start: 0.8765 (mm) cc_final: 0.8482 (mm) REVERT: Am 431 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6724 (mm) REVERT: Am 441 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: An 301 PHE cc_start: 0.9409 (m-80) cc_final: 0.9190 (m-80) REVERT: An 370 LYS cc_start: 0.7790 (mttt) cc_final: 0.7420 (mttp) REVERT: An 376 TYR cc_start: 0.7994 (m-80) cc_final: 0.7647 (m-80) REVERT: An 379 ASP cc_start: 0.7998 (p0) cc_final: 0.7492 (p0) REVERT: An 385 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: An 426 SER cc_start: 0.8052 (m) cc_final: 0.7596 (p) REVERT: Ao 305 GLU cc_start: 0.7713 (mt-10) cc_final: 0.6786 (tt0) REVERT: Ao 385 GLU cc_start: 0.8019 (tm-30) cc_final: 0.6966 (tm-30) REVERT: Ao 387 LYS cc_start: 0.7938 (mmtp) cc_final: 0.7598 (mmtp) REVERT: Ao 431 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6834 (mm) REVERT: Ap 426 SER cc_start: 0.8605 (m) cc_final: 0.8033 (p) REVERT: Ap 429 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7554 (mm-40) REVERT: Ap 445 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8074 (tt) REVERT: Aq 296 ASP cc_start: 0.7829 (t70) cc_final: 0.7502 (t0) REVERT: Aq 299 LEU cc_start: 0.8981 (mp) cc_final: 0.8524 (mt) REVERT: Aq 301 PHE cc_start: 0.9140 (m-80) cc_final: 0.8876 (m-80) REVERT: Aq 385 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7108 (tm-30) REVERT: Ar 265 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7803 (mt-10) REVERT: Ar 266 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9045 (tm) REVERT: Ar 376 TYR cc_start: 0.7898 (m-80) cc_final: 0.6903 (m-80) REVERT: Ar 377 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7661 (tm-30) REVERT: Ar 379 ASP cc_start: 0.8089 (p0) cc_final: 0.7732 (p0) REVERT: Ar 385 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6208 (tm-30) REVERT: Ar 386 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7172 (ttm-80) REVERT: Ar 429 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: As 309 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: As 378 LEU cc_start: 0.7834 (mt) cc_final: 0.7595 (mt) REVERT: As 385 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7375 (tm-30) REVERT: As 430 VAL cc_start: 0.6460 (t) cc_final: 0.6243 (t) REVERT: At 296 ASP cc_start: 0.7651 (t0) cc_final: 0.7344 (t0) REVERT: At 393 ASN cc_start: 0.8462 (t0) cc_final: 0.8231 (p0) REVERT: At 426 SER cc_start: 0.8004 (m) cc_final: 0.7686 (p) REVERT: At 429 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: At 446 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7533 (p0) REVERT: Au 282 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7006 (mm) REVERT: Au 305 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6733 (tp30) REVERT: Au 376 TYR cc_start: 0.7914 (m-80) cc_final: 0.7501 (m-80) REVERT: Au 450 MET cc_start: 0.8238 (pmm) cc_final: 0.7294 (pmm) REVERT: Av 266 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8718 (tm) REVERT: Av 272 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7958 (tp30) REVERT: Av 376 TYR cc_start: 0.7843 (m-80) cc_final: 0.7568 (m-10) REVERT: Av 439 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6349 (pp20) REVERT: Av 446 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6422 (p0) REVERT: Aw 387 LYS cc_start: 0.8455 (mmtp) cc_final: 0.8134 (mmtp) REVERT: Aw 394 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8432 (ttt180) REVERT: Aw 428 ARG cc_start: 0.8401 (tpt90) cc_final: 0.8151 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8235 (mm) cc_final: 0.7924 (mt) REVERT: Aw 446 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7138 (p0) REVERT: Ax 309 LYS cc_start: 0.8888 (tttt) cc_final: 0.8122 (mttp) REVERT: Ax 393 ASN cc_start: 0.8626 (t0) cc_final: 0.8254 (t0) REVERT: Ax 425 ASN cc_start: 0.8472 (p0) cc_final: 0.7789 (p0) REVERT: Ax 429 GLN cc_start: 0.7268 (mp10) cc_final: 0.6883 (mp10) REVERT: Ax 431 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7167 (mm) REVERT: Ay 385 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: Az 432 ILE cc_start: 0.7812 (mm) cc_final: 0.7497 (mt) REVERT: Ba 376 TYR cc_start: 0.7550 (m-10) cc_final: 0.7216 (m-10) REVERT: Ba 385 GLU cc_start: 0.7697 (tm-30) cc_final: 0.6743 (tm-30) REVERT: Ba 425 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.7931 (p0) REVERT: Bb 272 GLU cc_start: 0.8512 (tp30) cc_final: 0.8177 (tp30) REVERT: Bb 423 ASP cc_start: 0.8057 (m-30) cc_final: 0.7548 (t0) REVERT: Bb 432 ILE cc_start: 0.7705 (mt) cc_final: 0.7307 (mt) REVERT: Bc 296 ASP cc_start: 0.7761 (t70) cc_final: 0.7398 (t0) REVERT: Bc 298 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7185 (mt-10) REVERT: Bc 425 ASN cc_start: 0.8506 (p0) cc_final: 0.8154 (p0) REVERT: Bd 296 ASP cc_start: 0.8088 (t0) cc_final: 0.7807 (t0) REVERT: Bd 395 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: Bd 450 MET cc_start: 0.9032 (pmm) cc_final: 0.8333 (pmm) REVERT: Be 296 ASP cc_start: 0.7824 (t70) cc_final: 0.7379 (t0) REVERT: Be 299 LEU cc_start: 0.8927 (mt) cc_final: 0.8625 (mt) REVERT: Be 385 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: Be 387 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8440 (mmtp) REVERT: Be 426 SER cc_start: 0.8287 (m) cc_final: 0.7775 (p) REVERT: Be 446 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.6574 (p0) REVERT: Bf 374 ARG cc_start: 0.7553 (ptp-110) cc_final: 0.7176 (ttm110) REVERT: Bg 268 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8002 (tptp) REVERT: Bg 305 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6522 (tp30) REVERT: Bg 309 LYS cc_start: 0.8549 (tttt) cc_final: 0.7268 (mttm) REVERT: Bg 324 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7437 (tt) REVERT: Bg 376 TYR cc_start: 0.7964 (m-10) cc_final: 0.7189 (m-10) REVERT: Bg 432 ILE cc_start: 0.7790 (mm) cc_final: 0.7543 (mt) REVERT: Bh 312 ASP cc_start: 0.8324 (t0) cc_final: 0.8017 (t0) REVERT: Bh 425 ASN cc_start: 0.8501 (p0) cc_final: 0.7879 (p0) REVERT: Bh 429 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7138 (mp10) outliers start: 250 outliers final: 175 residues processed: 1361 average time/residue: 0.2139 time to fit residues: 480.2478 Evaluate side-chains 1408 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1195 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 310 VAL Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 391 VAL Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 282 LEU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 310 VAL Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 391 VAL Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 430 VAL Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 420 SER Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 369 HIS Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ag residue 450 MET Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 309 LYS Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 369 HIS Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 424 LEU Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 280 SER Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Aj residue 445 LEU Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Ak residue 448 LEU Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 280 SER Chi-restraints excluded: chain Al residue 305 GLU Chi-restraints excluded: chain Al residue 324 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 449 SER Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 391 VAL Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 385 GLU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 389 SER Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Ap residue 445 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 429 GLN Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain As residue 444 LEU Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 298 GLU Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 439 GLU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 280 SER Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 378 LEU Chi-restraints excluded: chain Ax residue 380 THR Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 431 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 378 LEU Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 266 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 266 LEU Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 378 LEU Chi-restraints excluded: chain Bb residue 383 SER Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 281 VAL Chi-restraints excluded: chain Bc residue 373 THR Chi-restraints excluded: chain Bc residue 420 SER Chi-restraints excluded: chain Bc residue 444 LEU Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 395 GLN Chi-restraints excluded: chain Bd residue 420 SER Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 321 GLU Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 420 SER Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 310 VAL Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 445 LEU Chi-restraints excluded: chain Bh residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 19 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 199 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 396 optimal weight: 0.7980 chunk 303 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ae 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 369 HIS ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 395 GLN ** Bf 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.241715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173713 restraints weight = 30753.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.174396 restraints weight = 23593.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.173976 restraints weight = 14089.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.174992 restraints weight = 12196.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.175261 restraints weight = 9941.903| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38930 Z= 0.130 Angle : 0.532 8.163 52564 Z= 0.275 Chirality : 0.042 0.305 6188 Planarity : 0.003 0.032 6902 Dihedral : 5.283 59.978 5367 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.21 % Allowed : 20.80 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.13), residues: 4692 helix: 2.27 (0.14), residues: 1293 sheet: -2.16 (0.11), residues: 2188 loop : -3.04 (0.14), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 374 TYR 0.026 0.001 TYRAv 291 PHE 0.015 0.001 PHEAc 301 HIS 0.006 0.001 HISAh 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (38930) covalent geometry : angle 0.53189 / 0.28 (52564) hydrogen bonds : bond 0.02917 / 1.95 ( 1783) hydrogen bonds : angle 5.07499 / 3.54 ( 5061) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 1214 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 261 ARG cc_start: 0.7894 (tmm160) cc_final: 0.7294 (tmm160) REVERT: Aa 384 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.7138 (t-90) REVERT: Ab 283 ILE cc_start: 0.9072 (mm) cc_final: 0.8806 (mt) REVERT: Ab 298 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7735 (mt-10) REVERT: Ab 385 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6862 (tm-30) REVERT: Ab 429 GLN cc_start: 0.7627 (mp10) cc_final: 0.7392 (mp10) REVERT: Ac 262 LYS cc_start: 0.9090 (tptm) cc_final: 0.8865 (tttt) REVERT: Ac 296 ASP cc_start: 0.7676 (t0) cc_final: 0.7325 (t0) REVERT: Ad 305 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7413 (t0) REVERT: Ad 443 ASP cc_start: 0.7655 (m-30) cc_final: 0.7273 (m-30) REVERT: Ae 272 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8214 (mm-30) REVERT: Ae 379 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6833 (t0) REVERT: Ae 448 LEU cc_start: 0.9021 (mp) cc_final: 0.8734 (mt) REVERT: Af 321 GLU cc_start: 0.8305 (tp30) cc_final: 0.7502 (tt0) REVERT: Af 377 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7900 (tm-30) REVERT: Af 378 LEU cc_start: 0.8054 (mt) cc_final: 0.7410 (mt) REVERT: Af 385 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7127 (tm-30) REVERT: Af 429 GLN cc_start: 0.7399 (mp10) cc_final: 0.7127 (mp10) REVERT: Af 444 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7060 (tt) REVERT: Ag 266 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8892 (tt) REVERT: Ag 296 ASP cc_start: 0.7880 (t70) cc_final: 0.7480 (t0) REVERT: Ag 369 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8095 (t-90) REVERT: Ag 425 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.7908 (p0) REVERT: Ag 429 GLN cc_start: 0.7442 (mp10) cc_final: 0.7064 (mp10) REVERT: Ah 309 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7649 (mttp) REVERT: Ah 312 ASP cc_start: 0.8367 (t70) cc_final: 0.7916 (t0) REVERT: Ah 319 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7483 (ttm-80) REVERT: Ah 377 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7440 (tp30) REVERT: Ai 296 ASP cc_start: 0.7768 (t70) cc_final: 0.7403 (t0) REVERT: Ai 309 LYS cc_start: 0.8333 (tttt) cc_final: 0.7569 (mttp) REVERT: Ai 376 TYR cc_start: 0.7805 (m-80) cc_final: 0.7443 (m-10) REVERT: Ai 425 ASN cc_start: 0.8501 (p0) cc_final: 0.8205 (p0) REVERT: Aj 299 LEU cc_start: 0.8422 (mt) cc_final: 0.8152 (mt) REVERT: Aj 328 ASN cc_start: 0.7491 (m-40) cc_final: 0.7044 (m-40) REVERT: Aj 376 TYR cc_start: 0.7689 (m-10) cc_final: 0.7427 (m-10) REVERT: Aj 429 GLN cc_start: 0.7801 (mp10) cc_final: 0.7465 (mp10) REVERT: Ak 266 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8777 (tm) REVERT: Ak 309 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8259 (pttt) REVERT: Ak 429 GLN cc_start: 0.8382 (tt0) cc_final: 0.8159 (mm110) REVERT: Al 266 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8820 (tm) REVERT: Al 283 ILE cc_start: 0.8968 (mt) cc_final: 0.8717 (mp) REVERT: Al 296 ASP cc_start: 0.8156 (t70) cc_final: 0.7575 (t0) REVERT: Al 298 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7091 (mt-10) REVERT: Al 305 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: Al 385 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6611 (tm-30) REVERT: Am 296 ASP cc_start: 0.8664 (t0) cc_final: 0.8318 (t70) REVERT: Am 424 LEU cc_start: 0.8753 (mm) cc_final: 0.8481 (mm) REVERT: Am 431 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6708 (mm) REVERT: Am 441 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7992 (ttp80) REVERT: An 370 LYS cc_start: 0.7763 (mttt) cc_final: 0.7379 (mttp) REVERT: An 376 TYR cc_start: 0.7982 (m-80) cc_final: 0.7668 (m-80) REVERT: An 379 ASP cc_start: 0.7983 (p0) cc_final: 0.7468 (p0) REVERT: An 385 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: An 426 SER cc_start: 0.8244 (m) cc_final: 0.7588 (p) REVERT: Ao 305 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6710 (tt0) REVERT: Ao 379 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7525 (t0) REVERT: Ao 385 GLU cc_start: 0.7966 (tm-30) cc_final: 0.6845 (tm-30) REVERT: Ao 387 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7611 (mmtp) REVERT: Ao 431 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6792 (mm) REVERT: Ap 272 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7731 (tp30) REVERT: Ap 426 SER cc_start: 0.8578 (m) cc_final: 0.7987 (p) REVERT: Ap 429 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7541 (mm-40) REVERT: Ap 445 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7802 (tt) REVERT: Aq 296 ASP cc_start: 0.7964 (t70) cc_final: 0.7636 (t0) REVERT: Aq 298 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6707 (mt-10) REVERT: Aq 299 LEU cc_start: 0.8980 (mp) cc_final: 0.8521 (mt) REVERT: Aq 301 PHE cc_start: 0.9173 (m-80) cc_final: 0.8877 (m-80) REVERT: Aq 385 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6934 (tm-30) REVERT: Ar 265 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7813 (mt-10) REVERT: Ar 266 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9132 (tm) REVERT: Ar 272 GLU cc_start: 0.8448 (tp30) cc_final: 0.8172 (tp30) REVERT: Ar 376 TYR cc_start: 0.7924 (m-80) cc_final: 0.6886 (m-80) REVERT: Ar 377 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7659 (tm-30) REVERT: Ar 379 ASP cc_start: 0.8046 (p0) cc_final: 0.7663 (p0) REVERT: Ar 385 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6184 (tm-30) REVERT: Ar 386 ARG cc_start: 0.7609 (ttm110) cc_final: 0.7210 (ttm-80) REVERT: As 309 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8148 (tttt) REVERT: As 378 LEU cc_start: 0.7862 (mt) cc_final: 0.7584 (mt) REVERT: As 385 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7310 (tm-30) REVERT: As 394 ARG cc_start: 0.8681 (tpt-90) cc_final: 0.8467 (tpt-90) REVERT: As 425 ASN cc_start: 0.8394 (p0) cc_final: 0.8123 (p0) REVERT: As 429 GLN cc_start: 0.7707 (mp10) cc_final: 0.7374 (mp10) REVERT: As 430 VAL cc_start: 0.5779 (t) cc_final: 0.5514 (t) REVERT: At 265 GLU cc_start: 0.8404 (tt0) cc_final: 0.8146 (tp30) REVERT: At 296 ASP cc_start: 0.7819 (t0) cc_final: 0.7494 (t0) REVERT: At 429 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7298 (mm-40) REVERT: At 446 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7374 (p0) REVERT: Au 282 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.6978 (mm) REVERT: Au 305 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: Au 376 TYR cc_start: 0.7932 (m-80) cc_final: 0.7514 (m-80) REVERT: Au 450 MET cc_start: 0.8222 (pmm) cc_final: 0.7214 (pmm) REVERT: Av 266 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8706 (tm) REVERT: Av 272 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7976 (tp30) REVERT: Av 376 TYR cc_start: 0.7832 (m-80) cc_final: 0.7594 (m-10) REVERT: Av 439 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6334 (pp20) REVERT: Av 446 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6405 (p0) REVERT: Aw 379 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7478 (t0) REVERT: Aw 387 LYS cc_start: 0.8421 (mmtp) cc_final: 0.8075 (mmtp) REVERT: Aw 394 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8381 (ttt180) REVERT: Aw 428 ARG cc_start: 0.8416 (tpt90) cc_final: 0.8145 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8208 (mm) cc_final: 0.7902 (mt) REVERT: Aw 446 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7247 (p0) REVERT: Ax 309 LYS cc_start: 0.8810 (tttt) cc_final: 0.8013 (mttp) REVERT: Ax 393 ASN cc_start: 0.8653 (t0) cc_final: 0.8276 (t0) REVERT: Ax 425 ASN cc_start: 0.8490 (p0) cc_final: 0.7523 (p0) REVERT: Ax 429 GLN cc_start: 0.7301 (mp10) cc_final: 0.6885 (mp10) REVERT: Ax 431 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7193 (mm) REVERT: Az 432 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7593 (mt) REVERT: Ba 376 TYR cc_start: 0.7374 (m-10) cc_final: 0.7064 (m-10) REVERT: Ba 385 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6764 (tm-30) REVERT: Ba 387 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8149 (mmtp) REVERT: Ba 425 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.7974 (p0) REVERT: Bb 272 GLU cc_start: 0.8497 (tp30) cc_final: 0.8176 (tp30) REVERT: Bb 423 ASP cc_start: 0.7981 (m-30) cc_final: 0.7633 (t0) REVERT: Bb 432 ILE cc_start: 0.7805 (mt) cc_final: 0.7468 (mp) REVERT: Bc 296 ASP cc_start: 0.7727 (t70) cc_final: 0.7357 (t0) REVERT: Bc 298 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7196 (mt-10) REVERT: Bc 393 ASN cc_start: 0.8641 (t0) cc_final: 0.8205 (p0) REVERT: Bc 425 ASN cc_start: 0.8580 (p0) cc_final: 0.8063 (p0) REVERT: Bc 429 GLN cc_start: 0.7172 (mp10) cc_final: 0.6738 (mp10) REVERT: Bc 432 ILE cc_start: 0.7382 (mp) cc_final: 0.7123 (mp) REVERT: Bd 296 ASP cc_start: 0.8060 (t0) cc_final: 0.7773 (t0) REVERT: Bd 395 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: Bd 450 MET cc_start: 0.9066 (pmm) cc_final: 0.8410 (pmm) REVERT: Be 296 ASP cc_start: 0.7826 (t70) cc_final: 0.7363 (t0) REVERT: Be 299 LEU cc_start: 0.9075 (mt) cc_final: 0.8729 (mt) REVERT: Be 385 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: Be 387 LYS cc_start: 0.8786 (mmtp) cc_final: 0.8412 (mmtp) REVERT: Be 426 SER cc_start: 0.8252 (m) cc_final: 0.7736 (p) REVERT: Be 446 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.6639 (p0) REVERT: Bf 374 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7062 (ttm110) REVERT: Bg 268 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7985 (tptp) REVERT: Bg 305 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6478 (tp30) REVERT: Bg 309 LYS cc_start: 0.8515 (tttt) cc_final: 0.7207 (mttm) REVERT: Bg 324 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7319 (tt) REVERT: Bg 376 TYR cc_start: 0.7943 (m-10) cc_final: 0.7237 (m-10) REVERT: Bg 432 ILE cc_start: 0.7778 (mm) cc_final: 0.7543 (mt) REVERT: Bh 312 ASP cc_start: 0.8325 (t0) cc_final: 0.7994 (t0) REVERT: Bh 425 ASN cc_start: 0.8507 (p0) cc_final: 0.7869 (p0) REVERT: Bh 429 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7139 (mp10) outliers start: 223 outliers final: 159 residues processed: 1338 average time/residue: 0.2150 time to fit residues: 474.0202 Evaluate side-chains 1387 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1189 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 391 VAL Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 282 LEU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 391 VAL Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 391 VAL Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 369 HIS Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ag residue 425 ASN Chi-restraints excluded: chain Ag residue 450 MET Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 309 LYS Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 369 HIS Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 280 SER Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Aj residue 445 LEU Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 280 SER Chi-restraints excluded: chain Al residue 305 GLU Chi-restraints excluded: chain Al residue 324 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 445 LEU Chi-restraints excluded: chain Al residue 449 SER Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 391 VAL Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 385 GLU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Ap residue 445 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 298 GLU Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 439 GLU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 280 SER Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 310 VAL Chi-restraints excluded: chain Ax residue 380 THR Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 431 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 378 LEU Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 432 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 266 LEU Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 378 LEU Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 281 VAL Chi-restraints excluded: chain Bc residue 420 SER Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 266 LEU Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 395 GLN Chi-restraints excluded: chain Bd residue 420 SER Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 420 SER Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 310 VAL Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Chi-restraints excluded: chain Bh residue 445 LEU Chi-restraints excluded: chain Bh residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 189 optimal weight: 0.9990 chunk 419 optimal weight: 0.8980 chunk 165 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Ae 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 369 HIS Bf 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.240568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.172214 restraints weight = 30847.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.168530 restraints weight = 22088.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.174052 restraints weight = 13785.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.174362 restraints weight = 10321.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.175456 restraints weight = 9529.354| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38930 Z= 0.142 Angle : 0.549 9.892 52564 Z= 0.285 Chirality : 0.043 0.306 6188 Planarity : 0.003 0.033 6902 Dihedral : 5.224 59.936 5363 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.18 % Allowed : 21.43 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.88 (0.13), residues: 4692 helix: 2.22 (0.14), residues: 1294 sheet: -2.23 (0.11), residues: 2221 loop : -2.86 (0.15), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 374 TYR 0.024 0.001 TYRAv 291 PHE 0.021 0.001 PHEAs 301 HIS 0.008 0.001 HISAh 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (38930) covalent geometry : angle 0.54937 / 0.28 (52564) hydrogen bonds : bond 0.02969 / 1.99 ( 1783) hydrogen bonds : angle 5.10265 / 3.57 ( 5061) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1203 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 272 GLU cc_start: 0.8690 (tp30) cc_final: 0.8479 (tp30) REVERT: Aa 296 ASP cc_start: 0.7922 (t70) cc_final: 0.7515 (t0) REVERT: Aa 384 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: Ab 283 ILE cc_start: 0.8990 (mm) cc_final: 0.8670 (mt) REVERT: Ab 298 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7807 (mt-10) REVERT: Ab 429 GLN cc_start: 0.7668 (mp10) cc_final: 0.7120 (mp10) REVERT: Ac 262 LYS cc_start: 0.9098 (tptm) cc_final: 0.8852 (tttt) REVERT: Ac 296 ASP cc_start: 0.7705 (t0) cc_final: 0.7326 (t0) REVERT: Ad 305 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7419 (t0) REVERT: Ad 443 ASP cc_start: 0.7717 (m-30) cc_final: 0.7445 (m-30) REVERT: Ae 272 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8176 (mm-30) REVERT: Ae 379 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.6826 (t0) REVERT: Ae 448 LEU cc_start: 0.9021 (mp) cc_final: 0.8730 (mt) REVERT: Af 321 GLU cc_start: 0.8181 (tp30) cc_final: 0.7446 (tt0) REVERT: Af 378 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7736 (mt) REVERT: Af 385 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7123 (tm-30) REVERT: Af 425 ASN cc_start: 0.8365 (p0) cc_final: 0.7974 (p0) REVERT: Af 444 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7054 (tt) REVERT: Ag 266 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8898 (tt) REVERT: Ag 296 ASP cc_start: 0.7894 (t70) cc_final: 0.7518 (t0) REVERT: Ag 369 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (t-90) REVERT: Ag 425 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7948 (p0) REVERT: Ag 429 GLN cc_start: 0.7463 (mp10) cc_final: 0.7066 (mp10) REVERT: Ah 309 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7496 (mttp) REVERT: Ah 312 ASP cc_start: 0.8368 (t70) cc_final: 0.7931 (t0) REVERT: Ah 319 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7468 (ttm-80) REVERT: Ai 309 LYS cc_start: 0.8322 (tttt) cc_final: 0.7580 (mttp) REVERT: Ai 376 TYR cc_start: 0.7769 (m-80) cc_final: 0.7403 (m-10) REVERT: Aj 262 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8633 (tptm) REVERT: Aj 299 LEU cc_start: 0.8316 (mt) cc_final: 0.8086 (mt) REVERT: Aj 328 ASN cc_start: 0.7482 (m-40) cc_final: 0.7062 (m-40) REVERT: Aj 376 TYR cc_start: 0.7706 (m-10) cc_final: 0.7489 (m-10) REVERT: Aj 429 GLN cc_start: 0.7846 (mp10) cc_final: 0.7483 (mp10) REVERT: Ak 266 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8761 (tm) REVERT: Ak 309 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8214 (pttt) REVERT: Ak 429 GLN cc_start: 0.8486 (tt0) cc_final: 0.8124 (mm110) REVERT: Ak 432 ILE cc_start: 0.7860 (mp) cc_final: 0.7614 (mp) REVERT: Al 266 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8840 (tm) REVERT: Al 283 ILE cc_start: 0.9030 (mt) cc_final: 0.8785 (mp) REVERT: Al 296 ASP cc_start: 0.8111 (t70) cc_final: 0.7531 (t0) REVERT: Al 298 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7056 (mt-10) REVERT: Al 305 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: Al 385 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6663 (tm-30) REVERT: Am 296 ASP cc_start: 0.8649 (t0) cc_final: 0.8351 (t70) REVERT: Am 424 LEU cc_start: 0.8822 (mm) cc_final: 0.8539 (mm) REVERT: Am 431 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6650 (mm) REVERT: Am 441 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8078 (tmm-80) REVERT: An 262 LYS cc_start: 0.9087 (tptm) cc_final: 0.8884 (tptm) REVERT: An 370 LYS cc_start: 0.7819 (mttt) cc_final: 0.7441 (mttp) REVERT: An 376 TYR cc_start: 0.7968 (m-80) cc_final: 0.7653 (m-80) REVERT: An 379 ASP cc_start: 0.8000 (p0) cc_final: 0.7497 (p0) REVERT: An 385 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: An 426 SER cc_start: 0.8135 (m) cc_final: 0.7568 (p) REVERT: Ao 305 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6728 (tt0) REVERT: Ao 385 GLU cc_start: 0.7984 (tm-30) cc_final: 0.6864 (tm-30) REVERT: Ao 387 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7707 (mmtp) REVERT: Ao 431 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6712 (mm) REVERT: Ap 385 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7121 (tm-30) REVERT: Ap 426 SER cc_start: 0.8567 (m) cc_final: 0.7962 (p) REVERT: Ap 429 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7571 (mm-40) REVERT: Aq 298 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6762 (mt-10) REVERT: Aq 299 LEU cc_start: 0.8990 (mp) cc_final: 0.8563 (mt) REVERT: Aq 301 PHE cc_start: 0.9188 (m-80) cc_final: 0.8873 (m-80) REVERT: Aq 385 GLU cc_start: 0.7746 (tm-30) cc_final: 0.6997 (tm-30) REVERT: Ar 265 GLU cc_start: 0.8641 (mm-30) cc_final: 0.7839 (mt-10) REVERT: Ar 266 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9137 (tm) REVERT: Ar 272 GLU cc_start: 0.8461 (tp30) cc_final: 0.8208 (tp30) REVERT: Ar 376 TYR cc_start: 0.7983 (m-80) cc_final: 0.7003 (m-80) REVERT: Ar 377 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7682 (tm-30) REVERT: Ar 379 ASP cc_start: 0.8142 (p0) cc_final: 0.7743 (p0) REVERT: Ar 385 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6197 (tm-30) REVERT: Ar 386 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7248 (ttm-80) REVERT: Ar 429 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7978 (mm-40) REVERT: As 309 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: As 378 LEU cc_start: 0.7803 (mt) cc_final: 0.7536 (mt) REVERT: As 385 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7291 (tm-30) REVERT: As 425 ASN cc_start: 0.8405 (p0) cc_final: 0.8093 (p0) REVERT: As 429 GLN cc_start: 0.7578 (mp10) cc_final: 0.7049 (mp10) REVERT: As 430 VAL cc_start: 0.5114 (t) cc_final: 0.4839 (t) REVERT: At 265 GLU cc_start: 0.8412 (tt0) cc_final: 0.8143 (tp30) REVERT: At 426 SER cc_start: 0.8021 (m) cc_final: 0.7658 (p) REVERT: At 429 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7346 (mm-40) REVERT: At 446 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7292 (p0) REVERT: Au 282 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6880 (mm) REVERT: Au 305 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: Au 376 TYR cc_start: 0.7915 (m-80) cc_final: 0.7475 (m-80) REVERT: Au 429 GLN cc_start: 0.7178 (mp10) cc_final: 0.6975 (mp10) REVERT: Au 450 MET cc_start: 0.8181 (pmm) cc_final: 0.7238 (pmm) REVERT: Av 266 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8712 (tm) REVERT: Av 272 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7805 (tp30) REVERT: Av 376 TYR cc_start: 0.7887 (m-80) cc_final: 0.7617 (m-10) REVERT: Av 397 VAL cc_start: 0.8542 (t) cc_final: 0.8196 (t) REVERT: Av 439 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6376 (pp20) REVERT: Av 446 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6369 (p0) REVERT: Aw 379 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7389 (t0) REVERT: Aw 387 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8046 (mmtp) REVERT: Aw 428 ARG cc_start: 0.8422 (tpt90) cc_final: 0.8124 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8179 (mm) cc_final: 0.7857 (mt) REVERT: Aw 446 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7219 (p0) REVERT: Ax 309 LYS cc_start: 0.8740 (tttt) cc_final: 0.7978 (mttp) REVERT: Ax 393 ASN cc_start: 0.8681 (t0) cc_final: 0.8294 (t0) REVERT: Ax 425 ASN cc_start: 0.8413 (p0) cc_final: 0.7544 (p0) REVERT: Ax 429 GLN cc_start: 0.7321 (mp10) cc_final: 0.6868 (mp10) REVERT: Ax 431 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6966 (mm) REVERT: Ay 385 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: Az 432 ILE cc_start: 0.8050 (mm) cc_final: 0.7782 (mt) REVERT: Ba 376 TYR cc_start: 0.7410 (m-10) cc_final: 0.7071 (m-10) REVERT: Ba 425 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.7838 (p0) REVERT: Bb 272 GLU cc_start: 0.8483 (tp30) cc_final: 0.8156 (tp30) REVERT: Bb 376 TYR cc_start: 0.8427 (m-10) cc_final: 0.8078 (m-10) REVERT: Bb 423 ASP cc_start: 0.7979 (m-30) cc_final: 0.7646 (t0) REVERT: Bb 432 ILE cc_start: 0.7905 (mt) cc_final: 0.7633 (mp) REVERT: Bc 296 ASP cc_start: 0.7696 (t70) cc_final: 0.7304 (t0) REVERT: Bc 298 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7205 (mt-10) REVERT: Bc 393 ASN cc_start: 0.8658 (t0) cc_final: 0.8213 (p0) REVERT: Bc 425 ASN cc_start: 0.8485 (p0) cc_final: 0.8172 (p0) REVERT: Bc 429 GLN cc_start: 0.7242 (mp10) cc_final: 0.7009 (mp10) REVERT: Bd 296 ASP cc_start: 0.8049 (t0) cc_final: 0.7776 (t0) REVERT: Bd 450 MET cc_start: 0.8981 (pmm) cc_final: 0.8399 (pmm) REVERT: Be 296 ASP cc_start: 0.7831 (t70) cc_final: 0.7379 (t0) REVERT: Be 299 LEU cc_start: 0.9062 (mt) cc_final: 0.8489 (mt) REVERT: Be 385 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: Be 387 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8398 (mmtp) REVERT: Be 426 SER cc_start: 0.8205 (m) cc_final: 0.7700 (p) REVERT: Be 446 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.6606 (p0) REVERT: Bf 374 ARG cc_start: 0.7577 (ptp-110) cc_final: 0.7100 (ttm110) REVERT: Bg 268 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7835 (tptp) REVERT: Bg 305 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6448 (tp30) REVERT: Bg 309 LYS cc_start: 0.8531 (tttt) cc_final: 0.7217 (mttm) REVERT: Bg 324 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7315 (tt) REVERT: Bg 376 TYR cc_start: 0.8015 (m-10) cc_final: 0.7282 (m-10) REVERT: Bg 432 ILE cc_start: 0.7812 (mm) cc_final: 0.7572 (mt) REVERT: Bh 312 ASP cc_start: 0.8322 (t0) cc_final: 0.7989 (t0) REVERT: Bh 425 ASN cc_start: 0.8510 (p0) cc_final: 0.7861 (p0) REVERT: Bh 429 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7177 (mp10) outliers start: 222 outliers final: 167 residues processed: 1330 average time/residue: 0.2314 time to fit residues: 506.7583 Evaluate side-chains 1388 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1184 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 391 VAL Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 387 LYS Chi-restraints excluded: chain Ac residue 266 LEU Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 391 VAL Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 420 SER Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 262 LYS Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 378 LEU Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 286 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 369 HIS Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ag residue 425 ASN Chi-restraints excluded: chain Ag residue 450 MET Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 309 LYS Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 280 SER Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 427 ILE Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Aj residue 445 LEU Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 378 LEU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 280 SER Chi-restraints excluded: chain Al residue 305 GLU Chi-restraints excluded: chain Al residue 324 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 445 LEU Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 391 VAL Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 427 ILE Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 369 HIS Chi-restraints excluded: chain An residue 385 GLU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 424 LEU Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 438 SER Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 389 SER Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain As residue 391 VAL Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 298 GLU Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 444 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Au residue 445 LEU Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 439 GLU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 280 SER Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 310 VAL Chi-restraints excluded: chain Ax residue 380 THR Chi-restraints excluded: chain Ax residue 384 HIS Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 431 LEU Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 378 LEU Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 378 LEU Chi-restraints excluded: chain Bb residue 383 SER Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 281 VAL Chi-restraints excluded: chain Bc residue 373 THR Chi-restraints excluded: chain Bc residue 420 SER Chi-restraints excluded: chain Bc residue 445 LEU Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 321 GLU Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 391 VAL Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 282 LEU Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 384 HIS Chi-restraints excluded: chain Bf residue 420 SER Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 310 VAL Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Chi-restraints excluded: chain Bh residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 434 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 381 optimal weight: 0.9990 chunk 427 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 457 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 428 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 294 GLN Ac 429 GLN Ad 328 ASN ** Ae 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 369 HIS ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 294 GLN Ao 369 HIS Ap 328 ASN As 369 HIS ** Bb 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 369 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.234572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4097 r_free = 0.4097 target = 0.166531 restraints weight = 31214.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165260 restraints weight = 23698.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165367 restraints weight = 16166.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166528 restraints weight = 13732.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.167310 restraints weight = 10980.548| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38930 Z= 0.213 Angle : 0.619 8.772 52564 Z= 0.322 Chirality : 0.044 0.319 6188 Planarity : 0.003 0.035 6902 Dihedral : 5.544 59.881 5363 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.09 % Allowed : 22.34 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.13), residues: 4692 helix: 2.06 (0.14), residues: 1294 sheet: -2.51 (0.10), residues: 2314 loop : -2.73 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAa 374 TYR 0.024 0.002 TYRAv 291 PHE 0.017 0.002 PHEAb 311 HIS 0.006 0.001 HISAu 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (38930) covalent geometry : angle 0.61869 / 0.32 (52564) hydrogen bonds : bond 0.03303 / 2.21 ( 1783) hydrogen bonds : angle 5.28881 / 3.68 ( 5061) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 1267 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 261 ARG cc_start: 0.7854 (tmm160) cc_final: 0.7243 (tmm160) REVERT: Aa 272 GLU cc_start: 0.8732 (tp30) cc_final: 0.8513 (tp30) REVERT: Ab 283 ILE cc_start: 0.9124 (mm) cc_final: 0.8860 (mt) REVERT: Ab 429 GLN cc_start: 0.7665 (mp10) cc_final: 0.7405 (mp10) REVERT: Ac 262 LYS cc_start: 0.9111 (tptm) cc_final: 0.8861 (tttt) REVERT: Ac 296 ASP cc_start: 0.7821 (t0) cc_final: 0.7470 (t0) REVERT: Ac 309 LYS cc_start: 0.8548 (ttmm) cc_final: 0.7618 (mttm) REVERT: Ad 305 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: Ad 379 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7510 (t0) REVERT: Ae 272 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8268 (mm-30) REVERT: Ae 448 LEU cc_start: 0.9018 (mp) cc_final: 0.8746 (mt) REVERT: Af 321 GLU cc_start: 0.8220 (tp30) cc_final: 0.7612 (mt-10) REVERT: Af 385 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7339 (tm-30) REVERT: Af 444 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7184 (tt) REVERT: Ag 369 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: Ag 425 ASN cc_start: 0.8706 (p0) cc_final: 0.7924 (p0) REVERT: Ag 429 GLN cc_start: 0.7439 (mp10) cc_final: 0.7060 (mp10) REVERT: Ah 309 LYS cc_start: 0.8269 (tttm) cc_final: 0.7543 (mttp) REVERT: Ah 312 ASP cc_start: 0.8401 (t70) cc_final: 0.7923 (t0) REVERT: Ah 319 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7535 (ttm-80) REVERT: Ai 309 LYS cc_start: 0.8388 (tttt) cc_final: 0.7626 (mttp) REVERT: Ai 376 TYR cc_start: 0.7885 (m-80) cc_final: 0.7617 (m-10) REVERT: Ai 429 GLN cc_start: 0.7994 (pp30) cc_final: 0.7647 (mp10) REVERT: Aj 262 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8675 (tptm) REVERT: Aj 296 ASP cc_start: 0.8390 (t70) cc_final: 0.7925 (t70) REVERT: Aj 321 GLU cc_start: 0.8437 (tp30) cc_final: 0.7992 (tp30) REVERT: Aj 328 ASN cc_start: 0.7532 (m-40) cc_final: 0.7079 (m-40) REVERT: Ak 266 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8829 (tm) REVERT: Ak 321 GLU cc_start: 0.7055 (tt0) cc_final: 0.6789 (tt0) REVERT: Ak 385 GLU cc_start: 0.7824 (tm-30) cc_final: 0.6831 (tm-30) REVERT: Ak 432 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7467 (mp) REVERT: Al 266 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8860 (tm) REVERT: Al 283 ILE cc_start: 0.9056 (mt) cc_final: 0.8806 (mp) REVERT: Al 296 ASP cc_start: 0.8191 (t70) cc_final: 0.7725 (t0) REVERT: Al 298 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7124 (mt-10) REVERT: Al 299 LEU cc_start: 0.9010 (mt) cc_final: 0.8713 (mt) REVERT: Al 305 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7100 (tp30) REVERT: Al 425 ASN cc_start: 0.8277 (p0) cc_final: 0.7613 (p0) REVERT: Al 429 GLN cc_start: 0.7269 (mp10) cc_final: 0.6796 (mp10) REVERT: Am 268 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8034 (tptp) REVERT: Am 296 ASP cc_start: 0.8628 (t0) cc_final: 0.8303 (t70) REVERT: Am 424 LEU cc_start: 0.8863 (mm) cc_final: 0.8628 (mm) REVERT: Am 429 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7782 (mm-40) REVERT: Am 431 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7050 (mm) REVERT: Am 441 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8079 (ttp80) REVERT: An 370 LYS cc_start: 0.8091 (mttt) cc_final: 0.7775 (mttp) REVERT: An 376 TYR cc_start: 0.7992 (m-80) cc_final: 0.7721 (m-80) REVERT: An 385 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: An 426 SER cc_start: 0.8224 (m) cc_final: 0.7647 (p) REVERT: Ao 305 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6833 (tt0) REVERT: Ao 385 GLU cc_start: 0.7945 (tm-30) cc_final: 0.6897 (tm-30) REVERT: Ao 387 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7687 (mmtp) REVERT: Ao 431 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7103 (mm) REVERT: Ap 385 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7229 (tm-30) REVERT: Ap 426 SER cc_start: 0.8642 (m) cc_final: 0.8014 (p) REVERT: Ap 429 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7472 (mm-40) REVERT: Aq 296 ASP cc_start: 0.8058 (t70) cc_final: 0.7732 (t0) REVERT: Aq 298 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6867 (mt-10) REVERT: Aq 299 LEU cc_start: 0.9053 (mp) cc_final: 0.8613 (mt) REVERT: Aq 301 PHE cc_start: 0.9128 (m-80) cc_final: 0.8659 (m-80) REVERT: Aq 385 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7325 (tm-30) REVERT: Aq 391 VAL cc_start: 0.8551 (m) cc_final: 0.8273 (p) REVERT: Ar 265 GLU cc_start: 0.8665 (mm-30) cc_final: 0.7855 (mt-10) REVERT: Ar 266 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9144 (tm) REVERT: Ar 272 GLU cc_start: 0.8536 (tp30) cc_final: 0.8305 (tp30) REVERT: Ar 376 TYR cc_start: 0.7975 (m-80) cc_final: 0.7097 (m-80) REVERT: Ar 377 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7780 (tm-30) REVERT: Ar 379 ASP cc_start: 0.8277 (p0) cc_final: 0.7890 (p0) REVERT: Ar 385 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6146 (tm-30) REVERT: Ar 386 ARG cc_start: 0.7692 (ttm110) cc_final: 0.7297 (ttm-80) REVERT: Ar 429 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7937 (mm-40) REVERT: As 296 ASP cc_start: 0.8359 (t70) cc_final: 0.8140 (t70) REVERT: As 309 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8328 (tttt) REVERT: As 378 LEU cc_start: 0.7990 (mt) cc_final: 0.7736 (mt) REVERT: As 385 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7350 (tm-30) REVERT: As 429 GLN cc_start: 0.7774 (mp10) cc_final: 0.7348 (mp10) REVERT: As 430 VAL cc_start: 0.5374 (t) cc_final: 0.5086 (t) REVERT: At 265 GLU cc_start: 0.8436 (tt0) cc_final: 0.8195 (tp30) REVERT: At 296 ASP cc_start: 0.8091 (t70) cc_final: 0.7526 (t0) REVERT: At 426 SER cc_start: 0.8060 (m) cc_final: 0.7684 (p) REVERT: At 429 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: At 446 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7536 (p0) REVERT: Au 282 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7209 (mm) REVERT: Au 305 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: Au 376 TYR cc_start: 0.7986 (m-80) cc_final: 0.7631 (m-80) REVERT: Au 379 ASP cc_start: 0.8139 (p0) cc_final: 0.7844 (p0) REVERT: Au 450 MET cc_start: 0.8200 (pmm) cc_final: 0.7222 (pmm) REVERT: Av 266 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8817 (tm) REVERT: Av 272 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7878 (tp30) REVERT: Av 376 TYR cc_start: 0.7947 (m-80) cc_final: 0.7724 (m-10) REVERT: Aw 428 ARG cc_start: 0.8445 (tpt90) cc_final: 0.8188 (ttt180) REVERT: Aw 432 ILE cc_start: 0.8336 (mm) cc_final: 0.8001 (mt) REVERT: Ax 309 LYS cc_start: 0.8852 (tttt) cc_final: 0.8120 (mttp) REVERT: Ax 393 ASN cc_start: 0.8689 (t0) cc_final: 0.8339 (t0) REVERT: Ax 425 ASN cc_start: 0.8369 (p0) cc_final: 0.7661 (p0) REVERT: Ax 429 GLN cc_start: 0.7442 (mp10) cc_final: 0.6810 (mp10) REVERT: Ay 384 HIS cc_start: 0.7623 (t70) cc_final: 0.7403 (t70) REVERT: Ay 385 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: Az 385 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6887 (tm-30) REVERT: Az 432 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7796 (mt) REVERT: Ba 321 GLU cc_start: 0.8619 (tp30) cc_final: 0.8343 (tp30) REVERT: Ba 374 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7998 (ttm110) REVERT: Ba 376 TYR cc_start: 0.7599 (m-10) cc_final: 0.7238 (m-10) REVERT: Ba 385 GLU cc_start: 0.7627 (tm-30) cc_final: 0.6626 (tm-30) REVERT: Ba 425 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7781 (p0) REVERT: Bb 272 GLU cc_start: 0.8539 (tp30) cc_final: 0.8179 (tp30) REVERT: Bb 376 TYR cc_start: 0.8390 (m-10) cc_final: 0.8109 (m-10) REVERT: Bb 423 ASP cc_start: 0.8152 (m-30) cc_final: 0.7678 (t0) REVERT: Bb 432 ILE cc_start: 0.8107 (mt) cc_final: 0.7813 (mp) REVERT: Bc 296 ASP cc_start: 0.7867 (t70) cc_final: 0.7483 (t0) REVERT: Bc 298 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7350 (mt-10) REVERT: Bc 393 ASN cc_start: 0.8669 (t0) cc_final: 0.8230 (p0) REVERT: Bc 425 ASN cc_start: 0.8501 (p0) cc_final: 0.8217 (p0) REVERT: Bc 429 GLN cc_start: 0.7291 (mp10) cc_final: 0.7034 (mp10) REVERT: Bd 296 ASP cc_start: 0.8151 (t0) cc_final: 0.7884 (t0) REVERT: Bd 395 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: Bd 429 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7491 (mm-40) REVERT: Bd 450 MET cc_start: 0.8924 (pmm) cc_final: 0.8420 (pmm) REVERT: Be 299 LEU cc_start: 0.9071 (mt) cc_final: 0.8556 (mt) REVERT: Be 426 SER cc_start: 0.8284 (m) cc_final: 0.7795 (p) REVERT: Be 446 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.6693 (p0) REVERT: Bf 300 ASP cc_start: 0.8533 (m-30) cc_final: 0.7012 (m-30) REVERT: Bf 309 LYS cc_start: 0.8472 (tttt) cc_final: 0.7728 (ttmm) REVERT: Bf 374 ARG cc_start: 0.7707 (ptp-110) cc_final: 0.7358 (ttm110) REVERT: Bf 393 ASN cc_start: 0.8662 (p0) cc_final: 0.8027 (p0) REVERT: Bg 268 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8030 (tptt) REVERT: Bg 300 ASP cc_start: 0.8811 (p0) cc_final: 0.8485 (p0) REVERT: Bg 305 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: Bg 309 LYS cc_start: 0.8571 (tttt) cc_final: 0.7374 (mttm) REVERT: Bg 324 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7482 (tt) REVERT: Bg 432 ILE cc_start: 0.7905 (mm) cc_final: 0.7637 (mp) REVERT: Bh 312 ASP cc_start: 0.8348 (t0) cc_final: 0.8078 (t0) REVERT: Bh 425 ASN cc_start: 0.8542 (p0) cc_final: 0.7983 (p0) outliers start: 218 outliers final: 167 residues processed: 1392 average time/residue: 0.2255 time to fit residues: 516.4333 Evaluate side-chains 1439 residues out of total 4284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1243 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 280 SER Chi-restraints excluded: chain Aa residue 380 THR Chi-restraints excluded: chain Aa residue 383 SER Chi-restraints excluded: chain Aa residue 384 HIS Chi-restraints excluded: chain Aa residue 391 VAL Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Ab residue 267 GLU Chi-restraints excluded: chain Ab residue 286 LEU Chi-restraints excluded: chain Ab residue 380 THR Chi-restraints excluded: chain Ab residue 424 LEU Chi-restraints excluded: chain Ac residue 374 ARG Chi-restraints excluded: chain Ac residue 419 LEU Chi-restraints excluded: chain Ac residue 429 GLN Chi-restraints excluded: chain Ac residue 450 MET Chi-restraints excluded: chain Ad residue 266 LEU Chi-restraints excluded: chain Ad residue 305 GLU Chi-restraints excluded: chain Ad residue 379 ASP Chi-restraints excluded: chain Ad residue 380 THR Chi-restraints excluded: chain Ad residue 387 LYS Chi-restraints excluded: chain Ad residue 391 VAL Chi-restraints excluded: chain Ad residue 420 SER Chi-restraints excluded: chain Ad residue 445 LEU Chi-restraints excluded: chain Ad residue 448 LEU Chi-restraints excluded: chain Ad residue 449 SER Chi-restraints excluded: chain Ae residue 262 LYS Chi-restraints excluded: chain Ae residue 266 LEU Chi-restraints excluded: chain Ae residue 379 ASP Chi-restraints excluded: chain Ae residue 380 THR Chi-restraints excluded: chain Ae residue 424 LEU Chi-restraints excluded: chain Ae residue 427 ILE Chi-restraints excluded: chain Af residue 444 LEU Chi-restraints excluded: chain Ag residue 266 LEU Chi-restraints excluded: chain Ag residue 267 GLU Chi-restraints excluded: chain Ag residue 282 LEU Chi-restraints excluded: chain Ag residue 286 LEU Chi-restraints excluded: chain Ag residue 310 VAL Chi-restraints excluded: chain Ag residue 369 HIS Chi-restraints excluded: chain Ag residue 379 ASP Chi-restraints excluded: chain Ag residue 380 THR Chi-restraints excluded: chain Ag residue 391 VAL Chi-restraints excluded: chain Ag residue 420 SER Chi-restraints excluded: chain Ag residue 450 MET Chi-restraints excluded: chain Ah residue 266 LEU Chi-restraints excluded: chain Ah residue 280 SER Chi-restraints excluded: chain Ah residue 319 ARG Chi-restraints excluded: chain Ah residue 369 HIS Chi-restraints excluded: chain Ah residue 378 LEU Chi-restraints excluded: chain Ah residue 380 THR Chi-restraints excluded: chain Ah residue 391 VAL Chi-restraints excluded: chain Ah residue 450 MET Chi-restraints excluded: chain Ai residue 282 LEU Chi-restraints excluded: chain Ai residue 380 THR Chi-restraints excluded: chain Ai residue 445 LEU Chi-restraints excluded: chain Aj residue 380 THR Chi-restraints excluded: chain Aj residue 438 SER Chi-restraints excluded: chain Aj residue 445 LEU Chi-restraints excluded: chain Ak residue 264 GLN Chi-restraints excluded: chain Ak residue 266 LEU Chi-restraints excluded: chain Ak residue 318 THR Chi-restraints excluded: chain Ak residue 378 LEU Chi-restraints excluded: chain Ak residue 380 THR Chi-restraints excluded: chain Ak residue 396 THR Chi-restraints excluded: chain Ak residue 432 ILE Chi-restraints excluded: chain Al residue 266 LEU Chi-restraints excluded: chain Al residue 280 SER Chi-restraints excluded: chain Al residue 305 GLU Chi-restraints excluded: chain Al residue 324 LEU Chi-restraints excluded: chain Al residue 379 ASP Chi-restraints excluded: chain Al residue 383 SER Chi-restraints excluded: chain Al residue 391 VAL Chi-restraints excluded: chain Al residue 431 LEU Chi-restraints excluded: chain Al residue 445 LEU Chi-restraints excluded: chain Al residue 449 SER Chi-restraints excluded: chain Am residue 266 LEU Chi-restraints excluded: chain Am residue 268 LYS Chi-restraints excluded: chain Am residue 286 LEU Chi-restraints excluded: chain Am residue 380 THR Chi-restraints excluded: chain Am residue 391 VAL Chi-restraints excluded: chain Am residue 396 THR Chi-restraints excluded: chain Am residue 431 LEU Chi-restraints excluded: chain Am residue 438 SER Chi-restraints excluded: chain Am residue 441 ARG Chi-restraints excluded: chain Am residue 448 LEU Chi-restraints excluded: chain An residue 385 GLU Chi-restraints excluded: chain An residue 391 VAL Chi-restraints excluded: chain An residue 445 LEU Chi-restraints excluded: chain An residue 448 LEU Chi-restraints excluded: chain Ao residue 369 HIS Chi-restraints excluded: chain Ao residue 379 ASP Chi-restraints excluded: chain Ao residue 380 THR Chi-restraints excluded: chain Ao residue 420 SER Chi-restraints excluded: chain Ao residue 431 LEU Chi-restraints excluded: chain Ao residue 432 ILE Chi-restraints excluded: chain Ap residue 286 LEU Chi-restraints excluded: chain Ap residue 318 THR Chi-restraints excluded: chain Ap residue 427 ILE Chi-restraints excluded: chain Ap residue 438 SER Chi-restraints excluded: chain Ap residue 444 LEU Chi-restraints excluded: chain Aq residue 304 VAL Chi-restraints excluded: chain Aq residue 425 ASN Chi-restraints excluded: chain Aq residue 438 SER Chi-restraints excluded: chain Aq residue 448 LEU Chi-restraints excluded: chain Ar residue 266 LEU Chi-restraints excluded: chain Ar residue 310 VAL Chi-restraints excluded: chain Ar residue 380 THR Chi-restraints excluded: chain Ar residue 396 THR Chi-restraints excluded: chain Ar residue 431 LEU Chi-restraints excluded: chain As residue 266 LEU Chi-restraints excluded: chain As residue 309 LYS Chi-restraints excluded: chain As residue 310 VAL Chi-restraints excluded: chain As residue 373 THR Chi-restraints excluded: chain As residue 380 THR Chi-restraints excluded: chain At residue 280 SER Chi-restraints excluded: chain At residue 429 GLN Chi-restraints excluded: chain At residue 431 LEU Chi-restraints excluded: chain At residue 446 ASN Chi-restraints excluded: chain Au residue 266 LEU Chi-restraints excluded: chain Au residue 280 SER Chi-restraints excluded: chain Au residue 282 LEU Chi-restraints excluded: chain Au residue 305 GLU Chi-restraints excluded: chain Au residue 380 THR Chi-restraints excluded: chain Au residue 383 SER Chi-restraints excluded: chain Au residue 438 SER Chi-restraints excluded: chain Av residue 266 LEU Chi-restraints excluded: chain Av residue 379 ASP Chi-restraints excluded: chain Av residue 380 THR Chi-restraints excluded: chain Av residue 391 VAL Chi-restraints excluded: chain Av residue 424 LEU Chi-restraints excluded: chain Av residue 431 LEU Chi-restraints excluded: chain Av residue 446 ASN Chi-restraints excluded: chain Aw residue 263 GLU Chi-restraints excluded: chain Aw residue 266 LEU Chi-restraints excluded: chain Aw residue 379 ASP Chi-restraints excluded: chain Aw residue 380 THR Chi-restraints excluded: chain Aw residue 446 ASN Chi-restraints excluded: chain Ax residue 267 GLU Chi-restraints excluded: chain Ax residue 282 LEU Chi-restraints excluded: chain Ax residue 310 VAL Chi-restraints excluded: chain Ax residue 380 THR Chi-restraints excluded: chain Ax residue 384 HIS Chi-restraints excluded: chain Ax residue 420 SER Chi-restraints excluded: chain Ax residue 450 MET Chi-restraints excluded: chain Ay residue 378 LEU Chi-restraints excluded: chain Ay residue 380 THR Chi-restraints excluded: chain Ay residue 383 SER Chi-restraints excluded: chain Ay residue 385 GLU Chi-restraints excluded: chain Ay residue 419 LEU Chi-restraints excluded: chain Az residue 280 SER Chi-restraints excluded: chain Az residue 305 GLU Chi-restraints excluded: chain Az residue 318 THR Chi-restraints excluded: chain Az residue 369 HIS Chi-restraints excluded: chain Az residue 379 ASP Chi-restraints excluded: chain Az residue 380 THR Chi-restraints excluded: chain Az residue 427 ILE Chi-restraints excluded: chain Az residue 432 ILE Chi-restraints excluded: chain Az residue 445 LEU Chi-restraints excluded: chain Ba residue 315 THR Chi-restraints excluded: chain Ba residue 420 SER Chi-restraints excluded: chain Ba residue 425 ASN Chi-restraints excluded: chain Ba residue 438 SER Chi-restraints excluded: chain Ba residue 450 MET Chi-restraints excluded: chain Bb residue 315 THR Chi-restraints excluded: chain Bb residue 318 THR Chi-restraints excluded: chain Bb residue 378 LEU Chi-restraints excluded: chain Bb residue 380 THR Chi-restraints excluded: chain Bb residue 383 SER Chi-restraints excluded: chain Bb residue 420 SER Chi-restraints excluded: chain Bb residue 448 LEU Chi-restraints excluded: chain Bc residue 373 THR Chi-restraints excluded: chain Bc residue 420 SER Chi-restraints excluded: chain Bd residue 379 ASP Chi-restraints excluded: chain Bd residue 380 THR Chi-restraints excluded: chain Bd residue 395 GLN Chi-restraints excluded: chain Bd residue 438 SER Chi-restraints excluded: chain Be residue 369 HIS Chi-restraints excluded: chain Be residue 380 THR Chi-restraints excluded: chain Be residue 385 GLU Chi-restraints excluded: chain Be residue 446 ASN Chi-restraints excluded: chain Bf residue 379 ASP Chi-restraints excluded: chain Bf residue 380 THR Chi-restraints excluded: chain Bf residue 384 HIS Chi-restraints excluded: chain Bf residue 420 SER Chi-restraints excluded: chain Bf residue 446 ASN Chi-restraints excluded: chain Bg residue 268 LYS Chi-restraints excluded: chain Bg residue 305 GLU Chi-restraints excluded: chain Bg residue 310 VAL Chi-restraints excluded: chain Bg residue 324 LEU Chi-restraints excluded: chain Bg residue 380 THR Chi-restraints excluded: chain Bg residue 401 VAL Chi-restraints excluded: chain Bg residue 420 SER Chi-restraints excluded: chain Bg residue 448 LEU Chi-restraints excluded: chain Bh residue 286 LEU Chi-restraints excluded: chain Bh residue 380 THR Chi-restraints excluded: chain Bh residue 438 SER Chi-restraints excluded: chain Bh residue 445 LEU Chi-restraints excluded: chain Bh residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 400 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 434 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ac 429 GLN ** Ae 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 429 GLN An 369 HIS Ao 369 HIS ** Bb 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 369 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.235844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160994 restraints weight = 31381.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166249 restraints weight = 17652.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.168921 restraints weight = 12767.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170083 restraints weight = 10332.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.170286 restraints weight = 9699.173| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38930 Z= 0.181 Angle : 0.613 9.205 52564 Z= 0.319 Chirality : 0.044 0.313 6188 Planarity : 0.003 0.034 6902 Dihedral : 5.518 58.850 5363 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.93 % Allowed : 22.90 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.12), residues: 4692 helix: 2.46 (0.14), residues: 1228 sheet: -2.47 (0.10), residues: 2280 loop : -3.01 (0.15), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAr 374 TYR 0.024 0.002 TYRAv 291 PHE 0.018 0.002 PHEAs 301 HIS 0.006 0.001 HISAp 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (38930) covalent geometry : angle 0.61327 / 0.32 (52564) hydrogen bonds : bond 0.03205 / 2.15 ( 1783) hydrogen bonds : angle 5.29683 / 3.68 ( 5061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10742.65 seconds wall clock time: 184 minutes 15.23 seconds (11055.23 seconds total)