Starting phenix.real_space_refine on Fri Jan 24 17:53:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3x_42959/01_2025/8v3x_42959.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.005 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 306 5.16 5 C 48510 2.51 5 N 12366 2.21 5 O 14766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 291 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 75948 Number of models: 1 Model: "" Number of chains: 42 Chain: "g" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "d" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "i" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "A" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "B" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "V" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "S" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "Y" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "K" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "W" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "T" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "Z" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "I" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "L" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "F" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "C" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "D" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "X" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "U" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "a" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "J" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "Q" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "P" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "R" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "N" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "O" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "z" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "b" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "q" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "j" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "r" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "k" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "e" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "c" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "s" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "l" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "n" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2738 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 6, 'TRANS': 345} Chain: "m" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Time building chain proxies: 32.65, per 1000 atoms: 0.43 Number of scatterers: 75948 At special positions: 0 Unit cell: (202.95, 204.05, 182.05, 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 306 16.00 O 14766 8.00 N 12366 7.00 C 48510 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: 13.90 Conformation dependent library (CDL) restraints added in 7.6 seconds 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18120 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 120 sheets defined 30.2% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.26 Creating SS restraints... Processing helix chain 'g' and resid 54 through 66 removed outlier: 3.624A pdb=" N MET g 66 " --> pdb=" O ASN g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 94 removed outlier: 3.557A pdb=" N PHE g 92 " --> pdb=" O THR g 88 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 124 Processing helix chain 'g' and resid 160 through 162 No H-bonds generated for 'chain 'g' and resid 160 through 162' Processing helix chain 'g' and resid 163 through 173 Processing helix chain 'g' and resid 195 through 206 Processing helix chain 'g' and resid 234 through 238 Processing helix chain 'g' and resid 239 through 261 Processing helix chain 'g' and resid 268 through 289 removed outlier: 3.553A pdb=" N SER g 289 " --> pdb=" O GLU g 285 " (cutoff:3.500A) Processing helix chain 'g' and resid 301 through 312 Processing helix chain 'g' and resid 320 through 327 Processing helix chain 'd' and resid 54 through 65 removed outlier: 3.861A pdb=" N TYR d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE d 61 " --> pdb=" O ASN d 57 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN d 62 " --> pdb=" O LYS d 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 94 removed outlier: 4.192A pdb=" N ALA d 89 " --> pdb=" O ASP d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 124 Processing helix chain 'd' and resid 163 through 174 Processing helix chain 'd' and resid 195 through 205 Processing helix chain 'd' and resid 234 through 238 Processing helix chain 'd' and resid 239 through 261 Processing helix chain 'd' and resid 268 through 289 Processing helix chain 'd' and resid 301 through 312 Processing helix chain 'd' and resid 320 through 326 Processing helix chain 'i' and resid 5 through 9 Processing helix chain 'i' and resid 11 through 13 No H-bonds generated for 'chain 'i' and resid 11 through 13' Processing helix chain 'i' and resid 69 through 82 removed outlier: 5.843A pdb=" N GLU i 77 " --> pdb=" O LYS i 73 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS i 78 " --> pdb=" O LEU i 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 69 through 82 removed outlier: 5.941A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 69 through 82 removed outlier: 5.718A pdb=" N GLU B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 66 removed outlier: 3.606A pdb=" N MET V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 94 removed outlier: 3.769A pdb=" N PHE V 92 " --> pdb=" O THR V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 124 Processing helix chain 'V' and resid 163 through 173 Processing helix chain 'V' and resid 195 through 206 Processing helix chain 'V' and resid 234 through 238 Processing helix chain 'V' and resid 239 through 261 Processing helix chain 'V' and resid 268 through 289 removed outlier: 3.507A pdb=" N SER V 289 " --> pdb=" O GLU V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 312 Processing helix chain 'V' and resid 320 through 326 Processing helix chain 'S' and resid 54 through 65 removed outlier: 3.869A pdb=" N TYR S 60 " --> pdb=" O GLU S 56 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 94 removed outlier: 4.244A pdb=" N ALA S 89 " --> pdb=" O ASP S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 124 Processing helix chain 'S' and resid 163 through 174 Processing helix chain 'S' and resid 195 through 205 Processing helix chain 'S' and resid 234 through 238 Processing helix chain 'S' and resid 239 through 261 Processing helix chain 'S' and resid 268 through 289 Processing helix chain 'S' and resid 301 through 313 Processing helix chain 'S' and resid 320 through 326 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 11 through 13 No H-bonds generated for 'chain 'Y' and resid 11 through 13' Processing helix chain 'Y' and resid 69 through 82 removed outlier: 5.831A pdb=" N GLU Y 77 " --> pdb=" O LYS Y 73 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS Y 78 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 11 through 13 No H-bonds generated for 'chain 'H' and resid 11 through 13' Processing helix chain 'H' and resid 69 through 82 removed outlier: 5.933A pdb=" N GLU H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 69 through 82 removed outlier: 5.691A pdb=" N GLU K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 80 " --> pdb=" O GLY K 76 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 66 removed outlier: 3.654A pdb=" N MET W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 94 removed outlier: 3.529A pdb=" N PHE W 92 " --> pdb=" O THR W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 125 Processing helix chain 'W' and resid 163 through 173 Processing helix chain 'W' and resid 195 through 206 Processing helix chain 'W' and resid 234 through 238 Processing helix chain 'W' and resid 239 through 261 Processing helix chain 'W' and resid 268 through 289 removed outlier: 3.550A pdb=" N SER W 289 " --> pdb=" O GLU W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 312 Processing helix chain 'W' and resid 320 through 327 Processing helix chain 'T' and resid 54 through 65 removed outlier: 3.838A pdb=" N TYR T 60 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE T 61 " --> pdb=" O ASN T 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN T 62 " --> pdb=" O LYS T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 94 removed outlier: 4.277A pdb=" N ALA T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 124 Processing helix chain 'T' and resid 163 through 174 Processing helix chain 'T' and resid 195 through 205 Processing helix chain 'T' and resid 234 through 238 Processing helix chain 'T' and resid 239 through 261 Processing helix chain 'T' and resid 268 through 289 Processing helix chain 'T' and resid 301 through 312 Processing helix chain 'T' and resid 320 through 326 Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 11 through 13 No H-bonds generated for 'chain 'Z' and resid 11 through 13' Processing helix chain 'Z' and resid 69 through 82 removed outlier: 5.823A pdb=" N GLU Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS Z 80 " --> pdb=" O GLY Z 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG Z 81 " --> pdb=" O GLU Z 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 11 through 13 No H-bonds generated for 'chain 'I' and resid 11 through 13' Processing helix chain 'I' and resid 69 through 82 removed outlier: 5.959A pdb=" N GLU I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LYS I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 11 through 13 No H-bonds generated for 'chain 'L' and resid 11 through 13' Processing helix chain 'L' and resid 69 through 82 removed outlier: 5.666A pdb=" N GLU L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS L 80 " --> pdb=" O GLY L 76 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.620A pdb=" N MET F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.553A pdb=" N PHE F 92 " --> pdb=" O THR F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 124 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'F' and resid 195 through 206 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 239 through 261 Processing helix chain 'F' and resid 268 through 289 removed outlier: 3.553A pdb=" N SER F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 320 through 326 Processing helix chain 'E' and resid 54 through 65 removed outlier: 3.862A pdb=" N TYR E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 4.200A pdb=" N ALA E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 124 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 239 through 261 Processing helix chain 'E' and resid 268 through 289 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 69 through 82 removed outlier: 5.841A pdb=" N GLU G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 80 " --> pdb=" O GLY G 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 69 through 82 removed outlier: 5.942A pdb=" N GLU C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 69 through 82 removed outlier: 5.720A pdb=" N GLU D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 66 removed outlier: 3.586A pdb=" N MET X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 94 removed outlier: 3.770A pdb=" N PHE X 92 " --> pdb=" O THR X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 124 Processing helix chain 'X' and resid 159 through 162 Processing helix chain 'X' and resid 163 through 173 Processing helix chain 'X' and resid 195 through 206 Processing helix chain 'X' and resid 234 through 238 Processing helix chain 'X' and resid 239 through 261 Processing helix chain 'X' and resid 268 through 289 removed outlier: 3.509A pdb=" N SER X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 312 Processing helix chain 'X' and resid 320 through 326 Processing helix chain 'U' and resid 54 through 65 removed outlier: 3.871A pdb=" N TYR U 60 " --> pdb=" O GLU U 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE U 61 " --> pdb=" O ASN U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 94 removed outlier: 4.274A pdb=" N ALA U 89 " --> pdb=" O ASP U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 124 Processing helix chain 'U' and resid 163 through 174 Processing helix chain 'U' and resid 195 through 205 Processing helix chain 'U' and resid 234 through 238 Processing helix chain 'U' and resid 239 through 261 Processing helix chain 'U' and resid 268 through 289 Processing helix chain 'U' and resid 301 through 313 Processing helix chain 'U' and resid 320 through 326 Processing helix chain 'a' and resid 5 through 9 Processing helix chain 'a' and resid 11 through 13 No H-bonds generated for 'chain 'a' and resid 11 through 13' Processing helix chain 'a' and resid 69 through 82 removed outlier: 5.826A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 11 through 13 No H-bonds generated for 'chain 'J' and resid 11 through 13' Processing helix chain 'J' and resid 69 through 82 removed outlier: 5.945A pdb=" N GLU J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 11 through 13 No H-bonds generated for 'chain 'M' and resid 11 through 13' Processing helix chain 'M' and resid 69 through 82 removed outlier: 5.698A pdb=" N GLU M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS M 80 " --> pdb=" O GLY M 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 removed outlier: 3.657A pdb=" N MET Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 94 removed outlier: 3.525A pdb=" N PHE Q 92 " --> pdb=" O THR Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 124 Processing helix chain 'Q' and resid 163 through 173 Processing helix chain 'Q' and resid 195 through 206 Processing helix chain 'Q' and resid 234 through 238 Processing helix chain 'Q' and resid 239 through 261 Processing helix chain 'Q' and resid 268 through 289 removed outlier: 3.550A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 312 Processing helix chain 'Q' and resid 320 through 327 Processing helix chain 'P' and resid 54 through 65 removed outlier: 3.835A pdb=" N TYR P 60 " --> pdb=" O GLU P 56 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE P 61 " --> pdb=" O ASN P 57 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 94 removed outlier: 4.329A pdb=" N ALA P 89 " --> pdb=" O ASP P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 124 Processing helix chain 'P' and resid 163 through 174 Processing helix chain 'P' and resid 195 through 205 Processing helix chain 'P' and resid 234 through 238 Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 268 through 289 Processing helix chain 'P' and resid 301 through 312 Processing helix chain 'P' and resid 320 through 326 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 11 through 13 No H-bonds generated for 'chain 'R' and resid 11 through 13' Processing helix chain 'R' and resid 69 through 82 removed outlier: 5.828A pdb=" N GLU R 77 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS R 80 " --> pdb=" O GLY R 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 11 through 13 No H-bonds generated for 'chain 'N' and resid 11 through 13' Processing helix chain 'N' and resid 69 through 82 removed outlier: 5.958A pdb=" N GLU N 77 " --> pdb=" O LYS N 73 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS N 78 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 11 through 13 No H-bonds generated for 'chain 'O' and resid 11 through 13' Processing helix chain 'O' and resid 69 through 82 removed outlier: 5.665A pdb=" N GLU O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS O 80 " --> pdb=" O GLY O 76 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'z' and resid 54 through 65 removed outlier: 3.623A pdb=" N TYR z 60 " --> pdb=" O GLU z 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE z 61 " --> pdb=" O ASN z 57 " (cutoff:3.500A) Processing helix chain 'z' and resid 85 through 94 removed outlier: 4.128A pdb=" N ALA z 89 " --> pdb=" O ASP z 85 " (cutoff:3.500A) Processing helix chain 'z' and resid 107 through 124 Processing helix chain 'z' and resid 163 through 173 Processing helix chain 'z' and resid 195 through 206 Processing helix chain 'z' and resid 234 through 238 Processing helix chain 'z' and resid 239 through 261 Processing helix chain 'z' and resid 268 through 289 Processing helix chain 'z' and resid 301 through 313 Processing helix chain 'z' and resid 320 through 326 Processing helix chain 'b' and resid 5 through 9 Processing helix chain 'b' and resid 11 through 13 No H-bonds generated for 'chain 'b' and resid 11 through 13' Processing helix chain 'b' and resid 69 through 82 removed outlier: 5.986A pdb=" N GLU b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS b 78 " --> pdb=" O LEU b 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 54 through 65 removed outlier: 3.599A pdb=" N TYR q 60 " --> pdb=" O GLU q 56 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE q 61 " --> pdb=" O ASN q 57 " (cutoff:3.500A) Processing helix chain 'q' and resid 85 through 94 removed outlier: 4.091A pdb=" N ALA q 89 " --> pdb=" O ASP q 85 " (cutoff:3.500A) Processing helix chain 'q' and resid 107 through 124 Processing helix chain 'q' and resid 163 through 173 Processing helix chain 'q' and resid 195 through 206 Processing helix chain 'q' and resid 234 through 238 Processing helix chain 'q' and resid 239 through 261 Processing helix chain 'q' and resid 268 through 289 Processing helix chain 'q' and resid 301 through 313 Processing helix chain 'q' and resid 320 through 326 Processing helix chain 'j' and resid 5 through 9 Processing helix chain 'j' and resid 11 through 13 No H-bonds generated for 'chain 'j' and resid 11 through 13' Processing helix chain 'j' and resid 69 through 82 removed outlier: 5.940A pdb=" N GLU j 77 " --> pdb=" O LYS j 73 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS j 78 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 54 through 65 removed outlier: 3.627A pdb=" N TYR r 60 " --> pdb=" O GLU r 56 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE r 61 " --> pdb=" O ASN r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.046A pdb=" N ALA r 89 " --> pdb=" O ASP r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 107 through 124 Processing helix chain 'r' and resid 159 through 173 removed outlier: 4.495A pdb=" N SER r 165 " --> pdb=" O ASP r 161 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG r 166 " --> pdb=" O GLU r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 195 through 206 Processing helix chain 'r' and resid 234 through 238 Processing helix chain 'r' and resid 239 through 261 Processing helix chain 'r' and resid 268 through 289 Processing helix chain 'r' and resid 301 through 313 Processing helix chain 'r' and resid 320 through 326 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 11 through 13 No H-bonds generated for 'chain 'k' and resid 11 through 13' Processing helix chain 'k' and resid 69 through 82 removed outlier: 5.951A pdb=" N GLU k 77 " --> pdb=" O LYS k 73 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 65 removed outlier: 3.634A pdb=" N TYR e 60 " --> pdb=" O GLU e 56 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE e 61 " --> pdb=" O ASN e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 94 removed outlier: 4.100A pdb=" N ALA e 89 " --> pdb=" O ASP e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 124 Processing helix chain 'e' and resid 163 through 173 Processing helix chain 'e' and resid 195 through 206 Processing helix chain 'e' and resid 234 through 238 Processing helix chain 'e' and resid 239 through 261 Processing helix chain 'e' and resid 268 through 289 Processing helix chain 'e' and resid 301 through 313 Processing helix chain 'e' and resid 320 through 326 Processing helix chain 'c' and resid 5 through 9 Processing helix chain 'c' and resid 11 through 13 No H-bonds generated for 'chain 'c' and resid 11 through 13' Processing helix chain 'c' and resid 69 through 82 removed outlier: 5.985A pdb=" N GLU c 77 " --> pdb=" O LYS c 73 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS c 78 " --> pdb=" O LEU c 74 " (cutoff:3.500A) Processing helix chain 's' and resid 54 through 65 removed outlier: 3.584A pdb=" N TYR s 60 " --> pdb=" O GLU s 56 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 85 through 94 removed outlier: 4.086A pdb=" N ALA s 89 " --> pdb=" O ASP s 85 " (cutoff:3.500A) Processing helix chain 's' and resid 107 through 124 Processing helix chain 's' and resid 163 through 173 Processing helix chain 's' and resid 195 through 206 Processing helix chain 's' and resid 234 through 238 Processing helix chain 's' and resid 239 through 261 Processing helix chain 's' and resid 268 through 289 Processing helix chain 's' and resid 301 through 313 Processing helix chain 's' and resid 320 through 326 Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 11 through 13 No H-bonds generated for 'chain 'l' and resid 11 through 13' Processing helix chain 'l' and resid 69 through 82 removed outlier: 5.942A pdb=" N GLU l 77 " --> pdb=" O LYS l 73 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS l 78 " --> pdb=" O LEU l 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 65 removed outlier: 3.631A pdb=" N TYR n 60 " --> pdb=" O GLU n 56 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE n 61 " --> pdb=" O ASN n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 94 removed outlier: 4.033A pdb=" N ALA n 89 " --> pdb=" O ASP n 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 107 through 124 Processing helix chain 'n' and resid 163 through 173 Processing helix chain 'n' and resid 195 through 206 Processing helix chain 'n' and resid 234 through 238 Processing helix chain 'n' and resid 239 through 261 Processing helix chain 'n' and resid 268 through 289 Processing helix chain 'n' and resid 301 through 313 Processing helix chain 'n' and resid 320 through 326 Processing helix chain 'm' and resid 5 through 9 Processing helix chain 'm' and resid 11 through 13 No H-bonds generated for 'chain 'm' and resid 11 through 13' Processing helix chain 'm' and resid 69 through 82 removed outlier: 5.951A pdb=" N GLU m 77 " --> pdb=" O LYS m 73 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS m 78 " --> pdb=" O LEU m 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'g' and resid 8 through 13 removed outlier: 6.425A pdb=" N ASN g 9 " --> pdb=" O LEU Q 350 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE Q 352 " --> pdb=" O ASN g 9 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER g 11 " --> pdb=" O ILE Q 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g' and resid 39 through 43 removed outlier: 3.731A pdb=" N GLY g 39 " --> pdb=" O VAL g 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU g 101 " --> pdb=" O VAL g 132 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA g 131 " --> pdb=" O ILE g 144 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE g 146 " --> pdb=" O ALA g 131 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU g 133 " --> pdb=" O PHE g 146 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU g 208 " --> pdb=" O ILE g 143 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN g 145 " --> pdb=" O LEU g 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g' and resid 210 through 212 Processing sheet with id=AA4, first strand: chain 'g' and resid 297 through 300 removed outlier: 6.530A pdb=" N ASN z 9 " --> pdb=" O LEU n 350 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE n 352 " --> pdb=" O ASN z 9 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N SER z 11 " --> pdb=" O ILE n 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 297 through 300 Processing sheet with id=AA6, first strand: chain 'd' and resid 8 through 13 removed outlier: 6.461A pdb=" N ASN d 9 " --> pdb=" O LEU P 350 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE P 352 " --> pdb=" O ASN d 9 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER d 11 " --> pdb=" O ILE P 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'd' and resid 39 through 43 removed outlier: 6.652A pdb=" N ILE d 28 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR d 78 " --> pdb=" O ILE d 28 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET d 30 " --> pdb=" O TYR d 78 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE d 80 " --> pdb=" O MET d 30 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU d 32 " --> pdb=" O ILE d 80 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR d 100 " --> pdb=" O ILE d 27 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU d 101 " --> pdb=" O VAL d 132 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY d 134 " --> pdb=" O LEU d 101 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA d 131 " --> pdb=" O ILE d 144 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE d 146 " --> pdb=" O ALA d 131 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU d 133 " --> pdb=" O PHE d 146 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU d 208 " --> pdb=" O ILE d 143 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN d 145 " --> pdb=" O LEU d 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 156 through 158 removed outlier: 7.203A pdb=" N LEU d 152 " --> pdb=" O VAL d 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 184 through 185 removed outlier: 4.421A pdb=" N ILE d 217 " --> pdb=" O LEU d 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 348 through 353 Processing sheet with id=AB2, first strand: chain 'i' and resid 22 through 23 removed outlier: 5.613A pdb=" N PHE i 87 " --> pdb=" O ASN i 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU i 135 " --> pdb=" O LYS i 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'i' and resid 22 through 23 removed outlier: 5.613A pdb=" N PHE i 87 " --> pdb=" O ASN i 108 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY i 58 " --> pdb=" O PHE i 133 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR i 51 " --> pdb=" O ILE i 41 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE i 41 " --> pdb=" O THR i 51 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR i 53 " --> pdb=" O GLU i 39 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU i 39 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY i 55 " --> pdb=" O THR i 37 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR i 65 " --> pdb=" O VAL i 27 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL i 27 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET i 34 " --> pdb=" O THR Y 115 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR Y 115 " --> pdb=" O MET i 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE i 36 " --> pdb=" O ASP Y 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP Y 113 " --> pdb=" O PHE i 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 113 through 120 removed outlier: 6.412A pdb=" N ASP i 113 " --> pdb=" O PHE R 36 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE R 36 " --> pdb=" O ASP i 113 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR i 115 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET R 34 " --> pdb=" O THR i 115 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL R 27 " --> pdb=" O TYR R 65 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR R 65 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY R 55 " --> pdb=" O THR R 37 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU R 39 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR R 53 " --> pdb=" O GLU R 39 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE R 41 " --> pdb=" O THR R 51 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR R 51 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N PHE R 87 " --> pdb=" O ASN R 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 113 through 120 removed outlier: 6.412A pdb=" N ASP i 113 " --> pdb=" O PHE R 36 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE R 36 " --> pdb=" O ASP i 113 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR i 115 " --> pdb=" O MET R 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET R 34 " --> pdb=" O THR i 115 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL R 27 " --> pdb=" O TYR R 65 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR R 65 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY R 55 " --> pdb=" O THR R 37 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU R 39 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR R 53 " --> pdb=" O GLU R 39 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE R 41 " --> pdb=" O THR R 51 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR R 51 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU R 135 " --> pdb=" O LYS R 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.643A pdb=" N PHE A 87 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.643A pdb=" N PHE A 87 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 58 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR A 51 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A 40 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR A 53 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS A 38 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 55 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 36 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LYS A 57 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET A 34 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS A 59 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA A 32 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 61 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A 30 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 63 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LYS A 28 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU H 120 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 30 " --> pdb=" O ASP H 118 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP H 118 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 32 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 113 through 120 removed outlier: 6.552A pdb=" N ALA N 32 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 118 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE N 30 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 120 " --> pdb=" O LYS N 28 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LYS N 28 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR N 63 " --> pdb=" O LYS N 28 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE N 30 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER N 61 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA N 32 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS N 59 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET N 34 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS N 57 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE N 36 " --> pdb=" O GLY N 55 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY N 55 " --> pdb=" O PHE N 36 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS N 38 " --> pdb=" O TYR N 53 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR N 53 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP N 40 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR N 51 " --> pdb=" O ASP N 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY N 58 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N PHE N 87 " --> pdb=" O ASN N 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 113 through 120 removed outlier: 6.552A pdb=" N ALA N 32 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 118 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE N 30 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 120 " --> pdb=" O LYS N 28 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LYS N 28 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR N 63 " --> pdb=" O LYS N 28 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE N 30 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER N 61 " --> pdb=" O PHE N 30 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA N 32 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS N 59 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET N 34 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS N 57 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE N 36 " --> pdb=" O GLY N 55 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY N 55 " --> pdb=" O PHE N 36 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS N 38 " --> pdb=" O TYR N 53 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR N 53 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP N 40 " --> pdb=" O THR N 51 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR N 51 " --> pdb=" O ASP N 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY N 58 " --> pdb=" O PHE N 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.722A pdb=" N PHE B 87 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 135 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.722A pdb=" N PHE B 87 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 58 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR B 51 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR B 53 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS B 38 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 55 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 36 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS B 57 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET B 34 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS B 59 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA B 32 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER B 61 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE B 30 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR B 63 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS B 28 " --> pdb=" O GLU K 120 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU K 120 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 30 " --> pdb=" O ASP K 118 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP K 118 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 32 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 113 through 120 removed outlier: 6.529A pdb=" N ALA O 32 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 118 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE O 30 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU B 120 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS O 28 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR O 63 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE O 30 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER O 61 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA O 32 " --> pdb=" O LYS O 59 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS O 59 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET O 34 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS O 57 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE O 36 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY O 55 " --> pdb=" O PHE O 36 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS O 38 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR O 53 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP O 40 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR O 51 " --> pdb=" O ASP O 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY O 58 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE O 87 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 113 through 120 removed outlier: 6.529A pdb=" N ALA O 32 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 118 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE O 30 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU B 120 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS O 28 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR O 63 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE O 30 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER O 61 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA O 32 " --> pdb=" O LYS O 59 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS O 59 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET O 34 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS O 57 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE O 36 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY O 55 " --> pdb=" O PHE O 36 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS O 38 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR O 53 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP O 40 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR O 51 " --> pdb=" O ASP O 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY O 58 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU O 135 " --> pdb=" O LYS O 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 39 through 43 removed outlier: 3.740A pdb=" N GLY V 39 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE V 28 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TYR V 78 " --> pdb=" O ILE V 28 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET V 30 " --> pdb=" O TYR V 78 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE V 80 " --> pdb=" O MET V 30 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU V 32 " --> pdb=" O ILE V 80 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU V 101 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA V 131 " --> pdb=" O ILE V 144 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE V 146 " --> pdb=" O ALA V 131 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU V 133 " --> pdb=" O PHE V 146 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU V 208 " --> pdb=" O ILE V 143 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN V 145 " --> pdb=" O LEU V 208 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 210 through 212 Processing sheet with id=AC7, first strand: chain 'V' and resid 297 through 300 Processing sheet with id=AC8, first strand: chain 'S' and resid 297 through 300 Processing sheet with id=AC9, first strand: chain 'S' and resid 39 through 43 removed outlier: 6.632A pdb=" N ILE S 28 " --> pdb=" O LEU S 76 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR S 78 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET S 30 " --> pdb=" O TYR S 78 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE S 80 " --> pdb=" O MET S 30 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU S 32 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR S 100 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU S 101 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY S 134 " --> pdb=" O LEU S 101 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA S 131 " --> pdb=" O ILE S 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE S 146 " --> pdb=" O ALA S 131 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU S 133 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU S 208 " --> pdb=" O ILE S 143 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN S 145 " --> pdb=" O LEU S 208 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 156 through 158 removed outlier: 7.317A pdb=" N LEU S 152 " --> pdb=" O VAL S 189 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 184 through 185 removed outlier: 4.518A pdb=" N ILE S 217 " --> pdb=" O LEU S 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 348 through 353 Processing sheet with id=AD4, first strand: chain 'Y' and resid 22 through 23 removed outlier: 5.647A pdb=" N PHE Y 87 " --> pdb=" O ASN Y 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU Y 135 " --> pdb=" O LYS Y 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 22 through 23 removed outlier: 5.647A pdb=" N PHE Y 87 " --> pdb=" O ASN Y 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY Y 58 " --> pdb=" O PHE Y 133 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR Y 51 " --> pdb=" O ILE Y 41 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE Y 41 " --> pdb=" O THR Y 51 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR Y 53 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU Y 39 " --> pdb=" O TYR Y 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY Y 55 " --> pdb=" O THR Y 37 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR Y 65 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL Y 27 " --> pdb=" O TYR Y 65 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET Y 34 " --> pdb=" O THR Z 115 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR Z 115 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE Y 36 " --> pdb=" O ASP Z 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP Z 113 " --> pdb=" O PHE Y 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.625A pdb=" N PHE H 87 " --> pdb=" O ASN H 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.625A pdb=" N PHE H 87 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY H 58 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR H 51 " --> pdb=" O ASP H 40 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP H 40 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR H 53 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS H 38 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY H 55 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE H 36 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LYS H 57 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET H 34 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS H 59 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA H 32 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER H 61 " --> pdb=" O PHE H 30 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE H 30 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR H 63 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N LYS H 28 " --> pdb=" O GLU I 120 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU I 120 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE H 30 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP I 118 " --> pdb=" O PHE H 30 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA H 32 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.727A pdb=" N PHE K 87 " --> pdb=" O ASN K 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU K 135 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 22 through 23 removed outlier: 5.727A pdb=" N PHE K 87 " --> pdb=" O ASN K 108 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 58 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR K 51 " --> pdb=" O ASP K 40 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP K 40 " --> pdb=" O THR K 51 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR K 53 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS K 38 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY K 55 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE K 36 " --> pdb=" O GLY K 55 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS K 57 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N MET K 34 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS K 59 " --> pdb=" O ALA K 32 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA K 32 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER K 61 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE K 30 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR K 63 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS K 28 " --> pdb=" O GLU L 120 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU L 120 " --> pdb=" O LYS K 28 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE K 30 " --> pdb=" O ASP L 118 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP L 118 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA K 32 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 39 through 43 removed outlier: 3.733A pdb=" N GLY W 39 " --> pdb=" O VAL W 79 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE W 28 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR W 78 " --> pdb=" O ILE W 28 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET W 30 " --> pdb=" O TYR W 78 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE W 80 " --> pdb=" O MET W 30 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU W 32 " --> pdb=" O ILE W 80 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU W 101 " --> pdb=" O VAL W 132 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA W 131 " --> pdb=" O ILE W 144 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE W 146 " --> pdb=" O ALA W 131 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU W 133 " --> pdb=" O PHE W 146 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU W 208 " --> pdb=" O ILE W 143 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN W 145 " --> pdb=" O LEU W 208 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 210 through 212 Processing sheet with id=AE3, first strand: chain 'W' and resid 297 through 300 Processing sheet with id=AE4, first strand: chain 'T' and resid 297 through 300 Processing sheet with id=AE5, first strand: chain 'T' and resid 39 through 43 removed outlier: 6.666A pdb=" N ILE T 28 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TYR T 78 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET T 30 " --> pdb=" O TYR T 78 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE T 80 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU T 32 " --> pdb=" O ILE T 80 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR T 100 " --> pdb=" O ILE T 27 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU T 101 " --> pdb=" O VAL T 132 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY T 134 " --> pdb=" O LEU T 101 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA T 131 " --> pdb=" O ILE T 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE T 146 " --> pdb=" O ALA T 131 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU T 133 " --> pdb=" O PHE T 146 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N LEU T 208 " --> pdb=" O ILE T 143 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASN T 145 " --> pdb=" O LEU T 208 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 156 through 158 removed outlier: 7.216A pdb=" N LEU T 152 " --> pdb=" O VAL T 189 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 184 through 185 removed outlier: 4.416A pdb=" N ILE T 217 " --> pdb=" O LEU T 185 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 348 through 353 Processing sheet with id=AE9, first strand: chain 'Z' and resid 22 through 23 removed outlier: 5.594A pdb=" N PHE Z 87 " --> pdb=" O ASN Z 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU Z 135 " --> pdb=" O LYS Z 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 22 through 23 removed outlier: 5.594A pdb=" N PHE Z 87 " --> pdb=" O ASN Z 108 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR Z 51 " --> pdb=" O ILE Z 41 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE Z 41 " --> pdb=" O THR Z 51 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU Z 39 " --> pdb=" O TYR Z 53 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY Z 55 " --> pdb=" O THR Z 37 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR Z 65 " --> pdb=" O VAL Z 27 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL Z 27 " --> pdb=" O TYR Z 65 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET Z 34 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR G 115 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE Z 36 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP G 113 " --> pdb=" O PHE Z 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.635A pdb=" N PHE I 87 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.635A pdb=" N PHE I 87 " --> pdb=" O ASN I 108 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY I 58 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR I 51 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP I 40 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR I 53 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS I 38 " --> pdb=" O TYR I 53 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY I 55 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE I 36 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS I 57 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET I 34 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS I 59 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA I 32 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER I 61 " --> pdb=" O PHE I 30 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE I 30 " --> pdb=" O SER I 61 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR I 63 " --> pdb=" O LYS I 28 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N LYS I 28 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU C 120 " --> pdb=" O LYS I 28 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE I 30 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP C 118 " --> pdb=" O PHE I 30 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA I 32 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.739A pdb=" N PHE L 87 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU L 135 " --> pdb=" O LYS L 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.739A pdb=" N PHE L 87 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY L 58 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR L 51 " --> pdb=" O ASP L 40 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP L 40 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR L 53 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS L 38 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY L 55 " --> pdb=" O PHE L 36 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE L 36 " --> pdb=" O GLY L 55 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS L 57 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET L 34 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS L 59 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA L 32 " --> pdb=" O LYS L 59 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER L 61 " --> pdb=" O PHE L 30 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE L 30 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR L 63 " --> pdb=" O LYS L 28 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS L 28 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU D 120 " --> pdb=" O LYS L 28 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE L 30 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP D 118 " --> pdb=" O PHE L 30 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA L 32 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.734A pdb=" N GLY F 39 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F 101 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA F 131 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE F 146 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU F 133 " --> pdb=" O PHE F 146 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU F 208 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASN F 145 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 210 through 212 Processing sheet with id=AF8, first strand: chain 'F' and resid 297 through 300 Processing sheet with id=AF9, first strand: chain 'E' and resid 297 through 300 Processing sheet with id=AG1, first strand: chain 'E' and resid 39 through 43 removed outlier: 6.687A pdb=" N ILE E 28 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR E 78 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET E 30 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE E 80 " --> pdb=" O MET E 30 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU E 32 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR E 100 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 101 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY E 134 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA E 131 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE E 146 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU E 133 " --> pdb=" O PHE E 146 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N LEU E 208 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN E 145 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 156 through 158 removed outlier: 7.361A pdb=" N LEU E 152 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 184 through 185 removed outlier: 4.437A pdb=" N ILE E 217 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 348 through 353 Processing sheet with id=AG5, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.601A pdb=" N PHE G 87 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU G 135 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.601A pdb=" N PHE G 87 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY G 58 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR G 51 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE G 41 " --> pdb=" O THR G 51 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR G 53 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU G 39 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 55 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR G 65 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL G 27 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET G 34 " --> pdb=" O THR a 115 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR a 115 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE G 36 " --> pdb=" O ASP a 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP a 113 " --> pdb=" O PHE G 36 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.643A pdb=" N PHE C 87 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.643A pdb=" N PHE C 87 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 58 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR C 51 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 53 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS C 38 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY C 55 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE C 36 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS C 57 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N MET C 34 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS C 59 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 32 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 61 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE C 30 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR C 63 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LYS C 28 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU J 120 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE C 30 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP J 118 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C 32 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.722A pdb=" N PHE D 87 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 135 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.722A pdb=" N PHE D 87 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 58 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 51 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP D 40 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR D 53 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS D 38 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY D 55 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE D 36 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS D 57 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET D 34 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 59 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 32 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER D 61 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 30 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR D 63 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LYS D 28 " --> pdb=" O GLU M 120 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU M 120 " --> pdb=" O LYS D 28 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE D 30 " --> pdb=" O ASP M 118 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP M 118 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA D 32 " --> pdb=" O LEU M 116 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 39 through 43 removed outlier: 3.734A pdb=" N GLY X 39 " --> pdb=" O VAL X 79 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU X 101 " --> pdb=" O VAL X 132 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA X 131 " --> pdb=" O ILE X 144 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE X 146 " --> pdb=" O ALA X 131 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU X 133 " --> pdb=" O PHE X 146 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU X 208 " --> pdb=" O ILE X 143 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN X 145 " --> pdb=" O LEU X 208 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 210 through 212 Processing sheet with id=AH4, first strand: chain 'X' and resid 297 through 300 Processing sheet with id=AH5, first strand: chain 'U' and resid 297 through 300 Processing sheet with id=AH6, first strand: chain 'U' and resid 39 through 43 removed outlier: 6.630A pdb=" N ILE U 28 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR U 78 " --> pdb=" O ILE U 28 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET U 30 " --> pdb=" O TYR U 78 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE U 80 " --> pdb=" O MET U 30 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU U 32 " --> pdb=" O ILE U 80 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR U 100 " --> pdb=" O ILE U 27 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU U 101 " --> pdb=" O VAL U 132 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY U 134 " --> pdb=" O LEU U 101 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA U 131 " --> pdb=" O ILE U 144 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE U 146 " --> pdb=" O ALA U 131 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU U 133 " --> pdb=" O PHE U 146 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LEU U 208 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN U 145 " --> pdb=" O LEU U 208 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'U' and resid 156 through 158 removed outlier: 7.333A pdb=" N LEU U 152 " --> pdb=" O VAL U 189 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 184 through 185 removed outlier: 4.519A pdb=" N ILE U 217 " --> pdb=" O LEU U 185 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'U' and resid 348 through 353 Processing sheet with id=AI1, first strand: chain 'a' and resid 22 through 23 removed outlier: 5.648A pdb=" N PHE a 87 " --> pdb=" O ASN a 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU a 135 " --> pdb=" O LYS a 107 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 22 through 23 removed outlier: 5.648A pdb=" N PHE a 87 " --> pdb=" O ASN a 108 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY a 58 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR a 51 " --> pdb=" O ILE a 41 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE a 41 " --> pdb=" O THR a 51 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR a 53 " --> pdb=" O GLU a 39 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU a 39 " --> pdb=" O TYR a 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY a 55 " --> pdb=" O THR a 37 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR a 65 " --> pdb=" O VAL a 27 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL a 27 " --> pdb=" O TYR a 65 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET a 34 " --> pdb=" O THR R 115 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR R 115 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE a 36 " --> pdb=" O ASP R 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP R 113 " --> pdb=" O PHE a 36 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.628A pdb=" N PHE J 87 " --> pdb=" O ASN J 108 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.628A pdb=" N PHE J 87 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY J 58 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR J 51 " --> pdb=" O ASP J 40 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP J 40 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR J 53 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS J 38 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY J 55 " --> pdb=" O PHE J 36 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE J 36 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS J 57 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N MET J 34 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS J 59 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA J 32 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER J 61 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE J 30 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR J 63 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N LYS J 28 " --> pdb=" O GLU N 120 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU N 120 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE J 30 " --> pdb=" O ASP N 118 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP N 118 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA J 32 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.725A pdb=" N PHE M 87 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU M 135 " --> pdb=" O LYS M 107 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.725A pdb=" N PHE M 87 " --> pdb=" O ASN M 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY M 58 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR M 51 " --> pdb=" O ASP M 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP M 40 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR M 53 " --> pdb=" O LYS M 38 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS M 38 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY M 55 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE M 36 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS M 57 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET M 34 " --> pdb=" O LYS M 57 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS M 59 " --> pdb=" O ALA M 32 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA M 32 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER M 61 " --> pdb=" O PHE M 30 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE M 30 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR M 63 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS M 28 " --> pdb=" O GLU O 120 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU O 120 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE M 30 " --> pdb=" O ASP O 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP O 118 " --> pdb=" O PHE M 30 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA M 32 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 39 through 43 removed outlier: 3.736A pdb=" N GLY Q 39 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE Q 28 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR Q 78 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET Q 30 " --> pdb=" O TYR Q 78 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE Q 80 " --> pdb=" O MET Q 30 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU Q 32 " --> pdb=" O ILE Q 80 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU Q 101 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 144 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE Q 146 " --> pdb=" O ALA Q 131 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU Q 133 " --> pdb=" O PHE Q 146 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU Q 208 " --> pdb=" O ILE Q 143 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN Q 145 " --> pdb=" O LEU Q 208 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 210 through 212 Processing sheet with id=AI9, first strand: chain 'Q' and resid 297 through 300 Processing sheet with id=AJ1, first strand: chain 'P' and resid 39 through 43 removed outlier: 6.658A pdb=" N ILE P 28 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR P 78 " --> pdb=" O ILE P 28 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET P 30 " --> pdb=" O TYR P 78 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE P 80 " --> pdb=" O MET P 30 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU P 32 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR P 100 " --> pdb=" O ILE P 27 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU P 101 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLY P 134 " --> pdb=" O LEU P 101 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA P 131 " --> pdb=" O ILE P 144 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE P 146 " --> pdb=" O ALA P 131 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU P 133 " --> pdb=" O PHE P 146 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LEU P 208 " --> pdb=" O ILE P 143 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN P 145 " --> pdb=" O LEU P 208 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 156 through 158 removed outlier: 7.217A pdb=" N LEU P 152 " --> pdb=" O VAL P 189 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 184 through 185 removed outlier: 4.382A pdb=" N ILE P 217 " --> pdb=" O LEU P 185 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'z' and resid 39 through 43 removed outlier: 7.029A pdb=" N ILE z 28 " --> pdb=" O LEU z 76 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR z 78 " --> pdb=" O ILE z 28 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET z 30 " --> pdb=" O TYR z 78 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE z 80 " --> pdb=" O MET z 30 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU z 32 " --> pdb=" O ILE z 80 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR z 100 " --> pdb=" O ILE z 27 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU z 101 " --> pdb=" O VAL z 132 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY z 134 " --> pdb=" O LEU z 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA z 131 " --> pdb=" O ILE z 144 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE z 146 " --> pdb=" O ALA z 131 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU z 133 " --> pdb=" O PHE z 146 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU z 208 " --> pdb=" O ILE z 143 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN z 145 " --> pdb=" O LEU z 208 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'z' and resid 156 through 158 removed outlier: 7.505A pdb=" N LEU z 152 " --> pdb=" O VAL z 189 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL z 189 " --> pdb=" O LEU z 152 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'z' and resid 184 through 185 removed outlier: 4.222A pdb=" N ILE z 217 " --> pdb=" O LEU z 185 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'z' and resid 297 through 300 Processing sheet with id=AJ8, first strand: chain 'b' and resid 22 through 23 removed outlier: 5.724A pdb=" N PHE b 87 " --> pdb=" O ASN b 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU b 135 " --> pdb=" O LYS b 107 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'b' and resid 22 through 23 removed outlier: 5.724A pdb=" N PHE b 87 " --> pdb=" O ASN b 108 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY b 58 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR b 51 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE b 41 " --> pdb=" O THR b 51 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR b 53 " --> pdb=" O GLU b 39 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU b 39 " --> pdb=" O TYR b 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY b 55 " --> pdb=" O THR b 37 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR b 65 " --> pdb=" O VAL b 27 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL b 27 " --> pdb=" O TYR b 65 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LYS b 28 " --> pdb=" O GLU j 120 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU j 120 " --> pdb=" O LYS b 28 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE b 30 " --> pdb=" O ASP j 118 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP j 118 " --> pdb=" O PHE b 30 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA b 32 " --> pdb=" O LEU j 116 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'b' and resid 113 through 120 removed outlier: 6.596A pdb=" N ALA m 32 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP b 118 " --> pdb=" O PHE m 30 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE m 30 " --> pdb=" O ASP b 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU b 120 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LYS m 28 " --> pdb=" O GLU b 120 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL m 27 " --> pdb=" O TYR m 65 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR m 65 " --> pdb=" O VAL m 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY m 55 " --> pdb=" O THR m 37 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU m 39 " --> pdb=" O TYR m 53 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR m 53 " --> pdb=" O GLU m 39 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE m 41 " --> pdb=" O THR m 51 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR m 51 " --> pdb=" O ILE m 41 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY m 58 " --> pdb=" O PHE m 133 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE m 87 " --> pdb=" O ASN m 108 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'b' and resid 113 through 120 removed outlier: 6.596A pdb=" N ALA m 32 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP b 118 " --> pdb=" O PHE m 30 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE m 30 " --> pdb=" O ASP b 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU b 120 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LYS m 28 " --> pdb=" O GLU b 120 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL m 27 " --> pdb=" O TYR m 65 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR m 65 " --> pdb=" O VAL m 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY m 55 " --> pdb=" O THR m 37 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU m 39 " --> pdb=" O TYR m 53 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR m 53 " --> pdb=" O GLU m 39 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE m 41 " --> pdb=" O THR m 51 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR m 51 " --> pdb=" O ILE m 41 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY m 58 " --> pdb=" O PHE m 133 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU m 135 " --> pdb=" O LYS m 107 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 39 through 43 removed outlier: 6.899A pdb=" N ILE q 28 " --> pdb=" O LEU q 76 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR q 78 " --> pdb=" O ILE q 28 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET q 30 " --> pdb=" O TYR q 78 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE q 80 " --> pdb=" O MET q 30 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU q 32 " --> pdb=" O ILE q 80 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR q 100 " --> pdb=" O ILE q 27 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU q 101 " --> pdb=" O VAL q 132 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY q 134 " --> pdb=" O LEU q 101 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA q 131 " --> pdb=" O ILE q 144 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE q 146 " --> pdb=" O ALA q 131 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU q 133 " --> pdb=" O PHE q 146 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LEU q 208 " --> pdb=" O ILE q 143 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN q 145 " --> pdb=" O LEU q 208 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'q' and resid 156 through 158 removed outlier: 3.631A pdb=" N LEU q 152 " --> pdb=" O ASP q 190 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP q 190 " --> pdb=" O LEU q 152 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'q' and resid 184 through 185 removed outlier: 4.147A pdb=" N ILE q 217 " --> pdb=" O LEU q 185 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'q' and resid 297 through 300 Processing sheet with id=AK7, first strand: chain 'j' and resid 22 through 23 removed outlier: 5.700A pdb=" N PHE j 87 " --> pdb=" O ASN j 108 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU j 135 " --> pdb=" O LYS j 107 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'j' and resid 22 through 23 removed outlier: 5.700A pdb=" N PHE j 87 " --> pdb=" O ASN j 108 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY j 58 " --> pdb=" O PHE j 133 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR j 51 " --> pdb=" O ILE j 41 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE j 41 " --> pdb=" O THR j 51 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR j 53 " --> pdb=" O GLU j 39 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU j 39 " --> pdb=" O TYR j 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY j 55 " --> pdb=" O THR j 37 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR j 65 " --> pdb=" O VAL j 27 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL j 27 " --> pdb=" O TYR j 65 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LYS j 28 " --> pdb=" O GLU k 120 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU k 120 " --> pdb=" O LYS j 28 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE j 30 " --> pdb=" O ASP k 118 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP k 118 " --> pdb=" O PHE j 30 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA j 32 " --> pdb=" O LEU k 116 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'r' and resid 39 through 43 removed outlier: 7.078A pdb=" N ILE r 28 " --> pdb=" O LEU r 76 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TYR r 78 " --> pdb=" O ILE r 28 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET r 30 " --> pdb=" O TYR r 78 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE r 80 " --> pdb=" O MET r 30 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU r 32 " --> pdb=" O ILE r 80 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR r 100 " --> pdb=" O ILE r 27 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU r 101 " --> pdb=" O VAL r 132 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY r 134 " --> pdb=" O LEU r 101 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA r 131 " --> pdb=" O ILE r 144 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE r 146 " --> pdb=" O ALA r 131 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU r 133 " --> pdb=" O PHE r 146 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N LEU r 208 " --> pdb=" O ILE r 143 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN r 145 " --> pdb=" O LEU r 208 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'r' and resid 156 through 158 removed outlier: 7.388A pdb=" N LEU r 152 " --> pdb=" O VAL r 189 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL r 189 " --> pdb=" O LEU r 152 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'r' and resid 184 through 185 removed outlier: 4.082A pdb=" N ILE r 217 " --> pdb=" O LEU r 185 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'r' and resid 297 through 300 Processing sheet with id=AL4, first strand: chain 'k' and resid 22 through 23 removed outlier: 5.713A pdb=" N PHE k 87 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU k 135 " --> pdb=" O LYS k 107 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'k' and resid 22 through 23 removed outlier: 5.713A pdb=" N PHE k 87 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY k 58 " --> pdb=" O PHE k 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR k 51 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE k 41 " --> pdb=" O THR k 51 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR k 53 " --> pdb=" O GLU k 39 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU k 39 " --> pdb=" O TYR k 53 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY k 55 " --> pdb=" O THR k 37 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR k 65 " --> pdb=" O VAL k 27 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL k 27 " --> pdb=" O TYR k 65 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N LYS k 28 " --> pdb=" O GLU c 120 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU c 120 " --> pdb=" O LYS k 28 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE k 30 " --> pdb=" O ASP c 118 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP c 118 " --> pdb=" O PHE k 30 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA k 32 " --> pdb=" O LEU c 116 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'e' and resid 39 through 43 removed outlier: 7.136A pdb=" N ILE e 28 " --> pdb=" O LEU e 76 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N TYR e 78 " --> pdb=" O ILE e 28 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET e 30 " --> pdb=" O TYR e 78 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE e 80 " --> pdb=" O MET e 30 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU e 32 " --> pdb=" O ILE e 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR e 100 " --> pdb=" O ILE e 27 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU e 101 " --> pdb=" O VAL e 132 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLY e 134 " --> pdb=" O LEU e 101 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA e 131 " --> pdb=" O ILE e 144 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE e 146 " --> pdb=" O ALA e 131 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU e 133 " --> pdb=" O PHE e 146 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU e 208 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN e 145 " --> pdb=" O LEU e 208 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'e' and resid 156 through 158 removed outlier: 7.348A pdb=" N LEU e 152 " --> pdb=" O VAL e 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL e 189 " --> pdb=" O LEU e 152 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'e' and resid 184 through 185 removed outlier: 4.193A pdb=" N ILE e 217 " --> pdb=" O LEU e 185 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'e' and resid 297 through 300 Processing sheet with id=AM1, first strand: chain 'c' and resid 22 through 23 removed outlier: 5.723A pdb=" N PHE c 87 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU c 135 " --> pdb=" O LYS c 107 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'c' and resid 22 through 23 removed outlier: 5.723A pdb=" N PHE c 87 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY c 58 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR c 51 " --> pdb=" O ILE c 41 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE c 41 " --> pdb=" O THR c 51 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TYR c 53 " --> pdb=" O GLU c 39 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU c 39 " --> pdb=" O TYR c 53 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY c 55 " --> pdb=" O THR c 37 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR c 65 " --> pdb=" O VAL c 27 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL c 27 " --> pdb=" O TYR c 65 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LYS c 28 " --> pdb=" O GLU l 120 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU l 120 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE c 30 " --> pdb=" O ASP l 118 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP l 118 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA c 32 " --> pdb=" O LEU l 116 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 's' and resid 39 through 43 removed outlier: 6.901A pdb=" N ILE s 28 " --> pdb=" O LEU s 76 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR s 78 " --> pdb=" O ILE s 28 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET s 30 " --> pdb=" O TYR s 78 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE s 80 " --> pdb=" O MET s 30 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU s 32 " --> pdb=" O ILE s 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR s 100 " --> pdb=" O ILE s 27 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU s 101 " --> pdb=" O VAL s 132 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY s 134 " --> pdb=" O LEU s 101 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA s 131 " --> pdb=" O ILE s 144 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE s 146 " --> pdb=" O ALA s 131 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU s 133 " --> pdb=" O PHE s 146 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N LEU s 208 " --> pdb=" O ILE s 143 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN s 145 " --> pdb=" O LEU s 208 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 's' and resid 156 through 158 removed outlier: 7.288A pdb=" N LEU s 152 " --> pdb=" O VAL s 189 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 's' and resid 184 through 185 removed outlier: 4.175A pdb=" N ILE s 217 " --> pdb=" O LEU s 185 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 's' and resid 297 through 300 Processing sheet with id=AM7, first strand: chain 'l' and resid 22 through 23 removed outlier: 5.701A pdb=" N PHE l 87 " --> pdb=" O ASN l 108 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU l 135 " --> pdb=" O LYS l 107 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'l' and resid 22 through 23 removed outlier: 5.701A pdb=" N PHE l 87 " --> pdb=" O ASN l 108 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY l 58 " --> pdb=" O PHE l 133 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR l 51 " --> pdb=" O ILE l 41 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE l 41 " --> pdb=" O THR l 51 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR l 53 " --> pdb=" O GLU l 39 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU l 39 " --> pdb=" O TYR l 53 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY l 55 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR l 65 " --> pdb=" O VAL l 27 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL l 27 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LYS l 28 " --> pdb=" O GLU m 120 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU m 120 " --> pdb=" O LYS l 28 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE l 30 " --> pdb=" O ASP m 118 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP m 118 " --> pdb=" O PHE l 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA l 32 " --> pdb=" O LEU m 116 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'n' and resid 39 through 43 removed outlier: 6.973A pdb=" N ILE n 28 " --> pdb=" O LEU n 76 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR n 78 " --> pdb=" O ILE n 28 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N MET n 30 " --> pdb=" O TYR n 78 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE n 80 " --> pdb=" O MET n 30 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU n 32 " --> pdb=" O ILE n 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR n 100 " --> pdb=" O ILE n 27 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU n 101 " --> pdb=" O VAL n 132 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLY n 134 " --> pdb=" O LEU n 101 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA n 131 " --> pdb=" O ILE n 144 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE n 146 " --> pdb=" O ALA n 131 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU n 133 " --> pdb=" O PHE n 146 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU n 208 " --> pdb=" O ILE n 143 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN n 145 " --> pdb=" O LEU n 208 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'n' and resid 156 through 158 removed outlier: 7.371A pdb=" N LEU n 152 " --> pdb=" O VAL n 189 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL n 189 " --> pdb=" O LEU n 152 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'n' and resid 184 through 185 removed outlier: 4.085A pdb=" N ILE n 217 " --> pdb=" O LEU n 185 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'n' and resid 297 through 300 3540 hydrogen bonds defined for protein. 9903 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: 41.18 Time building geometry restraints manager: 16.36 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: 24522 1.34 - 1.46: 14731 1.46 - 1.58: 37151 1.58 - 1.70: 0 1.70 - 1.82: 576 Bond restraints: 76980 Sorted by residual: bond pdb=" N ASN U 68 " pdb=" CA ASN U 68 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.74e+00 bond pdb=" N ASN S 68 " pdb=" CA ASN S 68 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.68e+00 bond pdb=" N ASN E 68 " pdb=" CA ASN E 68 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.23e+00 bond pdb=" N ASN T 68 " pdb=" CA ASN T 68 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.42e+00 bond pdb=" CA GLU k 26 " pdb=" CB GLU k 26 " ideal model delta sigma weight residual 1.525 1.552 -0.027 1.36e-02 5.41e+03 3.96e+00 ... (remaining 76975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 99774 1.66 - 3.31: 3393 3.31 - 4.97: 371 4.97 - 6.63: 75 6.63 - 8.29: 37 Bond angle restraints: 103650 Sorted by residual: angle pdb=" N ASN S 68 " pdb=" CA ASN S 68 " pdb=" C ASN S 68 " ideal model delta sigma weight residual 111.07 119.20 -8.13 1.07e+00 8.73e-01 5.78e+01 angle pdb=" N ASN U 68 " pdb=" CA ASN U 68 " pdb=" C ASN U 68 " ideal model delta sigma weight residual 111.07 119.15 -8.08 1.07e+00 8.73e-01 5.70e+01 angle pdb=" N ASN E 68 " pdb=" CA ASN E 68 " pdb=" C ASN E 68 " ideal model delta sigma weight residual 111.07 118.80 -7.73 1.07e+00 8.73e-01 5.22e+01 angle pdb=" N ASN T 68 " pdb=" CA ASN T 68 " pdb=" C ASN T 68 " ideal model delta sigma weight residual 111.07 118.77 -7.70 1.07e+00 8.73e-01 5.17e+01 angle pdb=" N VAL X 69 " pdb=" CA VAL X 69 " pdb=" C VAL X 69 " ideal model delta sigma weight residual 112.96 106.59 6.37 1.00e+00 1.00e+00 4.05e+01 ... (remaining 103645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 40933 18.16 - 36.32: 4628 36.32 - 54.48: 1256 54.48 - 72.64: 291 72.64 - 90.80: 106 Dihedral angle restraints: 47214 sinusoidal: 19140 harmonic: 28074 Sorted by residual: dihedral pdb=" CA LEU c 64 " pdb=" C LEU c 64 " pdb=" N TYR c 65 " pdb=" CA TYR c 65 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU b 64 " pdb=" C LEU b 64 " pdb=" N TYR b 65 " pdb=" CA TYR b 65 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU G 64 " pdb=" C LEU G 64 " pdb=" N TYR G 65 " pdb=" CA TYR G 65 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 47211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8491 0.045 - 0.090: 2637 0.090 - 0.134: 873 0.134 - 0.179: 147 0.179 - 0.224: 8 Chirality restraints: 12156 Sorted by residual: chirality pdb=" CB VAL B 24 " pdb=" CA VAL B 24 " pdb=" CG1 VAL B 24 " pdb=" CG2 VAL B 24 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL K 24 " pdb=" CA VAL K 24 " pdb=" CG1 VAL K 24 " pdb=" CG2 VAL K 24 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASN S 68 " pdb=" N ASN S 68 " pdb=" C ASN S 68 " pdb=" CB ASN S 68 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 12153 not shown) Planarity restraints: 13002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU k 26 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C GLU k 26 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU k 26 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL k 27 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR n 60 " 0.020 2.00e-02 2.50e+03 1.44e-02 4.17e+00 pdb=" CG TYR n 60 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR n 60 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR n 60 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR n 60 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR n 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR n 60 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR n 60 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR r 60 " -0.018 2.00e-02 2.50e+03 1.39e-02 3.88e+00 pdb=" CG TYR r 60 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR r 60 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR r 60 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR r 60 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR r 60 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR r 60 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR r 60 " -0.006 2.00e-02 2.50e+03 ... (remaining 12999 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4351 2.74 - 3.28: 72485 3.28 - 3.82: 119783 3.82 - 4.36: 145596 4.36 - 4.90: 250820 Nonbonded interactions: 593035 Sorted by model distance: nonbonded pdb=" O GLY U 138 " pdb=" OG SER U 225 " model vdw 2.197 3.040 nonbonded pdb=" ND2 ASN P 68 " pdb=" OG1 THR P 183 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLU M 16 " pdb=" NZ LYS M 23 " model vdw 2.205 3.120 nonbonded pdb=" OE2 GLU z 287 " pdb=" OG SER z 296 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU e 287 " pdb=" OG SER e 296 " model vdw 2.212 3.040 ... (remaining 593030 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.940 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: 0.110 Extract box with map and model: 3.210 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 146.240 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.660 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: 0.020 Load rotamer database and sin/cos tables:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.051 76980 Z= 0.270 Angle : 0.732 8.287 103650 Z= 0.420 Chirality : 0.049 0.224 12156 Planarity : 0.004 0.048 13002 Dihedral : 17.262 90.802 29094 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.88 % Allowed : 23.00 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.08), residues: 9612 helix: 1.66 (0.10), residues: 2520 sheet: 0.24 (0.11), residues: 1932 loop : -0.94 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 119 HIS 0.007 0.002 HIS U 250 PHE 0.019 0.002 PHE T 146 TYR 0.034 0.002 TYR n 60 ARG 0.007 0.001 ARG W 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2318 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 2161 time to evaluate : 6.895 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: g 30 MET cc_start: 0.7184 (ttp) cc_final: 0.6805 (ttp) REVERT: i 4 MET cc_start: 0.7823 (tpt) cc_final: 0.7448 (tpt) REVERT: i 23 LYS cc_start: 0.8692 (tptp) cc_final: 0.8342 (tptt) REVERT: i 84 GLU cc_start: 0.7991 (tt0) cc_final: 0.7755 (tt0) REVERT: A 23 LYS cc_start: 0.8485 (tttt) cc_final: 0.8241 (tttp) REVERT: A 24 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8234 (t) REVERT: A 84 GLU cc_start: 0.8089 (tt0) cc_final: 0.7881 (tt0) REVERT: V 200 GLU cc_start: 0.7256 (tp30) cc_final: 0.6975 (tp30) REVERT: V 288 LYS cc_start: 0.7232 (mttp) cc_final: 0.6996 (mppt) REVERT: Y 23 LYS cc_start: 0.8670 (tptp) cc_final: 0.8269 (tptt) REVERT: H 4 MET cc_start: 0.7686 (tpt) cc_final: 0.7348 (tpt) REVERT: K 4 MET cc_start: 0.7677 (tpt) cc_final: 0.7343 (tpt) REVERT: W 111 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.5946 (mptp) REVERT: W 221 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7604 (tpt-90) REVERT: W 288 LYS cc_start: 0.7080 (mttp) cc_final: 0.6848 (mppt) REVERT: W 345 MET cc_start: 0.8029 (mtt) cc_final: 0.7758 (mtt) REVERT: T 316 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5412 (mm) REVERT: Z 23 LYS cc_start: 0.8692 (tptp) cc_final: 0.8277 (tptt) REVERT: Z 84 GLU cc_start: 0.8106 (tt0) cc_final: 0.7838 (tt0) REVERT: Z 126 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7297 (mm-30) REVERT: Z 128 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: I 4 MET cc_start: 0.7586 (tpt) cc_final: 0.7328 (tpt) REVERT: F 30 MET cc_start: 0.7169 (ttp) cc_final: 0.6688 (ttp) REVERT: F 224 ASN cc_start: 0.6905 (m-40) cc_final: 0.6621 (m110) REVERT: F 325 LYS cc_start: 0.8180 (tttt) cc_final: 0.7958 (tttp) REVERT: G 4 MET cc_start: 0.7913 (tpt) cc_final: 0.7551 (tpt) REVERT: G 23 LYS cc_start: 0.8731 (tptp) cc_final: 0.8324 (tptt) REVERT: G 84 GLU cc_start: 0.8020 (tt0) cc_final: 0.7764 (tt0) REVERT: C 23 LYS cc_start: 0.8501 (tttt) cc_final: 0.8271 (tttp) REVERT: C 24 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8226 (t) REVERT: C 84 GLU cc_start: 0.8107 (tt0) cc_final: 0.7901 (tt0) REVERT: X 200 GLU cc_start: 0.7212 (tp30) cc_final: 0.6956 (tp30) REVERT: a 23 LYS cc_start: 0.8659 (tptp) cc_final: 0.8279 (tptt) REVERT: J 4 MET cc_start: 0.7695 (tpt) cc_final: 0.7365 (tpt) REVERT: M 47 MET cc_start: 0.8425 (mmp) cc_final: 0.8211 (mmp) REVERT: Q 111 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.5966 (mptp) REVERT: Q 221 ARG cc_start: 0.8023 (tpp-160) cc_final: 0.7610 (tpt-90) REVERT: Q 288 LYS cc_start: 0.7111 (mttp) cc_final: 0.6886 (mppt) REVERT: P 9 ASN cc_start: 0.7951 (p0) cc_final: 0.7685 (t0) REVERT: R 4 MET cc_start: 0.7714 (tpt) cc_final: 0.7485 (tpt) REVERT: R 23 LYS cc_start: 0.8710 (tptp) cc_final: 0.8267 (tptt) REVERT: R 84 GLU cc_start: 0.8205 (tt0) cc_final: 0.7930 (tt0) REVERT: R 126 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7356 (mm-30) REVERT: z 288 LYS cc_start: 0.7405 (mttp) cc_final: 0.7123 (mtmt) REVERT: z 305 GLN cc_start: 0.8092 (tt0) cc_final: 0.7834 (tt0) REVERT: z 322 GLN cc_start: 0.7665 (tt0) cc_final: 0.7430 (tt0) REVERT: z 325 LYS cc_start: 0.7871 (tttt) cc_final: 0.7496 (tttt) REVERT: z 345 MET cc_start: 0.7862 (ttm) cc_final: 0.7384 (mtt) REVERT: q 13 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7219 (ptpp) REVERT: q 103 MET cc_start: 0.6349 (ttp) cc_final: 0.6065 (ttp) REVERT: q 305 GLN cc_start: 0.8035 (tt0) cc_final: 0.7786 (tt0) REVERT: q 345 MET cc_start: 0.7653 (ttm) cc_final: 0.7242 (ttp) REVERT: j 4 MET cc_start: 0.7272 (tpt) cc_final: 0.6865 (tpp) REVERT: j 126 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7854 (mm-30) REVERT: r 103 MET cc_start: 0.6302 (ttp) cc_final: 0.6022 (ttp) REVERT: r 182 TYR cc_start: 0.8595 (m-80) cc_final: 0.7959 (m-10) REVERT: r 305 GLN cc_start: 0.8104 (tt0) cc_final: 0.7887 (tt0) REVERT: k 78 LYS cc_start: 0.8879 (mttt) cc_final: 0.8642 (mtpt) REVERT: e 288 LYS cc_start: 0.7409 (mtmt) cc_final: 0.7205 (mtmt) REVERT: e 322 GLN cc_start: 0.7633 (tt0) cc_final: 0.7303 (tt0) REVERT: e 325 LYS cc_start: 0.7931 (tttt) cc_final: 0.7550 (tttt) REVERT: e 345 MET cc_start: 0.7806 (ttm) cc_final: 0.7350 (mtt) REVERT: c 29 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8095 (pptt) REVERT: s 13 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7325 (ptpp) REVERT: s 103 MET cc_start: 0.6264 (ttp) cc_final: 0.5969 (ttt) REVERT: s 305 GLN cc_start: 0.8035 (tt0) cc_final: 0.7810 (tt0) REVERT: s 345 MET cc_start: 0.7932 (ttm) cc_final: 0.7592 (mtt) REVERT: l 31 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: n 13 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7230 (ptpp) REVERT: n 103 MET cc_start: 0.6311 (ttp) cc_final: 0.5962 (ttp) REVERT: n 305 GLN cc_start: 0.8076 (tt0) cc_final: 0.7875 (tt0) REVERT: m 4 MET cc_start: 0.7440 (tpt) cc_final: 0.7233 (tpt) REVERT: m 78 LYS cc_start: 0.8890 (mttt) cc_final: 0.8653 (mtpt) outliers start: 157 outliers final: 88 residues processed: 2275 average time/residue: 1.8718 time to fit residues: 5352.6998 Evaluate side-chains 1973 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1877 time to evaluate : 6.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 118 ILE Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 118 ILE Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Y residue 140 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain T residue 110 ASP Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 316 LEU Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 118 ILE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain U residue 191 ILE Chi-restraints excluded: chain U residue 198 ASP Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 140 ASP Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain P residue 164 THR Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 191 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 13 LYS Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 311 SER Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 91 SER Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 112 THR Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 110 ASP Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 75 LEU Chi-restraints excluded: chain s residue 112 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 309 LEU Chi-restraints excluded: chain s residue 311 SER Chi-restraints excluded: chain l residue 31 GLN Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 112 THR Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 139 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 815 optimal weight: 8.9990 chunk 732 optimal weight: 10.0000 chunk 406 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 493 optimal weight: 7.9990 chunk 391 optimal weight: 6.9990 chunk 757 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 563 optimal weight: 20.0000 chunk 877 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 238 GLN g 305 GLN d 68 ASN d 305 GLN d 322 GLN i 108 ASN A 31 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN S 271 ASN S 322 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 9 ASN T 322 GLN I 31 GLN I 46 GLN ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN F 305 GLN E 305 GLN E 322 GLN C 31 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 9 ASN U 224 ASN U 322 GLN P 68 ASN P 322 GLN N 31 GLN N 46 GLN O 31 GLN b 31 GLN q 322 GLN j 46 GLN r 322 GLN e 140 HIS e 305 GLN c 31 GLN l 46 GLN n 322 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.202768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.189792 restraints weight = 49660.832| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 0.35 r_work: 0.3848 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 76980 Z= 0.351 Angle : 0.771 9.868 103650 Z= 0.426 Chirality : 0.052 0.256 12156 Planarity : 0.005 0.060 13002 Dihedral : 6.470 85.217 10384 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.00 % Allowed : 21.05 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.08), residues: 9612 helix: 1.27 (0.10), residues: 2700 sheet: 0.58 (0.11), residues: 1680 loop : -1.04 (0.08), residues: 5232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 119 HIS 0.007 0.002 HIS k 72 PHE 0.019 0.002 PHE A 111 TYR 0.024 0.003 TYR n 60 ARG 0.007 0.001 ARG G 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2511 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 501 poor density : 2010 time to evaluate : 7.006 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: g 66 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5989 (mtm) REVERT: g 232 GLU cc_start: 0.6035 (mm-30) cc_final: 0.5765 (mm-30) REVERT: g 241 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: g 285 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: d 130 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7392 (mppt) REVERT: d 218 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7504 (ptm160) REVERT: i 128 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 23 LYS cc_start: 0.8456 (tttt) cc_final: 0.8174 (tptt) REVERT: B 35 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: V 200 GLU cc_start: 0.7145 (tp30) cc_final: 0.6852 (tp30) REVERT: V 232 GLU cc_start: 0.6132 (mm-30) cc_final: 0.5806 (mm-30) REVERT: S 101 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7267 (tm) REVERT: S 107 VAL cc_start: 0.5770 (t) cc_final: 0.5569 (m) REVERT: S 144 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7459 (pt) REVERT: S 347 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7158 (p0) REVERT: Y 81 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7345 (mtt90) REVERT: W 200 GLU cc_start: 0.7207 (tp30) cc_final: 0.6979 (tp30) REVERT: T 101 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7387 (tm) REVERT: T 244 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6955 (t70) REVERT: T 336 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8483 (pttp) REVERT: Z 84 GLU cc_start: 0.8163 (tt0) cc_final: 0.7891 (tt0) REVERT: Z 126 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7254 (mm-30) REVERT: Z 128 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: I 23 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8165 (tptt) REVERT: F 66 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5975 (mtm) REVERT: F 150 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5741 (t70) REVERT: F 200 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: F 241 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: F 285 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: E 14 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5582 (mm-30) REVERT: E 107 VAL cc_start: 0.5935 (t) cc_final: 0.5713 (m) REVERT: E 130 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7373 (mppt) REVERT: E 144 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7452 (pt) REVERT: E 248 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (tp) REVERT: G 128 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: C 23 LYS cc_start: 0.8476 (tttt) cc_final: 0.8188 (tptt) REVERT: D 35 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: X 200 GLU cc_start: 0.7159 (tp30) cc_final: 0.6862 (tp30) REVERT: X 288 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6931 (mtpt) REVERT: U 101 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7300 (tm) REVERT: U 144 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7451 (pt) REVERT: U 347 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7204 (p0) REVERT: a 28 LYS cc_start: 0.8696 (ttmp) cc_final: 0.8308 (tttp) REVERT: a 81 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7364 (mtt90) REVERT: P 90 LEU cc_start: 0.6788 (mt) cc_final: 0.6535 (mt) REVERT: P 101 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7429 (tm) REVERT: P 316 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5659 (mm) REVERT: R 84 GLU cc_start: 0.8187 (tt0) cc_final: 0.7959 (tt0) REVERT: N 23 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8176 (tptt) REVERT: z 14 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5549 (mp0) REVERT: z 124 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6585 (mp) REVERT: z 182 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: z 218 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7778 (ptm160) REVERT: z 325 LYS cc_start: 0.7995 (tttt) cc_final: 0.7772 (tttt) REVERT: z 345 MET cc_start: 0.8166 (ttm) cc_final: 0.7754 (ttp) REVERT: b 47 MET cc_start: 0.8734 (mmp) cc_final: 0.8503 (mmp) REVERT: q 14 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: q 103 MET cc_start: 0.6363 (ttp) cc_final: 0.5994 (ttt) REVERT: q 264 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7536 (mptt) REVERT: q 280 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8223 (tppt) REVERT: j 4 MET cc_start: 0.7101 (tpt) cc_final: 0.6732 (tpp) REVERT: r 13 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7229 (ptpt) REVERT: r 14 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5368 (mp0) REVERT: r 103 MET cc_start: 0.6220 (ttp) cc_final: 0.5803 (ttp) REVERT: r 124 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6478 (mp) REVERT: r 305 GLN cc_start: 0.8056 (tt0) cc_final: 0.7849 (tt0) REVERT: k 81 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7346 (mtt90) REVERT: e 14 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: e 124 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6651 (mp) REVERT: e 182 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: e 218 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7783 (ptm160) REVERT: e 322 GLN cc_start: 0.7503 (tt0) cc_final: 0.7290 (tt0) REVERT: e 345 MET cc_start: 0.8105 (ttm) cc_final: 0.7698 (ttp) REVERT: c 47 MET cc_start: 0.8713 (mmp) cc_final: 0.8479 (mmp) REVERT: s 103 MET cc_start: 0.6305 (ttp) cc_final: 0.5948 (ttt) REVERT: s 264 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7545 (mptt) REVERT: s 280 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8226 (tppt) REVERT: l 84 GLU cc_start: 0.8074 (tt0) cc_final: 0.7859 (tt0) REVERT: n 13 LYS cc_start: 0.7539 (ttpt) cc_final: 0.7233 (ptpp) REVERT: n 14 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5471 (mp0) REVERT: n 27 ILE cc_start: 0.8065 (mt) cc_final: 0.7842 (mt) REVERT: n 103 MET cc_start: 0.6148 (ttp) cc_final: 0.5743 (ttp) REVERT: n 124 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6553 (mp) REVERT: n 182 TYR cc_start: 0.8528 (m-80) cc_final: 0.7983 (m-10) REVERT: n 228 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: m 4 MET cc_start: 0.7251 (tpt) cc_final: 0.7038 (tpt) REVERT: m 81 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7344 (mtt90) outliers start: 501 outliers final: 190 residues processed: 2283 average time/residue: 1.7958 time to fit residues: 5210.0593 Evaluate side-chains 2156 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 1911 time to evaluate : 6.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 95 THR Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 241 LYS Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain g residue 306 LYS Chi-restraints excluded: chain d residue 13 LYS Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 130 LYS Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 198 ASP Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 124 LYS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 347 ASP Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Y residue 81 ARG Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 111 LYS Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 306 LYS Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 212 LYS Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 347 ASP Chi-restraints excluded: chain a residue 81 ARG Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 306 LYS Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain z residue 13 LYS Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 75 LEU Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 227 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 86 ILE Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 248 ILE Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 81 ARG Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 86 ILE Chi-restraints excluded: chain r residue 112 THR Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 248 ILE Chi-restraints excluded: chain r residue 306 LYS Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 81 ARG Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 124 ILE Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 227 THR Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 112 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 81 ARG Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 112 THR Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 228 GLU Chi-restraints excluded: chain n residue 248 ILE Chi-restraints excluded: chain n residue 306 LYS Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 81 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 204 optimal weight: 6.9990 chunk 881 optimal weight: 2.9990 chunk 616 optimal weight: 7.9990 chunk 663 optimal weight: 0.4980 chunk 605 optimal weight: 5.9990 chunk 782 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 583 optimal weight: 0.7980 chunk 785 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 139 ASN g 204 ASN g 305 GLN d 68 ASN d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 ASN S 224 ASN W 44 HIS W 204 ASN T 322 GLN I 31 GLN I 46 GLN F 139 ASN F 204 ASN F 305 GLN E 322 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 139 ASN U 224 ASN U 271 ASN U 322 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 HIS Q 204 ASN P 322 GLN N 31 GLN N 46 GLN z 305 GLN z 322 GLN b 31 GLN q 305 GLN q 322 GLN j 46 GLN r 322 GLN e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN n 322 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.205105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.192227 restraints weight = 49993.921| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.35 r_work: 0.3878 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 76980 Z= 0.215 Angle : 0.627 9.169 103650 Z= 0.347 Chirality : 0.046 0.179 12156 Planarity : 0.004 0.048 13002 Dihedral : 5.538 57.311 10305 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.22 % Allowed : 22.38 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.08), residues: 9612 helix: 1.59 (0.10), residues: 2700 sheet: 0.31 (0.11), residues: 1776 loop : -0.98 (0.08), residues: 5136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 119 HIS 0.006 0.001 HIS l 72 PHE 0.020 0.002 PHE T 302 TYR 0.012 0.002 TYR Q 269 ARG 0.007 0.001 ARG X 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2415 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 436 poor density : 1979 time to evaluate : 6.970 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: g 66 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5955 (mtm) REVERT: g 150 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5564 (t70) REVERT: g 285 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: d 218 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7520 (ptm160) REVERT: i 128 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 23 LYS cc_start: 0.8444 (tttt) cc_final: 0.8219 (tptt) REVERT: B 35 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 40 ASP cc_start: 0.8060 (m-30) cc_final: 0.7851 (m-30) REVERT: V 22 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6238 (mmm-85) REVERT: V 59 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4930 (mt-10) REVERT: V 200 GLU cc_start: 0.7125 (tp30) cc_final: 0.6867 (tp30) REVERT: V 288 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6860 (mtpt) REVERT: S 101 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7225 (tm) REVERT: S 144 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7342 (pt) REVERT: S 236 MET cc_start: 0.7784 (mmm) cc_final: 0.7493 (mmm) REVERT: Y 81 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7299 (mtt90) REVERT: Y 128 GLU cc_start: 0.7406 (mp0) cc_final: 0.7180 (mp0) REVERT: H 81 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7448 (mmp-170) REVERT: K 59 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7998 (mmmt) REVERT: W 232 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5828 (mm-30) REVERT: W 288 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6581 (mtpt) REVERT: W 322 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: T 90 LEU cc_start: 0.6698 (mt) cc_final: 0.6462 (mt) REVERT: T 143 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7356 (pp) REVERT: T 244 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6837 (t70) REVERT: T 340 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (mppt) REVERT: Z 84 GLU cc_start: 0.8108 (tt0) cc_final: 0.7827 (tt0) REVERT: Z 128 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: I 23 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8188 (tptt) REVERT: L 141 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7577 (pp) REVERT: F 15 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7305 (mt) REVERT: F 66 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5948 (mtm) REVERT: F 150 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5720 (t70) REVERT: F 200 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: F 285 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 14 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5534 (mm-30) REVERT: G 128 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 23 LYS cc_start: 0.8449 (tttt) cc_final: 0.8227 (tptt) REVERT: D 40 ASP cc_start: 0.8036 (m-30) cc_final: 0.7829 (m-30) REVERT: X 22 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6199 (mmm-85) REVERT: X 200 GLU cc_start: 0.7148 (tp30) cc_final: 0.6864 (tp30) REVERT: X 288 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6833 (mtpt) REVERT: U 101 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7271 (tm) REVERT: U 143 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7411 (pp) REVERT: U 144 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7318 (pt) REVERT: U 236 MET cc_start: 0.7810 (mmm) cc_final: 0.7530 (mmm) REVERT: a 81 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7306 (mtt90) REVERT: a 128 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: J 81 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7470 (mmp-170) REVERT: Q 288 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6574 (mtpt) REVERT: Q 322 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: P 90 LEU cc_start: 0.6743 (mt) cc_final: 0.6513 (mt) REVERT: P 235 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: P 288 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7519 (mtmt) REVERT: P 336 LYS cc_start: 0.8771 (pttp) cc_final: 0.8553 (pttp) REVERT: P 340 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7840 (mppt) REVERT: R 84 GLU cc_start: 0.8217 (tt0) cc_final: 0.7991 (tt0) REVERT: N 23 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8148 (tptt) REVERT: N 102 GLU cc_start: 0.7838 (tt0) cc_final: 0.7623 (tt0) REVERT: O 141 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7582 (pp) REVERT: z 124 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6615 (mp) REVERT: z 182 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: z 218 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7690 (ptm160) REVERT: z 345 MET cc_start: 0.8191 (ttm) cc_final: 0.7762 (ttp) REVERT: q 13 LYS cc_start: 0.7515 (tttm) cc_final: 0.7245 (ptpp) REVERT: q 65 LEU cc_start: 0.6131 (tp) cc_final: 0.5913 (mm) REVERT: q 103 MET cc_start: 0.6288 (ttp) cc_final: 0.5926 (ttt) REVERT: q 124 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6604 (mp) REVERT: q 176 LEU cc_start: 0.7075 (tp) cc_final: 0.6813 (tp) REVERT: q 228 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: q 264 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7503 (mptt) REVERT: j 4 MET cc_start: 0.7149 (tpt) cc_final: 0.6801 (tpp) REVERT: j 64 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8606 (mt) REVERT: r 103 MET cc_start: 0.6215 (ttp) cc_final: 0.5812 (ttp) REVERT: r 124 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6400 (mp) REVERT: r 126 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6590 (mmmt) REVERT: r 228 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6292 (tm-30) REVERT: r 305 GLN cc_start: 0.8043 (tt0) cc_final: 0.7783 (tt0) REVERT: k 81 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7210 (mtt90) REVERT: e 182 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: e 218 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7681 (ptm160) REVERT: e 345 MET cc_start: 0.8119 (ttm) cc_final: 0.7699 (ttp) REVERT: s 103 MET cc_start: 0.6251 (ttp) cc_final: 0.5892 (ttt) REVERT: s 176 LEU cc_start: 0.7072 (tp) cc_final: 0.6825 (tp) REVERT: s 228 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: s 264 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7505 (mptt) REVERT: l 64 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (mt) REVERT: n 13 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7127 (ptpt) REVERT: n 103 MET cc_start: 0.6168 (ttp) cc_final: 0.5738 (ttp) REVERT: n 124 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6390 (mp) REVERT: n 126 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6622 (mmmt) REVERT: n 182 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: m 81 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7200 (mtt90) outliers start: 436 outliers final: 174 residues processed: 2199 average time/residue: 1.8222 time to fit residues: 5081.6245 Evaluate side-chains 2103 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 1866 time to evaluate : 6.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 95 THR Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain i residue 124 LYS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 165 SER Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain Y residue 81 ARG Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 288 LYS Chi-restraints excluded: chain W residue 306 LYS Chi-restraints excluded: chain W residue 322 GLN Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 340 LYS Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 191 ILE Chi-restraints excluded: chain a residue 81 ARG Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 288 LYS Chi-restraints excluded: chain Q residue 306 LYS Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 340 LYS Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain z residue 13 LYS Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 343 ASP Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 124 ILE Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 228 GLU Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 331 SER Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain q residue 343 ASP Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 193 LYS Chi-restraints excluded: chain r residue 195 THR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 228 GLU Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain r residue 343 ASP Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 81 ARG Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 326 GLU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 112 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 228 GLU Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain s residue 343 ASP Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 13 LYS Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 112 THR Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 343 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 821 optimal weight: 3.9990 chunk 461 optimal weight: 20.0000 chunk 859 optimal weight: 3.9990 chunk 483 optimal weight: 7.9990 chunk 524 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 708 optimal weight: 4.9990 chunk 603 optimal weight: 7.9990 chunk 467 optimal weight: 4.9990 chunk 376 optimal weight: 20.0000 chunk 842 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 204 ASN g 305 GLN d 68 ASN d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 ASN S 322 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 ASN T 322 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN F 204 ASN F 305 GLN E 322 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 224 ASN ** a 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 322 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN z 305 GLN b 31 GLN q 305 GLN q 322 GLN j 46 GLN e 305 GLN e 322 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN n 322 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.203575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.190758 restraints weight = 49913.847| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 0.34 r_work: 0.3861 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 76980 Z= 0.265 Angle : 0.675 9.109 103650 Z= 0.373 Chirality : 0.048 0.199 12156 Planarity : 0.004 0.048 13002 Dihedral : 5.541 57.928 10287 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.05 % Allowed : 21.68 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.08), residues: 9612 helix: 1.49 (0.10), residues: 2700 sheet: 0.29 (0.11), residues: 1728 loop : -1.06 (0.08), residues: 5184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP M 119 HIS 0.006 0.002 HIS b 72 PHE 0.016 0.002 PHE P 302 TYR 0.015 0.002 TYR g 78 ARG 0.006 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2451 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 505 poor density : 1946 time to evaluate : 6.930 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: g 15 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7399 (mt) REVERT: g 66 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.6037 (mtm) REVERT: g 150 ASP cc_start: 0.6095 (OUTLIER) cc_final: 0.5433 (t70) REVERT: g 232 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5643 (mm-30) REVERT: g 285 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: d 101 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7301 (tm) REVERT: d 218 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7463 (ptm160) REVERT: i 128 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 23 LYS cc_start: 0.8498 (tttt) cc_final: 0.8229 (tptt) REVERT: B 35 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 40 ASP cc_start: 0.8033 (m-30) cc_final: 0.7822 (m-30) REVERT: V 22 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6242 (mmm-85) REVERT: V 200 GLU cc_start: 0.7164 (tp30) cc_final: 0.6890 (tp30) REVERT: V 288 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6876 (mtpt) REVERT: S 101 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7231 (tm) REVERT: S 143 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7440 (pp) REVERT: S 144 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7334 (pt) REVERT: S 236 MET cc_start: 0.7774 (mmm) cc_final: 0.7507 (mmm) REVERT: Y 128 GLU cc_start: 0.7404 (mp0) cc_final: 0.7162 (mp0) REVERT: H 81 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7493 (mmp-170) REVERT: H 135 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7690 (mm-30) REVERT: K 59 LYS cc_start: 0.8244 (mmmt) cc_final: 0.8009 (mmmt) REVERT: W 232 GLU cc_start: 0.6056 (mm-30) cc_final: 0.5764 (mm-30) REVERT: W 288 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6627 (mtpt) REVERT: T 90 LEU cc_start: 0.6702 (mt) cc_final: 0.6467 (mt) REVERT: Z 84 GLU cc_start: 0.8130 (tt0) cc_final: 0.7832 (tt0) REVERT: Z 128 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: I 23 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8145 (tptt) REVERT: F 15 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7348 (mt) REVERT: F 66 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6030 (mtm) REVERT: F 150 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5491 (t70) REVERT: F 200 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: F 232 GLU cc_start: 0.5945 (mm-30) cc_final: 0.5736 (mm-30) REVERT: F 241 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7916 (tttm) REVERT: F 285 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: E 14 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5615 (mm-30) REVERT: E 101 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7311 (tm) REVERT: E 144 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7404 (pt) REVERT: G 128 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: C 23 LYS cc_start: 0.8509 (tttt) cc_final: 0.8243 (tptt) REVERT: X 22 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6212 (mmm-85) REVERT: X 200 GLU cc_start: 0.7152 (tp30) cc_final: 0.6860 (tp30) REVERT: X 202 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6775 (mtt90) REVERT: X 288 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6854 (mtpt) REVERT: U 101 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7228 (tm) REVERT: U 144 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7360 (pt) REVERT: U 236 MET cc_start: 0.7825 (mmm) cc_final: 0.7579 (mmm) REVERT: a 128 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: J 81 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7506 (mmp-170) REVERT: Q 288 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6627 (mtpt) REVERT: Q 322 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: P 90 LEU cc_start: 0.6740 (mt) cc_final: 0.6492 (mt) REVERT: P 336 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8482 (pttp) REVERT: R 84 GLU cc_start: 0.8239 (tt0) cc_final: 0.7981 (tt0) REVERT: N 23 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8145 (tptt) REVERT: z 14 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5425 (mp0) REVERT: z 182 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: z 218 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7746 (ptm160) REVERT: z 345 MET cc_start: 0.8248 (ttm) cc_final: 0.7814 (ttp) REVERT: q 103 MET cc_start: 0.6325 (ttp) cc_final: 0.5963 (ttt) REVERT: q 123 ASP cc_start: 0.5158 (m-30) cc_final: 0.4952 (m-30) REVERT: q 264 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7528 (mptt) REVERT: q 280 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8196 (tppt) REVERT: j 4 MET cc_start: 0.7099 (tpt) cc_final: 0.6786 (tpp) REVERT: r 13 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7225 (ptpt) REVERT: r 14 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.6030 (tp30) REVERT: r 124 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6446 (mp) REVERT: r 280 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8184 (tppt) REVERT: r 305 GLN cc_start: 0.8037 (tt0) cc_final: 0.7830 (tt0) REVERT: k 81 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7212 (mtt90) REVERT: e 14 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: e 182 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: e 218 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7734 (ptm160) REVERT: e 345 MET cc_start: 0.8127 (ttm) cc_final: 0.7674 (ttp) REVERT: s 103 MET cc_start: 0.6304 (ttp) cc_final: 0.5914 (ttt) REVERT: s 176 LEU cc_start: 0.7038 (tp) cc_final: 0.6786 (tp) REVERT: s 264 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7539 (mptt) REVERT: s 280 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8208 (tppt) REVERT: n 13 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7161 (ptpp) REVERT: n 14 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6085 (tp30) REVERT: n 124 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6451 (mp) REVERT: n 182 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: n 280 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8199 (tppt) REVERT: m 81 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7193 (mtt90) outliers start: 505 outliers final: 225 residues processed: 2228 average time/residue: 1.8082 time to fit residues: 5113.7911 Evaluate side-chains 2142 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 1858 time to evaluate : 6.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 95 THR Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain g residue 306 LYS Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 210 LEU Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 124 LYS Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 165 SER Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 198 ASP Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 288 LYS Chi-restraints excluded: chain W residue 306 LYS Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain F residue 306 LYS Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 115 LYS Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 202 ARG Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain X residue 306 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 212 LYS Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 288 LYS Chi-restraints excluded: chain Q residue 306 LYS Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 75 LEU Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 127 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 191 ILE Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 326 GLU Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 217 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain q residue 343 ASP Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 124 ILE Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 193 LYS Chi-restraints excluded: chain r residue 195 THR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 280 LYS Chi-restraints excluded: chain r residue 289 SER Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain r residue 343 ASP Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 81 ARG Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 326 GLU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 112 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 217 ILE Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 13 LYS Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 112 THR Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 280 LYS Chi-restraints excluded: chain n residue 289 SER Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 64 LEU Chi-restraints excluded: chain m residue 81 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 787 optimal weight: 3.9990 chunk 406 optimal weight: 9.9990 chunk 817 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 687 optimal weight: 0.8980 chunk 388 optimal weight: 0.7980 chunk 697 optimal weight: 8.9990 chunk 782 optimal weight: 9.9990 chunk 255 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 204 ASN g 305 GLN d 68 ASN d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 ASN S 322 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 322 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN F 204 ASN F 305 GLN E 322 GLN U 178 GLN U 224 ASN U 322 GLN ** a 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 ASN P 322 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN b 31 GLN q 305 GLN j 46 GLN k 31 GLN e 305 GLN e 322 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN m 31 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.205059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.192268 restraints weight = 50036.096| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.34 r_work: 0.3879 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 76980 Z= 0.208 Angle : 0.617 9.160 103650 Z= 0.340 Chirality : 0.046 0.166 12156 Planarity : 0.004 0.047 13002 Dihedral : 5.274 56.427 10283 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.35 % Allowed : 22.41 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 9612 helix: 1.66 (0.10), residues: 2700 sheet: 0.16 (0.11), residues: 1848 loop : -1.01 (0.08), residues: 5064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 119 HIS 0.006 0.001 HIS j 72 PHE 0.016 0.002 PHE q 302 TYR 0.012 0.002 TYR Q 269 ARG 0.008 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2390 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 447 poor density : 1943 time to evaluate : 7.754 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: g 15 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7357 (mt) REVERT: g 66 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6025 (mtm) REVERT: g 150 ASP cc_start: 0.6019 (OUTLIER) cc_final: 0.5384 (t70) REVERT: g 232 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5630 (mm-30) REVERT: g 285 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: d 101 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7234 (tm) REVERT: d 218 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7514 (ptm160) REVERT: d 340 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7557 (mppt) REVERT: i 128 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 23 LYS cc_start: 0.8488 (tttt) cc_final: 0.8197 (tptt) REVERT: B 35 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 40 ASP cc_start: 0.8005 (m-30) cc_final: 0.7804 (m-30) REVERT: V 22 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.6202 (mmm-85) REVERT: V 200 GLU cc_start: 0.7145 (tp30) cc_final: 0.6876 (tp30) REVERT: V 288 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6831 (mtpt) REVERT: S 101 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7183 (tm) REVERT: S 143 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7423 (pp) REVERT: S 144 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7315 (pt) REVERT: S 236 MET cc_start: 0.7716 (mmm) cc_final: 0.7430 (mmm) REVERT: Y 81 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7250 (mtt90) REVERT: Y 128 GLU cc_start: 0.7371 (mp0) cc_final: 0.7160 (mp0) REVERT: H 4 MET cc_start: 0.7492 (tpt) cc_final: 0.7272 (tpt) REVERT: H 81 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7460 (mmp-170) REVERT: H 135 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7599 (mm-30) REVERT: K 59 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7968 (mmmt) REVERT: W 288 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6559 (mtpt) REVERT: T 90 LEU cc_start: 0.6671 (mt) cc_final: 0.6445 (mt) REVERT: T 143 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7314 (pp) REVERT: T 244 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6784 (t70) REVERT: Z 84 GLU cc_start: 0.8084 (tt0) cc_final: 0.7787 (tt0) REVERT: Z 128 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: I 23 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8181 (tptt) REVERT: L 141 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7486 (pp) REVERT: F 15 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (mt) REVERT: F 66 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6059 (mtm) REVERT: F 150 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5471 (t70) REVERT: F 200 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: F 232 GLU cc_start: 0.5910 (mm-30) cc_final: 0.5615 (mm-30) REVERT: F 285 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: E 101 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7293 (tm) REVERT: E 144 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7351 (pt) REVERT: E 340 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7568 (mppt) REVERT: G 128 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: C 23 LYS cc_start: 0.8504 (tttt) cc_final: 0.8258 (tptt) REVERT: X 22 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6182 (mmm-85) REVERT: X 200 GLU cc_start: 0.7134 (tp30) cc_final: 0.6869 (tp30) REVERT: X 288 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6802 (mtpt) REVERT: U 101 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7203 (tm) REVERT: U 144 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7311 (pt) REVERT: U 236 MET cc_start: 0.7754 (mmm) cc_final: 0.7476 (mmm) REVERT: a 81 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7239 (mtt90) REVERT: a 128 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: J 4 MET cc_start: 0.7505 (tpt) cc_final: 0.7276 (tpt) REVERT: J 81 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (mmp-170) REVERT: Q 200 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6468 (tm-30) REVERT: Q 322 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: P 90 LEU cc_start: 0.6707 (mt) cc_final: 0.6469 (mt) REVERT: R 84 GLU cc_start: 0.8204 (tt0) cc_final: 0.7886 (tt0) REVERT: N 23 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8138 (tptt) REVERT: O 141 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7475 (pp) REVERT: z 14 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: z 182 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: z 218 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: z 345 MET cc_start: 0.8201 (ttm) cc_final: 0.7771 (ttp) REVERT: q 13 LYS cc_start: 0.7444 (tttm) cc_final: 0.7200 (ptpp) REVERT: q 103 MET cc_start: 0.6265 (ttp) cc_final: 0.5885 (ttt) REVERT: q 123 ASP cc_start: 0.5212 (m-30) cc_final: 0.4985 (m-30) REVERT: q 228 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: q 264 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7497 (mptt) REVERT: j 4 MET cc_start: 0.7107 (tpt) cc_final: 0.6804 (tpp) REVERT: j 64 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8624 (mt) REVERT: r 13 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7096 (ptpt) REVERT: r 14 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5937 (tp30) REVERT: r 126 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6609 (mmmt) REVERT: r 228 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: r 280 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8192 (tppt) REVERT: e 14 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5274 (mp0) REVERT: e 182 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8028 (m-10) REVERT: e 218 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: e 345 MET cc_start: 0.8100 (ttm) cc_final: 0.7664 (ttp) REVERT: s 103 MET cc_start: 0.6205 (ttp) cc_final: 0.5843 (ttt) REVERT: s 228 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6105 (tm-30) REVERT: s 264 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7500 (mptt) REVERT: l 64 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (mt) REVERT: n 13 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7095 (ptpp) REVERT: n 14 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: n 126 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6610 (mmmt) REVERT: n 182 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8053 (m-10) REVERT: n 228 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6242 (tm-30) outliers start: 447 outliers final: 201 residues processed: 2187 average time/residue: 1.8130 time to fit residues: 5026.8084 Evaluate side-chains 2132 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 1867 time to evaluate : 6.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 165 SER Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain S residue 343 ASP Chi-restraints excluded: chain Y residue 81 ARG Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 198 ASP Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 288 LYS Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 343 ASP Chi-restraints excluded: chain a residue 81 ARG Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 200 GLU Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 75 LEU Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 326 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 75 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 228 GLU Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 193 LYS Chi-restraints excluded: chain r residue 195 THR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 228 GLU Chi-restraints excluded: chain r residue 280 LYS Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain r residue 343 ASP Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 326 GLU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 217 ILE Chi-restraints excluded: chain s residue 228 GLU Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain s residue 343 ASP Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 13 LYS Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 228 GLU Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 341 VAL Chi-restraints excluded: chain n residue 343 ASP Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 727 optimal weight: 20.0000 chunk 467 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 909 optimal weight: 8.9990 chunk 632 optimal weight: 5.9990 chunk 373 optimal weight: 0.2980 chunk 336 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 537 optimal weight: 9.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 204 ASN d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 322 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 ASN T 322 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN F 204 ASN E 322 GLN U 322 GLN Q 204 ASN P 322 GLN N 46 GLN z 305 GLN b 31 GLN q 57 ASN q 305 GLN j 46 GLN r 305 GLN e 305 GLN c 31 GLN s 57 ASN s 305 GLN l 46 GLN n 305 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.202500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.189659 restraints weight = 49779.043| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 0.35 r_work: 0.3846 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 76980 Z= 0.302 Angle : 0.714 9.325 103650 Z= 0.393 Chirality : 0.049 0.170 12156 Planarity : 0.004 0.048 13002 Dihedral : 5.547 57.899 10274 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.84 % Allowed : 22.11 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.08), residues: 9612 helix: 1.39 (0.10), residues: 2700 sheet: 0.34 (0.11), residues: 1680 loop : -1.13 (0.08), residues: 5232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP N 119 HIS 0.007 0.002 HIS l 72 PHE 0.018 0.002 PHE P 146 TYR 0.017 0.002 TYR F 78 ARG 0.007 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2426 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 488 poor density : 1938 time to evaluate : 7.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.6133 (mtm) REVERT: g 150 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5553 (t70) REVERT: g 285 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: d 101 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7275 (tm) REVERT: d 144 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7480 (pt) REVERT: d 218 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7463 (ptm160) REVERT: d 288 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7571 (mtmt) REVERT: d 340 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7609 (mppt) REVERT: i 128 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 23 LYS cc_start: 0.8526 (tttt) cc_final: 0.8255 (tptt) REVERT: B 35 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: V 22 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.6283 (mmm-85) REVERT: V 200 GLU cc_start: 0.7211 (tp30) cc_final: 0.6919 (tp30) REVERT: V 288 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6905 (mtpt) REVERT: S 101 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7186 (tm) REVERT: S 144 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7394 (pt) REVERT: S 236 MET cc_start: 0.7862 (mmm) cc_final: 0.7662 (mmm) REVERT: Y 128 GLU cc_start: 0.7393 (mp0) cc_final: 0.7173 (mp0) REVERT: H 28 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8575 (ttmm) REVERT: H 81 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7511 (mmp-170) REVERT: K 59 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7994 (mmmt) REVERT: W 288 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6660 (mtpt) REVERT: T 90 LEU cc_start: 0.6752 (mt) cc_final: 0.6525 (mt) REVERT: T 144 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7422 (pt) REVERT: T 218 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6728 (ptp-170) REVERT: T 244 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6874 (t70) REVERT: T 321 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8035 (mm) REVERT: Z 84 GLU cc_start: 0.8132 (tt0) cc_final: 0.7824 (tt0) REVERT: Z 128 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: I 23 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8166 (tptt) REVERT: L 59 LYS cc_start: 0.8271 (mmmt) cc_final: 0.8037 (mmmt) REVERT: F 66 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.6147 (mtm) REVERT: F 150 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5576 (t70) REVERT: F 200 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: F 232 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5667 (mm-30) REVERT: F 285 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: E 101 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7261 (tm) REVERT: E 340 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7617 (mppt) REVERT: G 128 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 23 LYS cc_start: 0.8546 (tttt) cc_final: 0.8280 (tptt) REVERT: X 14 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6739 (pt0) REVERT: X 22 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6345 (mmm-85) REVERT: X 200 GLU cc_start: 0.7249 (tp30) cc_final: 0.6971 (tp30) REVERT: X 288 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6875 (mtpt) REVERT: U 101 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7193 (tm) REVERT: U 144 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7398 (pt) REVERT: U 236 MET cc_start: 0.7874 (mmm) cc_final: 0.7671 (mmm) REVERT: a 128 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: J 28 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8568 (ttmm) REVERT: J 81 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7518 (mmp-170) REVERT: Q 200 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: P 90 LEU cc_start: 0.6748 (mt) cc_final: 0.6534 (mt) REVERT: P 144 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7427 (pt) REVERT: R 84 GLU cc_start: 0.8190 (tt0) cc_final: 0.7918 (tt0) REVERT: N 23 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8164 (tptt) REVERT: z 14 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: z 182 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: z 218 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7843 (ptm160) REVERT: z 332 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6682 (mmpt) REVERT: z 345 MET cc_start: 0.8228 (ttm) cc_final: 0.7780 (ttp) REVERT: q 103 MET cc_start: 0.6374 (ttp) cc_final: 0.5993 (ttt) REVERT: q 264 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: q 280 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8202 (tppt) REVERT: j 4 MET cc_start: 0.7099 (tpt) cc_final: 0.6831 (tpp) REVERT: r 13 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7315 (ptpt) REVERT: r 14 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6036 (tp30) REVERT: r 280 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8188 (tppt) REVERT: e 14 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5324 (mp0) REVERT: e 182 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: e 218 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7850 (ptm160) REVERT: e 332 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6698 (mmpt) REVERT: e 345 MET cc_start: 0.8181 (ttm) cc_final: 0.7728 (ttp) REVERT: s 103 MET cc_start: 0.6333 (ttp) cc_final: 0.5930 (ttt) REVERT: s 176 LEU cc_start: 0.7017 (tp) cc_final: 0.6761 (tp) REVERT: s 264 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (mptt) REVERT: s 280 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8185 (tppt) REVERT: s 353 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: n 14 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6099 (tp30) REVERT: n 182 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: n 280 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8191 (tppt) outliers start: 488 outliers final: 236 residues processed: 2202 average time/residue: 1.8185 time to fit residues: 5076.2747 Evaluate side-chains 2187 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 1892 time to evaluate : 6.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 210 LEU Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 161 ASP Chi-restraints excluded: chain V residue 212 LYS Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 198 ASP Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 288 LYS Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 212 LYS Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 321 LEU Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 115 LYS Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 177 SER Chi-restraints excluded: chain X residue 212 LYS Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 200 GLU Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 184 LYS Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 75 LEU Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 127 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 332 LYS Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 217 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 280 LYS Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 326 GLU Chi-restraints excluded: chain e residue 332 LYS Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 217 ILE Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain s residue 353 GLU Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 280 LYS Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 341 VAL Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 684 optimal weight: 20.0000 chunk 746 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 688 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 549 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 808 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 644 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 322 GLN I 46 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN U 224 ASN P 322 GLN N 46 GLN z 44 HIS z 305 GLN b 31 GLN q 305 GLN j 46 GLN r 57 ASN r 305 GLN e 44 HIS e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 44 HIS n 305 GLN m 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.201997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.189132 restraints weight = 49773.335| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 0.35 r_work: 0.3844 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 76980 Z= 0.327 Angle : 0.745 9.411 103650 Z= 0.410 Chirality : 0.050 0.170 12156 Planarity : 0.005 0.056 13002 Dihedral : 5.642 58.605 10274 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.57 % Allowed : 22.65 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.08), residues: 9612 helix: 1.27 (0.10), residues: 2700 sheet: 0.26 (0.11), residues: 1680 loop : -1.16 (0.08), residues: 5232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K 119 HIS 0.007 0.002 HIS c 72 PHE 0.019 0.002 PHE P 146 TYR 0.018 0.002 TYR F 78 ARG 0.008 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2383 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 465 poor density : 1918 time to evaluate : 6.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6150 (mtm) REVERT: g 150 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5597 (t70) REVERT: g 200 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: g 232 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5673 (mm-30) REVERT: g 285 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: g 306 LYS cc_start: 0.7773 (ttpp) cc_final: 0.7563 (mtpt) REVERT: d 101 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7274 (tm) REVERT: d 144 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (pt) REVERT: d 218 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7364 (ptm160) REVERT: d 340 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7621 (mppt) REVERT: i 128 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: A 23 LYS cc_start: 0.8556 (tttt) cc_final: 0.8270 (tptt) REVERT: B 35 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: B 124 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8348 (pptt) REVERT: V 22 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6296 (mmm-85) REVERT: V 200 GLU cc_start: 0.7208 (tp30) cc_final: 0.6933 (tp30) REVERT: V 288 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6954 (mtpt) REVERT: S 101 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7180 (tm) REVERT: S 144 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7434 (pt) REVERT: Y 128 GLU cc_start: 0.7446 (mp0) cc_final: 0.7231 (mp0) REVERT: H 28 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: H 81 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7537 (mmp-170) REVERT: K 59 LYS cc_start: 0.8251 (mmmt) cc_final: 0.8048 (mmmt) REVERT: W 232 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5816 (mm-30) REVERT: W 288 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6712 (mtpt) REVERT: T 90 LEU cc_start: 0.6784 (mt) cc_final: 0.6544 (mt) REVERT: T 144 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7465 (pt) REVERT: T 218 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6741 (ptp-170) REVERT: T 244 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6936 (t70) REVERT: T 321 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8055 (mm) REVERT: Z 84 GLU cc_start: 0.8158 (tt0) cc_final: 0.7855 (tt0) REVERT: Z 128 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: I 23 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8174 (tptt) REVERT: L 59 LYS cc_start: 0.8299 (mmmt) cc_final: 0.8068 (mmmt) REVERT: F 66 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6157 (mtm) REVERT: F 150 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5621 (t70) REVERT: F 200 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: F 232 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5675 (mm-30) REVERT: F 285 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: F 315 ASP cc_start: 0.5565 (t70) cc_final: 0.5318 (t70) REVERT: E 101 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7255 (tm) REVERT: E 340 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7631 (mppt) REVERT: G 128 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: C 23 LYS cc_start: 0.8568 (tttt) cc_final: 0.8286 (tptt) REVERT: X 14 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6755 (pt0) REVERT: X 22 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6374 (mmm-85) REVERT: X 32 LEU cc_start: 0.6289 (mt) cc_final: 0.5892 (mm) REVERT: X 200 GLU cc_start: 0.7273 (tp30) cc_final: 0.6961 (tp30) REVERT: X 288 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6942 (mtpt) REVERT: U 101 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7209 (tm) REVERT: U 144 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7433 (pt) REVERT: a 128 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: J 28 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8544 (ttmm) REVERT: J 81 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7545 (mmp-170) REVERT: Q 319 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5481 (mtp) REVERT: P 90 LEU cc_start: 0.6801 (mt) cc_final: 0.6581 (mt) REVERT: P 144 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7462 (pt) REVERT: R 84 GLU cc_start: 0.8216 (tt0) cc_final: 0.7948 (tt0) REVERT: N 23 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8176 (tptt) REVERT: z 14 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: z 182 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: z 218 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (ptm160) REVERT: z 332 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6664 (mmpt) REVERT: z 345 MET cc_start: 0.8293 (ttm) cc_final: 0.7848 (ttp) REVERT: q 176 LEU cc_start: 0.7059 (tp) cc_final: 0.6805 (tp) REVERT: q 264 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7592 (mptt) REVERT: q 280 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8205 (tppt) REVERT: j 4 MET cc_start: 0.7142 (tpt) cc_final: 0.6918 (tpp) REVERT: r 13 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7296 (ptpt) REVERT: r 14 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6051 (tp30) REVERT: r 280 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8220 (tppt) REVERT: e 14 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5393 (mp0) REVERT: e 182 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: e 218 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: e 332 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6683 (mmpt) REVERT: e 345 MET cc_start: 0.8271 (ttm) cc_final: 0.7809 (ttp) REVERT: c 124 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (pttm) REVERT: s 103 MET cc_start: 0.6402 (ttp) cc_final: 0.5980 (ttt) REVERT: s 176 LEU cc_start: 0.7067 (tp) cc_final: 0.6810 (tp) REVERT: s 264 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7604 (mptt) REVERT: s 280 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8213 (tppt) REVERT: n 14 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6175 (tp30) REVERT: n 280 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8218 (tppt) outliers start: 465 outliers final: 252 residues processed: 2184 average time/residue: 1.7942 time to fit residues: 4976.5562 Evaluate side-chains 2175 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 1863 time to evaluate : 6.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 200 GLU Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 210 LEU Chi-restraints excluded: chain d residue 211 ILE Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 161 ASP Chi-restraints excluded: chain V residue 165 SER Chi-restraints excluded: chain V residue 177 SER Chi-restraints excluded: chain V residue 212 LYS Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 95 THR Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 288 LYS Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 195 THR Chi-restraints excluded: chain T residue 198 ASP Chi-restraints excluded: chain T residue 212 LYS Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 321 LEU Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 177 SER Chi-restraints excluded: chain X residue 212 LYS Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 319 MET Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 159 SER Chi-restraints excluded: chain P residue 184 LYS Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 75 LEU Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 127 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 227 THR Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 332 LYS Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 217 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 289 SER Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 193 LYS Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 280 LYS Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 332 LYS Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 217 ILE Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 123 ASP Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 198 ASP Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 280 LYS Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 341 VAL Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 562 optimal weight: 5.9990 chunk 814 optimal weight: 10.0000 chunk 656 optimal weight: 0.8980 chunk 279 optimal weight: 8.9990 chunk 782 optimal weight: 10.0000 chunk 596 optimal weight: 4.9990 chunk 428 optimal weight: 8.9990 chunk 417 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 204 ASN d 68 ASN d 322 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 322 GLN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 ASN T 322 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN E 322 GLN ** X 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 224 ASN ** a 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 ASN P 322 GLN N 46 GLN z 305 GLN b 31 GLN q 305 GLN j 46 GLN r 44 HIS r 305 GLN e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.203837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.191153 restraints weight = 50168.995| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 0.35 r_work: 0.3865 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 76980 Z= 0.239 Angle : 0.669 9.285 103650 Z= 0.366 Chirality : 0.047 0.172 12156 Planarity : 0.004 0.061 13002 Dihedral : 5.368 57.930 10272 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.97 % Allowed : 23.59 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.08), residues: 9612 helix: 1.49 (0.10), residues: 2700 sheet: 0.09 (0.11), residues: 1728 loop : -1.10 (0.08), residues: 5184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 119 HIS 0.006 0.001 HIS j 72 PHE 0.020 0.002 PHE n 302 TYR 0.013 0.002 TYR q 269 ARG 0.014 0.001 ARG V 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2318 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 415 poor density : 1903 time to evaluate : 6.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 15 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7362 (mt) REVERT: g 66 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6104 (mtm) REVERT: g 150 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.5501 (t70) REVERT: g 232 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5500 (mm-30) REVERT: g 285 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: d 101 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7206 (tm) REVERT: d 184 LYS cc_start: 0.7592 (ptmm) cc_final: 0.7211 (tptt) REVERT: d 210 LEU cc_start: 0.7726 (mt) cc_final: 0.7517 (mm) REVERT: d 218 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7360 (ptm160) REVERT: d 340 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7577 (mppt) REVERT: i 128 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 23 LYS cc_start: 0.8504 (tttt) cc_final: 0.8222 (tptt) REVERT: B 35 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: V 15 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7675 (tt) REVERT: V 22 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6267 (mmm-85) REVERT: V 200 GLU cc_start: 0.7130 (tp30) cc_final: 0.6856 (tp30) REVERT: V 288 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6836 (mtpt) REVERT: S 101 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7133 (tm) REVERT: S 143 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7462 (pp) REVERT: S 144 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7346 (pt) REVERT: Y 128 GLU cc_start: 0.7367 (mp0) cc_final: 0.7121 (mp0) REVERT: H 28 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8581 (ttmm) REVERT: H 81 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7457 (mmp-170) REVERT: H 135 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7645 (mm-30) REVERT: K 59 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7968 (mmmt) REVERT: W 232 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5761 (mm-30) REVERT: T 144 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7413 (pt) REVERT: T 218 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6636 (ptp-170) REVERT: T 321 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8009 (mm) REVERT: Z 84 GLU cc_start: 0.8104 (tt0) cc_final: 0.7803 (tt0) REVERT: Z 128 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: I 23 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8183 (tptt) REVERT: L 59 LYS cc_start: 0.8247 (mmmt) cc_final: 0.8018 (mmmt) REVERT: F 15 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7304 (mt) REVERT: F 66 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6107 (mtm) REVERT: F 150 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5512 (t70) REVERT: F 200 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: F 232 GLU cc_start: 0.5909 (mm-30) cc_final: 0.5667 (mm-30) REVERT: F 285 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: E 101 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7210 (tm) REVERT: E 340 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: G 128 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: C 23 LYS cc_start: 0.8521 (tttt) cc_final: 0.8226 (tptt) REVERT: X 14 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6677 (pt0) REVERT: X 22 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6191 (mmm-85) REVERT: X 32 LEU cc_start: 0.6257 (mt) cc_final: 0.5911 (mm) REVERT: X 194 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5750 (ttm) REVERT: X 200 GLU cc_start: 0.7201 (tp30) cc_final: 0.6899 (tp30) REVERT: X 288 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6814 (mtpt) REVERT: U 101 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7151 (tm) REVERT: U 144 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7360 (pt) REVERT: a 81 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7289 (mtt90) REVERT: a 128 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: J 28 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8572 (ttmm) REVERT: J 81 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7474 (mmp-170) REVERT: J 135 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7623 (mm-30) REVERT: Q 232 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5700 (mm-30) REVERT: Q 319 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5376 (mtp) REVERT: P 90 LEU cc_start: 0.6747 (mt) cc_final: 0.6531 (mt) REVERT: P 144 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7426 (pt) REVERT: R 84 GLU cc_start: 0.8172 (tt0) cc_final: 0.7902 (tt0) REVERT: N 23 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8163 (tptt) REVERT: O 141 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7651 (pp) REVERT: z 14 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5418 (mp0) REVERT: z 182 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: z 218 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (ptm160) REVERT: z 332 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6647 (mmpt) REVERT: z 345 MET cc_start: 0.8172 (ttm) cc_final: 0.7735 (ttp) REVERT: q 176 LEU cc_start: 0.6941 (tp) cc_final: 0.6683 (tp) REVERT: q 264 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7507 (mptt) REVERT: j 4 MET cc_start: 0.7098 (tpt) cc_final: 0.6874 (tpp) REVERT: r 14 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6059 (tp30) REVERT: r 126 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6630 (mmmt) REVERT: r 228 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: e 14 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5286 (mp0) REVERT: e 182 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8029 (m-10) REVERT: e 218 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7752 (ptm160) REVERT: e 332 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6699 (mmpt) REVERT: e 345 MET cc_start: 0.8177 (ttm) cc_final: 0.7735 (ttp) REVERT: s 103 MET cc_start: 0.6278 (ttp) cc_final: 0.5928 (ttt) REVERT: s 176 LEU cc_start: 0.6948 (tp) cc_final: 0.6685 (tp) REVERT: s 228 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: s 264 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7518 (mptt) REVERT: l 64 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8652 (mt) REVERT: n 14 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.6113 (tp30) REVERT: n 126 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6629 (mmmt) REVERT: n 228 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6283 (tm-30) outliers start: 415 outliers final: 229 residues processed: 2138 average time/residue: 1.8077 time to fit residues: 4920.0269 Evaluate side-chains 2132 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 1841 time to evaluate : 6.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 165 SER Chi-restraints excluded: chain V residue 177 SER Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 165 SER Chi-restraints excluded: chain W residue 198 ASP Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 159 SER Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 212 LYS Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 321 LEU Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 81 ARG Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 319 MET Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 184 LYS Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 205 LYS Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 227 THR Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 332 LYS Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 217 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 289 SER Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 79 ILE Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 191 ILE Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 228 GLU Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain r residue 319 MET Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain e residue 8 ILE Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 332 LYS Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 123 ASP Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 228 GLU Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 289 SER Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 228 GLU Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 319 MET Chi-restraints excluded: chain n residue 341 VAL Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 25 optimal weight: 7.9990 chunk 296 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 637 optimal weight: 7.9990 chunk 438 optimal weight: 9.9990 chunk 884 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 714 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 204 ASN d 322 GLN S 322 GLN T 322 GLN I 46 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN J 31 GLN P 322 GLN N 46 GLN z 305 GLN b 31 GLN q 305 GLN j 46 GLN r 305 GLN k 31 GLN e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 57 ASN n 305 GLN m 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.201738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.189201 restraints weight = 49712.037| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 0.35 r_work: 0.3838 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 76980 Z= 0.338 Angle : 0.767 9.492 103650 Z= 0.421 Chirality : 0.051 0.185 12156 Planarity : 0.005 0.050 13002 Dihedral : 5.684 58.849 10271 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.92 % Allowed : 23.92 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.08), residues: 9612 helix: 1.22 (0.10), residues: 2700 sheet: 0.09 (0.11), residues: 1704 loop : -1.15 (0.08), residues: 5208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 119 HIS 0.008 0.002 HIS z 44 PHE 0.024 0.002 PHE q 302 TYR 0.019 0.002 TYR X 78 ARG 0.013 0.001 ARG V 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2287 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 411 poor density : 1876 time to evaluate : 7.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 66 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6171 (mtm) REVERT: g 150 ASP cc_start: 0.6257 (OUTLIER) cc_final: 0.5593 (t70) REVERT: g 232 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5695 (mm-30) REVERT: g 285 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: d 101 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7256 (tm) REVERT: d 144 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7501 (pt) REVERT: d 159 SER cc_start: 0.7129 (OUTLIER) cc_final: 0.6902 (p) REVERT: d 218 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7499 (ptm160) REVERT: d 288 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7612 (mtmt) REVERT: d 340 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7599 (mppt) REVERT: i 128 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 23 LYS cc_start: 0.8546 (tttt) cc_final: 0.8263 (tptt) REVERT: B 35 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: V 15 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7740 (tt) REVERT: V 22 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6397 (mmm-85) REVERT: V 200 GLU cc_start: 0.7200 (tp30) cc_final: 0.6895 (tp30) REVERT: V 288 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6916 (mtpt) REVERT: S 101 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7166 (tm) REVERT: S 144 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7431 (pt) REVERT: Y 128 GLU cc_start: 0.7405 (mp0) cc_final: 0.7172 (mp0) REVERT: H 28 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: H 81 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7482 (mmp-170) REVERT: K 59 LYS cc_start: 0.8227 (mmmt) cc_final: 0.8017 (mmmt) REVERT: W 200 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: W 232 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5800 (mm-30) REVERT: T 144 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7471 (pt) REVERT: T 218 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6741 (ptp-170) REVERT: T 321 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8035 (mm) REVERT: Z 84 GLU cc_start: 0.8151 (tt0) cc_final: 0.7844 (tt0) REVERT: Z 128 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: I 23 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8177 (tptt) REVERT: F 66 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6177 (mtm) REVERT: F 150 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5624 (t70) REVERT: F 200 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6548 (tm-30) REVERT: F 232 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5704 (mm-30) REVERT: F 255 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7884 (ttpp) REVERT: F 285 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: E 101 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7244 (tm) REVERT: E 340 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7609 (mppt) REVERT: G 128 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 23 LYS cc_start: 0.8552 (tttt) cc_final: 0.8276 (tptt) REVERT: X 14 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6759 (pt0) REVERT: X 22 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6387 (mmm-85) REVERT: X 288 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6899 (mtpt) REVERT: U 101 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7160 (tm) REVERT: U 144 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7439 (pt) REVERT: a 128 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: J 28 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8586 (ttmm) REVERT: J 81 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7503 (mmp-170) REVERT: Q 232 GLU cc_start: 0.6017 (mm-30) cc_final: 0.5781 (mm-30) REVERT: Q 241 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7928 (tttm) REVERT: Q 319 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5537 (mtp) REVERT: P 90 LEU cc_start: 0.6795 (mt) cc_final: 0.6560 (mt) REVERT: P 144 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7477 (pt) REVERT: R 84 GLU cc_start: 0.8192 (tt0) cc_final: 0.7925 (tt0) REVERT: N 23 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: z 14 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5456 (mp0) REVERT: z 182 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: z 218 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: z 332 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6642 (mmpt) REVERT: z 345 MET cc_start: 0.8218 (ttm) cc_final: 0.7764 (ttp) REVERT: q 14 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5960 (tp30) REVERT: q 176 LEU cc_start: 0.6961 (tp) cc_final: 0.6697 (tp) REVERT: q 264 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7588 (mptt) REVERT: q 280 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8187 (tppt) REVERT: q 325 LYS cc_start: 0.7863 (tttt) cc_final: 0.7602 (tttt) REVERT: r 14 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: e 14 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5402 (mp0) REVERT: e 182 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: e 218 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7877 (ptm160) REVERT: e 332 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6698 (mmpt) REVERT: e 345 MET cc_start: 0.8188 (ttm) cc_final: 0.7728 (ttp) REVERT: s 14 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6017 (tp30) REVERT: s 103 MET cc_start: 0.6341 (ttp) cc_final: 0.5954 (ttt) REVERT: s 176 LEU cc_start: 0.6961 (tp) cc_final: 0.6700 (tp) REVERT: s 193 LYS cc_start: 0.5431 (OUTLIER) cc_final: 0.4949 (pptt) REVERT: s 264 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7597 (mptt) REVERT: s 280 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8204 (tppt) REVERT: s 325 LYS cc_start: 0.7893 (tttt) cc_final: 0.7654 (tttt) REVERT: s 353 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: n 14 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6150 (tp30) REVERT: n 45 GLU cc_start: 0.4528 (mp0) cc_final: 0.4246 (mm-30) outliers start: 411 outliers final: 238 residues processed: 2118 average time/residue: 1.8098 time to fit residues: 4867.2128 Evaluate side-chains 2146 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 298 poor density : 1848 time to evaluate : 6.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 159 SER Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 161 ASP Chi-restraints excluded: chain V residue 177 SER Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 200 GLU Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 159 SER Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 195 THR Chi-restraints excluded: chain T residue 212 LYS Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 321 LEU Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 241 LYS Chi-restraints excluded: chain Q residue 319 MET Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 159 SER Chi-restraints excluded: chain P residue 184 LYS Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 127 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 205 LYS Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 227 THR Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 332 LYS Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 289 SER Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 126 LYS Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 332 LYS Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 193 LYS Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 289 SER Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain s residue 353 GLU Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 75 LEU Chi-restraints excluded: chain n residue 126 LYS Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 198 ASP Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 341 VAL Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 837 optimal weight: 9.9990 chunk 658 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 chunk 242 optimal weight: 0.8980 chunk 639 optimal weight: 3.9990 chunk 508 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 702 optimal weight: 10.0000 chunk 422 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 322 GLN T 322 GLN I 46 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN E 322 GLN ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 322 GLN N 46 GLN z 305 GLN b 31 GLN q 305 GLN j 46 GLN r 305 GLN e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.202902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.190083 restraints weight = 49953.856| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 0.34 r_work: 0.3854 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 76980 Z= 0.277 Angle : 0.718 9.413 103650 Z= 0.394 Chirality : 0.049 0.176 12156 Planarity : 0.004 0.051 13002 Dihedral : 5.540 58.583 10271 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.14 % Allowed : 24.82 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.08), residues: 9612 helix: 1.32 (0.10), residues: 2700 sheet: 0.01 (0.11), residues: 1728 loop : -1.13 (0.08), residues: 5184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP O 119 HIS 0.006 0.002 HIS b 72 PHE 0.022 0.002 PHE P 146 TYR 0.014 0.002 TYR X 78 ARG 0.014 0.001 ARG V 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19224 Ramachandran restraints generated. 9612 Oldfield, 0 Emsley, 9612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2231 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 346 poor density : 1885 time to evaluate : 7.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 15 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7404 (mt) REVERT: g 66 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6149 (mtm) REVERT: g 150 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5560 (t70) REVERT: g 232 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5629 (mm-30) REVERT: g 285 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: d 101 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7231 (tm) REVERT: d 144 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7487 (pt) REVERT: d 184 LYS cc_start: 0.7638 (ptmm) cc_final: 0.7176 (tptt) REVERT: d 210 LEU cc_start: 0.7718 (mt) cc_final: 0.7490 (mm) REVERT: d 218 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7435 (ptm160) REVERT: d 340 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7625 (mppt) REVERT: i 128 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: A 23 LYS cc_start: 0.8551 (tttt) cc_final: 0.8231 (tptt) REVERT: B 35 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: V 15 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7737 (tt) REVERT: V 22 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6281 (mmm-85) REVERT: V 200 GLU cc_start: 0.7218 (tp30) cc_final: 0.6895 (tp30) REVERT: V 288 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6876 (mtpt) REVERT: S 101 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7171 (tm) REVERT: S 143 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7456 (pp) REVERT: S 144 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7388 (pt) REVERT: Y 128 GLU cc_start: 0.7384 (mp0) cc_final: 0.7167 (mp0) REVERT: H 28 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8583 (ttmm) REVERT: H 81 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7515 (mmp-170) REVERT: K 59 LYS cc_start: 0.8244 (mmmt) cc_final: 0.8031 (mmmt) REVERT: W 200 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: W 232 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5827 (mm-30) REVERT: W 241 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7839 (tttm) REVERT: T 144 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7460 (pt) REVERT: T 218 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6687 (ptp-170) REVERT: T 321 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8015 (mm) REVERT: Z 84 GLU cc_start: 0.8142 (tt0) cc_final: 0.7847 (tt0) REVERT: Z 128 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: I 23 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8138 (tptt) REVERT: F 15 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7383 (mt) REVERT: F 66 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6158 (mtm) REVERT: F 150 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5587 (t70) REVERT: F 200 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: F 232 GLU cc_start: 0.5985 (mm-30) cc_final: 0.5775 (mm-30) REVERT: F 255 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7867 (ttpp) REVERT: F 285 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: E 101 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7192 (tm) REVERT: E 340 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7633 (mppt) REVERT: G 128 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 23 LYS cc_start: 0.8557 (tttt) cc_final: 0.8282 (tptt) REVERT: X 14 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: X 22 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6363 (mmm-85) REVERT: X 200 GLU cc_start: 0.7187 (tp30) cc_final: 0.6927 (tp30) REVERT: X 288 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6881 (mtpt) REVERT: U 101 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7166 (tm) REVERT: U 144 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7387 (pt) REVERT: a 128 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: J 28 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8562 (ttmm) REVERT: J 81 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7532 (mmp-170) REVERT: Q 232 GLU cc_start: 0.6057 (mm-30) cc_final: 0.5829 (mm-30) REVERT: Q 288 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6625 (mtpt) REVERT: Q 319 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5456 (mtp) REVERT: P 90 LEU cc_start: 0.6781 (mt) cc_final: 0.6566 (mt) REVERT: P 144 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7463 (pt) REVERT: R 84 GLU cc_start: 0.8188 (tt0) cc_final: 0.7910 (tt0) REVERT: N 23 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8195 (tptt) REVERT: z 14 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5485 (mp0) REVERT: z 182 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: z 218 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7869 (ptm160) REVERT: z 332 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6689 (mmpt) REVERT: z 345 MET cc_start: 0.8222 (ttm) cc_final: 0.7778 (ttp) REVERT: q 14 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5954 (tp30) REVERT: q 176 LEU cc_start: 0.6900 (tp) cc_final: 0.6645 (tp) REVERT: q 264 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7559 (mptt) REVERT: q 269 TYR cc_start: 0.8331 (t80) cc_final: 0.7932 (t80) REVERT: q 280 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8220 (tppt) REVERT: q 325 LYS cc_start: 0.7849 (tttt) cc_final: 0.7582 (tttt) REVERT: q 326 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: r 14 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6060 (tp30) REVERT: r 45 GLU cc_start: 0.4479 (mp0) cc_final: 0.4149 (mm-30) REVERT: e 14 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: e 182 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: e 218 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7855 (ptm160) REVERT: e 332 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6696 (mmpt) REVERT: e 345 MET cc_start: 0.8220 (ttm) cc_final: 0.7766 (ttp) REVERT: s 13 LYS cc_start: 0.7517 (tttm) cc_final: 0.7151 (ptpp) REVERT: s 103 MET cc_start: 0.6344 (ttp) cc_final: 0.5970 (ttt) REVERT: s 176 LEU cc_start: 0.6925 (tp) cc_final: 0.6663 (tp) REVERT: s 193 LYS cc_start: 0.5416 (OUTLIER) cc_final: 0.4954 (pptt) REVERT: s 264 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: s 280 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8268 (tppt) REVERT: s 325 LYS cc_start: 0.7868 (tttt) cc_final: 0.7613 (tttt) REVERT: s 353 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: n 14 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6123 (tp30) REVERT: n 45 GLU cc_start: 0.4585 (mp0) cc_final: 0.4307 (mm-30) REVERT: n 124 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6365 (mp) outliers start: 346 outliers final: 235 residues processed: 2093 average time/residue: 1.8000 time to fit residues: 4778.5633 Evaluate side-chains 2139 residues out of total 8352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 1840 time to evaluate : 6.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 14 GLU Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 19 VAL Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 66 MET Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain g residue 127 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 161 ASP Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 230 THR Chi-restraints excluded: chain g residue 285 GLU Chi-restraints excluded: chain d residue 7 SER Chi-restraints excluded: chain d residue 95 THR Chi-restraints excluded: chain d residue 101 LEU Chi-restraints excluded: chain d residue 115 LYS Chi-restraints excluded: chain d residue 127 VAL Chi-restraints excluded: chain d residue 144 ILE Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain d residue 195 THR Chi-restraints excluded: chain d residue 197 VAL Chi-restraints excluded: chain d residue 218 ARG Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 331 SER Chi-restraints excluded: chain d residue 340 LYS Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 128 GLU Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 127 VAL Chi-restraints excluded: chain V residue 161 ASP Chi-restraints excluded: chain V residue 177 SER Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 288 LYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 143 ILE Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 187 ASP Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain S residue 198 ASP Chi-restraints excluded: chain S residue 314 VAL Chi-restraints excluded: chain S residue 341 VAL Chi-restraints excluded: chain Y residue 124 LYS Chi-restraints excluded: chain Y residue 139 LEU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 59 GLU Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 127 VAL Chi-restraints excluded: chain W residue 161 ASP Chi-restraints excluded: chain W residue 200 GLU Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 241 LYS Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 95 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 127 VAL Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 159 SER Chi-restraints excluded: chain T residue 191 ILE Chi-restraints excluded: chain T residue 212 LYS Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 321 LEU Chi-restraints excluded: chain Z residue 79 ILE Chi-restraints excluded: chain Z residue 124 LYS Chi-restraints excluded: chain Z residue 128 GLU Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain L residue 77 GLU Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 111 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 22 ARG Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 230 THR Chi-restraints excluded: chain X residue 288 LYS Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 144 ILE Chi-restraints excluded: chain U residue 159 SER Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 195 THR Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 124 LYS Chi-restraints excluded: chain a residue 128 GLU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain M residue 77 GLU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain Q residue 127 VAL Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 198 ASP Chi-restraints excluded: chain Q residue 212 LYS Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 288 LYS Chi-restraints excluded: chain Q residue 319 MET Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain P residue 115 LYS Chi-restraints excluded: chain P residue 127 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 159 SER Chi-restraints excluded: chain P residue 184 LYS Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 124 LYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain z residue 14 GLU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain z residue 107 VAL Chi-restraints excluded: chain z residue 112 THR Chi-restraints excluded: chain z residue 127 VAL Chi-restraints excluded: chain z residue 164 THR Chi-restraints excluded: chain z residue 182 TYR Chi-restraints excluded: chain z residue 193 LYS Chi-restraints excluded: chain z residue 195 THR Chi-restraints excluded: chain z residue 196 LYS Chi-restraints excluded: chain z residue 198 ASP Chi-restraints excluded: chain z residue 205 LYS Chi-restraints excluded: chain z residue 218 ARG Chi-restraints excluded: chain z residue 227 THR Chi-restraints excluded: chain z residue 314 VAL Chi-restraints excluded: chain z residue 332 LYS Chi-restraints excluded: chain z residue 353 GLU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 57 LYS Chi-restraints excluded: chain b residue 139 LEU Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain q residue 17 THR Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 164 THR Chi-restraints excluded: chain q residue 191 ILE Chi-restraints excluded: chain q residue 227 THR Chi-restraints excluded: chain q residue 264 LYS Chi-restraints excluded: chain q residue 280 LYS Chi-restraints excluded: chain q residue 310 LYS Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 326 GLU Chi-restraints excluded: chain q residue 341 VAL Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 39 GLU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 38 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 127 VAL Chi-restraints excluded: chain r residue 164 THR Chi-restraints excluded: chain r residue 182 TYR Chi-restraints excluded: chain r residue 198 ASP Chi-restraints excluded: chain r residue 227 THR Chi-restraints excluded: chain r residue 309 LEU Chi-restraints excluded: chain r residue 314 VAL Chi-restraints excluded: chain r residue 319 MET Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 164 THR Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 191 ILE Chi-restraints excluded: chain e residue 193 LYS Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 306 LYS Chi-restraints excluded: chain e residue 314 VAL Chi-restraints excluded: chain e residue 332 LYS Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 139 LEU Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain s residue 17 THR Chi-restraints excluded: chain s residue 164 THR Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 193 LYS Chi-restraints excluded: chain s residue 227 THR Chi-restraints excluded: chain s residue 248 ILE Chi-restraints excluded: chain s residue 264 LYS Chi-restraints excluded: chain s residue 280 LYS Chi-restraints excluded: chain s residue 289 SER Chi-restraints excluded: chain s residue 310 LYS Chi-restraints excluded: chain s residue 314 VAL Chi-restraints excluded: chain s residue 341 VAL Chi-restraints excluded: chain s residue 353 GLU Chi-restraints excluded: chain l residue 33 LYS Chi-restraints excluded: chain l residue 39 GLU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 139 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 17 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain n residue 127 VAL Chi-restraints excluded: chain n residue 162 GLU Chi-restraints excluded: chain n residue 164 THR Chi-restraints excluded: chain n residue 182 TYR Chi-restraints excluded: chain n residue 193 LYS Chi-restraints excluded: chain n residue 198 ASP Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 309 LEU Chi-restraints excluded: chain n residue 314 VAL Chi-restraints excluded: chain n residue 319 MET Chi-restraints excluded: chain n residue 353 GLU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 57 LYS Chi-restraints excluded: chain m residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 966 random chunks: chunk 902 optimal weight: 20.0000 chunk 923 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 949 optimal weight: 0.0060 chunk 744 optimal weight: 10.0000 chunk 934 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 773 optimal weight: 20.0000 chunk 294 optimal weight: 9.9990 chunk 885 optimal weight: 0.8980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 322 GLN S 322 GLN Y 31 GLN ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 204 ASN ** T 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 322 GLN ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN ** X 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 ASN P 322 GLN N 46 GLN z 305 GLN b 31 GLN q 305 GLN j 46 GLN r 305 GLN e 305 GLN c 31 GLN s 305 GLN l 46 GLN n 305 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.206038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.193867 restraints weight = 50411.013| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 0.34 r_work: 0.3895 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 76980 Z= 0.185 Angle : 0.628 8.929 103650 Z= 0.341 Chirality : 0.046 0.166 12156 Planarity : 0.003 0.051 13002 Dihedral : 5.119 56.238 10271 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.30 % Allowed : 25.86 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.08), residues: 9612 helix: 1.63 (0.10), residues: 2700 sheet: -0.04 (0.11), residues: 1848 loop : -1.03 (0.08), residues: 5064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 119 HIS 0.004 0.001 HIS l 72 PHE 0.031 0.001 PHE n 302 TYR 0.016 0.001 TYR T 78 ARG 0.011 0.000 ARG V 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 87541.53 seconds wall clock time: 1490 minutes 7.79 seconds (89407.79 seconds total)