Starting phenix.real_space_refine on Thu Sep 26 19:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/09_2024/8hqo_34952.cif" } resolution = 3.2 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= -0.017 sd= 0.972 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: 5 Type Number sf(0) Gaussians S 300 5.16 5 C 38460 2.51 5 N 10209 2.21 5 O 11742 1.98 5 H 1902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62613 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "1" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "2" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "3" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1233 Classifications: {'peptide': 80} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Restraints were copied for chains: 0, G, H, M, L, Q, P, S, R, W, V, I, N, X, a, b, C, B, E, D, F, K, J, U, T, Y, Z, O, x Time building chain proxies: 12.88, per 1000 atoms: 0.21 Number of scatterers: 62613 At special positions: 0 Unit cell: (158.2, 159.6, 288.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 300 16.00 O 11742 8.00 N 10209 7.00 C 38460 6.00 H 1902 1.00 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: 12.32 Conformation dependent library (CDL) restraints added in 6.0 seconds 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14424 Finding SS restraints... Secondary structure from input PDB file: 291 helices and 99 sheets defined 47.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 303 Proline residue: D 294 - end of helix removed outlier: 3.860A pdb=" N GLU D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.543A pdb=" N PHE E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS E 186 " --> pdb=" O ASP E 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN E 231 " --> pdb=" O GLN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 4.127A pdb=" N ASP E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE E 284 " --> pdb=" O PRO E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 303 Proline residue: E 294 - end of helix removed outlier: 3.860A pdb=" N GLU E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET E 307 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'R' and resid 5 through 14 Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 83 No H-bonds generated for 'chain 'R' and resid 81 through 83' Processing helix chain 'R' and resid 117 through 133 Processing helix chain 'R' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE R 163 " --> pdb=" O HIS R 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 14 Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 117 through 133 Processing helix chain 'S' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR S 162 " --> pdb=" O GLU S 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE S 163 " --> pdb=" O HIS S 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR S 167 " --> pdb=" O ILE S 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 20 Processing helix chain 'a' and resid 41 through 45 Processing helix chain 'a' and resid 85 through 103 Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 42 through 57 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 278 removed outlier: 3.639A pdb=" N PHE B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 Proline residue: B 294 - end of helix removed outlier: 3.859A pdb=" N GLU B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS C 186 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 Proline residue: C 294 - end of helix removed outlier: 3.860A pdb=" N GLU C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'P' and resid 5 through 14 Processing helix chain 'P' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA P 33 " --> pdb=" O THR P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 117 through 133 Processing helix chain 'P' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR P 162 " --> pdb=" O GLU P 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE P 163 " --> pdb=" O HIS P 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR P 167 " --> pdb=" O ILE P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 83 No H-bonds generated for 'chain 'Q' and resid 81 through 83' Processing helix chain 'Q' and resid 117 through 133 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE Q 163 " --> pdb=" O HIS Q 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR Q 167 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 20 Processing helix chain 'b' and resid 41 through 45 Processing helix chain 'b' and resid 85 through 103 Processing helix chain 'b' and resid 156 through 161 Processing helix chain 'x' and resid 2 through 15 removed outlier: 3.636A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU x 9 " --> pdb=" O LEU x 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP x 12 " --> pdb=" O GLU x 8 " (cutoff:3.500A) Processing helix chain 'x' and resid 15 through 21 removed outlier: 4.495A pdb=" N THR x 19 " --> pdb=" O GLN x 15 " (cutoff:3.500A) Processing helix chain 'x' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU x 40 " --> pdb=" O ALA x 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU x 44 " --> pdb=" O GLU x 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU x 46 " --> pdb=" O THR x 42 " (cutoff:3.500A) Processing helix chain 'x' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR x 54 " --> pdb=" O PRO x 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER x 55 " --> pdb=" O LYS x 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG x 58 " --> pdb=" O TYR x 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA x 63 " --> pdb=" O ALA x 59 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA x 64 " --> pdb=" O ALA x 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS x 65 " --> pdb=" O ASP x 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET x 76 " --> pdb=" O ALA x 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA x 77 " --> pdb=" O SER x 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 42 through 57 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 Proline residue: A 294 - end of helix removed outlier: 3.859A pdb=" N GLU A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 179 Processing helix chain 'F' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU F 198 " --> pdb=" O LYS F 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 4.127A pdb=" N ASP F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE F 284 " --> pdb=" O PRO F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 303 Proline residue: F 294 - end of helix removed outlier: 3.860A pdb=" N GLU F 297 " --> pdb=" O ARG F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 117 through 133 Processing helix chain 'G' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR G 162 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE G 163 " --> pdb=" O HIS G 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 117 through 133 Processing helix chain 'H' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE H 163 " --> pdb=" O HIS H 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 20 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 85 through 103 Processing helix chain 'I' and resid 156 through 161 Processing helix chain 'J' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU J 22 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 42 Processing helix chain 'J' and resid 42 through 57 Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 179 Processing helix chain 'J' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS J 186 " --> pdb=" O ASP J 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU J 198 " --> pdb=" O LYS J 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN J 231 " --> pdb=" O GLN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP J 261 " --> pdb=" O LYS J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 278 removed outlier: 3.640A pdb=" N PHE J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE J 284 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 303 Proline residue: J 294 - end of helix removed outlier: 3.859A pdb=" N GLU J 297 " --> pdb=" O ARG J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET J 307 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 362 Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 42 through 57 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 179 Processing helix chain 'K' and resid 180 through 200 removed outlier: 3.510A pdb=" N LYS K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU K 198 " --> pdb=" O LYS K 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN K 231 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP K 261 " --> pdb=" O LYS K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE K 277 " --> pdb=" O ILE K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 286 removed outlier: 3.699A pdb=" N ILE K 284 " --> pdb=" O PRO K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 303 Proline residue: K 294 - end of helix removed outlier: 3.860A pdb=" N GLU K 297 " --> pdb=" O ARG K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET K 307 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA K 341 " --> pdb=" O LYS K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'K' and resid 369 through 374 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 117 through 133 Processing helix chain 'L' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR L 162 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE L 163 " --> pdb=" O HIS L 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 14 Processing helix chain 'M' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA M 33 " --> pdb=" O THR M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 117 through 133 Processing helix chain 'M' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE M 163 " --> pdb=" O HIS M 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 167 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 20 Processing helix chain 'N' and resid 41 through 45 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 156 through 161 Processing helix chain 'O' and resid 2 through 15 removed outlier: 3.635A pdb=" N GLU O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU O 9 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP O 12 " --> pdb=" O GLU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 21 removed outlier: 4.494A pdb=" N THR O 19 " --> pdb=" O GLN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU O 40 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU O 44 " --> pdb=" O GLU O 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 46 " --> pdb=" O THR O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR O 54 " --> pdb=" O PRO O 50 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 58 " --> pdb=" O TYR O 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA O 77 " --> pdb=" O SER O 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU T 22 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 42 Processing helix chain 'T' and resid 42 through 57 Processing helix chain 'T' and resid 77 through 87 Processing helix chain 'T' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE T 98 " --> pdb=" O ASP T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 179 Processing helix chain 'T' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU T 198 " --> pdb=" O LYS T 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP T 199 " --> pdb=" O GLU T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP T 261 " --> pdb=" O LYS T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE T 277 " --> pdb=" O ILE T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 280 through 286 removed outlier: 3.699A pdb=" N ILE T 284 " --> pdb=" O PRO T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 288 through 303 Proline residue: T 294 - end of helix removed outlier: 3.860A pdb=" N GLU T 297 " --> pdb=" O ARG T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET T 307 " --> pdb=" O THR T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA T 341 " --> pdb=" O LYS T 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 354 through 362 Processing helix chain 'T' and resid 369 through 374 Processing helix chain 'U' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU U 22 " --> pdb=" O ILE U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 42 Processing helix chain 'U' and resid 42 through 57 Processing helix chain 'U' and resid 77 through 87 Processing helix chain 'U' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE U 98 " --> pdb=" O ASP U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 179 Processing helix chain 'U' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS U 186 " --> pdb=" O ASP U 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU U 198 " --> pdb=" O LYS U 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP U 199 " --> pdb=" O GLU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN U 231 " --> pdb=" O GLN U 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP U 261 " --> pdb=" O LYS U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE U 277 " --> pdb=" O ILE U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE U 284 " --> pdb=" O PRO U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 303 Proline residue: U 294 - end of helix removed outlier: 3.861A pdb=" N GLU U 297 " --> pdb=" O ARG U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET U 307 " --> pdb=" O THR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA U 341 " --> pdb=" O LYS U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 362 Processing helix chain 'U' and resid 369 through 374 Processing helix chain 'V' and resid 5 through 14 Processing helix chain 'V' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA V 33 " --> pdb=" O THR V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 83 No H-bonds generated for 'chain 'V' and resid 81 through 83' Processing helix chain 'V' and resid 117 through 133 Processing helix chain 'V' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR V 162 " --> pdb=" O GLU V 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE V 163 " --> pdb=" O HIS V 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR V 167 " --> pdb=" O ILE V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 14 Processing helix chain 'W' and resid 21 through 39 removed outlier: 3.599A pdb=" N ALA W 33 " --> pdb=" O THR W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 83 No H-bonds generated for 'chain 'W' and resid 81 through 83' Processing helix chain 'W' and resid 117 through 133 Processing helix chain 'W' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR W 162 " --> pdb=" O GLU W 158 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE W 163 " --> pdb=" O HIS W 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 20 Processing helix chain 'X' and resid 41 through 45 Processing helix chain 'X' and resid 85 through 103 Processing helix chain 'X' and resid 156 through 161 Processing helix chain 'Y' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP Y 20 " --> pdb=" O ARG Y 16 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU Y 22 " --> pdb=" O ILE Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 42 Processing helix chain 'Y' and resid 42 through 57 Processing helix chain 'Y' and resid 77 through 87 Processing helix chain 'Y' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE Y 98 " --> pdb=" O ASP Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 179 Processing helix chain 'Y' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS Y 186 " --> pdb=" O ASP Y 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU Y 198 " --> pdb=" O LYS Y 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP Y 199 " --> pdb=" O GLU Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN Y 231 " --> pdb=" O GLN Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP Y 261 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 278 removed outlier: 3.640A pdb=" N PHE Y 277 " --> pdb=" O ILE Y 273 " (cutoff:3.500A) Processing helix chain 'Y' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE Y 284 " --> pdb=" O PRO Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 303 Proline residue: Y 294 - end of helix removed outlier: 3.859A pdb=" N GLU Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET Y 307 " --> pdb=" O THR Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 336 through 350 removed outlier: 3.595A pdb=" N ALA Y 341 " --> pdb=" O LYS Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 362 Processing helix chain 'Y' and resid 369 through 374 Processing helix chain 'Z' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Z 22 " --> pdb=" O ILE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 42 Processing helix chain 'Z' and resid 42 through 57 Processing helix chain 'Z' and resid 77 through 87 Processing helix chain 'Z' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE Z 98 " --> pdb=" O ASP Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 179 Processing helix chain 'Z' and resid 180 through 200 removed outlier: 3.510A pdb=" N LYS Z 186 " --> pdb=" O ASP Z 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU Z 198 " --> pdb=" O LYS Z 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP Z 199 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN Z 231 " --> pdb=" O GLN Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE Z 277 " --> pdb=" O ILE Z 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE Z 284 " --> pdb=" O PRO Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 303 Proline residue: Z 294 - end of helix removed outlier: 3.860A pdb=" N GLU Z 297 " --> pdb=" O ARG Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET Z 307 " --> pdb=" O THR Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA Z 341 " --> pdb=" O LYS Z 337 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 362 Processing helix chain 'Z' and resid 369 through 374 Processing helix chain '0' and resid 5 through 14 Processing helix chain '0' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA 0 33 " --> pdb=" O THR 0 29 " (cutoff:3.500A) Processing helix chain '0' and resid 81 through 83 No H-bonds generated for 'chain '0' and resid 81 through 83' Processing helix chain '0' and resid 117 through 133 Processing helix chain '0' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR 0 162 " --> pdb=" O GLU 0 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE 0 164 " --> pdb=" O ILE 0 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR 0 167 " --> pdb=" O ILE 0 163 " (cutoff:3.500A) Processing helix chain '1' and resid 5 through 14 Processing helix chain '1' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA 1 33 " --> pdb=" O THR 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 81 through 83 No H-bonds generated for 'chain '1' and resid 81 through 83' Processing helix chain '1' and resid 117 through 133 Processing helix chain '1' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR 1 162 " --> pdb=" O GLU 1 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE 1 163 " --> pdb=" O HIS 1 159 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 1 164 " --> pdb=" O ILE 1 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR 1 167 " --> pdb=" O ILE 1 163 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 20 Processing helix chain '2' and resid 41 through 45 Processing helix chain '2' and resid 85 through 103 Processing helix chain '2' and resid 156 through 161 Processing helix chain '3' and resid 2 through 15 removed outlier: 3.635A pdb=" N GLU 3 8 " --> pdb=" O LYS 3 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 3 9 " --> pdb=" O LEU 3 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP 3 12 " --> pdb=" O GLU 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 15 through 21 removed outlier: 4.495A pdb=" N THR 3 19 " --> pdb=" O GLN 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU 3 26 " --> pdb=" O ALA 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU 3 40 " --> pdb=" O ALA 3 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU 3 44 " --> pdb=" O GLU 3 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 3 46 " --> pdb=" O THR 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR 3 54 " --> pdb=" O PRO 3 50 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 3 58 " --> pdb=" O TYR 3 54 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS 3 65 " --> pdb=" O ASP 3 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET 3 76 " --> pdb=" O ALA 3 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA 3 77 " --> pdb=" O SER 3 73 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'D' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR D 61 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN D 326 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL D 63 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 324 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP D 65 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'D' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR D 113 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS D 141 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=5, first strand: chain 'D' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU D 206 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 242 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 208 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'E' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR E 61 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN E 326 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL E 63 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 324 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP E 65 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR E 113 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS E 141 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=10, first strand: chain 'E' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU E 206 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 242 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU E 208 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'R' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR R 103 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE R 75 " --> pdb=" O TYR R 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP R 105 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET R 73 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU R 107 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER R 69 " --> pdb=" O THR R 109 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'R' and resid 59 through 61 Processing sheet with id=13, first strand: chain 'R' and resid 139 through 140 removed outlier: 3.811A pdb=" N ALA S 139 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA P 139 " --> pdb=" O THR S 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 139 " --> pdb=" O THR P 148 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'S' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR S 103 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE S 75 " --> pdb=" O TYR S 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP S 105 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET S 73 " --> pdb=" O ASP S 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU S 107 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER S 69 " --> pdb=" O THR S 109 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'S' and resid 59 through 61 Processing sheet with id=16, first strand: chain 'a' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER a 36 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY a 60 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 129 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR a 62 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N SER b 127 " --> pdb=" O TYR a 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN b 147 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL b 131 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU b 145 " --> pdb=" O VAL b 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR b 133 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU b 143 " --> pdb=" O THR b 133 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER b 36 " --> pdb=" O VAL b 53 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'a' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN a 147 " --> pdb=" O THR a 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL a 131 " --> pdb=" O GLU a 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU a 145 " --> pdb=" O VAL a 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR a 133 " --> pdb=" O LEU a 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU a 143 " --> pdb=" O THR a 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY a 60 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 129 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR a 62 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N SER b 127 " --> pdb=" O TYR a 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN b 147 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL b 131 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU b 145 " --> pdb=" O VAL b 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR b 133 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU b 143 " --> pdb=" O THR b 133 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'a' and resid 108 through 112 Processing sheet with id=19, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR B 61 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN B 326 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL B 63 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 324 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 65 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'B' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR B 113 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS B 141 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=23, first strand: chain 'B' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU B 206 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU C 242 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 208 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR C 61 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN C 326 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL C 63 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR C 324 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP C 65 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR C 113 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS C 141 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=28, first strand: chain 'C' and resid 208 through 209 Processing sheet with id=29, first strand: chain 'P' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR P 103 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE P 75 " --> pdb=" O TYR P 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP P 105 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET P 73 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU P 107 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER P 69 " --> pdb=" O THR P 109 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'P' and resid 59 through 61 Processing sheet with id=31, first strand: chain 'Q' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR Q 103 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE Q 75 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP Q 105 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET Q 73 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU Q 107 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER Q 69 " --> pdb=" O THR Q 109 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'Q' and resid 59 through 61 Processing sheet with id=33, first strand: chain 'b' and resid 108 through 112 Processing sheet with id=34, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR A 61 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN A 326 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL A 63 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 324 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 65 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR A 113 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS A 141 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=38, first strand: chain 'A' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU A 206 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU F 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 208 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'F' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR F 61 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN F 326 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 63 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR F 324 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP F 65 " --> pdb=" O LYS F 322 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'F' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR F 113 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS F 141 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'F' and resid 163 through 164 Processing sheet with id=43, first strand: chain 'F' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU F 206 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU J 242 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU F 208 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'G' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR G 103 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE G 75 " --> pdb=" O TYR G 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 105 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET G 73 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU G 107 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 69 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'G' and resid 59 through 61 Processing sheet with id=46, first strand: chain 'G' and resid 139 through 140 removed outlier: 3.811A pdb=" N ALA H 139 " --> pdb=" O THR G 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA L 139 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA M 139 " --> pdb=" O THR L 148 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'H' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR H 103 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE H 75 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP H 105 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET H 73 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU H 107 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 69 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'H' and resid 59 through 61 Processing sheet with id=49, first strand: chain 'I' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER I 36 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 60 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR N 129 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N TYR I 62 " --> pdb=" O SER N 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER N 127 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN N 147 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL N 131 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU N 145 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR N 133 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU N 143 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER N 36 " --> pdb=" O VAL N 53 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'I' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN I 147 " --> pdb=" O THR I 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL I 131 " --> pdb=" O GLU I 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU I 145 " --> pdb=" O VAL I 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR I 133 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU I 143 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 60 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR N 129 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N TYR I 62 " --> pdb=" O SER N 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER N 127 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN N 147 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL N 131 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU N 145 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR N 133 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU N 143 " --> pdb=" O THR N 133 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'I' and resid 108 through 112 Processing sheet with id=52, first strand: chain 'J' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR J 61 " --> pdb=" O ASN J 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN J 326 " --> pdb=" O TYR J 61 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL J 63 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR J 324 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP J 65 " --> pdb=" O LYS J 322 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'J' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS J 141 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'J' and resid 163 through 164 Processing sheet with id=56, first strand: chain 'J' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU J 206 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU K 242 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU J 208 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'K' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR K 61 " --> pdb=" O ASN K 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN K 326 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL K 63 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR K 324 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP K 65 " --> pdb=" O LYS K 322 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'K' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR K 113 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS K 141 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'K' and resid 163 through 164 Processing sheet with id=61, first strand: chain 'K' and resid 208 through 209 Processing sheet with id=62, first strand: chain 'L' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR L 103 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE L 75 " --> pdb=" O TYR L 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP L 105 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET L 73 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU L 107 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER L 69 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'L' and resid 59 through 61 Processing sheet with id=64, first strand: chain 'M' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR M 103 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE M 75 " --> pdb=" O TYR M 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP M 105 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET M 73 " --> pdb=" O ASP M 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU M 107 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 69 " --> pdb=" O THR M 109 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'M' and resid 59 through 61 Processing sheet with id=66, first strand: chain 'N' and resid 108 through 112 Processing sheet with id=67, first strand: chain 'T' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR T 61 " --> pdb=" O ASN T 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN T 326 " --> pdb=" O TYR T 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL T 63 " --> pdb=" O THR T 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR T 324 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP T 65 " --> pdb=" O LYS T 322 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'T' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR T 113 " --> pdb=" O VAL T 124 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'T' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS T 141 " --> pdb=" O GLU T 132 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'T' and resid 163 through 164 Processing sheet with id=71, first strand: chain 'T' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU T 206 " --> pdb=" O LEU U 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU U 242 " --> pdb=" O LEU T 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU T 208 " --> pdb=" O LEU U 242 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'U' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR U 61 " --> pdb=" O ASN U 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN U 326 " --> pdb=" O TYR U 61 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL U 63 " --> pdb=" O THR U 324 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR U 324 " --> pdb=" O VAL U 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP U 65 " --> pdb=" O LYS U 322 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'U' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR U 113 " --> pdb=" O VAL U 124 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'U' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS U 141 " --> pdb=" O GLU U 132 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'U' and resid 163 through 164 Processing sheet with id=76, first strand: chain 'U' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU U 206 " --> pdb=" O LEU Y 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU Y 242 " --> pdb=" O LEU U 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU U 208 " --> pdb=" O LEU Y 242 " (cutoff:3.500A) Processing sheet with id=77, first strand: chain 'V' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR V 103 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE V 75 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP V 105 " --> pdb=" O MET V 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET V 73 " --> pdb=" O ASP V 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU V 107 " --> pdb=" O THR V 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER V 69 " --> pdb=" O THR V 109 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'V' and resid 59 through 61 Processing sheet with id=79, first strand: chain 'V' and resid 139 through 140 removed outlier: 3.810A pdb=" N ALA W 139 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA 0 139 " --> pdb=" O THR W 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA 1 139 " --> pdb=" O THR 0 148 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'W' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR W 103 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE W 75 " --> pdb=" O TYR W 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP W 105 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET W 73 " --> pdb=" O ASP W 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU W 107 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER W 69 " --> pdb=" O THR W 109 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'W' and resid 59 through 61 Processing sheet with id=82, first strand: chain 'X' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER X 36 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY X 60 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 2 129 " --> pdb=" O GLY X 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR X 62 " --> pdb=" O SER 2 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER 2 127 " --> pdb=" O TYR X 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN 2 147 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL 2 131 " --> pdb=" O GLU 2 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU 2 145 " --> pdb=" O VAL 2 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR 2 133 " --> pdb=" O LEU 2 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU 2 143 " --> pdb=" O THR 2 133 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER 2 36 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'X' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN X 147 " --> pdb=" O THR X 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL X 131 " --> pdb=" O GLU X 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU X 145 " --> pdb=" O VAL X 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR X 133 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU X 143 " --> pdb=" O THR X 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY X 60 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 2 129 " --> pdb=" O GLY X 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR X 62 " --> pdb=" O SER 2 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER 2 127 " --> pdb=" O TYR X 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN 2 147 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL 2 131 " --> pdb=" O GLU 2 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU 2 145 " --> pdb=" O VAL 2 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR 2 133 " --> pdb=" O LEU 2 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU 2 143 " --> pdb=" O THR 2 133 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'X' and resid 108 through 112 Processing sheet with id=85, first strand: chain 'Y' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR Y 61 " --> pdb=" O ASN Y 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN Y 326 " --> pdb=" O TYR Y 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL Y 63 " --> pdb=" O THR Y 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR Y 324 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP Y 65 " --> pdb=" O LYS Y 322 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'Y' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR Y 113 " --> pdb=" O VAL Y 124 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'Y' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS Y 141 " --> pdb=" O GLU Y 132 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'Y' and resid 163 through 164 Processing sheet with id=89, first strand: chain 'Y' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU Y 206 " --> pdb=" O LEU Z 240 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU Z 242 " --> pdb=" O LEU Y 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU Y 208 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'Z' and resid 60 through 66 removed outlier: 4.924A pdb=" N TYR Z 61 " --> pdb=" O ASN Z 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN Z 326 " --> pdb=" O TYR Z 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL Z 63 " --> pdb=" O THR Z 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR Z 324 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP Z 65 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'Z' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR Z 113 " --> pdb=" O VAL Z 124 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'Z' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS Z 141 " --> pdb=" O GLU Z 132 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'Z' and resid 163 through 164 Processing sheet with id=94, first strand: chain 'Z' and resid 208 through 209 Processing sheet with id=95, first strand: chain '0' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR 0 103 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE 0 75 " --> pdb=" O TYR 0 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP 0 105 " --> pdb=" O MET 0 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET 0 73 " --> pdb=" O ASP 0 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU 0 107 " --> pdb=" O THR 0 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 0 69 " --> pdb=" O THR 0 109 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain '0' and resid 59 through 61 Processing sheet with id=97, first strand: chain '1' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR 1 103 " --> pdb=" O ILE 1 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE 1 75 " --> pdb=" O TYR 1 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP 1 105 " --> pdb=" O MET 1 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET 1 73 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU 1 107 " --> pdb=" O THR 1 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 1 69 " --> pdb=" O THR 1 109 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain '1' and resid 59 through 61 Processing sheet with id=99, first strand: chain '2' and resid 108 through 112 2967 hydrogen bonds defined for protein. 8334 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: 25.71 Time building geometry restraints manager: 14.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1902 1.03 - 1.23: 81 1.23 - 1.42: 25014 1.42 - 1.61: 36165 1.61 - 1.81: 534 Bond restraints: 63696 Sorted by residual: bond pdb=" CB TRP L 131 " pdb=" CG TRP L 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP V 131 " pdb=" CG TRP V 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP R 131 " pdb=" CG TRP R 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP P 131 " pdb=" CG TRP P 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 bond pdb=" CB TRP G 131 " pdb=" CG TRP G 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 ... (remaining 63691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 84532 1.85 - 3.69: 3153 3.69 - 5.54: 218 5.54 - 7.39: 24 7.39 - 9.23: 6 Bond angle restraints: 87933 Sorted by residual: angle pdb=" CB ARG O 62 " pdb=" CG ARG O 62 " pdb=" CD ARG O 62 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" CB ARG x 62 " pdb=" CG ARG x 62 " pdb=" CD ARG x 62 " ideal model delta sigma weight residual 111.30 120.52 -9.22 2.30e+00 1.89e-01 1.61e+01 angle pdb=" CB ARG 3 62 " pdb=" CG ARG 3 62 " pdb=" CD ARG 3 62 " ideal model delta sigma weight residual 111.30 120.51 -9.21 2.30e+00 1.89e-01 1.60e+01 angle pdb=" N LYS B 263 " pdb=" CA LYS B 263 " pdb=" C LYS B 263 " ideal model delta sigma weight residual 111.33 115.81 -4.48 1.21e+00 6.83e-01 1.37e+01 angle pdb=" N LYS Y 263 " pdb=" CA LYS Y 263 " pdb=" C LYS Y 263 " ideal model delta sigma weight residual 111.33 115.80 -4.47 1.21e+00 6.83e-01 1.37e+01 ... (remaining 87928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 35484 17.96 - 35.92: 2499 35.92 - 53.88: 267 53.88 - 71.84: 87 71.84 - 89.80: 75 Dihedral angle restraints: 38412 sinusoidal: 16020 harmonic: 22392 Sorted by residual: dihedral pdb=" CA MET I 19 " pdb=" C MET I 19 " pdb=" N ASP I 20 " pdb=" CA ASP I 20 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET X 19 " pdb=" C MET X 19 " pdb=" N ASP X 20 " pdb=" CA ASP X 20 " ideal model delta harmonic sigma weight residual 180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET a 19 " pdb=" C MET a 19 " pdb=" N ASP a 20 " pdb=" CA ASP a 20 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 38409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7035 0.054 - 0.107: 2054 0.107 - 0.161: 403 0.161 - 0.215: 12 0.215 - 0.268: 12 Chirality restraints: 9516 Sorted by residual: chirality pdb=" CA TYR B 230 " pdb=" N TYR B 230 " pdb=" C TYR B 230 " pdb=" CB TYR B 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA TYR Y 230 " pdb=" N TYR Y 230 " pdb=" C TYR Y 230 " pdb=" CB TYR Y 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR J 230 " pdb=" N TYR J 230 " pdb=" C TYR J 230 " pdb=" CB TYR J 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 9513 not shown) Planarity restraints: 11052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 27 " 0.002 2.00e-02 2.50e+03 2.85e-02 1.62e+01 pdb=" CG TYR I 27 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR I 27 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR I 27 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 27 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR I 27 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 27 " -0.038 2.00e-02 2.50e+03 pdb=" OH TYR I 27 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 27 " -0.002 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR b 27 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR b 27 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR b 27 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR b 27 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR b 27 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR b 27 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR b 27 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 27 " -0.002 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR a 27 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR a 27 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR a 27 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR a 27 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR a 27 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR a 27 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR a 27 " -0.041 2.00e-02 2.50e+03 ... (remaining 11049 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.11: 138 1.11 - 1.98: 624 1.98 - 2.85: 31216 2.85 - 3.73: 131614 3.73 - 4.60: 236946 Warning: very small nonbonded interaction distances. Nonbonded interactions: 400538 Sorted by model distance: nonbonded pdb=" HA THR x 2 " pdb=" HZ2 LYS 3 4 " model vdw 0.237 2.270 nonbonded pdb=" HZ2 LYS O 4 " pdb=" HA THR 3 2 " model vdw 0.238 2.270 nonbonded pdb=" HZ2 LYS x 4 " pdb=" HA THR O 2 " model vdw 0.238 2.270 nonbonded pdb=" HD3 LYS O 23 " pdb=" HB1 ALA 3 18 " model vdw 0.250 2.440 nonbonded pdb=" HD3 LYS x 23 " pdb=" HB1 ALA O 18 " model vdw 0.250 2.440 ... (remaining 400533 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: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain '2' selection = chain 'I' selection = chain 'N' selection = chain 'X' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain '3' selection = chain 'O' selection = chain 'x' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'T' selection = chain 'U' selection = chain 'Y' 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: 1.560 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: 1.330 Extract box with map and model: 1.790 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 97.430 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 : 0.006 0.044 61794 Z= 0.411 Angle : 0.794 9.232 83604 Z= 0.478 Chirality : 0.051 0.268 9516 Planarity : 0.011 0.108 10818 Dihedral : 13.198 89.799 23460 Min Nonbonded Distance : 0.497 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -1.42 (0.08), residues: 7590 helix: -0.79 (0.08), residues: 2997 sheet: -0.07 (0.16), residues: 948 loop : -1.22 (0.09), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.004 0.001 HIS N 54 PHE 0.027 0.002 PHE X 48 TYR 0.042 0.006 TYR I 27 ARG 0.023 0.004 ARG 2 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2426 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2426 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 260 LEU cc_start: 0.8657 (mt) cc_final: 0.8266 (mp) REVERT: E 29 ASN cc_start: 0.8665 (t0) cc_final: 0.8232 (t0) REVERT: E 54 ASP cc_start: 0.7662 (m-30) cc_final: 0.6409 (m-30) REVERT: R 142 ILE cc_start: 0.8615 (tt) cc_final: 0.8293 (tt) REVERT: R 170 VAL cc_start: 0.6797 (t) cc_final: 0.6488 (t) REVERT: S 133 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8285 (mttm) REVERT: a 126 MET cc_start: 0.8464 (tmm) cc_final: 0.7511 (pmm) REVERT: a 134 ASP cc_start: 0.6539 (t70) cc_final: 0.6076 (t0) REVERT: B 330 VAL cc_start: 0.7821 (t) cc_final: 0.7592 (m) REVERT: B 372 MET cc_start: 0.8475 (tpt) cc_final: 0.7104 (tpp) REVERT: C 174 GLN cc_start: 0.7495 (tp40) cc_final: 0.7281 (tp-100) REVERT: C 196 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8396 (ttpt) REVERT: C 357 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7485 (mt-10) REVERT: P 72 LYS cc_start: 0.7619 (tttt) cc_final: 0.7292 (tptm) REVERT: P 80 ILE cc_start: 0.8797 (pt) cc_final: 0.8516 (pt) REVERT: P 110 GLN cc_start: 0.5795 (pt0) cc_final: 0.5581 (pp30) REVERT: Q 126 MET cc_start: 0.8837 (mtm) cc_final: 0.8477 (mtm) REVERT: Q 145 GLU cc_start: 0.7021 (pt0) cc_final: 0.6165 (mm-30) REVERT: b 32 TYR cc_start: 0.6598 (m-80) cc_final: 0.6089 (m-80) REVERT: b 113 LYS cc_start: 0.7324 (mmtp) cc_final: 0.7082 (mmtt) REVERT: A 34 THR cc_start: 0.5800 (p) cc_final: 0.5303 (p) REVERT: A 98 PHE cc_start: 0.4897 (t80) cc_final: 0.4428 (t80) REVERT: A 227 GLN cc_start: 0.5927 (tm-30) cc_final: 0.5654 (tt0) REVERT: A 372 MET cc_start: 0.6389 (tpt) cc_final: 0.6090 (mmm) REVERT: A 376 ARG cc_start: 0.5531 (mtt90) cc_final: 0.4751 (ptm-80) REVERT: F 216 LYS cc_start: 0.7829 (ttpt) cc_final: 0.6755 (mptt) REVERT: F 369 ASP cc_start: 0.5152 (t0) cc_final: 0.4739 (t70) REVERT: J 84 LEU cc_start: 0.5624 (mt) cc_final: 0.5404 (mt) REVERT: J 117 ASP cc_start: 0.3348 (t0) cc_final: 0.2620 (t0) REVERT: J 375 ILE cc_start: 0.7441 (mm) cc_final: 0.6690 (mm) REVERT: K 95 ILE cc_start: 0.6629 (tp) cc_final: 0.5940 (pt) REVERT: K 375 ILE cc_start: 0.5242 (mm) cc_final: 0.4772 (pt) REVERT: L 4 ILE cc_start: 0.2538 (pt) cc_final: 0.1605 (pt) REVERT: L 53 THR cc_start: 0.5843 (p) cc_final: 0.5445 (p) REVERT: M 32 ASN cc_start: 0.4730 (m-40) cc_final: 0.3942 (m-40) REVERT: M 142 ILE cc_start: 0.7843 (tt) cc_final: 0.7497 (mm) REVERT: T 141 LYS cc_start: 0.6832 (pttt) cc_final: 0.6097 (pttt) REVERT: V 4 ILE cc_start: 0.3936 (pt) cc_final: 0.3236 (tt) REVERT: X 19 MET cc_start: 0.4393 (mmt) cc_final: 0.4129 (mmt) REVERT: X 53 VAL cc_start: 0.7097 (t) cc_final: 0.6685 (p) REVERT: X 81 LYS cc_start: 0.5348 (tttt) cc_final: 0.4961 (pttt) REVERT: Y 97 THR cc_start: 0.7303 (m) cc_final: 0.6941 (p) REVERT: Y 145 ASN cc_start: 0.4249 (t0) cc_final: 0.3753 (t0) REVERT: Y 312 THR cc_start: 0.6288 (p) cc_final: 0.5966 (p) REVERT: Z 26 HIS cc_start: 0.6839 (p90) cc_final: 0.6513 (p90) REVERT: Z 90 ASN cc_start: 0.2504 (p0) cc_final: 0.1877 (p0) REVERT: 1 160 ILE cc_start: 0.6869 (mt) cc_final: 0.6637 (mt) outliers start: 0 outliers final: 0 residues processed: 2426 average time/residue: 0.6472 time to fit residues: 2546.8364 Evaluate side-chains 1205 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1205 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 9.9990 chunk 573 optimal weight: 20.0000 chunk 317 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 592 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 360 optimal weight: 10.0000 chunk 441 optimal weight: 7.9990 chunk 686 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN D 223 GLN E 130 GLN E 223 GLN E 236 GLN R 49 GLN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS R 132 HIS R 150 ASN S 2 GLN S 150 ASN a 18 GLN a 23 GLN a 153 GLN B 26 HIS B 200 ASN B 223 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 ASN Q 49 GLN Q 132 HIS b 18 GLN b 153 GLN ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS G 150 ASN H 130 HIS ** H 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 23 GLN I 153 GLN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN J 168 ASN ** J 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 281 GLN J 289 ASN ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN K 170 GLN K 174 GLN K 200 ASN ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN L 130 HIS ** L 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS M 132 HIS ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS N 18 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 GLN ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN ** T 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN U 145 ASN U 200 ASN U 227 GLN ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 349 ASN U 350 ASN ** V 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN W 130 HIS W 150 ASN ** X 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 GLN X 153 GLN Y 145 ASN Y 161 ASN Y 168 ASN Y 174 GLN Y 200 ASN Y 289 ASN Y 373 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 ASN Z 200 ASN Z 289 ASN ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 349 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 84 GLN 0 132 HIS 0 150 ASN 1 114 ASN 1 132 HIS ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 18 GLN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 61794 Z= 0.276 Angle : 0.668 14.719 83604 Z= 0.360 Chirality : 0.044 0.234 9516 Planarity : 0.006 0.171 10818 Dihedral : 5.185 29.651 8313 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.45 % Allowed : 12.79 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -0.11 (0.09), residues: 7590 helix: 0.66 (0.09), residues: 3273 sheet: 0.05 (0.15), residues: 960 loop : -0.76 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 131 HIS 0.008 0.001 HIS A 123 PHE 0.022 0.002 PHE F 299 TYR 0.023 0.002 TYR J 230 ARG 0.020 0.001 ARG x 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1883 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1582 time to evaluate : 5.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8080 (mmp) cc_final: 0.7461 (ttp) REVERT: D 260 LEU cc_start: 0.8885 (mt) cc_final: 0.8334 (mp) REVERT: D 329 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7717 (mp0) REVERT: R 145 GLU cc_start: 0.6800 (mp0) cc_final: 0.6249 (mp0) REVERT: a 126 MET cc_start: 0.7961 (tmm) cc_final: 0.7338 (pmm) REVERT: B 100 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8083 (mtm-85) REVERT: B 372 MET cc_start: 0.8588 (tpt) cc_final: 0.6983 (tpp) REVERT: C 196 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8301 (tttm) REVERT: C 254 ILE cc_start: 0.7569 (pt) cc_final: 0.7233 (mt) REVERT: C 357 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7622 (mt-10) REVERT: b 32 TYR cc_start: 0.6765 (m-80) cc_final: 0.6513 (m-80) REVERT: b 113 LYS cc_start: 0.7135 (mmtp) cc_final: 0.6904 (mmtt) REVERT: x 8 GLU cc_start: 0.6074 (pt0) cc_final: 0.5830 (pt0) REVERT: A 98 PHE cc_start: 0.5986 (t80) cc_final: 0.5753 (t80) REVERT: A 141 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6377 (pttp) REVERT: A 227 GLN cc_start: 0.6516 (tm-30) cc_final: 0.5866 (tt0) REVERT: A 259 ASP cc_start: 0.6941 (m-30) cc_final: 0.6733 (t0) REVERT: A 348 VAL cc_start: 0.7570 (t) cc_final: 0.7369 (p) REVERT: F 84 LEU cc_start: 0.7599 (mm) cc_final: 0.7269 (mm) REVERT: F 321 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6247 (t80) REVERT: F 348 VAL cc_start: 0.7204 (t) cc_final: 0.6954 (t) REVERT: F 353 MET cc_start: 0.6208 (ptm) cc_final: 0.5989 (ptp) REVERT: F 356 ASN cc_start: 0.5905 (m-40) cc_final: 0.5455 (m110) REVERT: G 119 ASP cc_start: 0.4478 (p0) cc_final: 0.4072 (p0) REVERT: G 167 TYR cc_start: 0.6687 (m-80) cc_final: 0.6431 (m-10) REVERT: H 41 MET cc_start: 0.6721 (ptm) cc_final: 0.6324 (ppp) REVERT: I 70 MET cc_start: 0.6290 (mtp) cc_final: 0.6016 (mtp) REVERT: I 128 ILE cc_start: 0.5909 (tt) cc_final: 0.5139 (mt) REVERT: J 84 LEU cc_start: 0.6389 (mt) cc_final: 0.6063 (mt) REVERT: J 259 ASP cc_start: 0.7512 (m-30) cc_final: 0.7114 (m-30) REVERT: J 317 PHE cc_start: 0.6841 (t80) cc_final: 0.6631 (t80) REVERT: K 136 ASN cc_start: 0.7120 (OUTLIER) cc_final: 0.6758 (t0) REVERT: K 224 GLU cc_start: 0.5978 (tt0) cc_final: 0.5584 (tt0) REVERT: K 307 MET cc_start: 0.7329 (mmm) cc_final: 0.6400 (mtt) REVERT: L 94 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6607 (mm) REVERT: M 26 MET cc_start: 0.6740 (tmm) cc_final: 0.6263 (tmm) REVERT: M 100 PRO cc_start: 0.7695 (Cg_exo) cc_final: 0.7479 (Cg_endo) REVERT: M 126 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6697 (ttp) REVERT: N 81 LYS cc_start: 0.5989 (tttm) cc_final: 0.5377 (tttm) REVERT: N 146 ILE cc_start: 0.6904 (mt) cc_final: 0.6676 (mp) REVERT: O 49 MET cc_start: 0.7516 (mpp) cc_final: 0.6946 (mmt) REVERT: T 17 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6978 (mt) REVERT: T 115 TYR cc_start: 0.7992 (t80) cc_final: 0.7491 (t80) REVERT: T 372 MET cc_start: 0.7101 (tpp) cc_final: 0.6487 (tpp) REVERT: U 140 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7757 (mtmt) REVERT: V 105 ASP cc_start: 0.6197 (t0) cc_final: 0.5755 (t0) REVERT: W 41 MET cc_start: 0.8078 (mpp) cc_final: 0.7818 (mpp) REVERT: W 150 ASN cc_start: 0.6176 (m-40) cc_final: 0.5965 (m110) REVERT: W 168 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7117 (ttm170) REVERT: X 30 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7314 (t0) REVERT: X 81 LYS cc_start: 0.6403 (tttt) cc_final: 0.5698 (pttt) REVERT: Y 97 THR cc_start: 0.7586 (m) cc_final: 0.7254 (p) REVERT: Y 257 PHE cc_start: 0.7857 (t80) cc_final: 0.7338 (t80) REVERT: Y 271 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7588 (tppt) REVERT: Y 372 MET cc_start: 0.6544 (tpp) cc_final: 0.5762 (ttm) REVERT: Z 97 THR cc_start: 0.6849 (m) cc_final: 0.6329 (m) REVERT: Z 141 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7715 (ptpp) REVERT: Z 202 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7000 (p) REVERT: Z 307 MET cc_start: 0.7023 (mmp) cc_final: 0.6814 (mtt) REVERT: Z 337 LYS cc_start: 0.7602 (mttp) cc_final: 0.7386 (mmpt) REVERT: Z 338 GLU cc_start: 0.7682 (tp30) cc_final: 0.6228 (mm-30) REVERT: 0 1 MET cc_start: 0.6257 (ttm) cc_final: 0.5846 (ttm) REVERT: 0 5 THR cc_start: 0.7299 (p) cc_final: 0.6637 (p) REVERT: 0 25 GLU cc_start: 0.8114 (tp30) cc_final: 0.7473 (tm-30) REVERT: 0 79 GLU cc_start: 0.7747 (tt0) cc_final: 0.6970 (pm20) REVERT: 1 26 MET cc_start: 0.7586 (tmm) cc_final: 0.7248 (tmm) REVERT: 1 137 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7240 (mmt90) REVERT: 2 74 LEU cc_start: 0.6793 (mt) cc_final: 0.6458 (mt) REVERT: 2 98 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5360 (ptmt) outliers start: 301 outliers final: 168 residues processed: 1755 average time/residue: 0.5966 time to fit residues: 1760.3555 Evaluate side-chains 1372 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1192 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 153 LYS Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 321 TYR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 131 TRP Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 174 GLN Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 136 ASN Chi-restraints excluded: chain K residue 207 ILE Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain K residue 349 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 92 PHE Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 149 ASN Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 282 VAL Chi-restraints excluded: chain T residue 338 GLU Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 279 VAL Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 349 ASN Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 104 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 50 ASN Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 114 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 271 LYS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 141 LYS Chi-restraints excluded: chain Z residue 143 ILE Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 330 VAL Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 26 MET Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 95 LEU Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 1 residue 35 ILE Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 1 residue 73 MET Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 1 residue 147 VAL Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 2 residue 71 PHE Chi-restraints excluded: chain 2 residue 98 LYS Chi-restraints excluded: chain 2 residue 150 VAL Chi-restraints excluded: chain 3 residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 571 optimal weight: 7.9990 chunk 467 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 687 optimal weight: 9.9990 chunk 742 optimal weight: 20.0000 chunk 612 optimal weight: 0.0980 chunk 682 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 551 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN a 54 HIS B 223 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN Q 130 HIS Q 150 ASN ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A 147 GLN A 170 GLN A 200 ASN A 223 GLN A 291 ASN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 136 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 GLN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN J 130 GLN ** J 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN ** K 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN M 150 ASN M 159 HIS N 29 ASN N 30 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 223 GLN ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 350 ASN U 74 ASN ** U 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 ASN U 223 GLN U 289 ASN U 349 ASN U 350 ASN ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 145 ASN ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 349 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 371 GLN ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 84 GLN 1 138 GLN 1 150 ASN 2 23 GLN 3 15 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 61794 Z= 0.293 Angle : 0.651 14.875 83604 Z= 0.349 Chirality : 0.044 0.294 9516 Planarity : 0.005 0.095 10818 Dihedral : 4.885 32.436 8313 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 33.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.89 % Allowed : 16.82 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.10), residues: 7590 helix: 1.01 (0.09), residues: 3144 sheet: 0.13 (0.16), residues: 936 loop : -0.79 (0.11), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 131 HIS 0.009 0.002 HIS D 343 PHE 0.028 0.002 PHE Z 319 TYR 0.031 0.002 TYR 0 88 ARG 0.009 0.001 ARG U 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1383 time to evaluate : 6.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 THR cc_start: 0.8385 (m) cc_final: 0.8138 (m) REVERT: D 160 ASP cc_start: 0.7656 (t0) cc_final: 0.7322 (t0) REVERT: D 260 LEU cc_start: 0.8903 (mt) cc_final: 0.8347 (mp) REVERT: D 329 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7586 (mp0) REVERT: D 357 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7401 (mt-10) REVERT: E 281 GLN cc_start: 0.7497 (tp40) cc_final: 0.7160 (mm110) REVERT: R 113 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.5922 (m-10) REVERT: S 72 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8141 (ptmt) REVERT: a 126 MET cc_start: 0.8155 (tmm) cc_final: 0.7441 (pmm) REVERT: a 149 THR cc_start: 0.8475 (m) cc_final: 0.8018 (p) REVERT: B 372 MET cc_start: 0.8778 (tpt) cc_final: 0.7432 (tpp) REVERT: C 224 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: P 96 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8589 (ttmm) REVERT: P 98 SER cc_start: 0.8740 (m) cc_final: 0.8483 (p) REVERT: P 126 MET cc_start: 0.8358 (mtm) cc_final: 0.7781 (mtp) REVERT: Q 151 ASN cc_start: 0.8452 (t0) cc_final: 0.8199 (t0) REVERT: b 113 LYS cc_start: 0.7235 (mmtp) cc_final: 0.6996 (mmtt) REVERT: b 146 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8234 (mp) REVERT: x 62 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8701 (mtm110) REVERT: A 105 ASP cc_start: 0.7761 (m-30) cc_final: 0.7403 (m-30) REVERT: A 163 TYR cc_start: 0.5275 (t80) cc_final: 0.4937 (t80) REVERT: A 225 GLU cc_start: 0.6527 (tp30) cc_final: 0.6117 (tp30) REVERT: A 372 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (mmm) REVERT: F 50 ASN cc_start: 0.7867 (t0) cc_final: 0.7300 (m110) REVERT: F 53 ILE cc_start: 0.8906 (mt) cc_final: 0.8646 (mt) REVERT: F 259 ASP cc_start: 0.6635 (m-30) cc_final: 0.6364 (t0) REVERT: F 281 GLN cc_start: 0.7520 (pp30) cc_final: 0.6971 (mm110) REVERT: F 356 ASN cc_start: 0.6675 (m-40) cc_final: 0.5776 (m110) REVERT: F 357 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7583 (tp30) REVERT: G 27 MET cc_start: 0.7932 (mmp) cc_final: 0.7211 (mmm) REVERT: G 167 TYR cc_start: 0.8318 (m-80) cc_final: 0.7982 (m-10) REVERT: H 41 MET cc_start: 0.7201 (ptm) cc_final: 0.6803 (ppp) REVERT: H 85 TYR cc_start: 0.6079 (p90) cc_final: 0.5795 (p90) REVERT: H 145 GLU cc_start: 0.7329 (pt0) cc_final: 0.7094 (pt0) REVERT: I 128 ILE cc_start: 0.7234 (tt) cc_final: 0.6592 (mt) REVERT: J 21 MET cc_start: 0.7721 (tpp) cc_final: 0.7127 (tpp) REVERT: J 79 LYS cc_start: 0.6583 (pptt) cc_final: 0.6296 (pttm) REVERT: J 162 SER cc_start: 0.5016 (t) cc_final: 0.4768 (p) REVERT: J 164 VAL cc_start: 0.7599 (t) cc_final: 0.7313 (m) REVERT: J 228 LEU cc_start: 0.8525 (tp) cc_final: 0.8300 (tp) REVERT: J 259 ASP cc_start: 0.7903 (m-30) cc_final: 0.7358 (m-30) REVERT: K 46 ASN cc_start: 0.8413 (t0) cc_final: 0.7941 (t0) REVERT: K 102 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8576 (p) REVERT: K 115 TYR cc_start: 0.7982 (t80) cc_final: 0.7511 (t80) REVERT: K 116 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.6377 (t60) REVERT: K 307 MET cc_start: 0.8059 (mmm) cc_final: 0.7104 (mtt) REVERT: K 343 HIS cc_start: 0.6827 (t70) cc_final: 0.6548 (t70) REVERT: L 82 PRO cc_start: 0.8208 (Cg_exo) cc_final: 0.7915 (Cg_endo) REVERT: L 85 TYR cc_start: 0.6008 (p90) cc_final: 0.5787 (p90) REVERT: L 128 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8993 (t) REVERT: M 49 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7105 (tt0) REVERT: M 126 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7096 (ttm) REVERT: M 151 ASN cc_start: 0.7505 (t0) cc_final: 0.7295 (t0) REVERT: T 61 TYR cc_start: 0.7838 (m-80) cc_final: 0.7440 (m-80) REVERT: T 186 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8208 (ttmm) REVERT: T 307 MET cc_start: 0.7476 (mpp) cc_final: 0.7157 (mtt) REVERT: T 372 MET cc_start: 0.7724 (tpp) cc_final: 0.7369 (tpp) REVERT: U 33 PHE cc_start: 0.6032 (m-80) cc_final: 0.5749 (m-10) REVERT: U 115 TYR cc_start: 0.7843 (t80) cc_final: 0.7523 (t80) REVERT: U 213 ILE cc_start: 0.7146 (mt) cc_final: 0.6599 (mt) REVERT: V 2 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6153 (tp40) REVERT: V 27 MET cc_start: 0.8397 (mmm) cc_final: 0.7347 (mmm) REVERT: V 43 ASP cc_start: 0.6724 (t0) cc_final: 0.5825 (t70) REVERT: V 94 LEU cc_start: 0.8637 (tp) cc_final: 0.8396 (tp) REVERT: W 26 MET cc_start: 0.8316 (ppp) cc_final: 0.7940 (ttm) REVERT: W 27 MET cc_start: 0.8081 (tpp) cc_final: 0.7817 (mmp) REVERT: W 97 PHE cc_start: 0.7299 (p90) cc_final: 0.7074 (p90) REVERT: W 168 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7492 (ttm170) REVERT: X 63 LEU cc_start: 0.6657 (mt) cc_final: 0.6225 (mt) REVERT: X 113 LYS cc_start: 0.4415 (mmtp) cc_final: 0.3920 (mttt) REVERT: Y 340 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7176 (mt-10) REVERT: Y 372 MET cc_start: 0.6628 (tpp) cc_final: 0.6420 (tpp) REVERT: Z 93 MET cc_start: 0.8529 (ttp) cc_final: 0.8228 (ttm) REVERT: Z 140 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7549 (mtpt) REVERT: Z 141 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8285 (ptpp) REVERT: Z 241 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Z 300 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.6959 (t80) REVERT: Z 309 ASN cc_start: 0.8059 (t0) cc_final: 0.7859 (t0) REVERT: Z 326 ASN cc_start: 0.7402 (m-40) cc_final: 0.6743 (t0) REVERT: 0 25 GLU cc_start: 0.8510 (tp30) cc_final: 0.8067 (tm-30) REVERT: 1 107 GLU cc_start: 0.7926 (tp30) cc_final: 0.7656 (tp30) REVERT: 1 137 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (mmt90) REVERT: 2 151 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5724 (tpp80) REVERT: 3 57 GLU cc_start: 0.9274 (pt0) cc_final: 0.8985 (pt0) outliers start: 331 outliers final: 192 residues processed: 1598 average time/residue: 0.5662 time to fit residues: 1538.2574 Evaluate side-chains 1286 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1075 time to evaluate : 5.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain b residue 146 ILE Chi-restraints excluded: chain x residue 15 GLN Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 125 CYS Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 186 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 279 VAL Chi-restraints excluded: chain T residue 297 GLU Chi-restraints excluded: chain T residue 350 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain V residue 2 GLN Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 93 ILE Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 26 HIS Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 123 HIS Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 362 LEU Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 141 LYS Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 74 THR Chi-restraints excluded: chain 1 residue 93 ILE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 137 ARG Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 124 THR Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 10.0000 chunk 517 optimal weight: 0.9990 chunk 356 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 461 optimal weight: 9.9990 chunk 690 optimal weight: 7.9990 chunk 730 optimal weight: 4.9990 chunk 360 optimal weight: 0.0770 chunk 654 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A 170 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 192 ASN G 84 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN J 168 ASN ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN K 174 GLN ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 ASN ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 ASN M 150 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN T 223 GLN ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 223 GLN ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 30 ASN X 54 HIS Y 223 GLN Y 270 ASN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 114 ASN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 1.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 61794 Z= 0.270 Angle : 0.571 14.569 83604 Z= 0.310 Chirality : 0.043 0.226 9516 Planarity : 0.005 0.080 10818 Dihedral : 4.653 29.870 8313 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 34.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.19 % Allowed : 19.23 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.23 (0.10), residues: 7590 helix: 1.19 (0.09), residues: 3198 sheet: 0.21 (0.16), residues: 960 loop : -0.83 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 116 HIS 0.008 0.001 HIS D 343 PHE 0.020 0.002 PHE Z 157 TYR 0.016 0.002 TYR Z 61 ARG 0.008 0.001 ARG K 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1171 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8078 (mmp) cc_final: 0.7362 (ttp) REVERT: D 104 THR cc_start: 0.8461 (m) cc_final: 0.8223 (m) REVERT: D 160 ASP cc_start: 0.7821 (t0) cc_final: 0.7396 (t0) REVERT: D 260 LEU cc_start: 0.8962 (mt) cc_final: 0.8389 (mp) REVERT: D 329 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7679 (mp0) REVERT: D 357 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7549 (mt-10) REVERT: E 281 GLN cc_start: 0.7683 (tp40) cc_final: 0.7369 (mm110) REVERT: E 352 ILE cc_start: 0.9042 (mt) cc_final: 0.8787 (tp) REVERT: R 113 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6100 (m-10) REVERT: a 126 MET cc_start: 0.8170 (tmm) cc_final: 0.7327 (pmm) REVERT: a 149 THR cc_start: 0.8396 (m) cc_final: 0.7929 (p) REVERT: B 372 MET cc_start: 0.8686 (tpt) cc_final: 0.7466 (tpp) REVERT: C 224 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: C 357 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8106 (mt-10) REVERT: P 96 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8630 (ttmm) REVERT: P 98 SER cc_start: 0.8710 (m) cc_final: 0.8455 (p) REVERT: A 247 LYS cc_start: 0.7782 (mmtp) cc_final: 0.7397 (mtpp) REVERT: A 260 LEU cc_start: 0.8803 (mt) cc_final: 0.8536 (mp) REVERT: A 347 LEU cc_start: 0.9221 (mt) cc_final: 0.8846 (mt) REVERT: F 272 SER cc_start: 0.8972 (m) cc_final: 0.8622 (t) REVERT: F 274 CYS cc_start: 0.7553 (t) cc_final: 0.7280 (t) REVERT: G 27 MET cc_start: 0.8291 (mmp) cc_final: 0.7179 (mmt) REVERT: J 79 LYS cc_start: 0.7131 (pptt) cc_final: 0.6722 (pttp) REVERT: J 187 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7448 (tmm-80) REVERT: J 192 ASN cc_start: 0.8821 (m-40) cc_final: 0.8428 (m-40) REVERT: J 225 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8238 (tm-30) REVERT: J 228 LEU cc_start: 0.8767 (tp) cc_final: 0.8542 (tp) REVERT: J 246 MET cc_start: 0.8954 (mtp) cc_final: 0.8709 (mtm) REVERT: J 291 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7101 (m-40) REVERT: J 333 LEU cc_start: 0.8263 (tp) cc_final: 0.7910 (tp) REVERT: K 19 ARG cc_start: 0.8142 (tmm-80) cc_final: 0.7750 (tmm-80) REVERT: K 21 MET cc_start: 0.8044 (mmm) cc_final: 0.7801 (ttm) REVERT: K 40 SER cc_start: 0.8933 (t) cc_final: 0.8441 (m) REVERT: K 46 ASN cc_start: 0.8202 (t0) cc_final: 0.7991 (t0) REVERT: K 50 ASN cc_start: 0.7039 (m-40) cc_final: 0.6368 (m-40) REVERT: K 51 MET cc_start: 0.7079 (tmm) cc_final: 0.5876 (tmm) REVERT: K 54 ASP cc_start: 0.7727 (m-30) cc_final: 0.7180 (p0) REVERT: K 58 GLU cc_start: 0.7542 (pt0) cc_final: 0.7187 (pm20) REVERT: K 115 TYR cc_start: 0.8370 (t80) cc_final: 0.8139 (t80) REVERT: K 116 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.6506 (t60) REVERT: K 141 LYS cc_start: 0.8045 (ptmt) cc_final: 0.7692 (ptmm) REVERT: K 293 ARG cc_start: 0.7932 (tpt90) cc_final: 0.7713 (tpt90) REVERT: K 307 MET cc_start: 0.7961 (mmm) cc_final: 0.7268 (mtm) REVERT: L 49 GLN cc_start: 0.6971 (tp40) cc_final: 0.6384 (tt0) REVERT: L 79 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7861 (mm-30) REVERT: M 81 ASP cc_start: 0.8503 (p0) cc_final: 0.8254 (p0) REVERT: N 70 MET cc_start: 0.8010 (mmt) cc_final: 0.7340 (mmt) REVERT: O 49 MET cc_start: 0.7623 (mpp) cc_final: 0.7016 (mmt) REVERT: T 58 GLU cc_start: 0.7029 (pp20) cc_final: 0.6822 (tm-30) REVERT: T 61 TYR cc_start: 0.8082 (m-80) cc_final: 0.7828 (m-80) REVERT: T 343 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6216 (t-170) REVERT: T 372 MET cc_start: 0.7946 (tpp) cc_final: 0.7541 (tpp) REVERT: U 54 ASP cc_start: 0.7878 (m-30) cc_final: 0.7665 (m-30) REVERT: U 101 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8324 (mp) REVERT: U 211 ASP cc_start: 0.7123 (m-30) cc_final: 0.6815 (t0) REVERT: V 118 GLU cc_start: 0.6513 (tp30) cc_final: 0.5866 (tm-30) REVERT: V 145 GLU cc_start: 0.6416 (pt0) cc_final: 0.5881 (mt-10) REVERT: W 2 GLN cc_start: 0.8723 (tp40) cc_final: 0.8504 (tp40) REVERT: W 54 LYS cc_start: 0.7530 (mttm) cc_final: 0.7269 (mmtm) REVERT: W 105 ASP cc_start: 0.7709 (t0) cc_final: 0.7361 (t70) REVERT: W 168 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: X 73 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7017 (pp20) REVERT: Y 16 ARG cc_start: 0.7250 (ptp-110) cc_final: 0.7022 (mtm-85) REVERT: Y 152 VAL cc_start: 0.8970 (p) cc_final: 0.8751 (m) REVERT: Y 265 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7038 (p0) REVERT: Y 328 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8316 (mttp) REVERT: Y 340 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7504 (mt-10) REVERT: Y 342 LYS cc_start: 0.8836 (tppt) cc_final: 0.8344 (tppt) REVERT: Y 372 MET cc_start: 0.7476 (tpp) cc_final: 0.7128 (tpp) REVERT: Z 93 MET cc_start: 0.8522 (ttp) cc_final: 0.8274 (ttm) REVERT: Z 150 TYR cc_start: 0.7869 (m-80) cc_final: 0.7174 (m-80) REVERT: Z 225 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6541 (mt-10) REVERT: Z 300 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7289 (t80) REVERT: Z 315 LEU cc_start: 0.9212 (mp) cc_final: 0.8958 (mp) REVERT: 0 79 GLU cc_start: 0.8685 (tt0) cc_final: 0.8275 (tt0) REVERT: 1 50 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8425 (tp) REVERT: 1 79 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6782 (tm-30) REVERT: 3 49 MET cc_start: 0.8582 (mpp) cc_final: 0.8326 (mpp) outliers start: 351 outliers final: 226 residues processed: 1400 average time/residue: 0.5934 time to fit residues: 1418.2908 Evaluate side-chains 1243 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1004 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 119 ASP Chi-restraints excluded: chain M residue 125 CYS Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 128 ILE Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 46 ASN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 105 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 254 ILE Chi-restraints excluded: chain T residue 343 HIS Chi-restraints excluded: chain T residue 346 SER Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 148 ILE Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 279 VAL Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 216 LYS Chi-restraints excluded: chain Y residue 238 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 265 ASP Chi-restraints excluded: chain Y residue 311 LEU Chi-restraints excluded: chain Y residue 322 LYS Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 362 LEU Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 271 LYS Chi-restraints excluded: chain Z residue 279 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 344 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 ASP Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 83 GLU Chi-restraints excluded: chain 0 residue 127 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 50 LEU Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 46 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 10.0000 chunk 414 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 544 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 623 optimal weight: 8.9990 chunk 505 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 chunk 655 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN a 34 ASN B 223 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN C 291 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 HIS ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 130 GLN F 192 ASN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 GLN ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN K 168 ASN ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 223 GLN U 371 GLN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Y 149 ASN Y 168 ASN Y 270 ASN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 ASN ** Z 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 281 GLN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 54 HIS ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 1.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 61794 Z= 0.463 Angle : 0.763 11.389 83604 Z= 0.406 Chirality : 0.047 0.180 9516 Planarity : 0.006 0.067 10818 Dihedral : 5.438 31.386 8313 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 38.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.43 % Allowed : 19.73 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.72 (0.09), residues: 7590 helix: 0.53 (0.09), residues: 3021 sheet: -0.24 (0.16), residues: 972 loop : -1.42 (0.10), residues: 3597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 131 HIS 0.009 0.002 HIS A 343 PHE 0.033 0.003 PHE A 299 TYR 0.037 0.002 TYR 0 88 ARG 0.011 0.001 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 435 poor density : 1013 time to evaluate : 5.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 160 ASP cc_start: 0.8041 (t0) cc_final: 0.7558 (t0) REVERT: D 258 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7885 (mmtp) REVERT: E 81 LEU cc_start: 0.9263 (tt) cc_final: 0.8947 (tt) REVERT: E 281 GLN cc_start: 0.7681 (tp40) cc_final: 0.7469 (mm110) REVERT: E 352 ILE cc_start: 0.8983 (mt) cc_final: 0.8736 (tp) REVERT: R 27 MET cc_start: 0.8021 (mtm) cc_final: 0.7315 (mtp) REVERT: R 113 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6621 (m-10) REVERT: a 126 MET cc_start: 0.8324 (tmm) cc_final: 0.7471 (pmm) REVERT: a 149 THR cc_start: 0.8487 (m) cc_final: 0.8049 (p) REVERT: B 372 MET cc_start: 0.8437 (tpt) cc_final: 0.7378 (tpp) REVERT: C 199 ASP cc_start: 0.8058 (m-30) cc_final: 0.7855 (m-30) REVERT: C 224 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: P 98 SER cc_start: 0.8851 (m) cc_final: 0.8494 (p) REVERT: Q 73 MET cc_start: 0.7621 (ptp) cc_final: 0.7270 (ptm) REVERT: x 62 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8767 (mtm110) REVERT: A 26 HIS cc_start: 0.8161 (p90) cc_final: 0.7910 (p90) REVERT: A 47 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7326 (tpp-160) REVERT: A 129 MET cc_start: 0.8206 (mmm) cc_final: 0.7982 (mmm) REVERT: A 188 SER cc_start: 0.9407 (t) cc_final: 0.9084 (p) REVERT: A 220 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 225 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 247 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7310 (mtpp) REVERT: A 337 LYS cc_start: 0.6057 (pptt) cc_final: 0.5649 (ptpp) REVERT: F 85 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8495 (tp) REVERT: F 176 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8505 (tpp80) REVERT: F 264 GLU cc_start: 0.8552 (mp0) cc_final: 0.8335 (mm-30) REVERT: F 309 ASN cc_start: 0.7335 (m-40) cc_final: 0.6752 (m-40) REVERT: H 76 ASN cc_start: 0.8316 (m-40) cc_final: 0.8058 (m110) REVERT: H 103 TYR cc_start: 0.6988 (m-80) cc_final: 0.6770 (m-10) REVERT: H 105 ASP cc_start: 0.8228 (m-30) cc_final: 0.7755 (t0) REVERT: I 2 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6911 (p0) REVERT: I 70 MET cc_start: 0.7458 (mtp) cc_final: 0.7233 (mtm) REVERT: I 126 MET cc_start: 0.7752 (tmm) cc_final: 0.6710 (pmm) REVERT: J 21 MET cc_start: 0.7662 (tpp) cc_final: 0.7358 (ttp) REVERT: J 187 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7412 (tmm-80) REVERT: J 238 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (p) REVERT: J 333 LEU cc_start: 0.8803 (tp) cc_final: 0.8561 (tt) REVERT: J 340 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: K 54 ASP cc_start: 0.7777 (m-30) cc_final: 0.7150 (m-30) REVERT: K 116 TRP cc_start: 0.7761 (OUTLIER) cc_final: 0.7426 (t60) REVERT: K 307 MET cc_start: 0.7781 (mmm) cc_final: 0.7504 (mtm) REVERT: L 49 GLN cc_start: 0.7344 (tp40) cc_final: 0.6927 (tt0) REVERT: L 72 LYS cc_start: 0.8245 (pptt) cc_final: 0.7870 (pptt) REVERT: M 27 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: O 8 GLU cc_start: 0.3406 (OUTLIER) cc_final: 0.2149 (pt0) REVERT: O 9 LEU cc_start: 0.6291 (mt) cc_final: 0.5539 (mp) REVERT: T 16 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8002 (ttm110) REVERT: T 61 TYR cc_start: 0.8327 (m-80) cc_final: 0.7934 (m-80) REVERT: T 293 ARG cc_start: 0.7641 (tpt90) cc_final: 0.7283 (mmm160) REVERT: U 96 SER cc_start: 0.8742 (m) cc_final: 0.8089 (p) REVERT: U 101 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8507 (mp) REVERT: U 115 TYR cc_start: 0.8174 (t80) cc_final: 0.7700 (t80) REVERT: U 192 ASN cc_start: 0.7968 (m-40) cc_final: 0.7744 (m-40) REVERT: U 261 ASP cc_start: 0.7721 (p0) cc_final: 0.7407 (p0) REVERT: U 336 ASP cc_start: 0.7482 (p0) cc_final: 0.6979 (p0) REVERT: V 2 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7719 (mm-40) REVERT: V 151 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7526 (m-40) REVERT: W 16 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8117 (mttp) REVERT: W 114 ASN cc_start: 0.7589 (m-40) cc_final: 0.7328 (p0) REVERT: W 168 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7788 (ttm170) REVERT: X 3 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6302 (m90) REVERT: Y 148 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8062 (tp) REVERT: Y 150 TYR cc_start: 0.7624 (m-80) cc_final: 0.6854 (m-80) REVERT: Y 229 ASP cc_start: 0.7738 (m-30) cc_final: 0.7515 (m-30) REVERT: Y 259 ASP cc_start: 0.7453 (m-30) cc_final: 0.7112 (m-30) REVERT: Y 265 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7366 (p0) REVERT: Y 333 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8382 (tp) REVERT: Y 340 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7578 (mt-10) REVERT: Y 342 LYS cc_start: 0.8953 (tppt) cc_final: 0.8541 (tppt) REVERT: Y 369 ASP cc_start: 0.7138 (t0) cc_final: 0.6553 (p0) REVERT: Y 372 MET cc_start: 0.7680 (tpp) cc_final: 0.6877 (tpp) REVERT: Z 300 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: Z 372 MET cc_start: 0.6292 (tpp) cc_final: 0.5685 (tmm) REVERT: 0 98 SER cc_start: 0.8659 (m) cc_final: 0.8337 (p) REVERT: 1 97 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8363 (p90) REVERT: 1 113 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.6001 (m-80) outliers start: 435 outliers final: 288 residues processed: 1315 average time/residue: 0.5712 time to fit residues: 1279.5244 Evaluate side-chains 1174 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 860 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 21 GLU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 83 GLU Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 TYR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 23 LYS Chi-restraints excluded: chain x residue 27 ASN Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 122 GLU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 190 MET Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 353 MET Chi-restraints excluded: chain J residue 375 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 119 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 65 ASP Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 343 HIS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 50 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 148 ILE Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 255 SER Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 342 LYS Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain V residue 2 GLN Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 3 HIS Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain X residue 101 ILE Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain Y residue 213 ILE Chi-restraints excluded: chain Y residue 216 LYS Chi-restraints excluded: chain Y residue 238 SER Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 265 ASP Chi-restraints excluded: chain Y residue 322 LYS Chi-restraints excluded: chain Y residue 333 LEU Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 279 VAL Chi-restraints excluded: chain Z residue 292 ILE Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 ASP Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 0 residue 93 ILE Chi-restraints excluded: chain 0 residue 127 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 97 PHE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 127 SER Chi-restraints excluded: chain 2 residue 145 GLU Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 46 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 0.8980 chunk 658 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 429 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 731 optimal weight: 6.9990 chunk 607 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 241 optimal weight: 6.9990 chunk 384 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 GLN ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 84 GLN ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN Y 270 ASN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 350 ASN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 23 GLN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 54 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 1.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61794 Z= 0.224 Angle : 0.508 9.964 83604 Z= 0.277 Chirality : 0.041 0.179 9516 Planarity : 0.004 0.063 10818 Dihedral : 4.636 27.260 8313 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 33.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.12 % Allowed : 22.47 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -0.15 (0.10), residues: 7590 helix: 1.06 (0.09), residues: 3165 sheet: -0.07 (0.16), residues: 936 loop : -1.20 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 116 HIS 0.009 0.001 HIS D 343 PHE 0.015 0.001 PHE Z 157 TYR 0.020 0.001 TYR 1 85 ARG 0.005 0.000 ARG 3 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 976 time to evaluate : 5.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8121 (mmp) cc_final: 0.7390 (ttp) REVERT: D 160 ASP cc_start: 0.7999 (t0) cc_final: 0.7714 (t0) REVERT: E 281 GLN cc_start: 0.7530 (tp40) cc_final: 0.7174 (mm110) REVERT: E 352 ILE cc_start: 0.9035 (mt) cc_final: 0.8780 (tp) REVERT: R 90 ASP cc_start: 0.7216 (t70) cc_final: 0.7014 (t70) REVERT: R 113 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6496 (m-10) REVERT: a 126 MET cc_start: 0.8242 (tmm) cc_final: 0.7375 (pmm) REVERT: a 134 ASP cc_start: 0.7638 (t0) cc_final: 0.6683 (p0) REVERT: a 149 THR cc_start: 0.8402 (m) cc_final: 0.7985 (p) REVERT: B 109 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: B 271 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8435 (tptp) REVERT: B 372 MET cc_start: 0.8482 (tpt) cc_final: 0.7440 (tpp) REVERT: C 44 ILE cc_start: 0.8662 (mp) cc_final: 0.8426 (mp) REVERT: C 199 ASP cc_start: 0.8102 (m-30) cc_final: 0.7877 (m-30) REVERT: C 224 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: P 98 SER cc_start: 0.8753 (m) cc_final: 0.8472 (p) REVERT: Q 73 MET cc_start: 0.7802 (ptp) cc_final: 0.7451 (ptm) REVERT: Q 103 TYR cc_start: 0.7743 (m-80) cc_final: 0.7285 (m-10) REVERT: x 26 GLU cc_start: 0.8532 (mp0) cc_final: 0.8068 (pm20) REVERT: A 21 MET cc_start: 0.7945 (tpp) cc_final: 0.7282 (ttp) REVERT: A 26 HIS cc_start: 0.8164 (p90) cc_final: 0.7906 (p90) REVERT: A 101 LEU cc_start: 0.9018 (mt) cc_final: 0.8781 (mt) REVERT: A 188 SER cc_start: 0.9330 (t) cc_final: 0.8971 (p) REVERT: A 220 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: A 225 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7826 (tt0) REVERT: A 337 LYS cc_start: 0.6062 (pptt) cc_final: 0.5768 (ptpp) REVERT: F 163 TYR cc_start: 0.7144 (t80) cc_final: 0.6853 (t80) REVERT: G 27 MET cc_start: 0.8108 (mmm) cc_final: 0.7124 (mmm) REVERT: H 76 ASN cc_start: 0.8268 (m-40) cc_final: 0.8037 (m110) REVERT: H 103 TYR cc_start: 0.7083 (m-80) cc_final: 0.6882 (m-10) REVERT: I 2 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6510 (p0) REVERT: I 126 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.6797 (pmm) REVERT: J 33 PHE cc_start: 0.8167 (t80) cc_final: 0.7949 (t80) REVERT: J 187 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7432 (tmm-80) REVERT: J 333 LEU cc_start: 0.8718 (tp) cc_final: 0.8504 (tt) REVERT: K 54 ASP cc_start: 0.7289 (m-30) cc_final: 0.7088 (m-30) REVERT: K 97 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8848 (p) REVERT: K 116 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7207 (t60) REVERT: O 8 GLU cc_start: 0.3141 (OUTLIER) cc_final: 0.1928 (pt0) REVERT: O 49 MET cc_start: 0.7935 (mpp) cc_final: 0.7513 (mpp) REVERT: T 61 TYR cc_start: 0.8253 (m-80) cc_final: 0.7920 (m-80) REVERT: T 342 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8427 (mmmt) REVERT: U 101 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8509 (mp) REVERT: U 192 ASN cc_start: 0.7944 (m-40) cc_final: 0.7646 (m-40) REVERT: U 261 ASP cc_start: 0.7645 (p0) cc_final: 0.7292 (p0) REVERT: W 2 GLN cc_start: 0.8860 (tp40) cc_final: 0.8596 (tp40) REVERT: W 16 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7935 (mttp) REVERT: W 27 MET cc_start: 0.8330 (tpp) cc_final: 0.8092 (mmt) REVERT: W 114 ASN cc_start: 0.7665 (m-40) cc_final: 0.7385 (m-40) REVERT: Y 150 TYR cc_start: 0.7600 (m-80) cc_final: 0.6723 (m-80) REVERT: Y 229 ASP cc_start: 0.7666 (m-30) cc_final: 0.7453 (m-30) REVERT: Y 265 ASP cc_start: 0.7725 (m-30) cc_final: 0.7361 (p0) REVERT: Y 333 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8449 (tp) REVERT: Y 342 LYS cc_start: 0.8646 (tppt) cc_final: 0.8165 (tppt) REVERT: Y 369 ASP cc_start: 0.7108 (t0) cc_final: 0.6537 (p0) REVERT: Y 372 MET cc_start: 0.7756 (tpp) cc_final: 0.6977 (tpp) REVERT: Z 26 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6596 (p90) REVERT: Z 31 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8086 (mmmt) REVERT: Z 51 MET cc_start: 0.6886 (ttm) cc_final: 0.6555 (ptp) REVERT: Z 300 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: Z 360 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7982 (tt) REVERT: Z 372 MET cc_start: 0.6316 (tpp) cc_final: 0.5784 (tmm) REVERT: 0 98 SER cc_start: 0.8667 (m) cc_final: 0.8402 (p) outliers start: 279 outliers final: 204 residues processed: 1164 average time/residue: 0.5588 time to fit residues: 1118.9010 Evaluate side-chains 1110 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 889 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 23 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 265 ASP Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 131 TRP Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 105 ASP Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 360 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 148 ILE Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 255 SER Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 266 ILE Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 146 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 238 SER Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 333 LEU Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 292 ILE Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 308 LEU Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 120 LEU Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 127 SER Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 chunk 534 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 chunk 615 optimal weight: 5.9990 chunk 408 optimal weight: 0.0970 chunk 728 optimal weight: 6.9990 chunk 456 optimal weight: 9.9990 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 ASN ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 350 ASN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 1.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 61794 Z= 0.353 Angle : 0.608 8.611 83604 Z= 0.327 Chirality : 0.043 0.159 9516 Planarity : 0.005 0.064 10818 Dihedral : 4.850 27.873 8313 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 35.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.38 % Favored : 94.61 % Rotamer: Outliers : 5.11 % Allowed : 22.59 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -0.36 (0.10), residues: 7590 helix: 0.97 (0.09), residues: 3081 sheet: -0.24 (0.16), residues: 972 loop : -1.34 (0.10), residues: 3537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 116 HIS 0.009 0.002 HIS A 343 PHE 0.027 0.002 PHE A 299 TYR 0.019 0.002 TYR J 115 ARG 0.005 0.001 ARG 3 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 888 time to evaluate : 5.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 LEU cc_start: 0.9241 (tt) cc_final: 0.8941 (tt) REVERT: E 281 GLN cc_start: 0.7560 (tp40) cc_final: 0.7359 (mm110) REVERT: E 352 ILE cc_start: 0.9034 (mt) cc_final: 0.8793 (tp) REVERT: R 113 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: S 28 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7894 (mt) REVERT: a 126 MET cc_start: 0.8302 (tmm) cc_final: 0.7423 (pmm) REVERT: a 134 ASP cc_start: 0.7756 (t0) cc_final: 0.7013 (p0) REVERT: a 149 THR cc_start: 0.8427 (m) cc_final: 0.7991 (p) REVERT: B 109 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: B 372 MET cc_start: 0.8486 (tpt) cc_final: 0.7419 (tpp) REVERT: C 41 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7780 (ptpt) REVERT: C 199 ASP cc_start: 0.8164 (m-30) cc_final: 0.7912 (m-30) REVERT: C 224 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: P 98 SER cc_start: 0.8775 (m) cc_final: 0.8495 (p) REVERT: Q 103 TYR cc_start: 0.7841 (m-80) cc_final: 0.7535 (m-80) REVERT: A 51 MET cc_start: 0.8133 (mtt) cc_final: 0.7794 (mtm) REVERT: A 101 LEU cc_start: 0.9062 (mt) cc_final: 0.8813 (mt) REVERT: A 188 SER cc_start: 0.9396 (t) cc_final: 0.9073 (p) REVERT: A 225 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7843 (tt0) REVERT: A 365 GLU cc_start: 0.8364 (pm20) cc_final: 0.8159 (mp0) REVERT: F 85 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8548 (tp) REVERT: F 146 ASN cc_start: 0.8537 (m110) cc_final: 0.8260 (m-40) REVERT: F 163 TYR cc_start: 0.7255 (t80) cc_final: 0.6894 (t80) REVERT: F 176 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8537 (tpp80) REVERT: G 27 MET cc_start: 0.8104 (mmm) cc_final: 0.7258 (mmm) REVERT: H 76 ASN cc_start: 0.8290 (m-40) cc_final: 0.8078 (m110) REVERT: H 146 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8067 (p) REVERT: I 2 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6229 (p0) REVERT: I 126 MET cc_start: 0.7450 (tmm) cc_final: 0.6684 (pmm) REVERT: I 134 ASP cc_start: 0.7683 (t0) cc_final: 0.7223 (p0) REVERT: J 187 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7294 (tmm-80) REVERT: J 333 LEU cc_start: 0.8851 (tp) cc_final: 0.8636 (tt) REVERT: K 116 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.7115 (t60) REVERT: M 27 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7483 (mtt) REVERT: N 23 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6232 (mp10) REVERT: O 8 GLU cc_start: 0.3393 (OUTLIER) cc_final: 0.2031 (pt0) REVERT: O 9 LEU cc_start: 0.6536 (mt) cc_final: 0.5712 (mp) REVERT: T 33 PHE cc_start: 0.8022 (t80) cc_final: 0.7769 (t80) REVERT: T 61 TYR cc_start: 0.8233 (m-80) cc_final: 0.7914 (m-80) REVERT: U 96 SER cc_start: 0.8739 (m) cc_final: 0.8088 (p) REVERT: U 101 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8538 (mp) REVERT: U 115 TYR cc_start: 0.8171 (t80) cc_final: 0.7758 (t80) REVERT: U 261 ASP cc_start: 0.7481 (p0) cc_final: 0.7163 (p0) REVERT: V 151 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: W 10 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7552 (tpp-160) REVERT: W 16 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7836 (mttp) REVERT: W 114 ASN cc_start: 0.7670 (m-40) cc_final: 0.7329 (m-40) REVERT: Y 148 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8059 (tp) REVERT: Y 150 TYR cc_start: 0.7774 (m-80) cc_final: 0.6638 (m-80) REVERT: Y 229 ASP cc_start: 0.7689 (m-30) cc_final: 0.7477 (m-30) REVERT: Y 265 ASP cc_start: 0.7661 (m-30) cc_final: 0.7261 (p0) REVERT: Y 369 ASP cc_start: 0.7092 (t0) cc_final: 0.6490 (p0) REVERT: Z 26 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6742 (p90) REVERT: Z 31 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8082 (mmmt) REVERT: Z 300 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: Z 372 MET cc_start: 0.6521 (tpp) cc_final: 0.5771 (tmm) REVERT: 0 83 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: 1 37 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8687 (p) REVERT: 1 97 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8090 (p90) outliers start: 346 outliers final: 264 residues processed: 1140 average time/residue: 0.5612 time to fit residues: 1104.6414 Evaluate side-chains 1129 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 842 time to evaluate : 5.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 21 GLU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 TYR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 27 ASN Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 176 ARG Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 151 ASN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 375 ILE Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 265 ASP Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 131 TRP Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 164 ILE Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 105 ASP Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 360 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 148 ILE Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 255 SER Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 146 THR Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain X residue 115 ASN Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 238 SER Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 322 LYS Chi-restraints excluded: chain Y residue 350 ASN Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 213 ILE Chi-restraints excluded: chain Z residue 272 SER Chi-restraints excluded: chain Z residue 282 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 308 LEU Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 43 ASP Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 83 GLU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 97 PHE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 46 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 435 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 463 optimal weight: 10.0000 chunk 496 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 572 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 ASN ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 350 ASN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 1.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61794 Z= 0.204 Angle : 0.489 10.818 83604 Z= 0.266 Chirality : 0.040 0.163 9516 Planarity : 0.004 0.061 10818 Dihedral : 4.439 26.797 8313 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 33.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.56 % Favored : 96.43 % Rotamer: Outliers : 4.17 % Allowed : 23.81 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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 (0.10), residues: 7590 helix: 1.32 (0.10), residues: 3135 sheet: -0.05 (0.17), residues: 936 loop : -1.21 (0.10), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 116 HIS 0.010 0.001 HIS C 343 PHE 0.013 0.001 PHE A 299 TYR 0.019 0.001 TYR 1 85 ARG 0.004 0.000 ARG 3 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 915 time to evaluate : 5.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8102 (mmp) cc_final: 0.7350 (ttp) REVERT: D 104 THR cc_start: 0.8429 (m) cc_final: 0.8169 (m) REVERT: D 129 MET cc_start: 0.8686 (tpp) cc_final: 0.8170 (mmm) REVERT: E 281 GLN cc_start: 0.7635 (tp40) cc_final: 0.7300 (mm110) REVERT: E 352 ILE cc_start: 0.9029 (mt) cc_final: 0.8771 (tp) REVERT: R 90 ASP cc_start: 0.7067 (t70) cc_final: 0.6566 (t70) REVERT: R 113 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: a 126 MET cc_start: 0.8307 (tmm) cc_final: 0.7314 (pmm) REVERT: a 134 ASP cc_start: 0.7732 (t0) cc_final: 0.7060 (p0) REVERT: a 149 THR cc_start: 0.8371 (m) cc_final: 0.7934 (p) REVERT: B 109 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: B 271 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8462 (tptp) REVERT: B 372 MET cc_start: 0.8490 (tpt) cc_final: 0.7439 (tpp) REVERT: C 199 ASP cc_start: 0.8018 (m-30) cc_final: 0.7763 (m-30) REVERT: C 224 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: P 98 SER cc_start: 0.8689 (m) cc_final: 0.8456 (p) REVERT: Q 103 TYR cc_start: 0.7805 (m-80) cc_final: 0.7362 (m-10) REVERT: Q 104 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8149 (ttp) REVERT: A 21 MET cc_start: 0.7514 (tpp) cc_final: 0.6887 (ttp) REVERT: A 101 LEU cc_start: 0.9039 (mt) cc_final: 0.8812 (mt) REVERT: A 188 SER cc_start: 0.9353 (t) cc_final: 0.9055 (p) REVERT: A 225 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7816 (tt0) REVERT: A 365 GLU cc_start: 0.8317 (pm20) cc_final: 0.8107 (mp0) REVERT: F 146 ASN cc_start: 0.8439 (m110) cc_final: 0.8191 (m-40) REVERT: F 163 TYR cc_start: 0.7147 (t80) cc_final: 0.6871 (t80) REVERT: F 281 GLN cc_start: 0.7202 (tp40) cc_final: 0.6925 (mm110) REVERT: F 337 LYS cc_start: 0.6042 (ttpp) cc_final: 0.5825 (ptmm) REVERT: G 27 MET cc_start: 0.8106 (mmm) cc_final: 0.7342 (mmm) REVERT: G 73 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7206 (ptm) REVERT: H 168 ARG cc_start: 0.8463 (ttt90) cc_final: 0.7858 (ttt-90) REVERT: I 80 ASP cc_start: 0.7326 (p0) cc_final: 0.7093 (p0) REVERT: I 126 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6518 (pmm) REVERT: I 134 ASP cc_start: 0.7534 (t0) cc_final: 0.7031 (p0) REVERT: J 41 LYS cc_start: 0.8645 (tppp) cc_final: 0.8382 (mtpp) REVERT: J 187 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7614 (tmm-80) REVERT: J 333 LEU cc_start: 0.8808 (tp) cc_final: 0.8591 (tt) REVERT: K 97 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8890 (p) REVERT: K 116 TRP cc_start: 0.7746 (OUTLIER) cc_final: 0.7150 (t60) REVERT: L 39 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8066 (mm) REVERT: M 27 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7756 (mtt) REVERT: N 70 MET cc_start: 0.7912 (mmm) cc_final: 0.7686 (mpp) REVERT: O 8 GLU cc_start: 0.3224 (OUTLIER) cc_final: 0.1985 (pt0) REVERT: T 16 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7962 (ttm110) REVERT: T 33 PHE cc_start: 0.7985 (t80) cc_final: 0.7750 (t80) REVERT: T 61 TYR cc_start: 0.8191 (m-80) cc_final: 0.7916 (m-80) REVERT: U 96 SER cc_start: 0.8698 (m) cc_final: 0.8019 (p) REVERT: U 101 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8565 (mp) REVERT: U 115 TYR cc_start: 0.8089 (t80) cc_final: 0.7664 (t80) REVERT: U 261 ASP cc_start: 0.7372 (p0) cc_final: 0.7166 (p0) REVERT: U 357 GLU cc_start: 0.8293 (tt0) cc_final: 0.7718 (tp30) REVERT: V 2 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7598 (mm110) REVERT: W 114 ASN cc_start: 0.7783 (m-40) cc_final: 0.7485 (m-40) REVERT: Y 148 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7977 (tp) REVERT: Y 150 TYR cc_start: 0.7721 (m-80) cc_final: 0.6553 (m-80) REVERT: Y 229 ASP cc_start: 0.7650 (m-30) cc_final: 0.7439 (m-30) REVERT: Y 265 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7292 (p0) REVERT: Y 350 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8613 (t0) REVERT: Y 369 ASP cc_start: 0.7064 (t0) cc_final: 0.6466 (p0) REVERT: Z 26 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6696 (p90) REVERT: Z 31 LYS cc_start: 0.8631 (mmtt) cc_final: 0.7982 (mmmt) REVERT: Z 150 TYR cc_start: 0.7834 (m-80) cc_final: 0.6984 (m-80) REVERT: Z 300 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: Z 372 MET cc_start: 0.6404 (tpp) cc_final: 0.5639 (tmm) REVERT: 0 81 ASP cc_start: 0.7233 (t70) cc_final: 0.6658 (t0) REVERT: 0 83 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7908 (pm20) outliers start: 282 outliers final: 224 residues processed: 1106 average time/residue: 0.5811 time to fit residues: 1114.0569 Evaluate side-chains 1110 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 864 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 255 SER Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 307 MET Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 2 GLN Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 146 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 213 ILE Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 265 ASP Chi-restraints excluded: chain Y residue 350 ASN Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain Z residue 213 ILE Chi-restraints excluded: chain Z residue 282 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 308 LEU Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 83 GLU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 120 LEU Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 127 SER Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 6.9990 chunk 698 optimal weight: 10.0000 chunk 636 optimal weight: 2.9990 chunk 679 optimal weight: 5.9990 chunk 697 optimal weight: 4.9990 chunk 408 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 533 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 613 optimal weight: 7.9990 chunk 642 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 ASN ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN W 110 GLN ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN Y 373 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 49 GLN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 1.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 61794 Z= 0.207 Angle : 0.496 8.741 83604 Z= 0.269 Chirality : 0.040 0.148 9516 Planarity : 0.004 0.060 10818 Dihedral : 4.308 25.584 8313 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 33.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 4.14 % Allowed : 24.05 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.16 (0.10), residues: 7590 helix: 1.47 (0.10), residues: 3126 sheet: 0.04 (0.17), residues: 936 loop : -1.15 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 116 HIS 0.010 0.001 HIS C 343 PHE 0.015 0.001 PHE A 299 TYR 0.019 0.001 TYR 1 85 ARG 0.004 0.000 ARG 3 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 880 time to evaluate : 5.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 THR cc_start: 0.8425 (m) cc_final: 0.8160 (m) REVERT: E 281 GLN cc_start: 0.7722 (tp40) cc_final: 0.7344 (mm110) REVERT: E 352 ILE cc_start: 0.9031 (mt) cc_final: 0.8777 (tp) REVERT: R 27 MET cc_start: 0.7940 (mtm) cc_final: 0.7698 (mtp) REVERT: R 90 ASP cc_start: 0.6992 (t70) cc_final: 0.6672 (t70) REVERT: S 28 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7761 (mt) REVERT: a 126 MET cc_start: 0.8321 (tmm) cc_final: 0.7287 (pmm) REVERT: a 134 ASP cc_start: 0.7745 (t0) cc_final: 0.7120 (p0) REVERT: a 149 THR cc_start: 0.8387 (m) cc_final: 0.7937 (p) REVERT: B 109 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: B 271 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8510 (tptp) REVERT: B 372 MET cc_start: 0.8489 (tpt) cc_final: 0.7441 (tpp) REVERT: C 199 ASP cc_start: 0.7992 (m-30) cc_final: 0.7760 (m-30) REVERT: C 224 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: Q 103 TYR cc_start: 0.7639 (m-80) cc_final: 0.7231 (m-10) REVERT: Q 104 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8161 (ttp) REVERT: A 21 MET cc_start: 0.7557 (tpp) cc_final: 0.7209 (ttp) REVERT: A 101 LEU cc_start: 0.9013 (mt) cc_final: 0.8770 (mt) REVERT: A 188 SER cc_start: 0.9346 (t) cc_final: 0.9062 (p) REVERT: A 225 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7832 (tt0) REVERT: A 365 GLU cc_start: 0.8311 (pm20) cc_final: 0.8108 (mp0) REVERT: F 146 ASN cc_start: 0.8434 (m110) cc_final: 0.8206 (m-40) REVERT: F 163 TYR cc_start: 0.7156 (t80) cc_final: 0.6844 (t80) REVERT: F 281 GLN cc_start: 0.7112 (tp40) cc_final: 0.6845 (mm110) REVERT: G 27 MET cc_start: 0.8073 (mmm) cc_final: 0.7418 (mmm) REVERT: I 80 ASP cc_start: 0.7285 (p0) cc_final: 0.7054 (p0) REVERT: I 126 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6578 (pmm) REVERT: I 134 ASP cc_start: 0.7520 (t0) cc_final: 0.7064 (p0) REVERT: J 187 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7613 (tmm-80) REVERT: K 95 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8360 (tp) REVERT: K 116 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7173 (t60) REVERT: L 39 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8069 (mm) REVERT: M 27 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.6714 (mpp) REVERT: N 70 MET cc_start: 0.7926 (mmm) cc_final: 0.7666 (mpp) REVERT: O 8 GLU cc_start: 0.3067 (OUTLIER) cc_final: 0.1686 (pt0) REVERT: O 9 LEU cc_start: 0.6395 (mt) cc_final: 0.5641 (mp) REVERT: T 16 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7945 (ttm110) REVERT: T 33 PHE cc_start: 0.8088 (t80) cc_final: 0.7860 (t80) REVERT: T 61 TYR cc_start: 0.8135 (m-80) cc_final: 0.7871 (m-80) REVERT: U 96 SER cc_start: 0.8657 (m) cc_final: 0.7994 (p) REVERT: U 101 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (mp) REVERT: U 115 TYR cc_start: 0.8064 (t80) cc_final: 0.7626 (t80) REVERT: U 261 ASP cc_start: 0.7564 (p0) cc_final: 0.7202 (p0) REVERT: U 338 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7164 (tm-30) REVERT: U 342 LYS cc_start: 0.8601 (tptm) cc_final: 0.7988 (mmtt) REVERT: U 357 GLU cc_start: 0.8274 (tt0) cc_final: 0.7723 (tp30) REVERT: V 126 MET cc_start: 0.8306 (mtm) cc_final: 0.8089 (mtm) REVERT: V 151 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7461 (m-40) REVERT: W 10 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7424 (ttp-170) REVERT: Y 148 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7938 (tp) REVERT: Y 150 TYR cc_start: 0.7733 (m-80) cc_final: 0.6476 (m-80) REVERT: Y 229 ASP cc_start: 0.7658 (m-30) cc_final: 0.7443 (m-30) REVERT: Y 265 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7204 (p0) REVERT: Y 369 ASP cc_start: 0.7136 (t0) cc_final: 0.6513 (p0) REVERT: Z 26 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6712 (p90) REVERT: Z 31 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8301 (mmmt) REVERT: Z 140 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8128 (ttpt) REVERT: Z 150 TYR cc_start: 0.7814 (m-80) cc_final: 0.6898 (m-80) REVERT: Z 300 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: Z 372 MET cc_start: 0.6421 (tpp) cc_final: 0.5751 (tmm) REVERT: 1 37 SER cc_start: 0.9062 (OUTLIER) cc_final: 0.8594 (p) outliers start: 280 outliers final: 235 residues processed: 1076 average time/residue: 0.5539 time to fit residues: 1034.8641 Evaluate side-chains 1114 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 857 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain a residue 12 VAL Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 323 ILE Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 26 HIS Chi-restraints excluded: chain K residue 51 MET Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain T residue 16 ARG Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 105 ASP Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 360 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 148 ILE Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 255 SER Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 307 MET Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 73 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 146 THR Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 254 ILE Chi-restraints excluded: chain Y residue 265 ASP Chi-restraints excluded: chain Y residue 322 LYS Chi-restraints excluded: chain Y residue 324 THR Chi-restraints excluded: chain Y residue 350 ASN Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 282 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 308 LEU Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 120 LEU Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 127 SER Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 3 residue 53 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 718 optimal weight: 5.9990 chunk 438 optimal weight: 9.9990 chunk 340 optimal weight: 3.9990 chunk 499 optimal weight: 5.9990 chunk 753 optimal weight: 8.9990 chunk 693 optimal weight: 0.9980 chunk 599 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 463 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN O 71 GLN T 145 ASN ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 ASN V 134 GLN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 130 HIS 0 151 ASN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 1.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 61794 Z= 0.142 Angle : 0.454 8.276 83604 Z= 0.245 Chirality : 0.039 0.143 9516 Planarity : 0.004 0.058 10818 Dihedral : 4.024 25.715 8313 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 32.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 2.85 % Allowed : 25.35 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.46 (0.10), residues: 7590 helix: 1.74 (0.10), residues: 3138 sheet: 0.18 (0.16), residues: 1050 loop : -1.04 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 116 HIS 0.010 0.001 HIS D 343 PHE 0.021 0.001 PHE V 113 TYR 0.019 0.001 TYR 1 85 ARG 0.004 0.000 ARG 3 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 916 time to evaluate : 5.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.7972 (mmp) cc_final: 0.7375 (ttp) REVERT: D 104 THR cc_start: 0.8411 (m) cc_final: 0.8130 (m) REVERT: E 281 GLN cc_start: 0.7655 (tp40) cc_final: 0.7415 (mm110) REVERT: E 352 ILE cc_start: 0.8997 (mt) cc_final: 0.8753 (tp) REVERT: E 372 MET cc_start: 0.8628 (tpt) cc_final: 0.8133 (tpp) REVERT: R 27 MET cc_start: 0.7979 (mtm) cc_final: 0.7587 (mtp) REVERT: R 90 ASP cc_start: 0.6884 (t70) cc_final: 0.6519 (t70) REVERT: S 28 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7642 (mt) REVERT: a 80 ASP cc_start: 0.7264 (t70) cc_final: 0.6948 (t70) REVERT: a 126 MET cc_start: 0.8197 (tmm) cc_final: 0.7259 (pmm) REVERT: a 134 ASP cc_start: 0.7715 (t0) cc_final: 0.7159 (p0) REVERT: a 149 THR cc_start: 0.8314 (m) cc_final: 0.7865 (p) REVERT: B 109 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: B 372 MET cc_start: 0.8513 (tpt) cc_final: 0.7389 (tpp) REVERT: C 224 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: b 85 ASP cc_start: 0.4694 (t70) cc_final: 0.4229 (t0) REVERT: A 21 MET cc_start: 0.7488 (tpp) cc_final: 0.7191 (ttp) REVERT: A 101 LEU cc_start: 0.9024 (mt) cc_final: 0.8796 (mt) REVERT: A 188 SER cc_start: 0.9335 (t) cc_final: 0.9060 (p) REVERT: A 225 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7837 (tt0) REVERT: F 163 TYR cc_start: 0.7090 (t80) cc_final: 0.6846 (t80) REVERT: F 165 CYS cc_start: 0.7349 (m) cc_final: 0.6828 (t) REVERT: F 281 GLN cc_start: 0.7056 (tp40) cc_final: 0.6793 (mm110) REVERT: G 27 MET cc_start: 0.8051 (mmm) cc_final: 0.7489 (mmm) REVERT: H 38 LEU cc_start: 0.9052 (mm) cc_final: 0.8795 (mp) REVERT: I 80 ASP cc_start: 0.7285 (p0) cc_final: 0.6507 (p0) REVERT: I 126 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6575 (pmm) REVERT: I 134 ASP cc_start: 0.7524 (t0) cc_final: 0.6944 (p0) REVERT: J 187 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7575 (tmm-80) REVERT: J 361 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7726 (tm-30) REVERT: K 95 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8270 (tp) REVERT: K 116 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.7152 (t60) REVERT: K 291 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7579 (p0) REVERT: L 39 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8011 (mm) REVERT: M 27 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6713 (mpp) REVERT: O 8 GLU cc_start: 0.2891 (OUTLIER) cc_final: 0.1911 (pt0) REVERT: O 9 LEU cc_start: 0.6260 (mt) cc_final: 0.5866 (mp) REVERT: T 33 PHE cc_start: 0.8042 (t80) cc_final: 0.7828 (t80) REVERT: T 61 TYR cc_start: 0.8215 (m-80) cc_final: 0.7941 (m-80) REVERT: U 115 TYR cc_start: 0.8021 (t80) cc_final: 0.7585 (t80) REVERT: U 229 ASP cc_start: 0.8107 (t70) cc_final: 0.7876 (t0) REVERT: U 261 ASP cc_start: 0.7363 (p0) cc_final: 0.7046 (p0) REVERT: U 282 VAL cc_start: 0.9510 (t) cc_final: 0.9048 (t) REVERT: U 338 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7141 (tm-30) REVERT: U 342 LYS cc_start: 0.8509 (tptm) cc_final: 0.7885 (mmtt) REVERT: U 357 GLU cc_start: 0.8231 (tt0) cc_final: 0.7718 (tp30) REVERT: V 126 MET cc_start: 0.8274 (mtm) cc_final: 0.8025 (mtm) REVERT: W 10 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7405 (ttp-170) REVERT: Y 21 MET cc_start: 0.7239 (mmp) cc_final: 0.6995 (ptm) REVERT: Y 148 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8156 (tp) REVERT: Y 150 TYR cc_start: 0.7724 (m-80) cc_final: 0.6421 (m-80) REVERT: Y 229 ASP cc_start: 0.7727 (m-30) cc_final: 0.7525 (m-30) REVERT: Y 350 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8578 (t0) REVERT: Y 369 ASP cc_start: 0.7056 (t0) cc_final: 0.6633 (p0) REVERT: Z 31 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8263 (mmmt) REVERT: Z 150 TYR cc_start: 0.7713 (m-80) cc_final: 0.6715 (m-80) REVERT: Z 271 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8263 (mtpt) REVERT: Z 300 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: Z 372 MET cc_start: 0.6498 (tpp) cc_final: 0.5659 (tmm) REVERT: 0 88 TYR cc_start: 0.5783 (m-80) cc_final: 0.5444 (m-80) REVERT: 1 37 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8590 (t) outliers start: 193 outliers final: 157 residues processed: 1042 average time/residue: 0.5656 time to fit residues: 1014.8998 Evaluate side-chains 1046 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 873 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 15 GLN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 94 ASP Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 224 GLU Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 311 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 274 CYS Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 307 MET Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 104 MET Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 146 THR Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 10 ARG Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 148 ILE Chi-restraints excluded: chain Y residue 350 ASN Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 282 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 308 LEU Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 120 LEU Chi-restraints excluded: chain 1 residue 146 THR Chi-restraints excluded: chain 2 residue 2 ASP Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 3 residue 53 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 8.9990 chunk 476 optimal weight: 9.9990 chunk 638 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 553 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 600 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 616 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 7.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 110 GLN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.112479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099532 restraints weight = 180583.852| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.11 r_work: 0.3490 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 1.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 61794 Z= 0.295 Angle : 0.563 59.186 83604 Z= 0.333 Chirality : 0.042 0.304 9516 Planarity : 0.004 0.198 10818 Dihedral : 4.024 25.579 8313 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 33.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 2.87 % Allowed : 25.37 % Favored : 71.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.96 % 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: 0.47 (0.10), residues: 7590 helix: 1.74 (0.10), residues: 3138 sheet: 0.20 (0.16), residues: 1056 loop : -1.03 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 116 HIS 0.008 0.001 HIS D 343 PHE 0.019 0.001 PHE V 113 TYR 0.017 0.001 TYR 1 85 ARG 0.004 0.000 ARG K 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19478.53 seconds wall clock time: 335 minutes 59.11 seconds (20159.11 seconds total)