Starting phenix.real_space_refine on Wed Nov 20 03:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/11_2024/8hdw_34681.cif" } resolution = 3.0 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 34452 2.51 5 N 9312 2.21 5 O 10584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54552 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "2" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "M" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "N" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "O" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "P" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "Q" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "R" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "S" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "T" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "U" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "V" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "W" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "X" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "Y" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "m" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "n" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "o" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "p" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "q" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "r" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "s" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "t" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "u" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "v" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "w" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "x" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "y" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Time building chain proxies: 27.29, per 1000 atoms: 0.50 Number of scatterers: 54552 At special positions: 0 Unit cell: (195.509, 197.535, 136.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 10584 8.00 N 9312 7.00 C 34452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 6.6 seconds 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 114 sheets defined 21.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain '1' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG 1 73 " --> pdb=" O SER 1 69 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG 2 73 " --> pdb=" O SER 2 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 8 Processing helix chain 'M' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 109 Processing helix chain 'M' and resid 129 through 131 No H-bonds generated for 'chain 'M' and resid 129 through 131' Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL M 136 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER M 190 " --> pdb=" O TYR M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE M 274 " --> pdb=" O PHE M 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN M 294 " --> pdb=" O SER M 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN M 295 " --> pdb=" O LEU M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL M 311 " --> pdb=" O GLN M 307 " (cutoff:3.500A) Proline residue: M 312 - end of helix Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'N' and resid 5 through 8 Processing helix chain 'N' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 109 Processing helix chain 'N' and resid 129 through 131 No H-bonds generated for 'chain 'N' and resid 129 through 131' Processing helix chain 'N' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL N 136 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 168 Processing helix chain 'N' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER N 190 " --> pdb=" O TYR N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE N 274 " --> pdb=" O PHE N 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 294 " --> pdb=" O SER N 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL N 311 " --> pdb=" O GLN N 307 " (cutoff:3.500A) Proline residue: N 312 - end of helix Processing helix chain 'N' and resid 351 through 356 Processing helix chain 'O' and resid 5 through 8 Processing helix chain 'O' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 109 Processing helix chain 'O' and resid 129 through 131 No H-bonds generated for 'chain 'O' and resid 129 through 131' Processing helix chain 'O' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL O 136 " --> pdb=" O LEU O 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 168 Processing helix chain 'O' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER O 190 " --> pdb=" O TYR O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE O 274 " --> pdb=" O PHE O 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN O 294 " --> pdb=" O SER O 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) Proline residue: O 312 - end of helix Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'P' and resid 5 through 8 Processing helix chain 'P' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 109 Processing helix chain 'P' and resid 129 through 131 No H-bonds generated for 'chain 'P' and resid 129 through 131' Processing helix chain 'P' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL P 136 " --> pdb=" O LEU P 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 168 Processing helix chain 'P' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER P 190 " --> pdb=" O TYR P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE P 274 " --> pdb=" O PHE P 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN P 294 " --> pdb=" O SER P 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN P 295 " --> pdb=" O LEU P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL P 311 " --> pdb=" O GLN P 307 " (cutoff:3.500A) Proline residue: P 312 - end of helix Processing helix chain 'P' and resid 351 through 356 Processing helix chain 'Q' and resid 5 through 8 Processing helix chain 'Q' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 109 Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL Q 136 " --> pdb=" O LEU Q 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 168 Processing helix chain 'Q' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER Q 190 " --> pdb=" O TYR Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE Q 274 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN Q 294 " --> pdb=" O SER Q 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN Q 295 " --> pdb=" O LEU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL Q 311 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) Proline residue: Q 312 - end of helix Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'R' and resid 5 through 8 Processing helix chain 'R' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 109 Processing helix chain 'R' and resid 129 through 131 No H-bonds generated for 'chain 'R' and resid 129 through 131' Processing helix chain 'R' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 168 Processing helix chain 'R' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE R 274 " --> pdb=" O PHE R 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 295 " --> pdb=" O LEU R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL R 311 " --> pdb=" O GLN R 307 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 351 through 356 Processing helix chain 'S' and resid 5 through 8 Processing helix chain 'S' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER S 72 " --> pdb=" O LYS S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 109 Processing helix chain 'S' and resid 129 through 131 No H-bonds generated for 'chain 'S' and resid 129 through 131' Processing helix chain 'S' and resid 132 through 140 removed outlier: 3.582A pdb=" N VAL S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 168 Processing helix chain 'S' and resid 186 through 191 removed outlier: 3.798A pdb=" N SER S 190 " --> pdb=" O TYR S 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE S 274 " --> pdb=" O PHE S 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN S 294 " --> pdb=" O SER S 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN S 295 " --> pdb=" O LEU S 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL S 311 " --> pdb=" O GLN S 307 " (cutoff:3.500A) Proline residue: S 312 - end of helix Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'T' and resid 5 through 8 Processing helix chain 'T' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER T 72 " --> pdb=" O LYS T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 109 Processing helix chain 'T' and resid 129 through 131 No H-bonds generated for 'chain 'T' and resid 129 through 131' Processing helix chain 'T' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL T 136 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 168 Processing helix chain 'T' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER T 190 " --> pdb=" O TYR T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE T 274 " --> pdb=" O PHE T 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN T 294 " --> pdb=" O SER T 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN T 295 " --> pdb=" O LEU T 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL T 311 " --> pdb=" O GLN T 307 " (cutoff:3.500A) Proline residue: T 312 - end of helix Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'U' and resid 5 through 8 Processing helix chain 'U' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER U 72 " --> pdb=" O LYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 109 Processing helix chain 'U' and resid 129 through 131 No H-bonds generated for 'chain 'U' and resid 129 through 131' Processing helix chain 'U' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL U 136 " --> pdb=" O LEU U 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER U 190 " --> pdb=" O TYR U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE U 274 " --> pdb=" O PHE U 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN U 294 " --> pdb=" O SER U 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN U 295 " --> pdb=" O LEU U 291 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL U 311 " --> pdb=" O GLN U 307 " (cutoff:3.500A) Proline residue: U 312 - end of helix Processing helix chain 'U' and resid 351 through 356 Processing helix chain 'V' and resid 5 through 8 Processing helix chain 'V' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER V 72 " --> pdb=" O LYS V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 109 Processing helix chain 'V' and resid 129 through 131 No H-bonds generated for 'chain 'V' and resid 129 through 131' Processing helix chain 'V' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER V 190 " --> pdb=" O TYR V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE V 274 " --> pdb=" O PHE V 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN V 294 " --> pdb=" O SER V 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN V 295 " --> pdb=" O LEU V 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL V 311 " --> pdb=" O GLN V 307 " (cutoff:3.500A) Proline residue: V 312 - end of helix Processing helix chain 'V' and resid 351 through 356 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 109 Processing helix chain 'W' and resid 129 through 131 No H-bonds generated for 'chain 'W' and resid 129 through 131' Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 168 Processing helix chain 'W' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER W 190 " --> pdb=" O TYR W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE W 274 " --> pdb=" O PHE W 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN W 294 " --> pdb=" O SER W 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN W 295 " --> pdb=" O LEU W 291 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL W 311 " --> pdb=" O GLN W 307 " (cutoff:3.500A) Proline residue: W 312 - end of helix Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER X 72 " --> pdb=" O LYS X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 109 Processing helix chain 'X' and resid 129 through 131 No H-bonds generated for 'chain 'X' and resid 129 through 131' Processing helix chain 'X' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 168 Processing helix chain 'X' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER X 190 " --> pdb=" O TYR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE X 274 " --> pdb=" O PHE X 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN X 294 " --> pdb=" O SER X 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN X 295 " --> pdb=" O LEU X 291 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL X 311 " --> pdb=" O GLN X 307 " (cutoff:3.500A) Proline residue: X 312 - end of helix Processing helix chain 'X' and resid 351 through 356 Processing helix chain 'Y' and resid 7 through 9 No H-bonds generated for 'chain 'Y' and resid 7 through 9' Processing helix chain 'Y' and resid 69 through 85 removed outlier: 3.589A pdb=" N ARG Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 9 No H-bonds generated for 'chain 'Z' and resid 7 through 9' Processing helix chain 'Z' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG Z 73 " --> pdb=" O SER Z 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 9 No H-bonds generated for 'chain 'm' and resid 7 through 9' Processing helix chain 'm' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG m 73 " --> pdb=" O SER m 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 9 No H-bonds generated for 'chain 'n' and resid 7 through 9' Processing helix chain 'n' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG n 73 " --> pdb=" O SER n 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 7 through 9 No H-bonds generated for 'chain 'o' and resid 7 through 9' Processing helix chain 'o' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG o 73 " --> pdb=" O SER o 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 9 No H-bonds generated for 'chain 'p' and resid 7 through 9' Processing helix chain 'p' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG p 73 " --> pdb=" O SER p 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG q 73 " --> pdb=" O SER q 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG r 73 " --> pdb=" O SER r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG s 73 " --> pdb=" O SER s 69 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG t 73 " --> pdb=" O SER t 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG u 73 " --> pdb=" O SER u 69 " (cutoff:3.500A) Processing helix chain 'v' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG v 73 " --> pdb=" O SER v 69 " (cutoff:3.500A) Processing helix chain 'w' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG w 73 " --> pdb=" O SER w 69 " (cutoff:3.500A) Processing helix chain 'x' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG x 73 " --> pdb=" O SER x 69 " (cutoff:3.500A) Processing helix chain 'y' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG y 73 " --> pdb=" O SER y 69 " (cutoff:3.500A) Processing helix chain 'z' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG z 73 " --> pdb=" O SER z 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU 1 101 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY 1 102 " --> pdb=" O THR 1 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR 1 128 " --> pdb=" O GLN 1 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 1 59 " --> pdb=" O THR 1 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 39 through 43 Processing sheet with id=AA5, first strand: chain '1' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA 2 59 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR 2 128 " --> pdb=" O GLN 2 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 6 through 7 removed outlier: 6.881A pdb=" N TYR 2 6 " --> pdb=" O GLN r 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU 2 101 " --> pdb=" O ASP 2 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY 2 102 " --> pdb=" O THR 2 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 39 through 43 Processing sheet with id=AA9, first strand: chain '2' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA w 59 " --> pdb=" O THR w 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR w 128 " --> pdb=" O GLN w 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.184A pdb=" N ASN M 11 " --> pdb=" O ILE N 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 15 through 16 removed outlier: 6.316A pdb=" N THR M 15 " --> pdb=" O MET N 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU M 122 " --> pdb=" O MET M 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'M' and resid 251 through 252 Processing sheet with id=AB6, first strand: chain 'M' and resid 342 through 343 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.859A pdb=" N TYR M 375 " --> pdb=" O ALA S 360 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA S 362 " --> pdb=" O TYR M 375 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL M 377 " --> pdb=" O ALA S 362 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN S 364 " --> pdb=" O VAL M 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 381 through 382 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.386A pdb=" N ASN N 11 " --> pdb=" O ILE Q 378 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR Q 375 " --> pdb=" O ALA W 360 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA W 362 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL Q 377 " --> pdb=" O ALA W 362 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN W 364 " --> pdb=" O VAL Q 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU N 122 " --> pdb=" O MET N 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AC3, first strand: chain 'N' and resid 251 through 252 Processing sheet with id=AC4, first strand: chain 'N' and resid 342 through 343 Processing sheet with id=AC5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.705A pdb=" N ASN O 11 " --> pdb=" O ILE P 378 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR P 375 " --> pdb=" O ALA V 360 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA V 362 " --> pdb=" O TYR P 375 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL P 377 " --> pdb=" O ALA V 362 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN V 364 " --> pdb=" O VAL P 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU O 122 " --> pdb=" O MET O 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 47 through 49 Processing sheet with id=AC8, first strand: chain 'O' and resid 251 through 252 Processing sheet with id=AC9, first strand: chain 'O' and resid 342 through 343 Processing sheet with id=AD1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.761A pdb=" N TYR O 375 " --> pdb=" O ALA U 360 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA U 362 " --> pdb=" O TYR O 375 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL O 377 " --> pdb=" O ALA U 362 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN U 364 " --> pdb=" O VAL O 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU P 122 " --> pdb=" O MET P 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 47 through 49 Processing sheet with id=AD4, first strand: chain 'P' and resid 251 through 252 Processing sheet with id=AD5, first strand: chain 'P' and resid 342 through 343 Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.578A pdb=" N ASN Q 11 " --> pdb=" O ILE R 378 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR R 375 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA X 362 " --> pdb=" O TYR R 375 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL R 377 " --> pdb=" O ALA X 362 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN X 364 " --> pdb=" O VAL R 377 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU Q 122 " --> pdb=" O MET Q 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 47 through 49 Processing sheet with id=AD9, first strand: chain 'Q' and resid 251 through 252 Processing sheet with id=AE1, first strand: chain 'Q' and resid 342 through 343 Processing sheet with id=AE2, first strand: chain 'R' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU R 122 " --> pdb=" O MET R 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 47 through 49 Processing sheet with id=AE4, first strand: chain 'R' and resid 251 through 252 Processing sheet with id=AE5, first strand: chain 'R' and resid 342 through 343 Processing sheet with id=AE6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N ASN S 11 " --> pdb=" O ILE T 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'S' and resid 15 through 16 removed outlier: 6.369A pdb=" N THR S 15 " --> pdb=" O MET T 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'S' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU S 122 " --> pdb=" O MET S 147 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'S' and resid 251 through 252 Processing sheet with id=AF2, first strand: chain 'S' and resid 376 through 378 Processing sheet with id=AF3, first strand: chain 'S' and resid 381 through 382 Processing sheet with id=AF4, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.414A pdb=" N ASN T 11 " --> pdb=" O ILE W 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'T' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU T 122 " --> pdb=" O MET T 147 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 47 through 49 Processing sheet with id=AF7, first strand: chain 'T' and resid 251 through 252 Processing sheet with id=AF8, first strand: chain 'T' and resid 342 through 343 Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.465A pdb=" N ASN U 11 " --> pdb=" O ILE V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'U' and resid 15 through 16 removed outlier: 6.487A pdb=" N THR U 15 " --> pdb=" O MET V 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'U' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU U 122 " --> pdb=" O MET U 147 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 47 through 49 Processing sheet with id=AG4, first strand: chain 'U' and resid 251 through 252 Processing sheet with id=AG5, first strand: chain 'U' and resid 381 through 382 Processing sheet with id=AG6, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU V 122 " --> pdb=" O MET V 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AG8, first strand: chain 'V' and resid 251 through 252 Processing sheet with id=AG9, first strand: chain 'W' and resid 15 through 16 removed outlier: 6.195A pdb=" N THR W 15 " --> pdb=" O MET X 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'W' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU W 122 " --> pdb=" O MET W 147 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 47 through 49 Processing sheet with id=AH3, first strand: chain 'W' and resid 251 through 252 Processing sheet with id=AH4, first strand: chain 'X' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU X 122 " --> pdb=" O MET X 147 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 47 through 49 Processing sheet with id=AH6, first strand: chain 'X' and resid 251 through 252 Processing sheet with id=AH7, first strand: chain 'Y' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU Y 101 " --> pdb=" O ASP Y 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY Y 102 " --> pdb=" O THR Y 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Y' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR Y 128 " --> pdb=" O GLN Y 111 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA Y 59 " --> pdb=" O THR Y 131 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 39 through 43 Processing sheet with id=AI1, first strand: chain 'Y' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA Z 59 " --> pdb=" O THR Z 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR Z 128 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Z' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU Z 101 " --> pdb=" O ASP Z 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY Z 102 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 39 through 43 removed outlier: 7.957A pdb=" N TYR r 6 " --> pdb=" O TRP Z 49 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE Z 51 " --> pdb=" O TYR r 6 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA m 59 " --> pdb=" O THR m 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR m 128 " --> pdb=" O GLN m 111 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'm' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU m 101 " --> pdb=" O ASP m 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY m 102 " --> pdb=" O THR m 137 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'm' and resid 39 through 43 removed outlier: 7.967A pdb=" N TYR s 6 " --> pdb=" O TRP m 49 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE m 51 " --> pdb=" O TYR s 6 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'm' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA n 59 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR n 128 " --> pdb=" O GLN n 111 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'n' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU n 101 " --> pdb=" O ASP n 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY n 102 " --> pdb=" O THR n 137 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'n' and resid 39 through 43 Processing sheet with id=AJ1, first strand: chain 'n' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA o 59 " --> pdb=" O THR o 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR o 128 " --> pdb=" O GLN o 111 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'o' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU o 101 " --> pdb=" O ASP o 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY o 102 " --> pdb=" O THR o 137 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'o' and resid 39 through 43 removed outlier: 8.113A pdb=" N TYR u 6 " --> pdb=" O TRP o 49 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE o 51 " --> pdb=" O TYR u 6 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'o' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA p 59 " --> pdb=" O THR p 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR p 128 " --> pdb=" O GLN p 111 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'p' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU p 101 " --> pdb=" O ASP p 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY p 102 " --> pdb=" O THR p 137 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'p' and resid 39 through 43 Processing sheet with id=AJ7, first strand: chain 'q' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU q 101 " --> pdb=" O ASP q 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY q 102 " --> pdb=" O THR q 137 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR q 128 " --> pdb=" O GLN q 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA q 59 " --> pdb=" O THR q 131 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 116 through 117 removed outlier: 3.524A pdb=" N THR r 32 " --> pdb=" O ASP q 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA r 59 " --> pdb=" O THR r 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR r 128 " --> pdb=" O GLN r 111 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'r' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU r 101 " --> pdb=" O ASP r 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY r 102 " --> pdb=" O THR r 137 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'r' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA s 59 " --> pdb=" O THR s 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR s 128 " --> pdb=" O GLN s 111 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 's' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU s 101 " --> pdb=" O ASP s 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY s 102 " --> pdb=" O THR s 137 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 's' and resid 39 through 43 Processing sheet with id=AK5, first strand: chain 's' and resid 116 through 117 removed outlier: 3.563A pdb=" N ALA t 59 " --> pdb=" O THR t 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR t 128 " --> pdb=" O GLN t 111 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 't' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU t 101 " --> pdb=" O ASP t 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY t 102 " --> pdb=" O THR t 137 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 't' and resid 39 through 43 Processing sheet with id=AK8, first strand: chain 't' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA u 59 " --> pdb=" O THR u 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR u 128 " --> pdb=" O GLN u 111 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'u' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU u 101 " --> pdb=" O ASP u 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY u 102 " --> pdb=" O THR u 137 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'u' and resid 39 through 43 Processing sheet with id=AL2, first strand: chain 'u' and resid 116 through 117 removed outlier: 3.563A pdb=" N ALA v 59 " --> pdb=" O THR v 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR v 128 " --> pdb=" O GLN v 111 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'v' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU v 101 " --> pdb=" O ASP v 96 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY v 102 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'v' and resid 39 through 43 Processing sheet with id=AL5, first strand: chain 'w' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU w 101 " --> pdb=" O ASP w 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY w 102 " --> pdb=" O THR w 137 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'w' and resid 39 through 43 Processing sheet with id=AL7, first strand: chain 'w' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA x 59 " --> pdb=" O THR x 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR x 128 " --> pdb=" O GLN x 111 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'x' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU x 101 " --> pdb=" O ASP x 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY x 102 " --> pdb=" O THR x 137 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'x' and resid 39 through 43 Processing sheet with id=AM1, first strand: chain 'x' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA y 59 " --> pdb=" O THR y 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR y 128 " --> pdb=" O GLN y 111 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'y' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU y 101 " --> pdb=" O ASP y 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY y 102 " --> pdb=" O THR y 137 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'y' and resid 39 through 43 Processing sheet with id=AM4, first strand: chain 'y' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA z 59 " --> pdb=" O THR z 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR z 128 " --> pdb=" O GLN z 111 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'z' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU z 101 " --> pdb=" O ASP z 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY z 102 " --> pdb=" O THR z 137 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'z' and resid 39 through 43 1646 hydrogen bonds defined for protein. 4545 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: 23.62 Time building geometry restraints manager: 13.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18113 1.34 - 1.46: 9156 1.46 - 1.57: 28003 1.57 - 1.69: 0 1.69 - 1.81: 396 Bond restraints: 55668 Sorted by residual: bond pdb=" CB ARG O 297 " pdb=" CG ARG O 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB ARG P 297 " pdb=" CG ARG P 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB ARG W 297 " pdb=" CG ARG W 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.50e+00 bond pdb=" CB ARG X 297 " pdb=" CG ARG X 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.49e+00 bond pdb=" CB ARG T 297 " pdb=" CG ARG T 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.47e+00 ... (remaining 55663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 75367 3.48 - 6.96: 395 6.96 - 10.43: 24 10.43 - 13.91: 0 13.91 - 17.39: 12 Bond angle restraints: 75798 Sorted by residual: angle pdb=" C PRO U 78 " pdb=" N ARG U 79 " pdb=" CA ARG U 79 " ideal model delta sigma weight residual 122.15 104.76 17.39 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO Q 78 " pdb=" N ARG Q 79 " pdb=" CA ARG Q 79 " ideal model delta sigma weight residual 122.15 104.77 17.38 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO M 78 " pdb=" N ARG M 79 " pdb=" CA ARG M 79 " ideal model delta sigma weight residual 122.15 104.78 17.37 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO N 78 " pdb=" N ARG N 79 " pdb=" CA ARG N 79 " ideal model delta sigma weight residual 122.15 104.78 17.37 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO R 78 " pdb=" N ARG R 79 " pdb=" CA ARG R 79 " ideal model delta sigma weight residual 122.15 104.79 17.36 3.47e+00 8.31e-02 2.50e+01 ... (remaining 75793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 29708 17.96 - 35.92: 2392 35.92 - 53.88: 804 53.88 - 71.84: 270 71.84 - 89.80: 24 Dihedral angle restraints: 33198 sinusoidal: 12594 harmonic: 20604 Sorted by residual: dihedral pdb=" CA TYR R 87 " pdb=" C TYR R 87 " pdb=" N ALA R 88 " pdb=" CA ALA R 88 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TYR V 87 " pdb=" C TYR V 87 " pdb=" N ALA V 88 " pdb=" CA ALA V 88 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA TYR Q 87 " pdb=" C TYR Q 87 " pdb=" N ALA Q 88 " pdb=" CA ALA Q 88 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 33195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5987 0.044 - 0.087: 1961 0.087 - 0.131: 720 0.131 - 0.174: 92 0.174 - 0.218: 18 Chirality restraints: 8778 Sorted by residual: chirality pdb=" CA PHE t 90 " pdb=" N PHE t 90 " pdb=" C PHE t 90 " pdb=" CB PHE t 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE x 90 " pdb=" N PHE x 90 " pdb=" C PHE x 90 " pdb=" CB PHE x 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE v 90 " pdb=" N PHE v 90 " pdb=" C PHE v 90 " pdb=" CB PHE v 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 8775 not shown) Planarity restraints: 9822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE s 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C PHE s 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE s 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO s 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE u 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C PHE u 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE u 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO u 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE v 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C PHE v 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE v 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO v 91 " -0.017 2.00e-02 2.50e+03 ... (remaining 9819 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 444 2.53 - 3.12: 41154 3.12 - 3.72: 80812 3.72 - 4.31: 117204 4.31 - 4.90: 197051 Nonbonded interactions: 436665 Sorted by model distance: nonbonded pdb=" OG1 THR M 10 " pdb=" OE1 GLU T 285 " model vdw 1.939 3.040 nonbonded pdb=" OG1 THR P 10 " pdb=" OE1 GLU S 285 " model vdw 2.098 3.040 nonbonded pdb=" O THR R 197 " pdb=" OG1 THR R 197 " model vdw 2.136 3.040 nonbonded pdb=" O THR S 197 " pdb=" OG1 THR S 197 " model vdw 2.136 3.040 nonbonded pdb=" O THR Q 197 " pdb=" OG1 THR Q 197 " model vdw 2.136 3.040 ... (remaining 436660 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 '1' selection = chain '2' selection = chain 'Y' selection = chain 'Z' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.060 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 109.660 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.460 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 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 0.056 55668 Z= 0.387 Angle : 0.834 17.389 75798 Z= 0.478 Chirality : 0.050 0.218 8778 Planarity : 0.005 0.052 9822 Dihedral : 15.954 89.802 19926 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 11.19 % Allowed : 10.79 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.09), residues: 7080 helix: -0.78 (0.14), residues: 1476 sheet: -0.30 (0.13), residues: 1560 loop : -2.78 (0.08), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP p 127 HIS 0.004 0.001 HIS s 72 PHE 0.035 0.003 PHE m 90 TYR 0.015 0.002 TYR S 131 ARG 0.005 0.001 ARG N 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1914 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 645 poor density : 1269 time to evaluate : 4.469 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: 1 18 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7376 (mtt180) REVERT: 1 80 MET cc_start: 0.8338 (mmm) cc_final: 0.8060 (mmt) REVERT: 1 97 SER cc_start: 0.7983 (m) cc_final: 0.7461 (p) REVERT: 1 112 LYS cc_start: 0.8449 (mttp) cc_final: 0.8066 (mtpt) REVERT: 2 27 ASP cc_start: 0.7623 (m-30) cc_final: 0.7346 (m-30) REVERT: 2 97 SER cc_start: 0.8044 (m) cc_final: 0.7591 (p) REVERT: 2 100 ASN cc_start: 0.7891 (m-40) cc_final: 0.7681 (m-40) REVERT: 2 112 LYS cc_start: 0.8501 (mttp) cc_final: 0.8179 (mtpt) REVERT: 2 120 ASN cc_start: 0.8019 (t0) cc_final: 0.7681 (t0) REVERT: M 117 PHE cc_start: 0.5110 (p90) cc_final: 0.4758 (p90) REVERT: M 123 ASP cc_start: 0.3208 (OUTLIER) cc_final: 0.2954 (p0) REVERT: M 139 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6845 (t) REVERT: M 318 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8605 (mt) REVERT: M 332 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6665 (mt) REVERT: M 341 THR cc_start: 0.8412 (p) cc_final: 0.8006 (t) REVERT: M 383 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7257 (t) REVERT: N 10 THR cc_start: 0.8711 (p) cc_final: 0.8381 (t) REVERT: N 29 GLN cc_start: 0.4280 (pt0) cc_final: 0.2688 (pm20) REVERT: N 48 LYS cc_start: 0.5890 (ttpt) cc_final: 0.4769 (tttm) REVERT: N 59 ASP cc_start: 0.0740 (OUTLIER) cc_final: 0.0413 (t0) REVERT: N 123 ASP cc_start: 0.3075 (OUTLIER) cc_final: 0.2564 (p0) REVERT: N 139 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6814 (t) REVERT: N 210 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6344 (tppp) REVERT: N 252 ASP cc_start: 0.6916 (p0) cc_final: 0.6662 (p0) REVERT: N 256 GLN cc_start: 0.6441 (mp10) cc_final: 0.6190 (mm-40) REVERT: N 287 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7133 (mm-30) REVERT: N 341 THR cc_start: 0.8360 (p) cc_final: 0.8030 (t) REVERT: N 364 GLN cc_start: 0.8119 (mt0) cc_final: 0.7689 (mm110) REVERT: O 29 GLN cc_start: 0.4259 (pt0) cc_final: 0.2574 (pm20) REVERT: O 81 ILE cc_start: 0.4263 (OUTLIER) cc_final: 0.3978 (mm) REVERT: O 123 ASP cc_start: 0.2871 (OUTLIER) cc_final: 0.2379 (p0) REVERT: O 139 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6769 (m) REVERT: O 156 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5842 (mt-10) REVERT: O 169 LYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4492 (ptmm) REVERT: O 287 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7109 (mm-30) REVERT: O 290 SER cc_start: 0.8295 (t) cc_final: 0.7758 (p) REVERT: O 318 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8562 (mt) REVERT: O 341 THR cc_start: 0.8340 (p) cc_final: 0.7944 (t) REVERT: O 364 GLN cc_start: 0.7871 (mt0) cc_final: 0.7635 (mm110) REVERT: P 55 GLU cc_start: 0.4288 (OUTLIER) cc_final: 0.3880 (mp0) REVERT: P 59 ASP cc_start: 0.0600 (OUTLIER) cc_final: 0.0191 (t0) REVERT: P 81 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4436 (mm) REVERT: P 123 ASP cc_start: 0.2968 (OUTLIER) cc_final: 0.2521 (p0) REVERT: P 139 VAL cc_start: 0.6994 (OUTLIER) cc_final: 0.6645 (m) REVERT: P 169 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.4305 (ptmm) REVERT: P 202 ASP cc_start: 0.8012 (m-30) cc_final: 0.7752 (m-30) REVERT: P 252 ASP cc_start: 0.6837 (p0) cc_final: 0.6582 (p0) REVERT: P 290 SER cc_start: 0.7952 (t) cc_final: 0.7507 (p) REVERT: P 321 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7934 (tmm-80) REVERT: Q 48 LYS cc_start: 0.6210 (ttpt) cc_final: 0.5544 (ttpt) REVERT: Q 55 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.3747 (mp0) REVERT: Q 123 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.2723 (p0) REVERT: Q 139 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6801 (t) REVERT: Q 169 LYS cc_start: 0.4636 (OUTLIER) cc_final: 0.4193 (ptmm) REVERT: Q 210 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.6031 (tttp) REVERT: Q 290 SER cc_start: 0.8397 (t) cc_final: 0.8057 (p) REVERT: R 59 ASP cc_start: 0.1278 (OUTLIER) cc_final: 0.0853 (t0) REVERT: R 117 PHE cc_start: 0.4863 (p90) cc_final: 0.4557 (p90) REVERT: R 123 ASP cc_start: 0.2805 (OUTLIER) cc_final: 0.2429 (p0) REVERT: R 139 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6778 (t) REVERT: R 332 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6786 (mt) REVERT: R 341 THR cc_start: 0.8356 (p) cc_final: 0.8060 (t) REVERT: S 32 LEU cc_start: 0.6792 (pp) cc_final: 0.6430 (tt) REVERT: S 55 GLU cc_start: 0.4555 (OUTLIER) cc_final: 0.4054 (mp0) REVERT: S 76 GLN cc_start: 0.6689 (tp40) cc_final: 0.5768 (mm110) REVERT: S 81 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.4041 (mt) REVERT: S 123 ASP cc_start: 0.2851 (OUTLIER) cc_final: 0.2449 (p0) REVERT: S 252 ASP cc_start: 0.7214 (p0) cc_final: 0.6978 (p0) REVERT: S 288 MET cc_start: 0.8069 (mmm) cc_final: 0.7795 (mmt) REVERT: S 290 SER cc_start: 0.8531 (t) cc_final: 0.8294 (p) REVERT: T 17 THR cc_start: 0.6591 (m) cc_final: 0.6183 (m) REVERT: T 23 ARG cc_start: 0.5329 (tpt170) cc_final: 0.3448 (mtm180) REVERT: T 29 GLN cc_start: 0.4113 (pt0) cc_final: 0.3741 (pt0) REVERT: T 32 LEU cc_start: 0.6618 (pp) cc_final: 0.6191 (tt) REVERT: T 48 LYS cc_start: 0.6109 (ttpt) cc_final: 0.5854 (ttpt) REVERT: T 123 ASP cc_start: 0.3466 (OUTLIER) cc_final: 0.3005 (p0) REVERT: T 169 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5503 (ptmm) REVERT: T 318 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7909 (mp) REVERT: U 29 GLN cc_start: 0.4084 (pt0) cc_final: 0.3708 (pt0) REVERT: U 32 LEU cc_start: 0.6565 (pp) cc_final: 0.6087 (tt) REVERT: U 55 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.4039 (mp0) REVERT: U 68 LYS cc_start: 0.5166 (mttt) cc_final: 0.4931 (tptp) REVERT: U 123 ASP cc_start: 0.2427 (OUTLIER) cc_final: 0.1946 (p0) REVERT: U 195 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7519 (ttp) REVERT: U 290 SER cc_start: 0.8602 (t) cc_final: 0.8362 (m) REVERT: U 382 MET cc_start: 0.7657 (ttp) cc_final: 0.7424 (ttm) REVERT: V 29 GLN cc_start: 0.4054 (pt0) cc_final: 0.3708 (pt0) REVERT: V 32 LEU cc_start: 0.6765 (pp) cc_final: 0.6323 (tt) REVERT: V 55 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4438 (mp0) REVERT: V 76 GLN cc_start: 0.6675 (tp40) cc_final: 0.6265 (tp-100) REVERT: V 123 ASP cc_start: 0.2660 (OUTLIER) cc_final: 0.2230 (p0) REVERT: V 252 ASP cc_start: 0.7019 (p0) cc_final: 0.6794 (p0) REVERT: V 367 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5994 (t80) REVERT: W 29 GLN cc_start: 0.4050 (pt0) cc_final: 0.3719 (pt0) REVERT: W 32 LEU cc_start: 0.6666 (pp) cc_final: 0.6223 (tt) REVERT: W 55 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4228 (mp0) REVERT: W 76 GLN cc_start: 0.6713 (tp40) cc_final: 0.6316 (tp-100) REVERT: W 81 ILE cc_start: 0.4027 (OUTLIER) cc_final: 0.3765 (mp) REVERT: W 123 ASP cc_start: 0.2712 (OUTLIER) cc_final: 0.2285 (p0) REVERT: W 204 ASN cc_start: 0.7957 (m-40) cc_final: 0.7660 (m110) REVERT: W 252 ASP cc_start: 0.6804 (p0) cc_final: 0.6526 (p0) REVERT: W 305 MET cc_start: 0.7870 (mmm) cc_final: 0.7594 (mmp) REVERT: W 343 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (m) REVERT: W 367 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: X 55 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.4334 (mp0) REVERT: X 76 GLN cc_start: 0.6517 (tp40) cc_final: 0.5599 (mm110) REVERT: X 123 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2902 (p0) REVERT: X 162 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.4868 (m) REVERT: X 212 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6767 (mptt) REVERT: X 290 SER cc_start: 0.8525 (t) cc_final: 0.8233 (p) REVERT: Y 12 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8243 (t) REVERT: Y 16 ASP cc_start: 0.7654 (t0) cc_final: 0.7315 (t70) REVERT: Y 101 GLU cc_start: 0.8127 (tt0) cc_final: 0.7884 (tt0) REVERT: Y 112 LYS cc_start: 0.8477 (mttp) cc_final: 0.8166 (mtpt) REVERT: Y 120 ASN cc_start: 0.7945 (t0) cc_final: 0.7679 (t0) REVERT: Z 12 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8269 (t) REVERT: Z 16 ASP cc_start: 0.7722 (t0) cc_final: 0.7340 (t0) REVERT: Z 31 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8426 (p) REVERT: Z 54 THR cc_start: 0.8264 (p) cc_final: 0.8039 (t) REVERT: Z 112 LYS cc_start: 0.8489 (mttp) cc_final: 0.8203 (mtpt) REVERT: m 3 MET cc_start: 0.3706 (tmm) cc_final: 0.3460 (tmm) REVERT: m 16 ASP cc_start: 0.7805 (t0) cc_final: 0.7387 (t0) REVERT: m 31 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (p) REVERT: m 73 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7925 (tmt90) REVERT: m 96 ASP cc_start: 0.8291 (t0) cc_final: 0.7892 (t0) REVERT: m 101 GLU cc_start: 0.8152 (tt0) cc_final: 0.7924 (tt0) REVERT: n 16 ASP cc_start: 0.7747 (t0) cc_final: 0.7486 (t70) REVERT: n 19 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6769 (ttt-90) REVERT: n 86 ARG cc_start: 0.8148 (ttt90) cc_final: 0.7947 (ttt90) REVERT: n 96 ASP cc_start: 0.8145 (t0) cc_final: 0.7912 (t70) REVERT: n 112 LYS cc_start: 0.8509 (mttp) cc_final: 0.8193 (mtpt) REVERT: n 120 ASN cc_start: 0.7940 (t0) cc_final: 0.7717 (t0) REVERT: o 16 ASP cc_start: 0.7543 (t0) cc_final: 0.7247 (t70) REVERT: o 19 ARG cc_start: 0.7408 (mtp180) cc_final: 0.7184 (ttt-90) REVERT: o 41 MET cc_start: 0.8507 (tpp) cc_final: 0.8111 (tpp) REVERT: o 112 LYS cc_start: 0.8335 (mttp) cc_final: 0.8123 (mtpt) REVERT: p 3 MET cc_start: 0.3456 (tmm) cc_final: 0.3220 (tmm) REVERT: p 16 ASP cc_start: 0.7779 (t0) cc_final: 0.7362 (t0) REVERT: p 19 ARG cc_start: 0.7306 (mtp180) cc_final: 0.6984 (ttt-90) REVERT: p 93 ASP cc_start: 0.7922 (t70) cc_final: 0.7617 (t0) REVERT: p 96 ASP cc_start: 0.8154 (t0) cc_final: 0.7692 (t70) REVERT: p 133 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: q 33 SER cc_start: 0.8398 (p) cc_final: 0.8171 (t) REVERT: q 112 LYS cc_start: 0.8378 (mttp) cc_final: 0.8168 (mtpt) REVERT: q 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: r 76 THR cc_start: 0.8588 (t) cc_final: 0.8379 (m) REVERT: s 3 MET cc_start: 0.2483 (tmm) cc_final: 0.2227 (tmt) REVERT: s 8 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7709 (tpt) REVERT: s 90 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6588 (p90) REVERT: t 33 SER cc_start: 0.8544 (p) cc_final: 0.8173 (t) REVERT: t 97 SER cc_start: 0.7975 (m) cc_final: 0.7536 (p) REVERT: u 24 MET cc_start: 0.8142 (mmm) cc_final: 0.7602 (tpt) REVERT: v 8 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7403 (tpt) REVERT: v 33 SER cc_start: 0.8550 (p) cc_final: 0.8207 (t) REVERT: v 90 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7169 (p90) REVERT: w 3 MET cc_start: 0.2671 (tmm) cc_final: 0.2226 (tmt) REVERT: w 12 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8123 (m) REVERT: w 31 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8098 (p) REVERT: w 32 THR cc_start: 0.8652 (p) cc_final: 0.8419 (t) REVERT: w 64 LYS cc_start: 0.8956 (mttt) cc_final: 0.8723 (mtmm) REVERT: w 133 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: x 16 ASP cc_start: 0.8101 (t0) cc_final: 0.7641 (t70) REVERT: x 80 MET cc_start: 0.8218 (mmm) cc_final: 0.8013 (mmt) REVERT: x 97 SER cc_start: 0.7875 (m) cc_final: 0.7359 (p) REVERT: x 112 LYS cc_start: 0.8658 (mttp) cc_final: 0.8252 (mtpt) REVERT: y 1 MET cc_start: 0.2217 (mtp) cc_final: 0.1943 (mpt) REVERT: y 12 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (m) REVERT: y 97 SER cc_start: 0.8022 (m) cc_final: 0.7685 (p) REVERT: y 112 LYS cc_start: 0.8535 (mttp) cc_final: 0.8187 (mtpt) REVERT: y 120 ASN cc_start: 0.7960 (t0) cc_final: 0.7636 (t0) REVERT: y 133 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: z 1 MET cc_start: 0.2599 (mtp) cc_final: 0.2128 (mtt) REVERT: z 16 ASP cc_start: 0.8027 (t0) cc_final: 0.7688 (t70) REVERT: z 31 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8200 (m) REVERT: z 64 LYS cc_start: 0.8977 (mttt) cc_final: 0.8662 (mtmm) REVERT: z 97 SER cc_start: 0.8066 (m) cc_final: 0.7466 (p) REVERT: z 112 LYS cc_start: 0.8387 (mttp) cc_final: 0.8176 (mtpt) outliers start: 645 outliers final: 260 residues processed: 1728 average time/residue: 1.3280 time to fit residues: 2971.0487 Evaluate side-chains 1226 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 327 poor density : 899 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 94 PHE Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 123 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 LYS Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 169 LYS Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 208 THR Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 209 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 169 LYS Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 318 LEU Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 195 MET Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 343 THR Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 343 THR Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 212 LYS Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 31 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 94 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 31 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 133 GLU Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 94 PHE Chi-restraints excluded: chain r residue 95 ILE Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 12 THR Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 31 THR Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 31 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 61 VAL Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 94 PHE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 31 THR Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 12 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 31 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 12 THR Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 31 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 61 VAL Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 12 THR Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 31 THR Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 12 THR Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 31 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 90 PHE Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 6.9990 chunk 536 optimal weight: 9.9990 chunk 297 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 554 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 337 optimal weight: 0.3980 chunk 413 optimal weight: 0.0050 chunk 642 optimal weight: 10.0000 overall best weight: 2.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 100 ASN 1 121 ASN 2 121 ASN N 307 GLN O 307 GLN P 295 ASN U 317 GLN p 121 ASN q 121 ASN r 120 ASN v 121 ASN x 121 ASN y 100 ASN y 121 ASN z 100 ASN z 121 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55668 Z= 0.188 Angle : 0.640 8.881 75798 Z= 0.345 Chirality : 0.046 0.155 8778 Planarity : 0.005 0.045 9822 Dihedral : 10.280 75.207 8204 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 8.97 % Allowed : 17.66 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.09), residues: 7080 helix: -0.00 (0.14), residues: 1476 sheet: -0.16 (0.13), residues: 1410 loop : -2.43 (0.08), residues: 4194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP w 127 HIS 0.005 0.001 HIS V 34 PHE 0.028 0.002 PHE q 90 TYR 0.017 0.002 TYR O 67 ARG 0.008 0.001 ARG R 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1553 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 517 poor density : 1036 time to evaluate : 6.032 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: 1 93 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7201 (t0) REVERT: 1 97 SER cc_start: 0.8109 (m) cc_final: 0.7603 (p) REVERT: 1 112 LYS cc_start: 0.8424 (mttp) cc_final: 0.8045 (mtpt) REVERT: 2 12 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8426 (m) REVERT: 2 27 ASP cc_start: 0.7492 (m-30) cc_final: 0.7257 (m-30) REVERT: 2 31 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8080 (m) REVERT: 2 97 SER cc_start: 0.8012 (m) cc_final: 0.7701 (p) REVERT: 2 100 ASN cc_start: 0.7959 (m-40) cc_final: 0.7658 (m-40) REVERT: 2 112 LYS cc_start: 0.8420 (mttp) cc_final: 0.8168 (mtpt) REVERT: 2 120 ASN cc_start: 0.7694 (t0) cc_final: 0.7456 (t0) REVERT: 2 133 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: M 40 GLN cc_start: 0.3607 (OUTLIER) cc_final: 0.2566 (mp10) REVERT: M 55 GLU cc_start: 0.4154 (OUTLIER) cc_final: 0.2012 (pp20) REVERT: M 117 PHE cc_start: 0.5106 (p90) cc_final: 0.4806 (p90) REVERT: M 332 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6489 (tm) REVERT: N 29 GLN cc_start: 0.4260 (pt0) cc_final: 0.3965 (pt0) REVERT: N 48 LYS cc_start: 0.5804 (ttpt) cc_final: 0.4699 (tttm) REVERT: N 139 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6879 (t) REVERT: N 147 MET cc_start: 0.2407 (tpp) cc_final: 0.1949 (tpp) REVERT: N 195 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7080 (mtp) REVERT: N 341 THR cc_start: 0.8211 (p) cc_final: 0.7993 (t) REVERT: O 10 THR cc_start: 0.8670 (p) cc_final: 0.8463 (t) REVERT: O 81 ILE cc_start: 0.4659 (OUTLIER) cc_final: 0.4337 (mp) REVERT: O 139 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6824 (t) REVERT: O 305 MET cc_start: 0.8037 (mmp) cc_final: 0.7607 (mmm) REVERT: O 341 THR cc_start: 0.8278 (p) cc_final: 0.7981 (t) REVERT: P 55 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3850 (mp0) REVERT: P 59 ASP cc_start: 0.0401 (OUTLIER) cc_final: -0.0023 (t0) REVERT: P 252 ASP cc_start: 0.6776 (p0) cc_final: 0.6563 (p0) REVERT: P 290 SER cc_start: 0.8241 (t) cc_final: 0.7745 (p) REVERT: Q 18 ASP cc_start: 0.4763 (OUTLIER) cc_final: 0.4520 (m-30) REVERT: Q 48 LYS cc_start: 0.5725 (ttpt) cc_final: 0.5144 (ttpt) REVERT: Q 55 GLU cc_start: 0.3803 (OUTLIER) cc_final: 0.3448 (mp0) REVERT: Q 139 VAL cc_start: 0.6989 (p) cc_final: 0.6744 (t) REVERT: Q 147 MET cc_start: 0.2782 (tpp) cc_final: 0.1790 (tpp) REVERT: Q 164 ILE cc_start: 0.4536 (OUTLIER) cc_final: 0.4185 (tp) REVERT: Q 290 SER cc_start: 0.8439 (t) cc_final: 0.7967 (p) REVERT: Q 343 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8486 (t) REVERT: R 117 PHE cc_start: 0.4986 (p90) cc_final: 0.4645 (p90) REVERT: R 139 VAL cc_start: 0.6938 (p) cc_final: 0.6701 (t) REVERT: R 147 MET cc_start: 0.3264 (tpp) cc_final: 0.2769 (tpp) REVERT: R 332 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6493 (mt) REVERT: R 341 THR cc_start: 0.8255 (p) cc_final: 0.8039 (t) REVERT: S 55 GLU cc_start: 0.4984 (OUTLIER) cc_final: 0.4410 (mp0) REVERT: S 76 GLN cc_start: 0.6365 (tp40) cc_final: 0.5845 (mm110) REVERT: S 81 ILE cc_start: 0.4129 (OUTLIER) cc_final: 0.3774 (mp) REVERT: S 84 LYS cc_start: 0.3712 (OUTLIER) cc_final: 0.3492 (tppt) REVERT: S 148 ILE cc_start: 0.5010 (mp) cc_final: 0.4803 (mt) REVERT: S 201 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7243 (t70) REVERT: S 220 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5592 (pt) REVERT: S 348 PHE cc_start: 0.5690 (OUTLIER) cc_final: 0.5099 (m-10) REVERT: T 23 ARG cc_start: 0.5316 (tpt170) cc_final: 0.3229 (mtp180) REVERT: T 29 GLN cc_start: 0.4051 (pt0) cc_final: 0.3766 (pt0) REVERT: T 48 LYS cc_start: 0.5950 (ttpt) cc_final: 0.5733 (ttpt) REVERT: T 59 ASP cc_start: 0.2074 (OUTLIER) cc_final: 0.1645 (t0) REVERT: T 81 ILE cc_start: 0.4471 (OUTLIER) cc_final: 0.4189 (mp) REVERT: T 169 LYS cc_start: 0.5824 (ttpm) cc_final: 0.5375 (ptmm) REVERT: T 211 PHE cc_start: 0.7113 (t80) cc_final: 0.6871 (t80) REVERT: T 220 ILE cc_start: 0.6392 (OUTLIER) cc_final: 0.5968 (pp) REVERT: T 290 SER cc_start: 0.8485 (t) cc_final: 0.8177 (m) REVERT: T 296 ASP cc_start: 0.7292 (t70) cc_final: 0.7004 (t70) REVERT: U 20 PHE cc_start: 0.6581 (m-80) cc_final: 0.6365 (m-80) REVERT: U 23 ARG cc_start: 0.5426 (tpt-90) cc_final: 0.3052 (mtm180) REVERT: U 29 GLN cc_start: 0.3768 (pt0) cc_final: 0.3330 (pt0) REVERT: U 55 GLU cc_start: 0.4550 (OUTLIER) cc_final: 0.4005 (mp0) REVERT: U 68 LYS cc_start: 0.5252 (mttt) cc_final: 0.4977 (tptp) REVERT: U 164 ILE cc_start: 0.4346 (OUTLIER) cc_final: 0.4086 (mp) REVERT: V 55 GLU cc_start: 0.4741 (OUTLIER) cc_final: 0.4115 (mp0) REVERT: V 76 GLN cc_start: 0.6599 (tp40) cc_final: 0.5454 (mm110) REVERT: V 81 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3812 (mt) REVERT: V 164 ILE cc_start: 0.4459 (OUTLIER) cc_final: 0.3976 (mp) REVERT: V 201 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7405 (t70) REVERT: V 211 PHE cc_start: 0.6663 (t80) cc_final: 0.6306 (t80) REVERT: V 220 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6030 (pt) REVERT: V 252 ASP cc_start: 0.6857 (p0) cc_final: 0.6593 (p0) REVERT: V 265 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5233 (mt) REVERT: W 55 GLU cc_start: 0.4595 (OUTLIER) cc_final: 0.4052 (mp0) REVERT: W 76 GLN cc_start: 0.6646 (tp40) cc_final: 0.5477 (mm110) REVERT: W 81 ILE cc_start: 0.4211 (OUTLIER) cc_final: 0.3872 (mp) REVERT: W 164 ILE cc_start: 0.4636 (OUTLIER) cc_final: 0.4288 (mp) REVERT: W 201 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7542 (t70) REVERT: W 211 PHE cc_start: 0.6656 (t80) cc_final: 0.6378 (t80) REVERT: W 220 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5883 (pt) REVERT: W 252 ASP cc_start: 0.6650 (p0) cc_final: 0.6273 (p0) REVERT: W 305 MET cc_start: 0.7885 (mmm) cc_final: 0.7603 (mmp) REVERT: W 348 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.5092 (m-10) REVERT: X 23 ARG cc_start: 0.5524 (tmt-80) cc_final: 0.3149 (mtm180) REVERT: X 55 GLU cc_start: 0.5060 (OUTLIER) cc_final: 0.4491 (mp0) REVERT: X 76 GLN cc_start: 0.6506 (tp40) cc_final: 0.5579 (mm110) REVERT: X 81 ILE cc_start: 0.4209 (OUTLIER) cc_final: 0.3697 (mp) REVERT: X 164 ILE cc_start: 0.4301 (OUTLIER) cc_final: 0.4001 (tp) REVERT: X 201 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7412 (t70) REVERT: X 220 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5665 (pp) REVERT: Y 19 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6760 (ttt-90) REVERT: Y 33 SER cc_start: 0.8339 (p) cc_final: 0.8019 (t) REVERT: Y 100 ASN cc_start: 0.7756 (m-40) cc_final: 0.7522 (m-40) REVERT: Y 112 LYS cc_start: 0.8482 (mttp) cc_final: 0.8237 (mtpt) REVERT: Z 16 ASP cc_start: 0.7785 (t0) cc_final: 0.7389 (t0) REVERT: Z 112 LYS cc_start: 0.8548 (mttp) cc_final: 0.8291 (mtpt) REVERT: m 93 ASP cc_start: 0.8030 (t0) cc_final: 0.7665 (t0) REVERT: n 6 TYR cc_start: 0.8633 (t80) cc_final: 0.8396 (t80) REVERT: n 19 ARG cc_start: 0.6875 (mtp180) cc_final: 0.6642 (ttt-90) REVERT: n 33 SER cc_start: 0.8235 (p) cc_final: 0.7896 (t) REVERT: n 112 LYS cc_start: 0.8476 (mttp) cc_final: 0.8221 (mtpt) REVERT: n 115 ASP cc_start: 0.8057 (m-30) cc_final: 0.7827 (m-30) REVERT: o 16 ASP cc_start: 0.7809 (t0) cc_final: 0.7491 (t0) REVERT: o 19 ARG cc_start: 0.7295 (mtp180) cc_final: 0.7074 (ttt-90) REVERT: o 112 LYS cc_start: 0.8467 (mttp) cc_final: 0.8188 (mtpt) REVERT: p 3 MET cc_start: 0.3618 (tmm) cc_final: 0.3362 (tmm) REVERT: p 19 ARG cc_start: 0.7084 (mtp180) cc_final: 0.6835 (ttt-90) REVERT: p 96 ASP cc_start: 0.8250 (t0) cc_final: 0.7878 (t70) REVERT: q 32 THR cc_start: 0.8831 (p) cc_final: 0.8587 (t) REVERT: q 86 ARG cc_start: 0.8291 (ttt90) cc_final: 0.7877 (ttt90) REVERT: q 97 SER cc_start: 0.7886 (m) cc_final: 0.7428 (p) REVERT: q 101 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: q 110 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8378 (mt) REVERT: q 112 LYS cc_start: 0.8525 (mttp) cc_final: 0.8298 (mtpt) REVERT: r 90 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6932 (p90) REVERT: s 8 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7541 (tpt) REVERT: t 97 SER cc_start: 0.7933 (m) cc_final: 0.7404 (p) REVERT: t 101 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: u 12 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7993 (m) REVERT: u 90 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.6786 (p90) REVERT: v 8 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7647 (tpt) REVERT: w 3 MET cc_start: 0.2784 (tmm) cc_final: 0.2335 (tmt) REVERT: w 133 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: x 12 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8431 (m) REVERT: x 16 ASP cc_start: 0.8093 (t0) cc_final: 0.7644 (t70) REVERT: x 80 MET cc_start: 0.8422 (mmm) cc_final: 0.8155 (mmp) REVERT: x 97 SER cc_start: 0.8097 (m) cc_final: 0.7653 (p) REVERT: x 112 LYS cc_start: 0.8598 (mttp) cc_final: 0.8273 (mtpt) REVERT: y 1 MET cc_start: 0.2454 (mtp) cc_final: 0.1944 (mpt) REVERT: y 3 MET cc_start: 0.2881 (tmm) cc_final: 0.2318 (tmt) REVERT: y 16 ASP cc_start: 0.7836 (t0) cc_final: 0.7601 (t70) REVERT: y 97 SER cc_start: 0.8162 (m) cc_final: 0.7866 (p) REVERT: y 112 LYS cc_start: 0.8489 (mttp) cc_final: 0.8187 (mtpt) REVERT: y 133 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: z 1 MET cc_start: 0.2653 (mtp) cc_final: 0.2115 (mtt) REVERT: z 16 ASP cc_start: 0.7840 (t0) cc_final: 0.7545 (t70) REVERT: z 97 SER cc_start: 0.8218 (m) cc_final: 0.7651 (p) REVERT: z 100 ASN cc_start: 0.8145 (m-40) cc_final: 0.7773 (m-40) REVERT: z 112 LYS cc_start: 0.8488 (mttp) cc_final: 0.8214 (mtpt) REVERT: z 133 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7838 (tm-30) outliers start: 517 outliers final: 204 residues processed: 1396 average time/residue: 1.3572 time to fit residues: 2494.0482 Evaluate side-chains 1142 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 880 time to evaluate : 5.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 95 ILE Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 208 THR Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 18 ASP Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 164 ILE Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 265 LEU Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 374 HIS Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 56 ASP Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 97 SER Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 12 THR Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 95 ILE Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 0.0000 chunk 199 optimal weight: 9.9990 chunk 535 optimal weight: 0.6980 chunk 437 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 644 optimal weight: 7.9990 chunk 695 optimal weight: 9.9990 chunk 573 optimal weight: 10.0000 chunk 638 optimal weight: 10.0000 chunk 219 optimal weight: 30.0000 chunk 516 optimal weight: 20.0000 overall best weight: 5.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 ASN N 307 GLN O 29 GLN O 295 ASN O 307 GLN P 29 GLN P 119 GLN P 364 GLN R 119 GLN T 119 GLN V 119 GLN W 63 ASN W 119 GLN X 374 HIS m 100 ASN u 120 ASN v 121 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 55668 Z= 0.320 Angle : 0.737 9.157 75798 Z= 0.396 Chirality : 0.049 0.220 8778 Planarity : 0.006 0.047 9822 Dihedral : 9.803 77.812 7959 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.59 % Favored : 89.38 % Rotamer: Outliers : 8.88 % Allowed : 19.68 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.09), residues: 7080 helix: 0.02 (0.14), residues: 1476 sheet: 0.21 (0.13), residues: 1266 loop : -2.52 (0.08), residues: 4338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP w 127 HIS 0.006 0.001 HIS V 34 PHE 0.042 0.003 PHE q 90 TYR 0.019 0.002 TYR o 6 ARG 0.005 0.001 ARG M 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1452 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 512 poor density : 940 time to evaluate : 5.688 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: 1 80 MET cc_start: 0.8432 (mmm) cc_final: 0.8165 (mmp) REVERT: 1 93 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7592 (t70) REVERT: 1 97 SER cc_start: 0.8232 (m) cc_final: 0.7718 (p) REVERT: 1 112 LYS cc_start: 0.8461 (mttp) cc_final: 0.8099 (mtpt) REVERT: 1 133 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: 2 1 MET cc_start: 0.3407 (mpt) cc_final: 0.2603 (mmm) REVERT: 2 12 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8552 (m) REVERT: 2 16 ASP cc_start: 0.7951 (t0) cc_final: 0.7674 (t70) REVERT: 2 97 SER cc_start: 0.8214 (m) cc_final: 0.7912 (p) REVERT: 2 112 LYS cc_start: 0.8429 (mttp) cc_final: 0.8138 (mtpt) REVERT: 2 115 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: 2 133 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: M 10 THR cc_start: 0.8911 (p) cc_final: 0.8639 (t) REVERT: M 16 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6736 (mtt90) REVERT: M 59 ASP cc_start: 0.1776 (OUTLIER) cc_final: 0.1348 (t0) REVERT: M 117 PHE cc_start: 0.5158 (p90) cc_final: 0.4899 (p90) REVERT: M 139 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6674 (t) REVERT: M 218 ARG cc_start: 0.3285 (OUTLIER) cc_final: 0.2103 (mmm160) REVERT: M 332 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6726 (mt) REVERT: M 341 THR cc_start: 0.8323 (p) cc_final: 0.8051 (t) REVERT: N 29 GLN cc_start: 0.4448 (pt0) cc_final: 0.4155 (pt0) REVERT: N 48 LYS cc_start: 0.5938 (ttpt) cc_final: 0.5598 (ttpp) REVERT: N 139 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.6996 (t) REVERT: N 147 MET cc_start: 0.2861 (tpp) cc_final: 0.2512 (tpp) REVERT: N 164 ILE cc_start: 0.4463 (OUTLIER) cc_final: 0.3724 (tp) REVERT: N 274 ILE cc_start: 0.7618 (mp) cc_final: 0.7310 (mt) REVERT: N 321 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: N 341 THR cc_start: 0.8299 (p) cc_final: 0.8045 (t) REVERT: O 10 THR cc_start: 0.8748 (p) cc_final: 0.8487 (t) REVERT: O 81 ILE cc_start: 0.4627 (OUTLIER) cc_final: 0.4172 (mp) REVERT: O 139 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6948 (t) REVERT: O 164 ILE cc_start: 0.4790 (OUTLIER) cc_final: 0.4117 (tp) REVERT: O 220 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.6007 (pt) REVERT: O 252 ASP cc_start: 0.7302 (p0) cc_final: 0.6649 (p0) REVERT: O 305 MET cc_start: 0.8046 (mmp) cc_final: 0.7608 (mmm) REVERT: O 321 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7085 (ttm170) REVERT: O 341 THR cc_start: 0.8320 (p) cc_final: 0.8015 (t) REVERT: P 3 LYS cc_start: 0.6722 (mppt) cc_final: 0.6449 (mttt) REVERT: P 59 ASP cc_start: 0.0706 (OUTLIER) cc_final: 0.0235 (m-30) REVERT: P 164 ILE cc_start: 0.5090 (OUTLIER) cc_final: 0.4362 (tt) REVERT: P 290 SER cc_start: 0.8558 (t) cc_final: 0.7949 (p) REVERT: P 341 THR cc_start: 0.8363 (p) cc_final: 0.8121 (t) REVERT: Q 48 LYS cc_start: 0.5960 (ttpt) cc_final: 0.5065 (ttmm) REVERT: Q 139 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6922 (t) REVERT: Q 147 MET cc_start: 0.2796 (tpp) cc_final: 0.2048 (tpp) REVERT: Q 164 ILE cc_start: 0.4861 (OUTLIER) cc_final: 0.4452 (tt) REVERT: Q 274 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7264 (mt) REVERT: Q 290 SER cc_start: 0.8581 (t) cc_final: 0.8083 (p) REVERT: Q 296 ASP cc_start: 0.6940 (m-30) cc_final: 0.6727 (m-30) REVERT: Q 343 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8460 (t) REVERT: R 10 THR cc_start: 0.8722 (p) cc_final: 0.8500 (t) REVERT: R 48 LYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4940 (ttpm) REVERT: R 139 VAL cc_start: 0.7079 (OUTLIER) cc_final: 0.6822 (t) REVERT: R 218 ARG cc_start: 0.3480 (OUTLIER) cc_final: 0.2993 (mmp80) REVERT: R 252 ASP cc_start: 0.7137 (p0) cc_final: 0.6804 (p0) REVERT: R 332 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6797 (mt) REVERT: R 341 THR cc_start: 0.8299 (p) cc_final: 0.8018 (t) REVERT: S 76 GLN cc_start: 0.6567 (tp40) cc_final: 0.5501 (mm110) REVERT: S 220 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6017 (pt) REVERT: S 294 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.7136 (t0) REVERT: S 348 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5429 (m-10) REVERT: T 23 ARG cc_start: 0.5383 (tpt170) cc_final: 0.3491 (mtm180) REVERT: T 59 ASP cc_start: 0.1696 (OUTLIER) cc_final: 0.1018 (t0) REVERT: T 76 GLN cc_start: 0.6282 (tp-100) cc_final: 0.5541 (mm110) REVERT: T 133 ASP cc_start: 0.5016 (t0) cc_final: 0.4694 (t70) REVERT: T 169 LYS cc_start: 0.5946 (ttpm) cc_final: 0.5385 (ptmm) REVERT: T 218 ARG cc_start: 0.3628 (OUTLIER) cc_final: 0.1811 (mmt-90) REVERT: T 220 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6180 (pp) REVERT: T 290 SER cc_start: 0.8543 (t) cc_final: 0.8256 (m) REVERT: U 55 GLU cc_start: 0.4497 (OUTLIER) cc_final: 0.4252 (mp0) REVERT: U 68 LYS cc_start: 0.5289 (mttt) cc_final: 0.4934 (tptp) REVERT: U 195 MET cc_start: 0.8072 (mtp) cc_final: 0.7772 (ttt) REVERT: U 220 ILE cc_start: 0.6437 (OUTLIER) cc_final: 0.5968 (pt) REVERT: U 256 GLN cc_start: 0.6117 (mp10) cc_final: 0.5898 (mp10) REVERT: U 288 MET cc_start: 0.8020 (mmt) cc_final: 0.7553 (mmt) REVERT: U 316 MET cc_start: 0.9028 (mmp) cc_final: 0.8823 (mmt) REVERT: U 348 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5582 (m-10) REVERT: V 55 GLU cc_start: 0.4516 (OUTLIER) cc_final: 0.4163 (mm-30) REVERT: V 76 GLN cc_start: 0.6694 (tp40) cc_final: 0.5864 (mm110) REVERT: V 201 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7563 (t70) REVERT: V 208 THR cc_start: 0.3512 (OUTLIER) cc_final: 0.3278 (m) REVERT: V 220 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6096 (pt) REVERT: V 252 ASP cc_start: 0.6857 (p0) cc_final: 0.6647 (p0) REVERT: V 348 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5423 (m-10) REVERT: V 367 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: W 23 ARG cc_start: 0.5764 (tpt90) cc_final: 0.3374 (mtm180) REVERT: W 55 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.4093 (mm-30) REVERT: W 76 GLN cc_start: 0.6742 (tp40) cc_final: 0.5772 (mm110) REVERT: W 81 ILE cc_start: 0.4321 (OUTLIER) cc_final: 0.3992 (mt) REVERT: W 201 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7618 (t70) REVERT: W 220 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.5956 (pt) REVERT: W 252 ASP cc_start: 0.6781 (p0) cc_final: 0.6569 (p0) REVERT: W 274 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6801 (mp) REVERT: W 294 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7222 (t0) REVERT: W 296 ASP cc_start: 0.7181 (t70) cc_final: 0.6890 (t0) REVERT: W 305 MET cc_start: 0.7889 (mmm) cc_final: 0.7684 (mmp) REVERT: W 348 PHE cc_start: 0.6215 (OUTLIER) cc_final: 0.5761 (m-10) REVERT: W 367 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: X 49 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5102 (tt) REVERT: X 76 GLN cc_start: 0.6488 (tp40) cc_final: 0.5471 (mm110) REVERT: X 139 VAL cc_start: 0.6595 (OUTLIER) cc_final: 0.6124 (m) REVERT: X 164 ILE cc_start: 0.4451 (OUTLIER) cc_final: 0.3684 (tp) REVERT: X 220 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6029 (pt) REVERT: X 348 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5499 (m-10) REVERT: Y 3 MET cc_start: 0.3286 (tmt) cc_final: 0.2961 (tmt) REVERT: Y 16 ASP cc_start: 0.7814 (t0) cc_final: 0.7445 (t0) REVERT: Y 66 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8495 (mtmp) REVERT: Y 100 ASN cc_start: 0.7883 (m-40) cc_final: 0.7604 (m-40) REVERT: Y 112 LYS cc_start: 0.8564 (mttp) cc_final: 0.8281 (mtpt) REVERT: Z 16 ASP cc_start: 0.7947 (t0) cc_final: 0.7552 (t0) REVERT: Z 54 THR cc_start: 0.8336 (p) cc_final: 0.8126 (t) REVERT: Z 112 LYS cc_start: 0.8431 (mttp) cc_final: 0.8188 (mtpt) REVERT: m 16 ASP cc_start: 0.7885 (t0) cc_final: 0.7489 (t70) REVERT: m 19 ARG cc_start: 0.7253 (mtp180) cc_final: 0.7015 (ttt-90) REVERT: m 73 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7467 (ttm-80) REVERT: m 93 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7634 (t0) REVERT: n 16 ASP cc_start: 0.7723 (t0) cc_final: 0.7371 (t0) REVERT: n 19 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6919 (ttt-90) REVERT: n 33 SER cc_start: 0.8491 (p) cc_final: 0.8145 (p) REVERT: n 100 ASN cc_start: 0.7954 (m-40) cc_final: 0.7613 (m-40) REVERT: n 112 LYS cc_start: 0.8574 (mttp) cc_final: 0.8289 (mtpt) REVERT: o 16 ASP cc_start: 0.7922 (t0) cc_final: 0.7545 (t0) REVERT: o 19 ARG cc_start: 0.7242 (mtp180) cc_final: 0.7024 (ttt-90) REVERT: o 112 LYS cc_start: 0.8493 (mttp) cc_final: 0.8196 (mtpt) REVERT: p 16 ASP cc_start: 0.7933 (t0) cc_final: 0.7547 (t70) REVERT: p 19 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7060 (ttt-90) REVERT: p 93 ASP cc_start: 0.8114 (t0) cc_final: 0.7770 (t0) REVERT: p 96 ASP cc_start: 0.8261 (t0) cc_final: 0.7967 (t0) REVERT: q 18 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: q 86 ARG cc_start: 0.8387 (ttt90) cc_final: 0.7928 (ttt90) REVERT: q 97 SER cc_start: 0.7970 (m) cc_final: 0.7352 (p) REVERT: q 101 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: q 111 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: q 112 LYS cc_start: 0.8494 (mttp) cc_final: 0.8227 (mtpt) REVERT: r 46 ASP cc_start: 0.7691 (p0) cc_final: 0.7478 (p0) REVERT: r 101 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: s 8 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7509 (tpt) REVERT: s 19 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6900 (ttt90) REVERT: s 90 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (p90) REVERT: t 18 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6335 (mtt-85) REVERT: t 97 SER cc_start: 0.8011 (m) cc_final: 0.7365 (p) REVERT: t 111 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: u 111 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: v 8 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7526 (tpt) REVERT: v 90 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (p90) REVERT: v 111 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: w 3 MET cc_start: 0.2861 (tmm) cc_final: 0.2271 (tmt) REVERT: w 16 ASP cc_start: 0.7813 (t0) cc_final: 0.7560 (t70) REVERT: w 93 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7569 (t70) REVERT: x 16 ASP cc_start: 0.8095 (t0) cc_final: 0.7658 (t70) REVERT: x 93 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7546 (t70) REVERT: x 97 SER cc_start: 0.8280 (m) cc_final: 0.7774 (p) REVERT: x 112 LYS cc_start: 0.8468 (mttp) cc_final: 0.8190 (mtpt) REVERT: x 133 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: y 3 MET cc_start: 0.2951 (tmm) cc_final: 0.2318 (tmt) REVERT: y 16 ASP cc_start: 0.7870 (t0) cc_final: 0.7632 (t70) REVERT: y 97 SER cc_start: 0.8157 (m) cc_final: 0.7843 (p) REVERT: y 112 LYS cc_start: 0.8364 (mttp) cc_final: 0.8102 (mtpt) REVERT: y 115 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: y 120 ASN cc_start: 0.7692 (t0) cc_final: 0.7439 (t0) REVERT: y 133 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: z 1 MET cc_start: 0.2938 (mtp) cc_final: 0.2412 (mtt) REVERT: z 19 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6787 (ttt-90) REVERT: z 93 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7556 (t70) REVERT: z 97 SER cc_start: 0.8328 (m) cc_final: 0.8003 (p) REVERT: z 112 LYS cc_start: 0.8451 (mttp) cc_final: 0.8190 (mtpt) outliers start: 512 outliers final: 275 residues processed: 1278 average time/residue: 1.3846 time to fit residues: 2317.1142 Evaluate side-chains 1215 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 864 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 95 ILE Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 218 ARG Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 212 LYS Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 208 THR Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 164 ILE Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 246 CYS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 341 THR Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 94 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 56 ASP Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 111 GLN Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain w residue 115 ASP Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Chi-restraints excluded: chain z residue 95 ILE Chi-restraints excluded: chain z residue 104 THR Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 20.0000 chunk 484 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 71 optimal weight: 0.0570 chunk 307 optimal weight: 0.0980 chunk 432 optimal weight: 8.9990 chunk 646 optimal weight: 9.9990 chunk 684 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 612 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 121 ASN M 119 GLN N 330 ASN P 294 ASN R 40 GLN R 119 GLN T 29 GLN m 121 ASN u 120 ASN v 121 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 55668 Z= 0.174 Angle : 0.609 8.205 75798 Z= 0.326 Chirality : 0.044 0.168 8778 Planarity : 0.005 0.047 9822 Dihedral : 8.812 77.572 7941 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 7.77 % Allowed : 21.47 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.09), residues: 7080 helix: 0.65 (0.14), residues: 1476 sheet: -0.10 (0.13), residues: 1338 loop : -2.37 (0.08), residues: 4266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP z 127 HIS 0.006 0.001 HIS V 34 PHE 0.028 0.002 PHE q 90 TYR 0.015 0.001 TYR z 6 ARG 0.004 0.000 ARG R 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 448 poor density : 924 time to evaluate : 6.240 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: 1 80 MET cc_start: 0.8419 (mmm) cc_final: 0.8149 (mmp) REVERT: 1 93 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7341 (t70) REVERT: 1 97 SER cc_start: 0.8276 (m) cc_final: 0.7757 (p) REVERT: 1 112 LYS cc_start: 0.8463 (mttp) cc_final: 0.8195 (mtpt) REVERT: 1 133 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: 2 1 MET cc_start: 0.3214 (mpt) cc_final: 0.2538 (mmm) REVERT: 2 16 ASP cc_start: 0.7957 (t0) cc_final: 0.7736 (t70) REVERT: 2 27 ASP cc_start: 0.7699 (m-30) cc_final: 0.7466 (m-30) REVERT: 2 31 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8088 (m) REVERT: 2 97 SER cc_start: 0.8217 (m) cc_final: 0.7913 (p) REVERT: 2 112 LYS cc_start: 0.8449 (mttp) cc_final: 0.8139 (mtpt) REVERT: M 10 THR cc_start: 0.8889 (p) cc_final: 0.8618 (t) REVERT: M 16 ARG cc_start: 0.6954 (mtt180) cc_final: 0.6734 (mtt90) REVERT: M 48 LYS cc_start: 0.4891 (OUTLIER) cc_final: 0.4074 (ttmt) REVERT: M 59 ASP cc_start: 0.1678 (OUTLIER) cc_final: 0.1287 (t0) REVERT: M 117 PHE cc_start: 0.5123 (p90) cc_final: 0.4875 (p90) REVERT: M 139 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6728 (t) REVERT: M 147 MET cc_start: 0.2852 (tpp) cc_final: 0.2484 (tpp) REVERT: M 218 ARG cc_start: 0.3171 (OUTLIER) cc_final: 0.1942 (mmm160) REVERT: M 252 ASP cc_start: 0.6767 (p0) cc_final: 0.6309 (p0) REVERT: M 332 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6622 (mt) REVERT: M 341 THR cc_start: 0.8329 (p) cc_final: 0.8109 (t) REVERT: N 29 GLN cc_start: 0.4247 (pt0) cc_final: 0.3976 (pt0) REVERT: N 147 MET cc_start: 0.3192 (tpp) cc_final: 0.2774 (tpp) REVERT: N 164 ILE cc_start: 0.4038 (OUTLIER) cc_final: 0.3480 (tp) REVERT: N 252 ASP cc_start: 0.6988 (p0) cc_final: 0.6777 (p0) REVERT: N 321 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7938 (tmm-80) REVERT: N 341 THR cc_start: 0.8234 (p) cc_final: 0.8033 (t) REVERT: N 382 MET cc_start: 0.7672 (ttp) cc_final: 0.7452 (ttm) REVERT: O 10 THR cc_start: 0.8643 (p) cc_final: 0.8429 (t) REVERT: O 81 ILE cc_start: 0.4458 (OUTLIER) cc_final: 0.4220 (mp) REVERT: O 139 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6935 (t) REVERT: O 164 ILE cc_start: 0.4885 (OUTLIER) cc_final: 0.4270 (tp) REVERT: O 220 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5987 (pt) REVERT: O 235 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: O 252 ASP cc_start: 0.7219 (p0) cc_final: 0.6784 (p0) REVERT: O 305 MET cc_start: 0.7976 (mmp) cc_final: 0.7569 (mmm) REVERT: O 341 THR cc_start: 0.8214 (p) cc_final: 0.7995 (t) REVERT: P 3 LYS cc_start: 0.6834 (mppt) cc_final: 0.6502 (mttt) REVERT: P 164 ILE cc_start: 0.4835 (OUTLIER) cc_final: 0.4342 (tt) REVERT: P 290 SER cc_start: 0.8638 (t) cc_final: 0.7954 (p) REVERT: P 341 THR cc_start: 0.8319 (p) cc_final: 0.8118 (t) REVERT: Q 48 LYS cc_start: 0.6093 (ttpt) cc_final: 0.5476 (ttpp) REVERT: Q 139 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6701 (t) REVERT: Q 147 MET cc_start: 0.2582 (tpp) cc_final: 0.2012 (tpp) REVERT: Q 191 MET cc_start: 0.4996 (OUTLIER) cc_final: 0.4415 (ttm) REVERT: Q 242 SER cc_start: 0.5735 (t) cc_final: 0.5528 (m) REVERT: Q 290 SER cc_start: 0.8695 (t) cc_final: 0.8033 (p) REVERT: Q 343 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8423 (t) REVERT: R 10 THR cc_start: 0.8834 (p) cc_final: 0.8537 (t) REVERT: R 48 LYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4280 (tttm) REVERT: R 147 MET cc_start: 0.3230 (tpp) cc_final: 0.2685 (tpp) REVERT: R 218 ARG cc_start: 0.3294 (OUTLIER) cc_final: 0.2082 (mmm160) REVERT: R 252 ASP cc_start: 0.6949 (p0) cc_final: 0.6689 (p0) REVERT: R 332 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6667 (mt) REVERT: R 341 THR cc_start: 0.8260 (p) cc_final: 0.8047 (t) REVERT: S 23 ARG cc_start: 0.5275 (tpt90) cc_final: 0.2959 (mtm180) REVERT: S 76 GLN cc_start: 0.6563 (tp40) cc_final: 0.5454 (mm110) REVERT: S 133 ASP cc_start: 0.5603 (t70) cc_final: 0.5097 (m-30) REVERT: S 202 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7360 (p0) REVERT: S 220 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5708 (pt) REVERT: S 296 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6860 (t70) REVERT: S 348 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5804 (m-10) REVERT: T 23 ARG cc_start: 0.5302 (tpt170) cc_final: 0.3384 (mtm180) REVERT: T 59 ASP cc_start: 0.1787 (OUTLIER) cc_final: 0.1144 (t0) REVERT: T 76 GLN cc_start: 0.6162 (tp-100) cc_final: 0.5474 (mm110) REVERT: T 133 ASP cc_start: 0.5072 (t0) cc_final: 0.4764 (t70) REVERT: T 169 LYS cc_start: 0.5851 (ttpm) cc_final: 0.5341 (ptmm) REVERT: T 218 ARG cc_start: 0.3639 (OUTLIER) cc_final: 0.2007 (mmt-90) REVERT: T 220 ILE cc_start: 0.6460 (OUTLIER) cc_final: 0.6033 (pp) REVERT: T 256 GLN cc_start: 0.6375 (mp10) cc_final: 0.6108 (mp10) REVERT: T 290 SER cc_start: 0.8577 (t) cc_final: 0.8258 (m) REVERT: U 55 GLU cc_start: 0.4152 (OUTLIER) cc_final: 0.3858 (mp0) REVERT: U 68 LYS cc_start: 0.5291 (mttt) cc_final: 0.4942 (tptp) REVERT: U 195 MET cc_start: 0.8044 (mtp) cc_final: 0.7730 (ttt) REVERT: U 220 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5588 (pt) REVERT: U 288 MET cc_start: 0.7976 (mmt) cc_final: 0.7502 (mmt) REVERT: U 348 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.6115 (m-10) REVERT: V 55 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.3905 (mm-30) REVERT: V 76 GLN cc_start: 0.6693 (tp40) cc_final: 0.5765 (mm110) REVERT: V 133 ASP cc_start: 0.5318 (t70) cc_final: 0.5100 (m-30) REVERT: V 164 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3832 (mp) REVERT: V 208 THR cc_start: 0.3298 (OUTLIER) cc_final: 0.3003 (m) REVERT: V 220 ILE cc_start: 0.6280 (OUTLIER) cc_final: 0.5860 (pt) REVERT: V 288 MET cc_start: 0.8194 (mmt) cc_final: 0.7724 (mmt) REVERT: V 294 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (t0) REVERT: V 296 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6972 (t70) REVERT: V 348 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5689 (m-10) REVERT: V 367 PHE cc_start: 0.6120 (OUTLIER) cc_final: 0.5653 (m-80) REVERT: W 55 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.3920 (mm-30) REVERT: W 76 GLN cc_start: 0.6761 (tp40) cc_final: 0.5823 (mm110) REVERT: W 81 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3874 (mt) REVERT: W 164 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3765 (mp) REVERT: W 201 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7611 (t70) REVERT: W 220 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.5838 (pt) REVERT: W 252 ASP cc_start: 0.6806 (p0) cc_final: 0.6597 (p0) REVERT: W 274 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6804 (mt) REVERT: W 294 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7244 (t0) REVERT: W 305 MET cc_start: 0.7901 (mmm) cc_final: 0.7671 (mmp) REVERT: W 348 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5878 (m-10) REVERT: W 367 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5782 (m-80) REVERT: X 55 GLU cc_start: 0.4513 (OUTLIER) cc_final: 0.4208 (mp0) REVERT: X 76 GLN cc_start: 0.6485 (tp40) cc_final: 0.5415 (mm110) REVERT: X 164 ILE cc_start: 0.4482 (OUTLIER) cc_final: 0.3976 (tp) REVERT: X 202 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7336 (p0) REVERT: X 220 ILE cc_start: 0.6004 (OUTLIER) cc_final: 0.5578 (pt) REVERT: X 294 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.7256 (t0) REVERT: X 303 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6840 (mm-40) REVERT: X 348 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5962 (m-10) REVERT: Y 16 ASP cc_start: 0.7740 (t0) cc_final: 0.7378 (t0) REVERT: Y 66 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8534 (mtmp) REVERT: Y 100 ASN cc_start: 0.7962 (m-40) cc_final: 0.7722 (m-40) REVERT: Y 112 LYS cc_start: 0.8501 (mttp) cc_final: 0.8257 (mtpt) REVERT: Z 16 ASP cc_start: 0.7903 (t0) cc_final: 0.7498 (t0) REVERT: Z 112 LYS cc_start: 0.8453 (mttp) cc_final: 0.8221 (mtpt) REVERT: n 6 TYR cc_start: 0.8572 (t80) cc_final: 0.8358 (t80) REVERT: n 33 SER cc_start: 0.8439 (p) cc_final: 0.8036 (t) REVERT: n 100 ASN cc_start: 0.7834 (m-40) cc_final: 0.7551 (m-40) REVERT: n 112 LYS cc_start: 0.8527 (mttp) cc_final: 0.8263 (mtpt) REVERT: o 16 ASP cc_start: 0.7885 (t0) cc_final: 0.7509 (t0) REVERT: o 19 ARG cc_start: 0.7171 (mtp180) cc_final: 0.6913 (ttt-90) REVERT: o 112 LYS cc_start: 0.8508 (mttp) cc_final: 0.8241 (mtpt) REVERT: p 16 ASP cc_start: 0.7836 (t0) cc_final: 0.7443 (t70) REVERT: p 19 ARG cc_start: 0.7241 (mtp180) cc_final: 0.7004 (ttt-90) REVERT: p 96 ASP cc_start: 0.8319 (t0) cc_final: 0.8042 (t70) REVERT: q 97 SER cc_start: 0.7924 (m) cc_final: 0.7345 (p) REVERT: q 101 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: q 111 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: q 112 LYS cc_start: 0.8485 (mttp) cc_final: 0.8208 (mtpt) REVERT: r 61 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8677 (t) REVERT: r 90 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.6897 (p90) REVERT: r 101 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: s 8 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7461 (tpt) REVERT: s 19 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6860 (ttt90) REVERT: s 24 MET cc_start: 0.8407 (tpp) cc_final: 0.8122 (tpp) REVERT: s 111 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: t 18 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6502 (mtm-85) REVERT: t 97 SER cc_start: 0.7899 (m) cc_final: 0.7285 (p) REVERT: t 111 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: u 12 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8116 (m) REVERT: u 88 VAL cc_start: 0.7041 (m) cc_final: 0.6763 (t) REVERT: u 90 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6910 (p90) REVERT: u 101 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: v 8 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7606 (tpt) REVERT: v 133 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: w 3 MET cc_start: 0.2919 (tmm) cc_final: 0.2412 (tmt) REVERT: w 16 ASP cc_start: 0.7796 (t0) cc_final: 0.7532 (t70) REVERT: w 133 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: x 16 ASP cc_start: 0.8120 (t0) cc_final: 0.7681 (t70) REVERT: x 80 MET cc_start: 0.8477 (mmm) cc_final: 0.8177 (mmp) REVERT: x 93 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7242 (t70) REVERT: x 97 SER cc_start: 0.8284 (m) cc_final: 0.7792 (p) REVERT: x 112 LYS cc_start: 0.8447 (mttp) cc_final: 0.8176 (mtpt) REVERT: x 133 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: y 16 ASP cc_start: 0.7888 (t0) cc_final: 0.7668 (t70) REVERT: y 27 ASP cc_start: 0.7772 (m-30) cc_final: 0.7479 (m-30) REVERT: y 97 SER cc_start: 0.8140 (m) cc_final: 0.7844 (p) REVERT: y 112 LYS cc_start: 0.8429 (mttp) cc_final: 0.8130 (mtpt) REVERT: z 1 MET cc_start: 0.2848 (mtp) cc_final: 0.2354 (mtt) REVERT: z 19 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6758 (ttt-90) REVERT: z 97 SER cc_start: 0.8150 (m) cc_final: 0.7869 (p) REVERT: z 112 LYS cc_start: 0.8469 (mttp) cc_final: 0.8194 (mtpt) REVERT: z 133 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8018 (tm-30) outliers start: 448 outliers final: 244 residues processed: 1228 average time/residue: 1.4179 time to fit residues: 2275.5807 Evaluate side-chains 1184 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 319 poor density : 865 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 218 ARG Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 235 GLU Chi-restraints excluded: chain O residue 246 CYS Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 272 ASP Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 246 CYS Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 191 MET Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 246 CYS Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 202 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 246 CYS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 296 ASP Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 246 CYS Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 246 CYS Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 246 CYS Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 202 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 303 GLN Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 12 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 93 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 115 ASP Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 509 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 583 optimal weight: 9.9990 chunk 473 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 614 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN Q 29 GLN S 119 GLN T 63 ASN U 29 GLN U 63 ASN V 76 GLN W 76 GLN X 256 GLN v 121 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 55668 Z= 0.397 Angle : 0.795 10.768 75798 Z= 0.427 Chirality : 0.052 0.248 8778 Planarity : 0.007 0.058 9822 Dihedral : 9.462 76.185 7912 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.33 % Favored : 88.47 % Rotamer: Outliers : 9.17 % Allowed : 21.30 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.09), residues: 7080 helix: 0.29 (0.14), residues: 1440 sheet: 0.18 (0.13), residues: 1230 loop : -2.49 (0.08), residues: 4410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP z 127 HIS 0.007 0.001 HIS W 34 PHE 0.048 0.003 PHE q 90 TYR 0.023 0.003 TYR Z 6 ARG 0.007 0.001 ARG Q 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 529 poor density : 879 time to evaluate : 5.907 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: 1 93 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7603 (t70) REVERT: 1 97 SER cc_start: 0.8315 (m) cc_final: 0.7824 (p) REVERT: 1 112 LYS cc_start: 0.8501 (mttp) cc_final: 0.8124 (mtpt) REVERT: 1 133 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: 2 1 MET cc_start: 0.4068 (mpt) cc_final: 0.2878 (mtm) REVERT: 2 16 ASP cc_start: 0.7932 (t0) cc_final: 0.7612 (t70) REVERT: 2 97 SER cc_start: 0.8204 (m) cc_final: 0.7939 (p) REVERT: 2 112 LYS cc_start: 0.8403 (mttp) cc_final: 0.8112 (mtpt) REVERT: M 10 THR cc_start: 0.8833 (p) cc_final: 0.8614 (t) REVERT: M 16 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6868 (mtt90) REVERT: M 48 LYS cc_start: 0.5083 (OUTLIER) cc_final: 0.4204 (tttm) REVERT: M 59 ASP cc_start: 0.1825 (OUTLIER) cc_final: 0.1103 (t70) REVERT: M 84 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.4048 (ttpp) REVERT: M 139 VAL cc_start: 0.6757 (OUTLIER) cc_final: 0.6412 (t) REVERT: M 212 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7043 (mmtm) REVERT: M 218 ARG cc_start: 0.3359 (OUTLIER) cc_final: 0.2719 (tpm170) REVERT: M 341 THR cc_start: 0.8407 (p) cc_final: 0.8127 (t) REVERT: N 29 GLN cc_start: 0.4764 (pt0) cc_final: 0.4299 (pt0) REVERT: N 55 GLU cc_start: 0.4189 (OUTLIER) cc_final: 0.3068 (mp0) REVERT: N 164 ILE cc_start: 0.4000 (OUTLIER) cc_final: 0.3334 (tp) REVERT: N 191 MET cc_start: 0.5302 (ttm) cc_final: 0.4775 (ttp) REVERT: N 252 ASP cc_start: 0.6935 (p0) cc_final: 0.6723 (p0) REVERT: N 321 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7267 (ttm170) REVERT: N 341 THR cc_start: 0.8310 (p) cc_final: 0.7993 (t) REVERT: O 10 THR cc_start: 0.8650 (p) cc_final: 0.8350 (t) REVERT: O 50 TYR cc_start: 0.4137 (t80) cc_final: 0.3885 (t80) REVERT: O 81 ILE cc_start: 0.4486 (OUTLIER) cc_final: 0.4185 (mp) REVERT: O 139 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7001 (t) REVERT: O 164 ILE cc_start: 0.4783 (OUTLIER) cc_final: 0.4286 (tp) REVERT: O 252 ASP cc_start: 0.7029 (p0) cc_final: 0.6651 (p0) REVERT: O 321 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7179 (ttm170) REVERT: O 341 THR cc_start: 0.8300 (p) cc_final: 0.8000 (t) REVERT: P 139 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6427 (t) REVERT: P 164 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4441 (tt) REVERT: P 169 LYS cc_start: 0.4563 (OUTLIER) cc_final: 0.4176 (ptmm) REVERT: P 252 ASP cc_start: 0.7117 (p0) cc_final: 0.6895 (p0) REVERT: P 290 SER cc_start: 0.8725 (t) cc_final: 0.8024 (p) REVERT: P 341 THR cc_start: 0.8362 (p) cc_final: 0.7988 (t) REVERT: P 367 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5264 (m-80) REVERT: Q 139 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6891 (t) REVERT: Q 147 MET cc_start: 0.2786 (tpp) cc_final: 0.2278 (tpp) REVERT: Q 274 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7368 (mt) REVERT: Q 290 SER cc_start: 0.8730 (t) cc_final: 0.8013 (p) REVERT: Q 343 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8530 (t) REVERT: Q 367 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: R 10 THR cc_start: 0.8763 (p) cc_final: 0.8489 (t) REVERT: R 32 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5402 (tt) REVERT: R 40 GLN cc_start: 0.3583 (mm-40) cc_final: 0.3328 (mm-40) REVERT: R 48 LYS cc_start: 0.5602 (OUTLIER) cc_final: 0.4685 (tttm) REVERT: R 50 TYR cc_start: 0.3950 (t80) cc_final: 0.3557 (t80) REVERT: R 117 PHE cc_start: 0.4794 (p90) cc_final: 0.4316 (p90) REVERT: R 147 MET cc_start: 0.3307 (tpp) cc_final: 0.3006 (tpp) REVERT: R 218 ARG cc_start: 0.3409 (OUTLIER) cc_final: 0.3184 (tpm170) REVERT: R 294 ASN cc_start: 0.6589 (m-40) cc_final: 0.6372 (m-40) REVERT: R 341 THR cc_start: 0.8395 (p) cc_final: 0.8105 (t) REVERT: S 55 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.4095 (mp0) REVERT: S 67 TYR cc_start: 0.4135 (t80) cc_final: 0.3914 (t80) REVERT: S 76 GLN cc_start: 0.6694 (tp40) cc_final: 0.5504 (mm110) REVERT: S 133 ASP cc_start: 0.5378 (t70) cc_final: 0.5003 (m-30) REVERT: S 212 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6893 (mptp) REVERT: S 220 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6167 (pt) REVERT: S 348 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: T 23 ARG cc_start: 0.5341 (tpt170) cc_final: 0.3591 (mtm180) REVERT: T 59 ASP cc_start: 0.2077 (OUTLIER) cc_final: 0.1380 (t0) REVERT: T 63 ASN cc_start: 0.4455 (OUTLIER) cc_final: 0.4189 (p0) REVERT: T 76 GLN cc_start: 0.6321 (tp-100) cc_final: 0.5500 (mm110) REVERT: T 133 ASP cc_start: 0.5163 (t0) cc_final: 0.4836 (t70) REVERT: T 169 LYS cc_start: 0.5914 (ttpm) cc_final: 0.5332 (ptmm) REVERT: T 220 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6287 (pp) REVERT: T 290 SER cc_start: 0.8620 (t) cc_final: 0.8326 (m) REVERT: U 68 LYS cc_start: 0.5206 (mttt) cc_final: 0.4917 (tptp) REVERT: U 220 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6038 (pt) REVERT: U 288 MET cc_start: 0.8010 (mmt) cc_final: 0.7531 (mmt) REVERT: U 348 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: V 55 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.3968 (mm-30) REVERT: V 169 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5437 (ptmt) REVERT: V 208 THR cc_start: 0.3376 (OUTLIER) cc_final: 0.3095 (m) REVERT: V 220 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6312 (pt) REVERT: V 294 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7249 (t0) REVERT: V 303 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7458 (mp10) REVERT: V 348 PHE cc_start: 0.6858 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: W 3 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6734 (mmtt) REVERT: W 48 LYS cc_start: 0.6088 (ttpt) cc_final: 0.5880 (ttpt) REVERT: W 55 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.4074 (mm-30) REVERT: W 81 ILE cc_start: 0.4444 (OUTLIER) cc_final: 0.4233 (mt) REVERT: W 169 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.5278 (ptmt) REVERT: W 201 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7595 (t70) REVERT: W 210 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5328 (tppt) REVERT: W 220 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6042 (pt) REVERT: W 274 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6787 (mp) REVERT: W 294 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7301 (t0) REVERT: W 303 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7511 (mp10) REVERT: W 348 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: X 55 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.4368 (mm-30) REVERT: X 220 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6314 (pt) REVERT: X 294 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7192 (t0) REVERT: X 348 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: Y 16 ASP cc_start: 0.7862 (t0) cc_final: 0.7475 (t0) REVERT: Y 66 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8516 (mtmp) REVERT: Y 112 LYS cc_start: 0.8555 (mttp) cc_final: 0.8283 (mtpt) REVERT: Z 16 ASP cc_start: 0.7936 (t0) cc_final: 0.7578 (t0) REVERT: Z 54 THR cc_start: 0.8350 (p) cc_final: 0.8131 (t) REVERT: Z 112 LYS cc_start: 0.8480 (mttp) cc_final: 0.8228 (mtpt) REVERT: m 16 ASP cc_start: 0.7984 (t0) cc_final: 0.7603 (t70) REVERT: m 73 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7496 (ttm-80) REVERT: m 93 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7836 (t0) REVERT: n 16 ASP cc_start: 0.7766 (t0) cc_final: 0.7397 (t0) REVERT: n 33 SER cc_start: 0.8574 (p) cc_final: 0.8217 (p) REVERT: n 100 ASN cc_start: 0.7900 (m-40) cc_final: 0.7546 (m-40) REVERT: n 112 LYS cc_start: 0.8559 (mttp) cc_final: 0.8259 (mtpt) REVERT: o 16 ASP cc_start: 0.7932 (t0) cc_final: 0.7584 (t0) REVERT: o 112 LYS cc_start: 0.8535 (mttp) cc_final: 0.8244 (mtpt) REVERT: p 16 ASP cc_start: 0.7971 (t0) cc_final: 0.7611 (t70) REVERT: p 19 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7200 (ttt-90) REVERT: p 86 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7669 (ttm-80) REVERT: p 93 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (t0) REVERT: p 96 ASP cc_start: 0.8289 (t0) cc_final: 0.7970 (t0) REVERT: q 18 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6499 (mtt-85) REVERT: q 111 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: q 112 LYS cc_start: 0.8480 (mttp) cc_final: 0.8215 (mtpt) REVERT: r 101 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: s 8 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7526 (tpt) REVERT: s 24 MET cc_start: 0.8503 (tpp) cc_final: 0.8269 (tpp) REVERT: s 90 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8051 (p90) REVERT: s 111 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: t 18 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6409 (mtt-85) REVERT: t 46 ASP cc_start: 0.7640 (p0) cc_final: 0.7377 (p0) REVERT: t 101 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: t 111 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: u 86 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8096 (ttt90) REVERT: u 101 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: v 8 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7575 (tpt) REVERT: v 90 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8022 (p90) REVERT: w 93 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (t70) REVERT: w 133 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: x 97 SER cc_start: 0.8314 (m) cc_final: 0.7840 (p) REVERT: x 112 LYS cc_start: 0.8510 (mttp) cc_final: 0.8133 (mtpt) REVERT: x 133 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: y 16 ASP cc_start: 0.7910 (t0) cc_final: 0.7611 (t70) REVERT: y 97 SER cc_start: 0.8260 (m) cc_final: 0.7949 (p) REVERT: y 112 LYS cc_start: 0.8450 (mttp) cc_final: 0.8168 (mtpt) REVERT: y 115 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: y 120 ASN cc_start: 0.7635 (t0) cc_final: 0.7429 (t0) REVERT: z 3 MET cc_start: 0.2964 (tmm) cc_final: 0.2237 (tmt) REVERT: z 19 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6885 (ttt-90) REVERT: z 66 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8177 (mtmp) REVERT: z 97 SER cc_start: 0.8314 (m) cc_final: 0.8035 (p) REVERT: z 112 LYS cc_start: 0.8505 (mttp) cc_final: 0.8212 (mtpt) REVERT: z 133 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7126 (tm-30) outliers start: 529 outliers final: 300 residues processed: 1242 average time/residue: 1.4275 time to fit residues: 2319.0277 Evaluate side-chains 1225 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 379 poor density : 846 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 218 ARG Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 55 GLU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 246 CYS Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 231 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain Q residue 383 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 246 CYS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 63 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 246 CYS Chi-restraints excluded: chain T residue 265 LEU Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 353 SER Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 240 SER Chi-restraints excluded: chain U residue 246 CYS Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 246 CYS Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 341 THR Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 3 LYS Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 169 LYS Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 210 LYS Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 246 CYS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 296 ASP Chi-restraints excluded: chain W residue 341 THR Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 231 THR Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 93 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 86 ARG Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 93 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 14 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 40 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 66 LYS Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 10.0000 chunk 616 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 401 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 685 optimal weight: 3.9990 chunk 568 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 GLN P 294 ASN Q 294 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 HIS w 121 ASN z 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55668 Z= 0.198 Angle : 0.636 8.617 75798 Z= 0.340 Chirality : 0.045 0.167 8778 Planarity : 0.005 0.059 9822 Dihedral : 8.468 73.321 7882 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 7.72 % Allowed : 23.47 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.09), residues: 7080 helix: 0.73 (0.14), residues: 1464 sheet: -0.13 (0.13), residues: 1338 loop : -2.36 (0.08), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP z 127 HIS 0.005 0.001 HIS W 34 PHE 0.032 0.002 PHE q 90 TYR 0.020 0.002 TYR R 113 ARG 0.007 0.000 ARG Q 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 445 poor density : 876 time to evaluate : 6.105 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: 1 93 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7448 (t70) REVERT: 1 97 SER cc_start: 0.8313 (m) cc_final: 0.7820 (p) REVERT: 1 112 LYS cc_start: 0.8470 (mttp) cc_final: 0.8213 (mtpt) REVERT: 1 133 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: 2 1 MET cc_start: 0.3614 (mpt) cc_final: 0.2679 (mmm) REVERT: 2 16 ASP cc_start: 0.7995 (t0) cc_final: 0.7683 (t70) REVERT: 2 31 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8087 (m) REVERT: 2 97 SER cc_start: 0.8186 (m) cc_final: 0.7946 (p) REVERT: 2 112 LYS cc_start: 0.8412 (mttp) cc_final: 0.8107 (mtpt) REVERT: M 10 THR cc_start: 0.8863 (p) cc_final: 0.8563 (t) REVERT: M 16 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6771 (mtt90) REVERT: M 59 ASP cc_start: 0.1729 (OUTLIER) cc_final: 0.1092 (t70) REVERT: M 139 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6625 (t) REVERT: M 145 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.5867 (tp) REVERT: M 147 MET cc_start: 0.2935 (tpp) cc_final: 0.2658 (tpp) REVERT: M 201 ASP cc_start: 0.7544 (m-30) cc_final: 0.7322 (m-30) REVERT: M 218 ARG cc_start: 0.3351 (OUTLIER) cc_final: 0.2154 (mmm160) REVERT: M 321 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7975 (ttm170) REVERT: M 341 THR cc_start: 0.8364 (p) cc_final: 0.8125 (t) REVERT: N 29 GLN cc_start: 0.4665 (pt0) cc_final: 0.4261 (pt0) REVERT: N 84 LYS cc_start: 0.4129 (ttpp) cc_final: 0.3794 (mtmm) REVERT: N 139 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6596 (t) REVERT: N 147 MET cc_start: 0.2665 (tpp) cc_final: 0.2432 (tpp) REVERT: N 164 ILE cc_start: 0.3694 (OUTLIER) cc_final: 0.3168 (tp) REVERT: N 191 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4961 (ttp) REVERT: N 321 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7976 (tmm-80) REVERT: N 341 THR cc_start: 0.8245 (p) cc_final: 0.8044 (t) REVERT: O 10 THR cc_start: 0.8630 (p) cc_final: 0.8359 (t) REVERT: O 81 ILE cc_start: 0.4720 (OUTLIER) cc_final: 0.4280 (mp) REVERT: O 139 VAL cc_start: 0.7136 (p) cc_final: 0.6922 (t) REVERT: O 164 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4225 (tp) REVERT: O 235 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6489 (tp3------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 390 optimal weight: 2.9990 chunk 500 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 576 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 427 optimal weight: 9.9990 chunk 416 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN P 294 ASN Q 294 ASN S 29 GLN S 168 HIS U 63 ASN V 29 GLN V 168 HIS Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 55668 Z= 0.443 Angle : 0.830 11.524 75798 Z= 0.444 Chirality : 0.053 0.383 8778 Planarity : 0.007 0.066 9822 Dihedral : 9.110 80.865 7852 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.41 % Favored : 88.35 % Rotamer: Outliers : 8.67 % Allowed : 23.36 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.09), residues: 7080 helix: 0.13 (0.14), residues: 1476 sheet: -0.13 (0.13), residues: 1278 loop : -2.51 (0.08), residues: 4326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP w 127 HIS 0.006 0.001 HIS W 34 PHE 0.051 0.004 PHE q 90 TYR 0.026 0.003 TYR M 50 ARG 0.008 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 500 poor density : 868 time to evaluate : 5.885 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: 1 97 SER cc_start: 0.8299 (m) cc_final: 0.7841 (p) REVERT: 1 112 LYS cc_start: 0.8531 (mttp) cc_final: 0.8147 (mtpt) REVERT: 1 133 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: 2 1 MET cc_start: 0.3328 (mpt) cc_final: 0.2221 (mtm) REVERT: 2 16 ASP cc_start: 0.7955 (t0) cc_final: 0.7633 (t70) REVERT: 2 97 SER cc_start: 0.8203 (m) cc_final: 0.7941 (p) REVERT: 2 112 LYS cc_start: 0.8492 (mttp) cc_final: 0.8124 (mtpt) REVERT: 2 115 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: M 10 THR cc_start: 0.8829 (p) cc_final: 0.8550 (t) REVERT: M 16 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6907 (mtt90) REVERT: M 48 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.4197 (tttm) REVERT: M 59 ASP cc_start: 0.1944 (OUTLIER) cc_final: 0.1494 (t70) REVERT: M 117 PHE cc_start: 0.5209 (p90) cc_final: 0.4851 (p90) REVERT: M 139 VAL cc_start: 0.6637 (OUTLIER) cc_final: 0.6325 (t) REVERT: M 321 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (ttm170) REVERT: M 341 THR cc_start: 0.8401 (p) cc_final: 0.8089 (t) REVERT: N 29 GLN cc_start: 0.4808 (pt0) cc_final: 0.4363 (pt0) REVERT: N 50 TYR cc_start: 0.3979 (t80) cc_final: 0.1617 (m-80) REVERT: N 59 ASP cc_start: 0.0759 (OUTLIER) cc_final: 0.0541 (m-30) REVERT: N 84 LYS cc_start: 0.4634 (OUTLIER) cc_final: 0.4188 (ttpp) REVERT: N 132 LEU cc_start: 0.4021 (OUTLIER) cc_final: 0.3778 (mp) REVERT: N 164 ILE cc_start: 0.3768 (OUTLIER) cc_final: 0.3246 (tp) REVERT: N 321 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7284 (ttm170) REVERT: N 341 THR cc_start: 0.8383 (p) cc_final: 0.8051 (t) REVERT: O 10 THR cc_start: 0.8665 (p) cc_final: 0.8335 (t) REVERT: O 81 ILE cc_start: 0.4593 (OUTLIER) cc_final: 0.4279 (mp) REVERT: O 139 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7080 (t) REVERT: O 164 ILE cc_start: 0.4696 (OUTLIER) cc_final: 0.4247 (tp) REVERT: O 321 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7179 (ttm170) REVERT: O 341 THR cc_start: 0.8345 (p) cc_final: 0.8056 (t) REVERT: P 139 VAL cc_start: 0.6665 (OUTLIER) cc_final: 0.6315 (t) REVERT: P 164 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4461 (tt) REVERT: P 290 SER cc_start: 0.8703 (t) cc_final: 0.7996 (p) REVERT: P 341 THR cc_start: 0.8403 (p) cc_final: 0.7970 (t) REVERT: Q 68 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5135 (mtmm) REVERT: Q 139 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6889 (t) REVERT: Q 147 MET cc_start: 0.2884 (tpp) cc_final: 0.2562 (tpp) REVERT: Q 274 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7370 (mt) REVERT: Q 343 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8550 (t) REVERT: R 10 THR cc_start: 0.8801 (p) cc_final: 0.8494 (t) REVERT: R 32 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5540 (tt) REVERT: R 40 GLN cc_start: 0.3660 (mm-40) cc_final: 0.3402 (mm-40) REVERT: R 48 LYS cc_start: 0.5650 (OUTLIER) cc_final: 0.4716 (tttm) REVERT: R 117 PHE cc_start: 0.4800 (p90) cc_final: 0.4357 (p90) REVERT: R 147 MET cc_start: 0.3430 (tpp) cc_final: 0.3155 (tpp) REVERT: R 202 ASP cc_start: 0.8086 (m-30) cc_final: 0.7860 (m-30) REVERT: R 297 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7099 (ptm160) REVERT: R 341 THR cc_start: 0.8387 (p) cc_final: 0.8071 (t) REVERT: S 210 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5167 (tppt) REVERT: S 212 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7010 (mptp) REVERT: S 220 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6204 (pt) REVERT: T 59 ASP cc_start: 0.2271 (OUTLIER) cc_final: 0.1347 (t0) REVERT: T 123 ASP cc_start: 0.2228 (OUTLIER) cc_final: 0.1695 (p0) REVERT: T 133 ASP cc_start: 0.5235 (t0) cc_final: 0.4911 (t70) REVERT: T 169 LYS cc_start: 0.5906 (ttpm) cc_final: 0.5507 (ptmt) REVERT: T 220 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6293 (pp) REVERT: T 256 GLN cc_start: 0.6363 (mp10) cc_final: 0.5963 (mp10) REVERT: T 290 SER cc_start: 0.8716 (t) cc_final: 0.8331 (m) REVERT: T 294 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7263 (t0) REVERT: T 296 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: U 68 LYS cc_start: 0.5285 (mttt) cc_final: 0.4909 (tptp) REVERT: U 127 ARG cc_start: 0.5225 (mpt-90) cc_final: 0.5008 (mtt-85) REVERT: U 220 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6065 (pt) REVERT: U 288 MET cc_start: 0.7998 (mmt) cc_final: 0.7558 (mmt) REVERT: V 169 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5359 (ptmt) REVERT: V 201 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7625 (t70) REVERT: V 208 THR cc_start: 0.3406 (OUTLIER) cc_final: 0.3129 (m) REVERT: V 210 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.5180 (tppt) REVERT: V 220 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6291 (pt) REVERT: V 245 HIS cc_start: 0.6016 (OUTLIER) cc_final: 0.5168 (m-70) REVERT: V 294 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7342 (t0) REVERT: V 303 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7527 (mp10) REVERT: W 81 ILE cc_start: 0.4544 (OUTLIER) cc_final: 0.4230 (mt) REVERT: W 169 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5141 (ptmt) REVERT: W 201 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7660 (t70) REVERT: W 220 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6048 (pt) REVERT: W 245 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.5182 (m-70) REVERT: W 274 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.6936 (mp) REVERT: W 294 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7309 (t0) REVERT: W 303 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7493 (mp10) REVERT: X 139 VAL cc_start: 0.6498 (OUTLIER) cc_final: 0.6210 (m) REVERT: X 220 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6234 (pt) REVERT: Y 16 ASP cc_start: 0.7771 (t0) cc_final: 0.7424 (t0) REVERT: Y 28 ASP cc_start: 0.6930 (p0) cc_final: 0.6671 (p0) REVERT: Y 66 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8501 (mtmp) REVERT: Y 112 LYS cc_start: 0.8576 (mttp) cc_final: 0.8254 (mtpt) REVERT: Z 16 ASP cc_start: 0.7996 (t0) cc_final: 0.7624 (t70) REVERT: Z 112 LYS cc_start: 0.8500 (mttp) cc_final: 0.8229 (mtpt) REVERT: m 16 ASP cc_start: 0.7971 (t0) cc_final: 0.7629 (t70) REVERT: m 73 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7447 (ttm-80) REVERT: n 16 ASP cc_start: 0.7770 (t0) cc_final: 0.7436 (t0) REVERT: n 33 SER cc_start: 0.8574 (p) cc_final: 0.8209 (p) REVERT: n 100 ASN cc_start: 0.7953 (m-40) cc_final: 0.7606 (m-40) REVERT: n 112 LYS cc_start: 0.8552 (mttp) cc_final: 0.8246 (mtpt) REVERT: o 16 ASP cc_start: 0.7983 (t0) cc_final: 0.7623 (t70) REVERT: o 86 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7668 (ttm-80) REVERT: o 112 LYS cc_start: 0.8480 (mttp) cc_final: 0.8202 (mtpt) REVERT: p 16 ASP cc_start: 0.7977 (t0) cc_final: 0.7635 (t70) REVERT: p 19 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7274 (ttt-90) REVERT: p 93 ASP cc_start: 0.8128 (t0) cc_final: 0.7833 (t0) REVERT: p 96 ASP cc_start: 0.8318 (t0) cc_final: 0.8003 (t0) REVERT: p 101 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: q 18 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6522 (mtt-85) REVERT: q 111 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: q 112 LYS cc_start: 0.8365 (mttp) cc_final: 0.8160 (mtpt) REVERT: r 101 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: s 8 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: s 24 MET cc_start: 0.8470 (tpp) cc_final: 0.8248 (tpp) REVERT: s 90 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7799 (p90) REVERT: s 111 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: t 18 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6433 (mtt-85) REVERT: t 101 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: t 111 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: u 86 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7965 (ttp80) REVERT: u 101 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: v 8 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7580 (tpt) REVERT: v 86 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8099 (ttt90) REVERT: v 90 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7803 (p90) REVERT: w 93 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7588 (t70) REVERT: x 93 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7737 (t70) REVERT: x 97 SER cc_start: 0.8264 (m) cc_final: 0.7809 (p) REVERT: x 112 LYS cc_start: 0.8523 (mttp) cc_final: 0.8147 (mtpt) REVERT: x 133 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: y 16 ASP cc_start: 0.7935 (t0) cc_final: 0.7677 (t70) REVERT: y 93 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7636 (t70) REVERT: y 97 SER cc_start: 0.8260 (m) cc_final: 0.7938 (p) REVERT: y 112 LYS cc_start: 0.8413 (mttp) cc_final: 0.8119 (mtpt) REVERT: y 115 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: y 120 ASN cc_start: 0.7638 (t0) cc_final: 0.7434 (t0) REVERT: z 3 MET cc_start: 0.2986 (tmm) cc_final: 0.2360 (tmt) REVERT: z 93 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7558 (t70) REVERT: z 97 SER cc_start: 0.8331 (m) cc_final: 0.8028 (p) REVERT: z 112 LYS cc_start: 0.8532 (mttp) cc_final: 0.8227 (mtpt) REVERT: z 133 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7143 (tm-30) outliers start: 500 outliers final: 315 residues processed: 1207 average time/residue: 1.4292 time to fit residues: 2247.6657 Evaluate side-chains 1235 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 389 poor density : 846 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 321 ARG Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 352 GLU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 383 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 231 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 383 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 381 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 210 LYS Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 246 CYS Chi-restraints excluded: chain S residue 264 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 246 CYS Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 294 ASN Chi-restraints excluded: chain T residue 296 ASP Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 240 SER Chi-restraints excluded: chain U residue 246 CYS Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 296 ASP Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 191 MET Chi-restraints excluded: chain V residue 201 ASP Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 LYS Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 245 HIS Chi-restraints excluded: chain V residue 246 CYS Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 341 THR Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 169 LYS Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 245 HIS Chi-restraints excluded: chain W residue 246 CYS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 296 ASP Chi-restraints excluded: chain W residue 341 THR Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 93 ASP Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 116 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 86 ARG Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 93 ASP Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 86 ARG Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain y residue 37 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 88 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Chi-restraints excluded: chain z residue 104 THR Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 407 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 chunk 464 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 536 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 330 ASN P 294 ASN Q 294 ASN S 29 GLN T 76 GLN T 119 GLN V 29 GLN Y 100 ASN p 120 ASN w 121 ASN z 121 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55668 Z= 0.214 Angle : 0.657 11.550 75798 Z= 0.350 Chirality : 0.046 0.254 8778 Planarity : 0.006 0.062 9822 Dihedral : 8.242 66.617 7846 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.16 % Allowed : 24.92 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.09), residues: 7080 helix: 0.62 (0.14), residues: 1476 sheet: -0.42 (0.13), residues: 1386 loop : -2.38 (0.08), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP w 127 HIS 0.005 0.001 HIS R 34 PHE 0.034 0.002 PHE q 90 TYR 0.019 0.002 TYR R 113 ARG 0.007 0.000 ARG N 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 413 poor density : 864 time to evaluate : 5.950 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: 1 97 SER cc_start: 0.8290 (m) cc_final: 0.7850 (p) REVERT: 1 112 LYS cc_start: 0.8498 (mttp) cc_final: 0.8213 (mtpt) REVERT: 1 133 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: 2 1 MET cc_start: 0.3357 (mpt) cc_final: 0.2217 (mtm) REVERT: 2 16 ASP cc_start: 0.7995 (t0) cc_final: 0.7678 (t70) REVERT: 2 31 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8083 (m) REVERT: 2 97 SER cc_start: 0.8189 (m) cc_final: 0.7943 (p) REVERT: 2 112 LYS cc_start: 0.8445 (mttp) cc_final: 0.8129 (mtpt) REVERT: M 16 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6793 (mtt90) REVERT: M 48 LYS cc_start: 0.4946 (tttm) cc_final: 0.4135 (tttm) REVERT: M 59 ASP cc_start: 0.1757 (OUTLIER) cc_final: 0.1378 (t70) REVERT: M 117 PHE cc_start: 0.5045 (p90) cc_final: 0.4724 (p90) REVERT: M 139 VAL cc_start: 0.7080 (OUTLIER) cc_final: 0.6710 (t) REVERT: M 147 MET cc_start: 0.2890 (tpp) cc_final: 0.2391 (tpp) REVERT: M 321 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7991 (ttm170) REVERT: M 332 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6624 (mt) REVERT: M 341 THR cc_start: 0.8381 (p) cc_final: 0.8123 (t) REVERT: N 84 LYS cc_start: 0.4307 (OUTLIER) cc_final: 0.3811 (mtmm) REVERT: N 139 VAL cc_start: 0.6922 (t) cc_final: 0.6639 (t) REVERT: N 321 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7978 (tmm-80) REVERT: N 341 THR cc_start: 0.8286 (p) cc_final: 0.8044 (t) REVERT: O 10 THR cc_start: 0.8598 (p) cc_final: 0.8350 (t) REVERT: O 81 ILE cc_start: 0.4693 (OUTLIER) cc_final: 0.4314 (mp) REVERT: O 84 LYS cc_start: 0.4256 (ttpp) cc_final: 0.3952 (mtmm) REVERT: O 139 VAL cc_start: 0.7130 (OUTLIER) cc_final: 0.6901 (t) REVERT: O 164 ILE cc_start: 0.4415 (OUTLIER) cc_final: 0.4196 (tp) REVERT: O 252 ASP cc_start: 0.6646 (p0) cc_final: 0.6180 (t70) REVERT: O 321 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6951 (ttm170) REVERT: O 341 THR cc_start: 0.8261 (p) cc_final: 0.8019 (t) REVERT: P 48 LYS cc_start: 0.5222 (ttpt) cc_final: 0.4931 (ttpp) REVERT: P 139 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6440 (t) REVERT: P 164 ILE cc_start: 0.4526 (OUTLIER) cc_final: 0.4277 (tt) REVERT: P 226 VAL cc_start: 0.6556 (OUTLIER) cc_final: 0.6317 (m) REVERT: P 290 SER cc_start: 0.8653 (t) cc_final: 0.7924 (p) REVERT: P 341 THR cc_start: 0.8282 (p) cc_final: 0.8000 (t) REVERT: Q 48 LYS cc_start: 0.5469 (ttpt) cc_final: 0.4966 (ttpp) REVERT: Q 139 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6691 (t) REVERT: Q 274 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7217 (mt) REVERT: Q 290 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.7871 (p) REVERT: Q 343 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8431 (t) REVERT: R 10 THR cc_start: 0.8760 (p) cc_final: 0.8500 (t) REVERT: R 32 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5289 (tt) REVERT: R 117 PHE cc_start: 0.4626 (p90) cc_final: 0.4220 (p90) REVERT: R 147 MET cc_start: 0.3337 (tpp) cc_final: 0.2741 (tpp) REVERT: R 297 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7045 (ptm160) REVERT: R 341 THR cc_start: 0.8329 (p) cc_final: 0.8060 (t) REVERT: S 55 GLU cc_start: 0.4119 (OUTLIER) cc_final: 0.3840 (mp0) REVERT: S 220 ILE cc_start: 0.6401 (OUTLIER) cc_final: 0.5979 (pt) REVERT: S 303 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: T 59 ASP cc_start: 0.2035 (OUTLIER) cc_final: 0.1357 (t0) REVERT: T 133 ASP cc_start: 0.5478 (t0) cc_final: 0.5198 (t70) REVERT: T 169 LYS cc_start: 0.5762 (ttpm) cc_final: 0.5178 (ptmt) REVERT: T 220 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6029 (pp) REVERT: T 290 SER cc_start: 0.8699 (t) cc_final: 0.8294 (m) REVERT: U 68 LYS cc_start: 0.5334 (mttt) cc_final: 0.4935 (tptp) REVERT: U 220 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5717 (pt) REVERT: U 288 MET cc_start: 0.7941 (mmt) cc_final: 0.7530 (mmt) REVERT: V 76 GLN cc_start: 0.6341 (tp-100) cc_final: 0.5342 (mm110) REVERT: V 164 ILE cc_start: 0.4372 (OUTLIER) cc_final: 0.3929 (mp) REVERT: V 169 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5302 (ptmt) REVERT: V 208 THR cc_start: 0.3159 (OUTLIER) cc_final: 0.2955 (m) REVERT: V 220 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6038 (pt) REVERT: V 245 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5138 (m-70) REVERT: V 288 MET cc_start: 0.8083 (mmt) cc_final: 0.7689 (mmt) REVERT: V 294 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7284 (t0) REVERT: V 303 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7421 (mp10) REVERT: V 316 MET cc_start: 0.9046 (mmp) cc_final: 0.8798 (mmt) REVERT: W 76 GLN cc_start: 0.6341 (tp-100) cc_final: 0.5340 (mm110) REVERT: W 81 ILE cc_start: 0.4246 (OUTLIER) cc_final: 0.4027 (mt) REVERT: W 164 ILE cc_start: 0.4344 (OUTLIER) cc_final: 0.3912 (mp) REVERT: W 201 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7638 (t70) REVERT: W 220 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5807 (pt) REVERT: W 245 HIS cc_start: 0.6100 (OUTLIER) cc_final: 0.5295 (m-70) REVERT: W 274 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7054 (mt) REVERT: W 288 MET cc_start: 0.8250 (mmt) cc_final: 0.7766 (mmt) REVERT: W 294 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7255 (t0) REVERT: W 303 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7434 (mp10) REVERT: W 316 MET cc_start: 0.9042 (mmp) cc_final: 0.8785 (mmt) REVERT: X 164 ILE cc_start: 0.4480 (OUTLIER) cc_final: 0.3750 (tp) REVERT: X 202 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7347 (p0) REVERT: X 220 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6031 (pt) REVERT: X 303 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.6831 (mm-40) REVERT: Y 16 ASP cc_start: 0.7814 (t0) cc_final: 0.7423 (t0) REVERT: Y 28 ASP cc_start: 0.6855 (p0) cc_final: 0.6565 (p0) REVERT: Y 66 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8552 (mtmp) REVERT: Y 112 LYS cc_start: 0.8542 (mttp) cc_final: 0.8253 (mtpt) REVERT: Z 16 ASP cc_start: 0.7945 (t0) cc_final: 0.7529 (t0) REVERT: Z 112 LYS cc_start: 0.8467 (mttp) cc_final: 0.8246 (mtpt) REVERT: m 16 ASP cc_start: 0.7883 (t0) cc_final: 0.7488 (t70) REVERT: m 73 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6895 (ttm-80) REVERT: n 6 TYR cc_start: 0.8529 (t80) cc_final: 0.8301 (t80) REVERT: n 16 ASP cc_start: 0.7732 (t0) cc_final: 0.7366 (t0) REVERT: n 33 SER cc_start: 0.8528 (p) cc_final: 0.8144 (p) REVERT: n 100 ASN cc_start: 0.7896 (m-40) cc_final: 0.7529 (m-40) REVERT: n 112 LYS cc_start: 0.8541 (mttp) cc_final: 0.8252 (mtpt) REVERT: o 16 ASP cc_start: 0.7954 (t0) cc_final: 0.7526 (t0) REVERT: o 112 LYS cc_start: 0.8488 (mttp) cc_final: 0.8251 (mtpt) REVERT: p 16 ASP cc_start: 0.7873 (t0) cc_final: 0.7502 (t70) REVERT: p 19 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7141 (ttt180) REVERT: p 96 ASP cc_start: 0.8435 (t0) cc_final: 0.8035 (t70) REVERT: p 101 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: q 32 THR cc_start: 0.8811 (p) cc_final: 0.8516 (t) REVERT: q 93 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7351 (t70) REVERT: q 111 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: q 112 LYS cc_start: 0.8494 (mttp) cc_final: 0.8225 (mtpt) REVERT: r 90 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.6797 (p90) REVERT: r 101 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: s 8 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: s 24 MET cc_start: 0.8440 (tpp) cc_final: 0.8236 (tpp) REVERT: s 111 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: t 101 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: t 111 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: u 88 VAL cc_start: 0.7326 (m) cc_final: 0.7045 (t) REVERT: u 90 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.6911 (p90) REVERT: u 101 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: v 8 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7414 (tpt) REVERT: v 86 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8002 (ttt90) REVERT: v 111 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: w 3 MET cc_start: 0.3028 (tmm) cc_final: 0.2584 (tmt) REVERT: w 93 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7467 (t70) REVERT: w 101 GLU cc_start: 0.8085 (tt0) cc_final: 0.7741 (tt0) REVERT: x 93 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7516 (t70) REVERT: x 97 SER cc_start: 0.8275 (m) cc_final: 0.7853 (p) REVERT: x 112 LYS cc_start: 0.8524 (mttp) cc_final: 0.8241 (mtpt) REVERT: x 133 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: y 16 ASP cc_start: 0.7916 (t0) cc_final: 0.7655 (t70) REVERT: y 93 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7394 (t0) REVERT: y 97 SER cc_start: 0.8245 (m) cc_final: 0.7931 (p) REVERT: y 112 LYS cc_start: 0.8413 (mttp) cc_final: 0.8127 (mtpt) REVERT: z 3 MET cc_start: 0.3110 (tmm) cc_final: 0.2571 (tmt) REVERT: z 93 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7413 (t70) REVERT: z 97 SER cc_start: 0.8299 (m) cc_final: 0.8032 (p) REVERT: z 112 LYS cc_start: 0.8486 (mttp) cc_final: 0.8222 (mtpt) outliers start: 413 outliers final: 275 residues processed: 1141 average time/residue: 1.4481 time to fit residues: 2150.8728 Evaluate side-chains 1189 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 340 poor density : 849 time to evaluate : 5.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 321 ARG Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 246 CYS Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 202 ASP Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 246 CYS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 246 CYS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 235 GLU Chi-restraints excluded: chain T residue 246 CYS Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 240 SER Chi-restraints excluded: chain U residue 246 CYS Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 245 HIS Chi-restraints excluded: chain V residue 246 CYS Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 245 HIS Chi-restraints excluded: chain W residue 246 CYS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 202 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 303 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 93 ASP Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 86 ARG Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 596 optimal weight: 9.9990 chunk 635 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 499 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 574 optimal weight: 6.9990 chunk 601 optimal weight: 5.9990 chunk 633 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN N 239 GLN P 294 ASN Q 294 ASN V 29 GLN Y 100 ASN p 120 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 55668 Z= 0.244 Angle : 0.677 9.684 75798 Z= 0.360 Chirality : 0.046 0.238 8778 Planarity : 0.006 0.063 9822 Dihedral : 8.168 62.247 7843 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 6.78 % Allowed : 25.48 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.10), residues: 7080 helix: 0.66 (0.14), residues: 1476 sheet: -0.26 (0.13), residues: 1488 loop : -2.38 (0.09), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP w 127 HIS 0.006 0.001 HIS R 34 PHE 0.038 0.002 PHE q 90 TYR 0.018 0.002 TYR R 113 ARG 0.008 0.001 ARG n 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 391 poor density : 868 time to evaluate : 6.038 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: 1 97 SER cc_start: 0.8254 (m) cc_final: 0.7801 (p) REVERT: 1 112 LYS cc_start: 0.8497 (mttp) cc_final: 0.8208 (mtpt) REVERT: 1 133 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: 2 1 MET cc_start: 0.3361 (mpt) cc_final: 0.2225 (mtm) REVERT: 2 16 ASP cc_start: 0.7941 (t0) cc_final: 0.7598 (t70) REVERT: 2 97 SER cc_start: 0.8195 (m) cc_final: 0.7935 (p) REVERT: 2 112 LYS cc_start: 0.8415 (mttp) cc_final: 0.8113 (mtpt) REVERT: M 16 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6778 (mtt90) REVERT: M 48 LYS cc_start: 0.5046 (tttm) cc_final: 0.4164 (tttm) REVERT: M 59 ASP cc_start: 0.1720 (OUTLIER) cc_final: 0.1380 (t70) REVERT: M 117 PHE cc_start: 0.4964 (p90) cc_final: 0.4663 (p90) REVERT: M 139 VAL cc_start: 0.7063 (OUTLIER) cc_final: 0.6672 (t) REVERT: M 147 MET cc_start: 0.2949 (tpp) cc_final: 0.2593 (tpp) REVERT: M 321 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: M 341 THR cc_start: 0.8354 (p) cc_final: 0.8081 (t) REVERT: N 50 TYR cc_start: 0.3674 (t80) cc_final: 0.3364 (t80) REVERT: N 84 LYS cc_start: 0.4292 (OUTLIER) cc_final: 0.3744 (mtmm) REVERT: N 139 VAL cc_start: 0.6958 (OUTLIER) cc_final: 0.6662 (t) REVERT: N 321 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7931 (tmm-80) REVERT: N 341 THR cc_start: 0.8283 (p) cc_final: 0.8041 (t) REVERT: O 10 THR cc_start: 0.8598 (p) cc_final: 0.8288 (t) REVERT: O 50 TYR cc_start: 0.3509 (t80) cc_final: 0.3248 (t80) REVERT: O 81 ILE cc_start: 0.4708 (OUTLIER) cc_final: 0.4303 (mp) REVERT: O 139 VAL cc_start: 0.7089 (OUTLIER) cc_final: 0.6844 (t) REVERT: O 164 ILE cc_start: 0.4472 (OUTLIER) cc_final: 0.4219 (tp) REVERT: O 235 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: O 252 ASP cc_start: 0.6674 (p0) cc_final: 0.6310 (OUTLIER) REVERT: O 321 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7100 (ttm170) REVERT: O 341 THR cc_start: 0.8268 (p) cc_final: 0.8021 (t) REVERT: P 48 LYS cc_start: 0.5301 (ttpt) cc_final: 0.5057 (ttpm) REVERT: P 139 VAL cc_start: 0.6678 (OUTLIER) cc_final: 0.6279 (t) REVERT: P 164 ILE cc_start: 0.4666 (OUTLIER) cc_final: 0.4396 (tt) REVERT: P 226 VAL cc_start: 0.6573 (OUTLIER) cc_final: 0.6318 (m) REVERT: P 290 SER cc_start: 0.8629 (t) cc_final: 0.7958 (p) REVERT: P 341 THR cc_start: 0.8283 (p) cc_final: 0.8000 (t) REVERT: Q 48 LYS cc_start: 0.5514 (ttpt) cc_final: 0.5015 (ttpp) REVERT: Q 274 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7244 (mt) REVERT: Q 290 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.7896 (p) REVERT: Q 343 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8522 (t) REVERT: R 10 THR cc_start: 0.8801 (p) cc_final: 0.8532 (t) REVERT: R 20 PHE cc_start: 0.6049 (m-80) cc_final: 0.5687 (m-80) REVERT: R 32 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5485 (tt) REVERT: R 147 MET cc_start: 0.3518 (tpp) cc_final: 0.3057 (tpp) REVERT: R 297 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: R 341 THR cc_start: 0.8316 (p) cc_final: 0.8026 (t) REVERT: S 55 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.4008 (mp0) REVERT: S 202 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: S 220 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.5993 (pt) REVERT: S 303 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: T 59 ASP cc_start: 0.2106 (OUTLIER) cc_final: 0.1326 (t0) REVERT: T 133 ASP cc_start: 0.5484 (t0) cc_final: 0.5184 (t70) REVERT: T 169 LYS cc_start: 0.6007 (ttpm) cc_final: 0.5403 (ptmt) REVERT: T 220 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6118 (pp) REVERT: T 290 SER cc_start: 0.8735 (t) cc_final: 0.8311 (m) REVERT: U 68 LYS cc_start: 0.5373 (mttt) cc_final: 0.5008 (tptp) REVERT: U 191 MET cc_start: 0.5829 (ttm) cc_final: 0.5589 (ttm) REVERT: U 220 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5571 (pt) REVERT: U 288 MET cc_start: 0.7959 (mmt) cc_final: 0.7543 (mmt) REVERT: U 294 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7276 (t0) REVERT: V 164 ILE cc_start: 0.4444 (OUTLIER) cc_final: 0.3905 (mp) REVERT: V 169 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5392 (ptmt) REVERT: V 208 THR cc_start: 0.3000 (OUTLIER) cc_final: 0.2762 (m) REVERT: V 220 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.5958 (pt) REVERT: V 245 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5162 (m-70) REVERT: V 294 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7272 (t0) REVERT: V 316 MET cc_start: 0.9040 (mmp) cc_final: 0.8799 (mmt) REVERT: W 81 ILE cc_start: 0.4247 (OUTLIER) cc_final: 0.4021 (mt) REVERT: W 164 ILE cc_start: 0.4448 (OUTLIER) cc_final: 0.3940 (mp) REVERT: W 201 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7637 (t70) REVERT: W 220 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.5720 (pt) REVERT: W 245 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5322 (m-70) REVERT: W 274 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6908 (mp) REVERT: W 288 MET cc_start: 0.8268 (mmt) cc_final: 0.7790 (mmt) REVERT: W 294 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7289 (t0) REVERT: W 303 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7422 (mp10) REVERT: W 316 MET cc_start: 0.9029 (mmp) cc_final: 0.8785 (mmt) REVERT: X 164 ILE cc_start: 0.4220 (OUTLIER) cc_final: 0.3614 (tp) REVERT: X 202 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7322 (p0) REVERT: X 220 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.6013 (pt) REVERT: X 303 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: X 383 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (p) REVERT: Y 16 ASP cc_start: 0.7747 (t0) cc_final: 0.7380 (t0) REVERT: Y 28 ASP cc_start: 0.6975 (p0) cc_final: 0.6666 (p0) REVERT: Y 66 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8522 (mtmp) REVERT: Y 112 LYS cc_start: 0.8561 (mttp) cc_final: 0.8277 (mtpt) REVERT: Z 16 ASP cc_start: 0.7965 (t0) cc_final: 0.7554 (t0) REVERT: Z 112 LYS cc_start: 0.8475 (mttp) cc_final: 0.8258 (mtpt) REVERT: m 16 ASP cc_start: 0.7896 (t0) cc_final: 0.7513 (t70) REVERT: m 73 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6970 (ttm-80) REVERT: n 16 ASP cc_start: 0.7753 (t0) cc_final: 0.7385 (t0) REVERT: n 33 SER cc_start: 0.8529 (p) cc_final: 0.8143 (p) REVERT: n 100 ASN cc_start: 0.7975 (m-40) cc_final: 0.7612 (m-40) REVERT: n 112 LYS cc_start: 0.8558 (mttp) cc_final: 0.8275 (mtpt) REVERT: o 16 ASP cc_start: 0.7971 (t0) cc_final: 0.7565 (t0) REVERT: o 112 LYS cc_start: 0.8473 (mttp) cc_final: 0.8245 (mtpt) REVERT: p 16 ASP cc_start: 0.7896 (t0) cc_final: 0.7523 (t70) REVERT: p 19 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7178 (ttt-90) REVERT: p 96 ASP cc_start: 0.8392 (t0) cc_final: 0.7999 (t70) REVERT: p 101 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: q 32 THR cc_start: 0.8824 (p) cc_final: 0.8509 (t) REVERT: q 93 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7373 (t70) REVERT: q 111 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: q 112 LYS cc_start: 0.8487 (mttp) cc_final: 0.8219 (mtpt) REVERT: r 90 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.6835 (p90) REVERT: r 101 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: s 8 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: s 111 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: t 101 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: t 111 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: u 88 VAL cc_start: 0.7339 (m) cc_final: 0.7043 (t) REVERT: u 90 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.6900 (p90) REVERT: u 101 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: v 8 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7442 (tpt) REVERT: v 86 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8034 (ttt90) REVERT: v 111 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: w 3 MET cc_start: 0.3108 (tmm) cc_final: 0.2634 (tmt) REVERT: w 93 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7508 (t70) REVERT: w 101 GLU cc_start: 0.8070 (tt0) cc_final: 0.7736 (tt0) REVERT: x 93 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7574 (t70) REVERT: x 97 SER cc_start: 0.8275 (m) cc_final: 0.7854 (p) REVERT: x 112 LYS cc_start: 0.8498 (mttp) cc_final: 0.8211 (mtpt) REVERT: x 133 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: y 16 ASP cc_start: 0.7903 (t0) cc_final: 0.7638 (t70) REVERT: y 93 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7476 (t0) REVERT: y 97 SER cc_start: 0.8246 (m) cc_final: 0.7928 (p) REVERT: y 112 LYS cc_start: 0.8406 (mttp) cc_final: 0.8106 (mtpt) REVERT: z 3 MET cc_start: 0.3095 (tmm) cc_final: 0.2522 (tmt) REVERT: z 93 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7521 (t70) REVERT: z 97 SER cc_start: 0.8297 (m) cc_final: 0.8018 (p) REVERT: z 112 LYS cc_start: 0.8492 (mttp) cc_final: 0.8200 (mtpt) outliers start: 391 outliers final: 285 residues processed: 1133 average time/residue: 1.4426 time to fit residues: 2130.4877 Evaluate side-chains 1200 residues out of total 5766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 849 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 246 CYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 321 ARG Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 235 GLU Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 202 ASP Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 246 CYS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 202 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 246 CYS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 246 CYS Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 240 SER Chi-restraints excluded: chain U residue 246 CYS Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 294 ASN Chi-restraints excluded: chain U residue 296 ASP Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 245 HIS Chi-restraints excluded: chain V residue 246 CYS Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 245 HIS Chi-restraints excluded: chain W residue 246 CYS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 202 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 303 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 32 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 93 ASP Chi-restraints excluded: chain p residue 101 GLU Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 93 ASP Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 14 THR Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 86 ARG Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 0.3980 chunk 672 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 318 optimal weight: 20.0000 chunk 467 optimal weight: 0.8980 chunk 705 optimal weight: 20.0000 chunk 649 optimal weight: 9.9990 chunk 561 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 433 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: