Starting phenix.real_space_refine on Tue Aug 26 14:23:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.map" model { file = "/net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tre_10560/08_2025/6tre_10560.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 96 5.16 5 C 23232 2.51 5 N 7136 2.21 5 O 7712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38176 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6 Time building chain proxies: 3.85, per 1000 atoms: 0.10 Number of scatterers: 38176 At special positions: 0 Unit cell: (239.202, 239.202, 97.818, 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 96 16.00 O 7712 8.00 N 7136 7.00 C 23232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9280 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 97 sheets defined 29.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 258 Proline residue: 1 255 - end of helix Processing helix chain '1' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 1 421 " --> pdb=" O ARG 1 417 " (cutoff:3.500A) Processing helix chain '2' and resid 232 through 258 Proline residue: 2 255 - end of helix Processing helix chain '2' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 2 421 " --> pdb=" O ARG 2 417 " (cutoff:3.500A) Processing helix chain '3' and resid 232 through 258 Proline residue: 3 255 - end of helix Processing helix chain '3' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 3 421 " --> pdb=" O ARG 3 417 " (cutoff:3.500A) Processing helix chain '4' and resid 232 through 258 Proline residue: 4 255 - end of helix Processing helix chain '4' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 4 421 " --> pdb=" O ARG 4 417 " (cutoff:3.500A) Processing helix chain '5' and resid 232 through 258 Proline residue: 5 255 - end of helix Processing helix chain '5' and resid 405 through 421 removed outlier: 3.584A pdb=" N GLY 5 421 " --> pdb=" O ARG 5 417 " (cutoff:3.500A) Processing helix chain '6' and resid 232 through 258 Proline residue: 6 255 - end of helix Processing helix chain '6' and resid 405 through 421 removed outlier: 3.585A pdb=" N GLY 6 421 " --> pdb=" O ARG 6 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP A 271 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 382 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.782A pdb=" N HIS A 374 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 276 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 274 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS B 374 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 276 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 274 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS C 374 " --> pdb=" O GLU D 276 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 276 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS D 374 " --> pdb=" O GLU E 276 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 276 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 274 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS E 374 " --> pdb=" O GLU F 276 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 276 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN F 274 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS F 374 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU G 276 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 274 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS G 374 " --> pdb=" O GLU H 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN I 274 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN J 274 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS J 374 " --> pdb=" O GLU K 276 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU K 276 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN K 274 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN L 274 " --> pdb=" O LYS K 376 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS L 374 " --> pdb=" O GLU M 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU M 276 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN M 274 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN N 274 " --> pdb=" O LYS M 376 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS N 374 " --> pdb=" O GLU O 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU O 276 " --> pdb=" O HIS N 374 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN O 274 " --> pdb=" O LYS N 376 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS O 374 " --> pdb=" O GLU P 276 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN P 274 " --> pdb=" O LYS O 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN Q 274 " --> pdb=" O LYS P 376 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN R 274 " --> pdb=" O LYS Q 376 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN S 274 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN T 274 " --> pdb=" O LYS S 376 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN U 274 " --> pdb=" O LYS T 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS U 374 " --> pdb=" O GLU V 276 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU V 276 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN V 274 " --> pdb=" O LYS U 376 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS V 374 " --> pdb=" O GLU W 276 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU W 276 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN X 274 " --> pdb=" O LYS W 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN Y 274 " --> pdb=" O LYS X 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS Y 374 " --> pdb=" O GLU Z 276 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Z 276 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN Z 274 " --> pdb=" O LYS Y 376 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN 1 274 " --> pdb=" O LYS Z 376 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS 1 374 " --> pdb=" O GLU 2 276 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU 2 276 " --> pdb=" O HIS 1 374 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN 2 274 " --> pdb=" O LYS 1 376 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS 2 374 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 3 276 " --> pdb=" O HIS 2 374 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN 3 274 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN 4 274 " --> pdb=" O LYS 3 376 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS 4 374 " --> pdb=" O GLU 5 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU 5 276 " --> pdb=" O HIS 4 374 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN 5 274 " --> pdb=" O LYS 4 376 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS 5 374 " --> pdb=" O GLU 6 276 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU 6 276 " --> pdb=" O HIS 5 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN 6 274 " --> pdb=" O LYS 5 376 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS 6 374 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP B 271 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 382 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AA7, first strand: chain 'B' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB1, first strand: chain 'C' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP D 271 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE D 382 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AB4, first strand: chain 'D' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP E 271 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE E 382 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 281 through 282 Processing sheet with id=AB7, first strand: chain 'E' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP F 271 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE F 382 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 281 through 282 Processing sheet with id=AC1, first strand: chain 'F' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP G 271 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE G 382 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 281 through 282 Processing sheet with id=AC4, first strand: chain 'G' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP H 271 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE H 382 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 281 through 282 Processing sheet with id=AC7, first strand: chain 'H' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP I 271 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE I 382 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AD1, first strand: chain 'I' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 281 through 282 Processing sheet with id=AD4, first strand: chain 'J' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 281 through 282 Processing sheet with id=AD7, first strand: chain 'K' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP L 271 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE L 382 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 281 through 282 Processing sheet with id=AE1, first strand: chain 'L' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 281 through 282 Processing sheet with id=AE4, first strand: chain 'M' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP N 271 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE N 382 " --> pdb=" O ASP N 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 281 through 282 Processing sheet with id=AE7, first strand: chain 'N' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 281 through 282 Processing sheet with id=AF1, first strand: chain 'O' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 281 through 282 Processing sheet with id=AF4, first strand: chain 'P' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Q 271 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE Q 382 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 281 through 282 Processing sheet with id=AF7, first strand: chain 'Q' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP R 271 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE R 382 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 281 through 282 Processing sheet with id=AG1, first strand: chain 'R' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP S 271 " --> pdb=" O ILE S 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE S 382 " --> pdb=" O ASP S 271 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 281 through 282 Processing sheet with id=AG4, first strand: chain 'S' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 281 through 282 Processing sheet with id=AG7, first strand: chain 'T' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP U 271 " --> pdb=" O ILE U 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE U 382 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 281 through 282 Processing sheet with id=AH1, first strand: chain 'U' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP V 271 " --> pdb=" O ILE V 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE V 382 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 281 through 282 Processing sheet with id=AH4, first strand: chain 'V' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP W 271 " --> pdb=" O ILE W 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE W 382 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 281 through 282 Processing sheet with id=AH7, first strand: chain 'W' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP X 271 " --> pdb=" O ILE X 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE X 382 " --> pdb=" O ASP X 271 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 281 through 282 Processing sheet with id=AI1, first strand: chain 'X' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Y 271 " --> pdb=" O ILE Y 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE Y 382 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 281 through 282 Processing sheet with id=AI4, first strand: chain 'Y' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP Z 271 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE Z 382 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 281 through 282 Processing sheet with id=AI7, first strand: chain 'Z' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '1' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 1 271 " --> pdb=" O ILE 1 382 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE 1 382 " --> pdb=" O ASP 1 271 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '1' and resid 281 through 282 Processing sheet with id=AJ1, first strand: chain '1' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN 1 365 " --> pdb=" O ARG 1 294 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '2' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 2 271 " --> pdb=" O ILE 2 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 2 382 " --> pdb=" O ASP 2 271 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '2' and resid 281 through 282 Processing sheet with id=AJ4, first strand: chain '2' and resid 293 through 295 removed outlier: 6.490A pdb=" N ASN 2 365 " --> pdb=" O ARG 2 294 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain '3' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 3 271 " --> pdb=" O ILE 3 382 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE 3 382 " --> pdb=" O ASP 3 271 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '3' and resid 281 through 282 Processing sheet with id=AJ7, first strand: chain '3' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 3 365 " --> pdb=" O ARG 3 294 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain '4' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 4 271 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 4 382 " --> pdb=" O ASP 4 271 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '4' and resid 281 through 282 Processing sheet with id=AK1, first strand: chain '4' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 4 365 " --> pdb=" O ARG 4 294 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain '5' and resid 262 through 271 removed outlier: 6.088A pdb=" N ASP 5 271 " --> pdb=" O ILE 5 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 5 382 " --> pdb=" O ASP 5 271 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain '5' and resid 281 through 282 Processing sheet with id=AK4, first strand: chain '5' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 5 365 " --> pdb=" O ARG 5 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain '6' and resid 262 through 271 removed outlier: 6.087A pdb=" N ASP 6 271 " --> pdb=" O ILE 6 382 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE 6 382 " --> pdb=" O ASP 6 271 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain '6' and resid 281 through 282 Processing sheet with id=AK7, first strand: chain '6' and resid 293 through 295 removed outlier: 6.491A pdb=" N ASN 6 365 " --> pdb=" O ARG 6 294 " (cutoff:3.500A) 1668 hydrogen bonds defined for protein. 4770 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: 9.17 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13728 1.34 - 1.45: 4786 1.45 - 1.57: 19854 1.57 - 1.68: 0 1.68 - 1.80: 192 Bond restraints: 38560 Sorted by residual: bond pdb=" C TYR A 282 " pdb=" N SER A 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.84e+00 bond pdb=" C TYR S 282 " pdb=" N SER S 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.83e+00 bond pdb=" C TYR G 282 " pdb=" N SER G 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 bond pdb=" C TYR L 282 " pdb=" N SER L 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 bond pdb=" C TYR B 282 " pdb=" N SER B 283 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.80e+00 ... (remaining 38555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 46787 1.41 - 2.83: 4448 2.83 - 4.24: 516 4.24 - 5.66: 153 5.66 - 7.07: 64 Bond angle restraints: 51968 Sorted by residual: angle pdb=" N ARG E 294 " pdb=" CA ARG E 294 " pdb=" C ARG E 294 " ideal model delta sigma weight residual 114.31 110.00 4.31 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N ARG C 294 " pdb=" CA ARG C 294 " pdb=" C ARG C 294 " ideal model delta sigma weight residual 114.31 110.00 4.31 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG P 294 " pdb=" CA ARG P 294 " pdb=" C ARG P 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG D 294 " pdb=" CA ARG D 294 " pdb=" C ARG D 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 angle pdb=" N ARG F 294 " pdb=" CA ARG F 294 " pdb=" C ARG F 294 " ideal model delta sigma weight residual 114.31 110.01 4.30 1.29e+00 6.01e-01 1.11e+01 ... (remaining 51963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.36: 19296 11.36 - 22.72: 3066 22.72 - 34.08: 1094 34.08 - 45.44: 480 45.44 - 56.79: 160 Dihedral angle restraints: 24096 sinusoidal: 9984 harmonic: 14112 Sorted by residual: dihedral pdb=" CA GLN J 297 " pdb=" C GLN J 297 " pdb=" N LEU J 298 " pdb=" CA LEU J 298 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN 3 297 " pdb=" C GLN 3 297 " pdb=" N LEU 3 298 " pdb=" CA LEU 3 298 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN W 297 " pdb=" C GLN W 297 " pdb=" N LEU W 298 " pdb=" CA LEU W 298 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 24093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2831 0.025 - 0.050: 1894 0.050 - 0.076: 718 0.076 - 0.101: 358 0.101 - 0.126: 151 Chirality restraints: 5952 Sorted by residual: chirality pdb=" CA ILE 4 382 " pdb=" N ILE 4 382 " pdb=" C ILE 4 382 " pdb=" CB ILE 4 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE 1 382 " pdb=" N ILE 1 382 " pdb=" C ILE 1 382 " pdb=" CB ILE 1 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE H 382 " pdb=" N ILE H 382 " pdb=" C ILE H 382 " pdb=" CB ILE H 382 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 5949 not shown) Planarity restraints: 6976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 300 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE C 300 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 300 " -0.011 2.00e-02 2.50e+03 pdb=" N SER C 301 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 300 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ILE Y 300 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE Y 300 " 0.011 2.00e-02 2.50e+03 pdb=" N SER Y 301 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 300 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ILE 1 300 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE 1 300 " -0.011 2.00e-02 2.50e+03 pdb=" N SER 1 301 " -0.010 2.00e-02 2.50e+03 ... (remaining 6973 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 870 2.59 - 3.17: 33027 3.17 - 3.75: 52231 3.75 - 4.32: 80878 4.32 - 4.90: 140393 Nonbonded interactions: 307399 Sorted by model distance: nonbonded pdb=" OE1 GLU L 418 " pdb=" OG1 THR M 429 " model vdw 2.016 3.040 nonbonded pdb=" OE1 GLU E 418 " pdb=" OG1 THR F 429 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU 4 418 " pdb=" OG1 THR 5 429 " model vdw 2.077 3.040 nonbonded pdb=" O ASN G 239 " pdb=" OG SER G 243 " model vdw 2.081 3.040 nonbonded pdb=" O ASN D 239 " pdb=" OG SER D 243 " model vdw 2.081 3.040 ... (remaining 307394 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain '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' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } 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: 6.520 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 32.130 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 38560 Z= 0.441 Angle : 0.886 7.073 51968 Z= 0.525 Chirality : 0.043 0.126 5952 Planarity : 0.005 0.029 6976 Dihedral : 14.700 56.794 14816 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 11.33 % Allowed : 14.11 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.12), residues: 4640 helix: -0.64 (0.12), residues: 1280 sheet: -2.44 (0.11), residues: 2208 loop : -2.92 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 294 TYR 0.005 0.001 TYR D 393 PHE 0.013 0.002 PHE D 422 HIS 0.001 0.000 HIS T 263 Details of bonding type rmsd covalent geometry : bond 0.00894 (38560) covalent geometry : angle 0.88617 (51968) hydrogen bonds : bond 0.14272 ( 1668) hydrogen bonds : angle 6.35576 ( 4770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1667 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 486 poor density : 1181 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8613 (t) REVERT: C 409 MET cc_start: 0.8111 (mmm) cc_final: 0.7806 (tpp) REVERT: C 413 GLU cc_start: 0.8188 (tt0) cc_final: 0.7668 (mt-10) REVERT: D 413 GLU cc_start: 0.8065 (tt0) cc_final: 0.7782 (mt-10) REVERT: E 301 SER cc_start: 0.8032 (t) cc_final: 0.7757 (m) REVERT: E 376 LYS cc_start: 0.8181 (tttt) cc_final: 0.7965 (tttm) REVERT: F 232 ASP cc_start: 0.7661 (t0) cc_final: 0.7391 (t0) REVERT: F 431 ASN cc_start: 0.7986 (t0) cc_final: 0.7771 (t0) REVERT: I 271 ASP cc_start: 0.7836 (t0) cc_final: 0.7528 (t0) REVERT: I 386 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8406 (p) REVERT: I 425 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8345 (ttpt) REVERT: J 376 LYS cc_start: 0.7818 (tttt) cc_final: 0.7546 (ttmm) REVERT: J 425 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8446 (ttpt) REVERT: J 435 SER cc_start: 0.7896 (OUTLIER) cc_final: 0.7633 (m) REVERT: K 386 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8711 (p) REVERT: K 425 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: K 434 ASN cc_start: 0.7385 (t0) cc_final: 0.7162 (p0) REVERT: K 435 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7684 (m) REVERT: L 386 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8513 (p) REVERT: L 409 MET cc_start: 0.8492 (mmm) cc_final: 0.8252 (mmm) REVERT: M 376 LYS cc_start: 0.8259 (tttt) cc_final: 0.8023 (tttm) REVERT: N 376 LYS cc_start: 0.8038 (tttt) cc_final: 0.7368 (tttp) REVERT: N 425 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8452 (ttpt) REVERT: O 425 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8394 (ttpt) REVERT: P 413 GLU cc_start: 0.8079 (tt0) cc_final: 0.7861 (mt-10) REVERT: P 418 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7498 (mt-10) REVERT: P 435 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (m) REVERT: Q 376 LYS cc_start: 0.7617 (tttt) cc_final: 0.7234 (tttp) REVERT: Q 386 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8407 (p) REVERT: Q 423 SER cc_start: 0.8093 (OUTLIER) cc_final: 0.7858 (p) REVERT: Q 425 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8508 (ttpt) REVERT: R 425 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8484 (ttpt) REVERT: S 423 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7932 (p) REVERT: S 425 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8457 (ttpt) REVERT: T 271 ASP cc_start: 0.7843 (t0) cc_final: 0.7575 (t0) REVERT: T 425 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8413 (ttpt) REVERT: W 271 ASP cc_start: 0.7713 (t0) cc_final: 0.7398 (t0) REVERT: W 425 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8345 (ttpt) REVERT: Y 303 GLN cc_start: 0.7246 (mt0) cc_final: 0.6949 (mp10) REVERT: Y 409 MET cc_start: 0.8313 (mmm) cc_final: 0.8110 (mmm) REVERT: Y 413 GLU cc_start: 0.8133 (tt0) cc_final: 0.7724 (mt-10) REVERT: Z 386 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8804 (t) REVERT: Z 425 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8298 (ttpt) REVERT: 1 409 MET cc_start: 0.8113 (mmm) cc_final: 0.7871 (mmm) REVERT: 1 413 GLU cc_start: 0.8137 (tt0) cc_final: 0.7827 (mt-10) REVERT: 3 232 ASP cc_start: 0.7635 (t0) cc_final: 0.7381 (t0) REVERT: 3 299 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7425 (m-40) REVERT: 3 376 LYS cc_start: 0.8306 (tttt) cc_final: 0.8101 (tttt) REVERT: 4 409 MET cc_start: 0.8269 (mmm) cc_final: 0.8056 (tpp) REVERT: 4 413 GLU cc_start: 0.8178 (tt0) cc_final: 0.7759 (mt-10) REVERT: 4 425 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (ttpt) REVERT: 5 417 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7778 (ttm110) REVERT: 6 425 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8284 (ttmm) outliers start: 486 outliers final: 315 residues processed: 1563 average time/residue: 0.2491 time to fit residues: 625.0803 Evaluate side-chains 1247 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 340 poor density : 907 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 357 SER Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 289 SER Chi-restraints excluded: chain H residue 299 ASN Chi-restraints excluded: chain H residue 357 SER Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 357 SER Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain I residue 425 LYS Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 231 ASN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 357 SER Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 416 THR Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain J residue 425 LYS Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 231 ASN Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 357 SER Chi-restraints excluded: chain K residue 358 THR Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 423 SER Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 425 LYS Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 289 SER Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 357 SER Chi-restraints excluded: chain L residue 358 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 386 SER Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 381 ASP Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 289 SER Chi-restraints excluded: chain N residue 357 SER Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 386 SER Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain N residue 425 LYS Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 357 SER Chi-restraints excluded: chain O residue 358 THR Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 SER Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain O residue 425 LYS Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 357 SER Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 386 SER Chi-restraints excluded: chain P residue 416 THR Chi-restraints excluded: chain P residue 423 SER Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 231 ASN Chi-restraints excluded: chain Q residue 299 ASN Chi-restraints excluded: chain Q residue 357 SER Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 386 SER Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain Q residue 423 SER Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain R residue 231 ASN Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 289 SER Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 357 SER Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 386 SER Chi-restraints excluded: chain R residue 423 SER Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain R residue 425 LYS Chi-restraints excluded: chain S residue 231 ASN Chi-restraints excluded: chain S residue 243 SER Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 357 SER Chi-restraints excluded: chain S residue 358 THR Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 381 ASP Chi-restraints excluded: chain S residue 386 SER Chi-restraints excluded: chain S residue 423 SER Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 425 LYS Chi-restraints excluded: chain S residue 430 LEU Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 243 SER Chi-restraints excluded: chain T residue 289 SER Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 386 SER Chi-restraints excluded: chain T residue 423 SER Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 425 LYS Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain U residue 243 SER Chi-restraints excluded: chain U residue 289 SER Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 386 SER Chi-restraints excluded: chain U residue 423 SER Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain U residue 430 LEU Chi-restraints excluded: chain V residue 243 SER Chi-restraints excluded: chain V residue 289 SER Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 386 SER Chi-restraints excluded: chain V residue 416 THR Chi-restraints excluded: chain V residue 423 SER Chi-restraints excluded: chain V residue 424 ASP Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 289 SER Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 357 SER Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 386 SER Chi-restraints excluded: chain W residue 416 THR Chi-restraints excluded: chain W residue 423 SER Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain W residue 425 LYS Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 289 SER Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 358 THR Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 416 THR Chi-restraints excluded: chain X residue 423 SER Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain X residue 430 LEU Chi-restraints excluded: chain Y residue 289 SER Chi-restraints excluded: chain Y residue 299 ASN Chi-restraints excluded: chain Y residue 357 SER Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 386 SER Chi-restraints excluded: chain Y residue 416 THR Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 231 ASN Chi-restraints excluded: chain Z residue 289 SER Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 357 SER Chi-restraints excluded: chain Z residue 358 THR Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 386 SER Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain Z residue 423 SER Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 425 LYS Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain 1 residue 243 SER Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 299 ASN Chi-restraints excluded: chain 1 residue 357 SER Chi-restraints excluded: chain 1 residue 358 THR Chi-restraints excluded: chain 1 residue 369 ASP Chi-restraints excluded: chain 1 residue 416 THR Chi-restraints excluded: chain 1 residue 423 SER Chi-restraints excluded: chain 1 residue 424 ASP Chi-restraints excluded: chain 1 residue 429 THR Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 243 SER Chi-restraints excluded: chain 2 residue 289 SER Chi-restraints excluded: chain 2 residue 299 ASN Chi-restraints excluded: chain 2 residue 358 THR Chi-restraints excluded: chain 2 residue 369 ASP Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 2 residue 424 ASP Chi-restraints excluded: chain 2 residue 429 THR Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 299 ASN Chi-restraints excluded: chain 3 residue 357 SER Chi-restraints excluded: chain 3 residue 358 THR Chi-restraints excluded: chain 3 residue 369 ASP Chi-restraints excluded: chain 3 residue 416 THR Chi-restraints excluded: chain 3 residue 424 ASP Chi-restraints excluded: chain 3 residue 429 THR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 4 residue 289 SER Chi-restraints excluded: chain 4 residue 299 ASN Chi-restraints excluded: chain 4 residue 357 SER Chi-restraints excluded: chain 4 residue 358 THR Chi-restraints excluded: chain 4 residue 369 ASP Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 4 residue 416 THR Chi-restraints excluded: chain 4 residue 423 SER Chi-restraints excluded: chain 4 residue 424 ASP Chi-restraints excluded: chain 4 residue 425 LYS Chi-restraints excluded: chain 4 residue 429 THR Chi-restraints excluded: chain 5 residue 243 SER Chi-restraints excluded: chain 5 residue 299 ASN Chi-restraints excluded: chain 5 residue 357 SER Chi-restraints excluded: chain 5 residue 358 THR Chi-restraints excluded: chain 5 residue 369 ASP Chi-restraints excluded: chain 5 residue 416 THR Chi-restraints excluded: chain 5 residue 423 SER Chi-restraints excluded: chain 5 residue 424 ASP Chi-restraints excluded: chain 5 residue 429 THR Chi-restraints excluded: chain 6 residue 289 SER Chi-restraints excluded: chain 6 residue 299 ASN Chi-restraints excluded: chain 6 residue 357 SER Chi-restraints excluded: chain 6 residue 358 THR Chi-restraints excluded: chain 6 residue 369 ASP Chi-restraints excluded: chain 6 residue 381 ASP Chi-restraints excluded: chain 6 residue 416 THR Chi-restraints excluded: chain 6 residue 423 SER Chi-restraints excluded: chain 6 residue 424 ASP Chi-restraints excluded: chain 6 residue 425 LYS Chi-restraints excluded: chain 6 residue 429 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 239 ASN A 365 ASN A 434 ASN B 263 HIS B 434 ASN C 263 HIS C 434 ASN D 263 HIS D 365 ASN D 434 ASN E 239 ASN E 263 HIS E 365 ASN E 434 ASN F 234 GLN F 239 ASN F 365 ASN F 431 ASN F 434 ASN G 365 ASN G 434 ASN H 234 GLN H 263 HIS H 365 ASN I 231 ASN I 234 GLN I 263 HIS I 434 ASN J 234 GLN J 263 HIS J 434 ASN K 234 GLN K 263 HIS K 365 ASN K 434 ASN L 263 HIS L 434 ASN M 234 GLN M 239 ASN M 263 HIS M 434 ASN N 263 HIS N 434 ASN O 263 HIS O 434 ASN P 234 GLN P 263 HIS P 434 ASN Q 234 GLN Q 261 ASN Q 263 HIS Q 411 GLN R 234 GLN R 263 HIS R 411 GLN S 263 HIS T 234 GLN T 263 HIS T 365 ASN U 234 GLN U 239 ASN U 263 HIS U 365 ASN V 234 GLN V 263 HIS V 434 ASN W 234 GLN W 263 HIS W 434 ASN X 234 GLN X 239 ASN X 263 HIS X 365 ASN X 434 ASN Y 234 GLN Y 263 HIS Y 434 ASN Z 234 GLN Z 263 HIS Z 434 ASN 1 263 HIS 1 365 ASN 1 434 ASN 2 234 GLN 2 263 HIS 2 365 ASN 2 434 ASN 3 234 GLN 3 263 HIS 3 434 ASN 4 263 HIS 4 365 ASN 4 434 ASN 5 234 GLN 5 434 ASN 6 365 ASN 6 434 ASN Total number of N/Q/H flips: 98 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.149709 restraints weight = 39025.012| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.74 r_work: 0.3856 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 38560 Z= 0.137 Angle : 0.610 7.889 51968 Z= 0.317 Chirality : 0.040 0.114 5952 Planarity : 0.004 0.029 6976 Dihedral : 6.704 59.530 5712 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.08 % Allowed : 18.45 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 4640 helix: 1.77 (0.14), residues: 1280 sheet: -1.88 (0.11), residues: 2336 loop : -2.14 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 417 TYR 0.017 0.001 TYR 6 393 PHE 0.022 0.001 PHE A 422 HIS 0.001 0.000 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00268 (38560) covalent geometry : angle 0.61038 (51968) hydrogen bonds : bond 0.03753 ( 1668) hydrogen bonds : angle 4.35936 ( 4770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 951 time to evaluate : 1.779 Fit side-chains REVERT: A 377 MET cc_start: 0.8366 (mmm) cc_final: 0.8094 (mmm) REVERT: A 409 MET cc_start: 0.8110 (tpp) cc_final: 0.7540 (tpp) REVERT: B 377 MET cc_start: 0.8355 (mmm) cc_final: 0.8063 (mmm) REVERT: B 386 SER cc_start: 0.9133 (m) cc_final: 0.8288 (t) REVERT: C 356 ARG cc_start: 0.7268 (ttt180) cc_final: 0.7054 (ttm-80) REVERT: C 377 MET cc_start: 0.8271 (mmm) cc_final: 0.8060 (mmm) REVERT: C 386 SER cc_start: 0.9082 (m) cc_final: 0.8283 (t) REVERT: D 237 PHE cc_start: 0.7921 (t80) cc_final: 0.7372 (t80) REVERT: D 377 MET cc_start: 0.8532 (mmm) cc_final: 0.8300 (mmm) REVERT: D 410 LYS cc_start: 0.9042 (tptt) cc_final: 0.8778 (tptp) REVERT: D 413 GLU cc_start: 0.8329 (tt0) cc_final: 0.7779 (mt-10) REVERT: E 376 LYS cc_start: 0.7935 (tttt) cc_final: 0.7719 (tttt) REVERT: F 232 ASP cc_start: 0.7867 (t0) cc_final: 0.7517 (t0) REVERT: G 377 MET cc_start: 0.8344 (mmm) cc_final: 0.8083 (mmm) REVERT: G 386 SER cc_start: 0.9104 (m) cc_final: 0.8320 (t) REVERT: H 377 MET cc_start: 0.8353 (mmm) cc_final: 0.8138 (mmm) REVERT: H 409 MET cc_start: 0.8473 (mmm) cc_final: 0.8235 (mmm) REVERT: H 418 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7687 (mm-30) REVERT: I 240 ASP cc_start: 0.7547 (m-30) cc_final: 0.7286 (m-30) REVERT: I 271 ASP cc_start: 0.7915 (t0) cc_final: 0.7460 (t0) REVERT: I 303 GLN cc_start: 0.7100 (mp10) cc_final: 0.6803 (mp10) REVERT: I 376 LYS cc_start: 0.7575 (tttt) cc_final: 0.7068 (tttp) REVERT: I 377 MET cc_start: 0.8308 (mmm) cc_final: 0.8057 (mmm) REVERT: I 386 SER cc_start: 0.8895 (m) cc_final: 0.7994 (t) REVERT: I 409 MET cc_start: 0.8566 (mmm) cc_final: 0.8103 (mmm) REVERT: I 413 GLU cc_start: 0.8262 (tt0) cc_final: 0.7781 (mt-10) REVERT: J 232 ASP cc_start: 0.7354 (t0) cc_final: 0.6537 (m-30) REVERT: J 271 ASP cc_start: 0.8093 (t0) cc_final: 0.7887 (t0) REVERT: J 386 SER cc_start: 0.9131 (m) cc_final: 0.8165 (p) REVERT: J 435 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7370 (m) REVERT: K 232 ASP cc_start: 0.7426 (t0) cc_final: 0.6568 (m-30) REVERT: K 377 MET cc_start: 0.8243 (mmm) cc_final: 0.8001 (mmm) REVERT: K 386 SER cc_start: 0.9166 (m) cc_final: 0.8477 (p) REVERT: L 377 MET cc_start: 0.8498 (mmm) cc_final: 0.8269 (mmm) REVERT: M 237 PHE cc_start: 0.8222 (t80) cc_final: 0.8007 (t80) REVERT: M 386 SER cc_start: 0.9259 (m) cc_final: 0.8476 (t) REVERT: N 386 SER cc_start: 0.9251 (m) cc_final: 0.8352 (p) REVERT: N 409 MET cc_start: 0.8627 (mmm) cc_final: 0.8362 (mmm) REVERT: N 413 GLU cc_start: 0.8323 (tt0) cc_final: 0.7751 (mt-10) REVERT: O 386 SER cc_start: 0.9318 (m) cc_final: 0.8358 (p) REVERT: O 409 MET cc_start: 0.8727 (mmm) cc_final: 0.8475 (mmm) REVERT: P 409 MET cc_start: 0.8663 (mmm) cc_final: 0.8278 (mmm) REVERT: P 413 GLU cc_start: 0.8369 (tt0) cc_final: 0.7842 (mt-10) REVERT: Q 271 ASP cc_start: 0.8031 (t0) cc_final: 0.7748 (t0) REVERT: Q 303 GLN cc_start: 0.6929 (mt0) cc_final: 0.6527 (mp10) REVERT: Q 376 LYS cc_start: 0.7708 (tttt) cc_final: 0.7140 (tttp) REVERT: Q 386 SER cc_start: 0.9009 (m) cc_final: 0.8246 (p) REVERT: Q 409 MET cc_start: 0.8146 (tpp) cc_final: 0.7530 (tpp) REVERT: R 377 MET cc_start: 0.8276 (mmm) cc_final: 0.8050 (mmm) REVERT: R 409 MET cc_start: 0.8282 (mmm) cc_final: 0.7964 (mmm) REVERT: R 418 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7788 (mm-30) REVERT: S 232 ASP cc_start: 0.7312 (t0) cc_final: 0.6520 (m-30) REVERT: S 386 SER cc_start: 0.9096 (m) cc_final: 0.8249 (p) REVERT: S 418 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7645 (mm-30) REVERT: S 430 LEU cc_start: 0.8629 (tp) cc_final: 0.8353 (tp) REVERT: T 232 ASP cc_start: 0.7407 (t0) cc_final: 0.6637 (m-30) REVERT: T 237 PHE cc_start: 0.8019 (t80) cc_final: 0.7412 (t80) REVERT: T 240 ASP cc_start: 0.7491 (m-30) cc_final: 0.7252 (m-30) REVERT: T 271 ASP cc_start: 0.7889 (t0) cc_final: 0.7432 (t0) REVERT: T 356 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6872 (ttm170) REVERT: T 377 MET cc_start: 0.8420 (mmm) cc_final: 0.8151 (mmm) REVERT: T 386 SER cc_start: 0.9237 (m) cc_final: 0.8398 (t) REVERT: V 232 ASP cc_start: 0.7568 (t0) cc_final: 0.7286 (t0) REVERT: V 386 SER cc_start: 0.9202 (m) cc_final: 0.8366 (t) REVERT: V 435 SER cc_start: 0.7305 (m) cc_final: 0.7059 (m) REVERT: W 242 GLU cc_start: 0.7089 (pt0) cc_final: 0.6882 (tt0) REVERT: W 377 MET cc_start: 0.8243 (mmm) cc_final: 0.7953 (mmm) REVERT: X 418 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7472 (mm-30) REVERT: Y 376 LYS cc_start: 0.7599 (tttt) cc_final: 0.6954 (mtpp) REVERT: Y 386 SER cc_start: 0.9046 (m) cc_final: 0.8145 (t) REVERT: Y 409 MET cc_start: 0.8408 (mmm) cc_final: 0.8037 (tpt) REVERT: Z 232 ASP cc_start: 0.7855 (t0) cc_final: 0.7639 (t70) REVERT: Z 377 MET cc_start: 0.8283 (mmm) cc_final: 0.7950 (mmm) REVERT: Z 386 SER cc_start: 0.9212 (m) cc_final: 0.8449 (t) REVERT: 1 409 MET cc_start: 0.8221 (mmm) cc_final: 0.7718 (mmm) REVERT: 1 412 ILE cc_start: 0.8414 (mm) cc_final: 0.8132 (tt) REVERT: 1 413 GLU cc_start: 0.8412 (tt0) cc_final: 0.7941 (mt-10) REVERT: 2 377 MET cc_start: 0.8405 (mmm) cc_final: 0.8107 (mmm) REVERT: 2 386 SER cc_start: 0.9166 (m) cc_final: 0.8472 (t) REVERT: 2 393 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: 2 418 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7552 (mm-30) REVERT: 3 242 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: 3 386 SER cc_start: 0.9156 (m) cc_final: 0.8361 (t) REVERT: 4 409 MET cc_start: 0.8381 (mmm) cc_final: 0.8054 (tpp) REVERT: 4 413 GLU cc_start: 0.8422 (tt0) cc_final: 0.7724 (mt-10) REVERT: 5 377 MET cc_start: 0.8376 (mmm) cc_final: 0.8146 (mmm) REVERT: 5 393 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: 5 420 MET cc_start: 0.8450 (ptm) cc_final: 0.8195 (ptm) REVERT: 6 386 SER cc_start: 0.9085 (m) cc_final: 0.8324 (t) REVERT: 6 408 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6608 (tp-100) outliers start: 89 outliers final: 34 residues processed: 977 average time/residue: 0.2184 time to fit residues: 360.9937 Evaluate side-chains 897 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 859 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 429 THR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 393 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 290 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 263 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 307 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 239 ASN C 239 ASN E 239 ASN F 239 ASN J 234 GLN J 239 ASN J 411 GLN L 239 ASN M 239 ASN R 411 GLN T 234 GLN U 239 ASN W 234 GLN X 239 ASN 1 239 ASN 3 239 ASN 4 411 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.180827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.143651 restraints weight = 39426.778| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.69 r_work: 0.3772 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38560 Z= 0.179 Angle : 0.623 8.634 51968 Z= 0.317 Chirality : 0.040 0.123 5952 Planarity : 0.004 0.028 6976 Dihedral : 5.233 32.149 5221 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.33 % Allowed : 22.48 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.13), residues: 4640 helix: 2.29 (0.14), residues: 1280 sheet: -1.80 (0.12), residues: 2336 loop : -2.08 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 417 TYR 0.016 0.001 TYR A 393 PHE 0.016 0.002 PHE A 422 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00380 (38560) covalent geometry : angle 0.62317 (51968) hydrogen bonds : bond 0.03728 ( 1668) hydrogen bonds : angle 4.32929 ( 4770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 924 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8070 (t80) cc_final: 0.7814 (t80) REVERT: A 377 MET cc_start: 0.8414 (mmm) cc_final: 0.8068 (mmm) REVERT: B 377 MET cc_start: 0.8360 (mmm) cc_final: 0.8001 (mmm) REVERT: B 386 SER cc_start: 0.9211 (m) cc_final: 0.8343 (p) REVERT: B 393 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6469 (m-10) REVERT: C 356 ARG cc_start: 0.7230 (ttt180) cc_final: 0.7008 (ttm-80) REVERT: C 393 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: D 237 PHE cc_start: 0.7969 (t80) cc_final: 0.7496 (t80) REVERT: D 377 MET cc_start: 0.8527 (mmm) cc_final: 0.8213 (mmm) REVERT: D 393 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: D 409 MET cc_start: 0.8489 (mmm) cc_final: 0.8061 (mmm) REVERT: D 410 LYS cc_start: 0.9059 (tptt) cc_final: 0.8821 (tptt) REVERT: D 413 GLU cc_start: 0.8332 (tt0) cc_final: 0.7725 (mt-10) REVERT: E 237 PHE cc_start: 0.8024 (t80) cc_final: 0.7813 (t80) REVERT: E 356 ARG cc_start: 0.6986 (ttt180) cc_final: 0.6733 (ttm-80) REVERT: F 356 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6910 (ttm-80) REVERT: G 377 MET cc_start: 0.8278 (mmm) cc_final: 0.7928 (mmm) REVERT: G 393 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7169 (m-10) REVERT: H 377 MET cc_start: 0.8351 (mmm) cc_final: 0.8035 (mmm) REVERT: H 409 MET cc_start: 0.8573 (mmm) cc_final: 0.8366 (mmm) REVERT: I 240 ASP cc_start: 0.7602 (m-30) cc_final: 0.7328 (m-30) REVERT: I 377 MET cc_start: 0.8370 (mmm) cc_final: 0.8081 (mmm) REVERT: I 386 SER cc_start: 0.9136 (m) cc_final: 0.8083 (p) REVERT: I 409 MET cc_start: 0.8625 (mmm) cc_final: 0.8155 (mmm) REVERT: I 413 GLU cc_start: 0.8314 (tt0) cc_final: 0.7743 (mt-10) REVERT: J 386 SER cc_start: 0.9233 (m) cc_final: 0.8230 (p) REVERT: K 413 GLU cc_start: 0.8124 (tt0) cc_final: 0.7577 (mt-10) REVERT: L 356 ARG cc_start: 0.7077 (ttt180) cc_final: 0.6872 (ttm-80) REVERT: L 377 MET cc_start: 0.8509 (mmm) cc_final: 0.8178 (mmm) REVERT: N 386 SER cc_start: 0.9324 (m) cc_final: 0.8309 (p) REVERT: N 413 GLU cc_start: 0.8268 (tt0) cc_final: 0.7760 (mt-10) REVERT: O 409 MET cc_start: 0.8723 (mmm) cc_final: 0.8467 (mmm) REVERT: P 356 ARG cc_start: 0.6961 (ttt180) cc_final: 0.6734 (ttm-80) REVERT: P 409 MET cc_start: 0.8662 (mmm) cc_final: 0.8304 (mmm) REVERT: P 413 GLU cc_start: 0.8304 (tt0) cc_final: 0.7762 (mt-10) REVERT: P 418 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7791 (mm-30) REVERT: Q 435 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.7861 (m) REVERT: R 244 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7042 (tpp80) REVERT: R 276 GLU cc_start: 0.7932 (mp0) cc_final: 0.7538 (mp0) REVERT: R 303 GLN cc_start: 0.7292 (mp10) cc_final: 0.6952 (mp10) REVERT: R 377 MET cc_start: 0.8379 (mmm) cc_final: 0.8058 (mmm) REVERT: R 409 MET cc_start: 0.8541 (mmm) cc_final: 0.8186 (tpp) REVERT: R 415 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8040 (mp) REVERT: S 276 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: S 435 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.7937 (m) REVERT: T 237 PHE cc_start: 0.8036 (t80) cc_final: 0.7452 (t80) REVERT: T 377 MET cc_start: 0.8526 (mmm) cc_final: 0.8165 (mmm) REVERT: U 232 ASP cc_start: 0.7893 (t0) cc_final: 0.7686 (t0) REVERT: W 377 MET cc_start: 0.8341 (mmm) cc_final: 0.7973 (mmm) REVERT: X 386 SER cc_start: 0.9330 (m) cc_final: 0.8418 (t) REVERT: X 413 GLU cc_start: 0.8317 (tt0) cc_final: 0.7762 (mt-10) REVERT: Y 376 LYS cc_start: 0.7586 (tttt) cc_final: 0.6971 (tttp) REVERT: Y 386 SER cc_start: 0.9266 (m) cc_final: 0.8391 (p) REVERT: Y 393 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7423 (m-10) REVERT: Y 409 MET cc_start: 0.8461 (mmm) cc_final: 0.8118 (mmm) REVERT: Y 412 ILE cc_start: 0.8301 (mm) cc_final: 0.8076 (tt) REVERT: Y 413 GLU cc_start: 0.8394 (tt0) cc_final: 0.7793 (mt-10) REVERT: Z 377 MET cc_start: 0.8343 (mmm) cc_final: 0.7983 (mmm) REVERT: Z 386 SER cc_start: 0.9195 (m) cc_final: 0.8304 (p) REVERT: 1 409 MET cc_start: 0.8328 (mmm) cc_final: 0.7981 (mmm) REVERT: 1 413 GLU cc_start: 0.8361 (tt0) cc_final: 0.7830 (mt-10) REVERT: 2 244 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6915 (mtt-85) REVERT: 2 377 MET cc_start: 0.8378 (mmm) cc_final: 0.8017 (mmm) REVERT: 2 386 SER cc_start: 0.9226 (m) cc_final: 0.8346 (t) REVERT: 2 393 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7119 (m-10) REVERT: 3 356 ARG cc_start: 0.7071 (ttt180) cc_final: 0.6817 (ttm-80) REVERT: 3 377 MET cc_start: 0.8338 (mmm) cc_final: 0.8090 (mmm) REVERT: 4 409 MET cc_start: 0.8506 (mmm) cc_final: 0.8047 (tpp) REVERT: 4 413 GLU cc_start: 0.8428 (tt0) cc_final: 0.7742 (mt-10) REVERT: 5 377 MET cc_start: 0.8389 (mmm) cc_final: 0.8081 (mmm) REVERT: 5 393 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: 6 386 SER cc_start: 0.9147 (m) cc_final: 0.8318 (t) outliers start: 143 outliers final: 60 residues processed: 998 average time/residue: 0.2284 time to fit residues: 378.5065 Evaluate side-chains 954 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 881 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 411 GLN Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 244 ARG Chi-restraints excluded: chain R residue 386 SER Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 430 LEU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 244 ARG Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 393 TYR Chi-restraints excluded: chain 6 residue 393 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 129 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 450 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 153 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 285 ASN B 239 ASN B 365 ASN C 239 ASN C 285 ASN C 365 ASN E 239 ASN F 239 ASN F 285 ASN G 239 ASN H 239 ASN I 239 ASN J 234 GLN J 239 ASN J 365 ASN K 239 ASN L 239 ASN M 239 ASN M 365 ASN N 285 ASN N 365 ASN O 239 ASN O 365 ASN P 365 ASN P 411 GLN Q 239 ASN R 239 ASN S 285 ASN S 411 GLN U 239 ASN V 239 ASN W 365 ASN X 239 ASN Z 239 ASN Z 365 ASN 1 239 ASN 1 285 ASN 3 239 ASN 3 285 ASN 4 285 ASN 4 411 GLN 5 239 ASN 5 285 ASN 5 365 ASN 6 239 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139110 restraints weight = 40059.771| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.70 r_work: 0.3705 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 38560 Z= 0.257 Angle : 0.709 10.380 51968 Z= 0.358 Chirality : 0.041 0.133 5952 Planarity : 0.004 0.031 6976 Dihedral : 5.555 19.093 5216 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.55 % Allowed : 22.60 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.13), residues: 4640 helix: 2.05 (0.14), residues: 1280 sheet: -1.87 (0.12), residues: 2336 loop : -2.22 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 417 TYR 0.014 0.001 TYR A 393 PHE 0.021 0.002 PHE 3 237 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00556 (38560) covalent geometry : angle 0.70896 (51968) hydrogen bonds : bond 0.04034 ( 1668) hydrogen bonds : angle 4.55502 ( 4770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 864 time to evaluate : 1.129 Fit side-chains REVERT: A 285 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7826 (p0) REVERT: A 377 MET cc_start: 0.8441 (mmm) cc_final: 0.8073 (mmm) REVERT: A 393 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: A 413 GLU cc_start: 0.8398 (tt0) cc_final: 0.7783 (mt-10) REVERT: B 276 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 377 MET cc_start: 0.8443 (mmm) cc_final: 0.8055 (mmm) REVERT: B 393 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: B 409 MET cc_start: 0.8403 (tpp) cc_final: 0.8172 (tpp) REVERT: C 285 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7915 (p0) REVERT: C 356 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6966 (ttm-80) REVERT: C 393 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: D 377 MET cc_start: 0.8467 (mmm) cc_final: 0.8128 (mmm) REVERT: D 393 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: E 303 GLN cc_start: 0.7166 (mt0) cc_final: 0.6775 (mp10) REVERT: E 356 ARG cc_start: 0.7102 (ttt180) cc_final: 0.6828 (ttm-80) REVERT: F 285 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7744 (p0) REVERT: F 356 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6910 (ttm-80) REVERT: G 303 GLN cc_start: 0.7150 (mt0) cc_final: 0.6873 (mp10) REVERT: G 356 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6816 (ttm-80) REVERT: G 377 MET cc_start: 0.8352 (mmm) cc_final: 0.7940 (mmm) REVERT: G 393 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: H 377 MET cc_start: 0.8405 (mmm) cc_final: 0.8067 (mmm) REVERT: H 405 THR cc_start: 0.8252 (p) cc_final: 0.8044 (p) REVERT: I 276 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: I 386 SER cc_start: 0.9196 (m) cc_final: 0.8176 (p) REVERT: I 393 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7452 (m-10) REVERT: I 409 MET cc_start: 0.8629 (mmm) cc_final: 0.8056 (mmm) REVERT: I 413 GLU cc_start: 0.8345 (tt0) cc_final: 0.7825 (mt-10) REVERT: K 276 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: K 423 SER cc_start: 0.7799 (t) cc_final: 0.7512 (t) REVERT: K 435 SER cc_start: 0.8606 (t) cc_final: 0.8260 (m) REVERT: L 377 MET cc_start: 0.8468 (mmm) cc_final: 0.8109 (mmm) REVERT: M 303 GLN cc_start: 0.7109 (mt0) cc_final: 0.6859 (mp10) REVERT: M 356 ARG cc_start: 0.7206 (ttt180) cc_final: 0.6919 (ttm-80) REVERT: N 285 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7746 (p0) REVERT: N 356 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6883 (ttm-80) REVERT: N 413 GLU cc_start: 0.8339 (tt0) cc_final: 0.7813 (mt-10) REVERT: O 409 MET cc_start: 0.8714 (mmm) cc_final: 0.8458 (mmm) REVERT: P 356 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6844 (ttm-80) REVERT: P 386 SER cc_start: 0.9324 (m) cc_final: 0.8435 (t) REVERT: P 409 MET cc_start: 0.8611 (mmm) cc_final: 0.8208 (mmm) REVERT: P 413 GLU cc_start: 0.8313 (tt0) cc_final: 0.7768 (mt-10) REVERT: Q 240 ASP cc_start: 0.7580 (m-30) cc_final: 0.7378 (m-30) REVERT: Q 435 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8446 (m) REVERT: R 377 MET cc_start: 0.8458 (mmm) cc_final: 0.8096 (mmm) REVERT: S 232 ASP cc_start: 0.7770 (t0) cc_final: 0.6758 (m-30) REVERT: S 276 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: T 237 PHE cc_start: 0.8137 (t80) cc_final: 0.7645 (t80) REVERT: T 377 MET cc_start: 0.8485 (mmm) cc_final: 0.8116 (mmm) REVERT: T 413 GLU cc_start: 0.8376 (tt0) cc_final: 0.7978 (tt0) REVERT: T 417 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7288 (ttm110) REVERT: V 232 ASP cc_start: 0.7901 (t0) cc_final: 0.7617 (t0) REVERT: V 410 LYS cc_start: 0.9045 (tptt) cc_final: 0.8822 (tptt) REVERT: V 417 ARG cc_start: 0.8298 (ttm110) cc_final: 0.8037 (ttm110) REVERT: Y 303 GLN cc_start: 0.7071 (mt0) cc_final: 0.6630 (mp10) REVERT: Y 386 SER cc_start: 0.9320 (m) cc_final: 0.8409 (p) REVERT: Y 393 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7543 (m-10) REVERT: Y 409 MET cc_start: 0.8507 (mmm) cc_final: 0.8072 (mmm) REVERT: Y 413 GLU cc_start: 0.8344 (tt0) cc_final: 0.7749 (mt-10) REVERT: 1 240 ASP cc_start: 0.7553 (m-30) cc_final: 0.7289 (m-30) REVERT: 1 409 MET cc_start: 0.8450 (mmm) cc_final: 0.8247 (mmm) REVERT: 1 413 GLU cc_start: 0.8403 (tt0) cc_final: 0.7901 (mt-10) REVERT: 2 377 MET cc_start: 0.8460 (mmm) cc_final: 0.8106 (mmm) REVERT: 2 393 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: 3 303 GLN cc_start: 0.7113 (mt0) cc_final: 0.6732 (mp10) REVERT: 3 356 ARG cc_start: 0.7152 (ttt180) cc_final: 0.6914 (ttm-80) REVERT: 3 377 MET cc_start: 0.8403 (mmm) cc_final: 0.8043 (mmm) REVERT: 4 285 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7756 (p0) REVERT: 4 409 MET cc_start: 0.8591 (mmm) cc_final: 0.8163 (mmm) REVERT: 4 413 GLU cc_start: 0.8406 (tt0) cc_final: 0.7774 (mt-10) REVERT: 5 285 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7890 (p0) REVERT: 5 303 GLN cc_start: 0.7127 (mt0) cc_final: 0.6789 (mp10) REVERT: 5 356 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6846 (ttm-80) REVERT: 5 377 MET cc_start: 0.8374 (mmm) cc_final: 0.7980 (mmm) REVERT: 5 393 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: 6 356 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6952 (ttm-80) outliers start: 195 outliers final: 99 residues processed: 979 average time/residue: 0.2212 time to fit residues: 356.0247 Evaluate side-chains 953 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 834 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 231 ASN Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 381 ASP Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 381 ASP Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 285 ASN Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 411 GLN Chi-restraints excluded: chain P residue 415 LEU Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 381 ASP Chi-restraints excluded: chain R residue 386 SER Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 411 GLN Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 381 ASP Chi-restraints excluded: chain T residue 410 LYS Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 386 SER Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 381 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain X residue 430 LEU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Z residue 410 LYS Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 1 residue 410 LYS Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 285 ASN Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 4 residue 393 TYR Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 285 ASN Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 393 TYR Chi-restraints excluded: chain 5 residue 430 LEU Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 393 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 241 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 460 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 315 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 263 HIS B 239 ASN C 239 ASN D 239 ASN E 239 ASN F 239 ASN F 263 HIS G 239 ASN G 263 HIS H 239 ASN I 239 ASN J 234 GLN K 239 ASN M 239 ASN N 239 ASN O 239 ASN P 239 ASN Q 239 ASN R 239 ASN S 239 ASN T 239 ASN U 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 2 239 ASN 3 239 ASN 4 239 ASN 6 239 ASN 6 261 ASN 6 263 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.183406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.147413 restraints weight = 38878.526| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.74 r_work: 0.3790 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38560 Z= 0.124 Angle : 0.568 8.223 51968 Z= 0.292 Chirality : 0.039 0.146 5952 Planarity : 0.003 0.028 6976 Dihedral : 4.884 17.918 5216 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.22 % Allowed : 23.48 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 4640 helix: 2.63 (0.14), residues: 1280 sheet: -1.76 (0.12), residues: 2336 loop : -2.12 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 417 TYR 0.012 0.001 TYR A 393 PHE 0.024 0.001 PHE 2 237 HIS 0.001 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00261 (38560) covalent geometry : angle 0.56755 (51968) hydrogen bonds : bond 0.03311 ( 1668) hydrogen bonds : angle 4.12123 ( 4770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 900 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8388 (mmm) cc_final: 0.8042 (mmm) REVERT: A 386 SER cc_start: 0.9208 (m) cc_final: 0.8242 (p) REVERT: A 413 GLU cc_start: 0.8348 (tt0) cc_final: 0.7650 (mt-10) REVERT: B 377 MET cc_start: 0.8353 (mmm) cc_final: 0.8035 (mmm) REVERT: B 393 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6363 (m-10) REVERT: B 413 GLU cc_start: 0.8319 (tt0) cc_final: 0.7733 (mt-10) REVERT: B 414 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: C 356 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6995 (ttm-80) REVERT: C 386 SER cc_start: 0.9145 (m) cc_final: 0.8150 (t) REVERT: C 393 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: D 237 PHE cc_start: 0.7983 (t80) cc_final: 0.7309 (t80) REVERT: D 377 MET cc_start: 0.8377 (mmm) cc_final: 0.8057 (mmm) REVERT: D 393 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7288 (m-10) REVERT: D 410 LYS cc_start: 0.9115 (tptt) cc_final: 0.8881 (tptp) REVERT: D 413 GLU cc_start: 0.8334 (tt0) cc_final: 0.7697 (mt-10) REVERT: E 414 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: F 232 ASP cc_start: 0.7804 (t0) cc_final: 0.7559 (t0) REVERT: F 413 GLU cc_start: 0.8330 (tt0) cc_final: 0.7701 (mt-10) REVERT: G 356 ARG cc_start: 0.7014 (ttt180) cc_final: 0.6763 (ttm-80) REVERT: G 377 MET cc_start: 0.8228 (mmm) cc_final: 0.7848 (mmm) REVERT: G 393 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7152 (m-10) REVERT: H 276 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: H 377 MET cc_start: 0.8342 (mmm) cc_final: 0.8041 (mmm) REVERT: H 418 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7552 (mm-30) REVERT: I 377 MET cc_start: 0.8328 (mmm) cc_final: 0.8035 (mmm) REVERT: I 393 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7435 (m-10) REVERT: K 409 MET cc_start: 0.8575 (mmm) cc_final: 0.8286 (mmm) REVERT: K 413 GLU cc_start: 0.8224 (tt0) cc_final: 0.7696 (mt-10) REVERT: K 435 SER cc_start: 0.8493 (t) cc_final: 0.8194 (m) REVERT: L 237 PHE cc_start: 0.7981 (t80) cc_final: 0.7348 (t80) REVERT: L 377 MET cc_start: 0.8411 (mmm) cc_final: 0.8048 (mmm) REVERT: M 356 ARG cc_start: 0.7132 (ttt180) cc_final: 0.6878 (ttm-80) REVERT: M 386 SER cc_start: 0.9206 (m) cc_final: 0.8272 (t) REVERT: N 413 GLU cc_start: 0.8308 (tt0) cc_final: 0.7729 (mt-10) REVERT: O 409 MET cc_start: 0.8736 (mmm) cc_final: 0.8441 (mmm) REVERT: P 276 GLU cc_start: 0.7740 (mp0) cc_final: 0.7200 (mp0) REVERT: P 409 MET cc_start: 0.8558 (mmm) cc_final: 0.8149 (mmm) REVERT: P 413 GLU cc_start: 0.8274 (tt0) cc_final: 0.7673 (mt-10) REVERT: P 418 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7716 (mm-30) REVERT: Q 376 LYS cc_start: 0.7432 (tttt) cc_final: 0.6910 (tttp) REVERT: Q 435 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8345 (m) REVERT: R 377 MET cc_start: 0.8346 (mmm) cc_final: 0.8020 (mmm) REVERT: T 237 PHE cc_start: 0.8004 (t80) cc_final: 0.7380 (t80) REVERT: T 377 MET cc_start: 0.8381 (mmm) cc_final: 0.8041 (mmm) REVERT: T 386 SER cc_start: 0.9162 (m) cc_final: 0.8191 (t) REVERT: T 413 GLU cc_start: 0.8354 (tt0) cc_final: 0.7827 (mt-10) REVERT: U 409 MET cc_start: 0.8568 (mmm) cc_final: 0.8342 (mmm) REVERT: V 232 ASP cc_start: 0.7901 (t0) cc_final: 0.7657 (t0) REVERT: W 377 MET cc_start: 0.8293 (mmm) cc_final: 0.7984 (mmm) REVERT: W 413 GLU cc_start: 0.8322 (tt0) cc_final: 0.7750 (mt-10) REVERT: X 413 GLU cc_start: 0.8299 (tt0) cc_final: 0.7823 (mt-10) REVERT: X 435 SER cc_start: 0.7706 (m) cc_final: 0.7473 (m) REVERT: Y 386 SER cc_start: 0.9170 (m) cc_final: 0.8225 (p) REVERT: Y 393 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: Y 409 MET cc_start: 0.8483 (mmm) cc_final: 0.7845 (mmm) REVERT: Y 413 GLU cc_start: 0.8326 (tt0) cc_final: 0.7656 (mt-10) REVERT: Z 232 ASP cc_start: 0.7634 (t0) cc_final: 0.6551 (m-30) REVERT: Z 377 MET cc_start: 0.8370 (mmm) cc_final: 0.8075 (mmm) REVERT: Z 386 SER cc_start: 0.9118 (m) cc_final: 0.8144 (p) REVERT: 1 409 MET cc_start: 0.8426 (mmm) cc_final: 0.7961 (mmm) REVERT: 1 413 GLU cc_start: 0.8363 (tt0) cc_final: 0.7844 (mt-10) REVERT: 1 431 ASN cc_start: 0.8520 (t0) cc_final: 0.8122 (t0) REVERT: 2 377 MET cc_start: 0.8343 (mmm) cc_final: 0.7997 (mmm) REVERT: 2 393 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6925 (m-10) REVERT: 2 414 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: 3 377 MET cc_start: 0.8328 (mmm) cc_final: 0.8039 (mmm) REVERT: 4 409 MET cc_start: 0.8551 (mmm) cc_final: 0.7893 (tpp) REVERT: 4 413 GLU cc_start: 0.8370 (tt0) cc_final: 0.7700 (mt-10) REVERT: 5 356 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6836 (ttm-80) REVERT: 5 377 MET cc_start: 0.8285 (mmm) cc_final: 0.7906 (mmm) REVERT: 5 413 GLU cc_start: 0.8387 (tt0) cc_final: 0.7704 (mt-10) REVERT: 6 356 ARG cc_start: 0.7087 (ttt180) cc_final: 0.6836 (ttm-80) REVERT: 6 386 SER cc_start: 0.9202 (m) cc_final: 0.8207 (t) REVERT: 6 409 MET cc_start: 0.8345 (tpp) cc_final: 0.7746 (tpp) outliers start: 138 outliers final: 57 residues processed: 957 average time/residue: 0.2083 time to fit residues: 336.1723 Evaluate side-chains 931 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 862 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 386 SER Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 414 ASP Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 386 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 262 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 347 optimal weight: 1.9990 chunk 408 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 460 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 448 optimal weight: 0.0970 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN D 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN I 411 GLN J 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN O 239 ASN P 239 ASN R 239 ASN S 239 ASN S 285 ASN T 239 ASN T 411 GLN U 239 ASN V 239 ASN W 411 GLN X 239 ASN Z 239 ASN 1 239 ASN 1 285 ASN 2 239 ASN 3 239 ASN 4 239 ASN 4 411 GLN 6 239 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142856 restraints weight = 39461.414| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.83 r_work: 0.3744 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38560 Z= 0.190 Angle : 0.631 9.587 51968 Z= 0.323 Chirality : 0.040 0.228 5952 Planarity : 0.004 0.024 6976 Dihedral : 5.068 18.813 5216 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.68 % Allowed : 23.83 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.14), residues: 4640 helix: 2.38 (0.14), residues: 1280 sheet: -1.71 (0.12), residues: 2304 loop : -2.19 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 417 TYR 0.017 0.001 TYR 5 393 PHE 0.022 0.002 PHE 2 237 HIS 0.003 0.001 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00421 (38560) covalent geometry : angle 0.63129 (51968) hydrogen bonds : bond 0.03521 ( 1668) hydrogen bonds : angle 4.33302 ( 4770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 907 time to evaluate : 1.662 Fit side-chains REVERT: A 377 MET cc_start: 0.8395 (mmm) cc_final: 0.8029 (mmm) REVERT: A 386 SER cc_start: 0.9283 (m) cc_final: 0.8339 (p) REVERT: A 393 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: A 413 GLU cc_start: 0.8329 (tt0) cc_final: 0.7719 (mt-10) REVERT: B 377 MET cc_start: 0.8403 (mmm) cc_final: 0.8039 (mmm) REVERT: B 393 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.6383 (m-10) REVERT: B 409 MET cc_start: 0.8432 (tpp) cc_final: 0.7934 (tpp) REVERT: B 413 GLU cc_start: 0.8288 (tt0) cc_final: 0.7908 (mt-10) REVERT: C 303 GLN cc_start: 0.7102 (mt0) cc_final: 0.6889 (mp10) REVERT: C 356 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6903 (ttm-80) REVERT: C 386 SER cc_start: 0.9238 (m) cc_final: 0.8233 (t) REVERT: C 393 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: C 413 GLU cc_start: 0.8268 (tt0) cc_final: 0.7600 (mt-10) REVERT: D 237 PHE cc_start: 0.8062 (t80) cc_final: 0.7401 (t80) REVERT: D 377 MET cc_start: 0.8377 (mmm) cc_final: 0.8016 (mmm) REVERT: D 393 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: D 413 GLU cc_start: 0.8422 (tt0) cc_final: 0.7786 (mt-10) REVERT: E 303 GLN cc_start: 0.7231 (mt0) cc_final: 0.6675 (mp10) REVERT: E 414 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: F 232 ASP cc_start: 0.7931 (t0) cc_final: 0.7697 (t0) REVERT: F 413 GLU cc_start: 0.8386 (tt0) cc_final: 0.7696 (mt-10) REVERT: G 356 ARG cc_start: 0.7026 (ttt180) cc_final: 0.6783 (ttm-80) REVERT: G 377 MET cc_start: 0.8304 (mmm) cc_final: 0.7912 (mmm) REVERT: G 386 SER cc_start: 0.9201 (m) cc_final: 0.8194 (p) REVERT: G 393 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: H 276 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: H 377 MET cc_start: 0.8349 (mmm) cc_final: 0.8017 (mmm) REVERT: H 409 MET cc_start: 0.8540 (mmm) cc_final: 0.7529 (mmm) REVERT: H 413 GLU cc_start: 0.8365 (tt0) cc_final: 0.7782 (mp0) REVERT: I 276 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: I 386 SER cc_start: 0.9150 (m) cc_final: 0.8131 (t) REVERT: I 393 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: I 413 GLU cc_start: 0.8296 (tt0) cc_final: 0.8000 (mt-10) REVERT: I 414 ASP cc_start: 0.7743 (t0) cc_final: 0.7527 (p0) REVERT: K 276 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: K 386 SER cc_start: 0.9230 (m) cc_final: 0.8251 (t) REVERT: K 409 MET cc_start: 0.8581 (mmm) cc_final: 0.8265 (mmm) REVERT: K 413 GLU cc_start: 0.8239 (tt0) cc_final: 0.7686 (mt-10) REVERT: K 423 SER cc_start: 0.7786 (t) cc_final: 0.7518 (t) REVERT: L 237 PHE cc_start: 0.8041 (t80) cc_final: 0.7511 (t80) REVERT: L 377 MET cc_start: 0.8382 (mmm) cc_final: 0.8000 (mmm) REVERT: M 356 ARG cc_start: 0.7227 (ttt180) cc_final: 0.6952 (ttm-80) REVERT: M 409 MET cc_start: 0.8528 (mmm) cc_final: 0.8324 (mmm) REVERT: N 413 GLU cc_start: 0.8348 (tt0) cc_final: 0.7742 (mt-10) REVERT: O 409 MET cc_start: 0.8693 (mmm) cc_final: 0.8461 (mmm) REVERT: O 410 LYS cc_start: 0.9082 (tptt) cc_final: 0.8829 (tptt) REVERT: P 276 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: P 386 SER cc_start: 0.9261 (m) cc_final: 0.8273 (t) REVERT: P 409 MET cc_start: 0.8563 (mmm) cc_final: 0.8159 (mmm) REVERT: P 413 GLU cc_start: 0.8294 (tt0) cc_final: 0.7693 (mt-10) REVERT: Q 435 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8495 (m) REVERT: R 377 MET cc_start: 0.8369 (mmm) cc_final: 0.8006 (mmm) REVERT: R 423 SER cc_start: 0.7801 (t) cc_final: 0.7547 (t) REVERT: S 412 ILE cc_start: 0.8012 (tt) cc_final: 0.7754 (mp) REVERT: T 237 PHE cc_start: 0.8052 (t80) cc_final: 0.7577 (t80) REVERT: T 377 MET cc_start: 0.8415 (mmm) cc_final: 0.8034 (mmm) REVERT: T 386 SER cc_start: 0.9232 (m) cc_final: 0.8301 (t) REVERT: T 413 GLU cc_start: 0.8366 (tt0) cc_final: 0.7834 (mt-10) REVERT: V 232 ASP cc_start: 0.8023 (t0) cc_final: 0.7805 (t0) REVERT: V 386 SER cc_start: 0.9206 (m) cc_final: 0.8216 (t) REVERT: V 413 GLU cc_start: 0.8334 (tt0) cc_final: 0.8070 (mt-10) REVERT: V 417 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7941 (ttm110) REVERT: W 377 MET cc_start: 0.8392 (mmm) cc_final: 0.8055 (mmm) REVERT: W 413 GLU cc_start: 0.8340 (tt0) cc_final: 0.7821 (mt-10) REVERT: W 414 ASP cc_start: 0.7633 (t0) cc_final: 0.7365 (p0) REVERT: X 413 GLU cc_start: 0.8364 (tt0) cc_final: 0.7900 (mt-10) REVERT: Y 386 SER cc_start: 0.9249 (m) cc_final: 0.8275 (t) REVERT: Y 393 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: Y 409 MET cc_start: 0.8458 (mmm) cc_final: 0.8241 (mmm) REVERT: Y 413 GLU cc_start: 0.8315 (tt0) cc_final: 0.7944 (mt-10) REVERT: Z 377 MET cc_start: 0.8408 (mmm) cc_final: 0.8095 (mmm) REVERT: Z 386 SER cc_start: 0.9193 (m) cc_final: 0.8193 (p) REVERT: Z 413 GLU cc_start: 0.8271 (tt0) cc_final: 0.7889 (mt-10) REVERT: 1 409 MET cc_start: 0.8456 (mmm) cc_final: 0.8136 (mmm) REVERT: 1 413 GLU cc_start: 0.8394 (tt0) cc_final: 0.7854 (mt-10) REVERT: 1 431 ASN cc_start: 0.8549 (t0) cc_final: 0.8236 (t0) REVERT: 2 377 MET cc_start: 0.8375 (mmm) cc_final: 0.7986 (mmm) REVERT: 2 393 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: 3 303 GLN cc_start: 0.7053 (mt0) cc_final: 0.6562 (mp10) REVERT: 3 377 MET cc_start: 0.8321 (mmm) cc_final: 0.7978 (mmm) REVERT: 3 413 GLU cc_start: 0.8371 (tt0) cc_final: 0.7715 (mt-10) REVERT: 4 409 MET cc_start: 0.8564 (mmm) cc_final: 0.8202 (mmm) REVERT: 4 413 GLU cc_start: 0.8390 (tt0) cc_final: 0.7748 (mt-10) REVERT: 5 356 ARG cc_start: 0.7197 (ttt180) cc_final: 0.6863 (ttm-80) REVERT: 5 377 MET cc_start: 0.8390 (mmm) cc_final: 0.8026 (mmm) REVERT: 5 413 GLU cc_start: 0.8323 (tt0) cc_final: 0.7710 (mt-10) REVERT: 6 356 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6856 (ttm-80) REVERT: 6 404 LEU cc_start: 0.6300 (mp) cc_final: 0.5973 (mp) REVERT: 6 409 MET cc_start: 0.8399 (tpp) cc_final: 0.7849 (tpp) outliers start: 158 outliers final: 75 residues processed: 985 average time/residue: 0.2141 time to fit residues: 357.8403 Evaluate side-chains 964 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 875 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 410 LYS Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 368 VAL Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 411 GLN Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 415 LEU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 391 VAL Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 381 ASP Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 4 residue 386 SER Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 262 VAL Chi-restraints excluded: chain 6 residue 430 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 44 optimal weight: 10.0000 chunk 289 optimal weight: 0.8980 chunk 463 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 443 optimal weight: 4.9990 chunk 436 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN D 239 ASN D 261 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN O 239 ASN P 239 ASN Q 239 ASN R 239 ASN S 239 ASN T 239 ASN U 239 ASN V 239 ASN V 411 GLN X 239 ASN Z 239 ASN 1 239 ASN 2 239 ASN 3 239 ASN 4 239 ASN 6 239 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145468 restraints weight = 39215.137| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.76 r_work: 0.3855 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 38560 Z= 0.154 Angle : 0.605 9.519 51968 Z= 0.312 Chirality : 0.040 0.211 5952 Planarity : 0.003 0.031 6976 Dihedral : 4.922 18.292 5216 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.38 % Allowed : 23.95 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.14), residues: 4640 helix: 2.37 (0.14), residues: 1280 sheet: -1.75 (0.12), residues: 2336 loop : -2.30 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 247 TYR 0.013 0.001 TYR 5 393 PHE 0.021 0.001 PHE K 237 HIS 0.002 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00343 (38560) covalent geometry : angle 0.60451 (51968) hydrogen bonds : bond 0.03361 ( 1668) hydrogen bonds : angle 4.31938 ( 4770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 881 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7762 (t0) cc_final: 0.7554 (t0) REVERT: A 377 MET cc_start: 0.8341 (mmm) cc_final: 0.8025 (mmm) REVERT: A 386 SER cc_start: 0.9228 (m) cc_final: 0.8354 (p) REVERT: A 393 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: A 413 GLU cc_start: 0.8261 (tt0) cc_final: 0.7928 (mt-10) REVERT: B 377 MET cc_start: 0.8364 (mmm) cc_final: 0.8072 (mmm) REVERT: B 393 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: B 413 GLU cc_start: 0.8214 (tt0) cc_final: 0.7974 (mt-10) REVERT: B 414 ASP cc_start: 0.7815 (t0) cc_final: 0.7602 (p0) REVERT: C 393 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: C 413 GLU cc_start: 0.8256 (tt0) cc_final: 0.7717 (mt-10) REVERT: D 237 PHE cc_start: 0.8056 (t80) cc_final: 0.7413 (t80) REVERT: D 377 MET cc_start: 0.8340 (mmm) cc_final: 0.8046 (mmm) REVERT: D 393 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7326 (m-10) REVERT: D 413 GLU cc_start: 0.8336 (tt0) cc_final: 0.7957 (mt-10) REVERT: E 413 GLU cc_start: 0.8352 (tt0) cc_final: 0.7783 (mt-10) REVERT: F 232 ASP cc_start: 0.7892 (t0) cc_final: 0.7674 (t0) REVERT: F 413 GLU cc_start: 0.8340 (tt0) cc_final: 0.7820 (mt-10) REVERT: G 356 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6897 (ttm-80) REVERT: G 377 MET cc_start: 0.8242 (mmm) cc_final: 0.7898 (mmm) REVERT: G 386 SER cc_start: 0.9130 (m) cc_final: 0.8177 (p) REVERT: G 393 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: H 276 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: H 377 MET cc_start: 0.8307 (mmm) cc_final: 0.8023 (mmm) REVERT: H 413 GLU cc_start: 0.8283 (tt0) cc_final: 0.7754 (mt-10) REVERT: H 418 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7495 (mm-30) REVERT: I 276 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: I 386 SER cc_start: 0.9082 (m) cc_final: 0.8092 (t) REVERT: I 393 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7525 (m-10) REVERT: I 413 GLU cc_start: 0.8201 (tt0) cc_final: 0.7983 (mt-10) REVERT: J 413 GLU cc_start: 0.8099 (tt0) cc_final: 0.7628 (mt-10) REVERT: K 276 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: K 410 LYS cc_start: 0.9151 (tptt) cc_final: 0.8829 (tptt) REVERT: K 413 GLU cc_start: 0.8228 (tt0) cc_final: 0.7752 (mt-10) REVERT: K 414 ASP cc_start: 0.7801 (t0) cc_final: 0.7527 (p0) REVERT: K 423 SER cc_start: 0.7822 (t) cc_final: 0.7615 (t) REVERT: K 435 SER cc_start: 0.8294 (t) cc_final: 0.7938 (m) REVERT: L 237 PHE cc_start: 0.8003 (t80) cc_final: 0.7411 (t80) REVERT: L 377 MET cc_start: 0.8355 (mmm) cc_final: 0.8006 (mmm) REVERT: L 386 SER cc_start: 0.9123 (m) cc_final: 0.8139 (t) REVERT: M 356 ARG cc_start: 0.7260 (ttt180) cc_final: 0.7045 (ttm-80) REVERT: N 413 GLU cc_start: 0.8265 (tt0) cc_final: 0.7936 (mt-10) REVERT: O 386 SER cc_start: 0.9306 (m) cc_final: 0.8346 (t) REVERT: O 409 MET cc_start: 0.8706 (mmm) cc_final: 0.8480 (mmm) REVERT: O 410 LYS cc_start: 0.9096 (tptt) cc_final: 0.8869 (tptt) REVERT: P 276 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: P 386 SER cc_start: 0.9195 (m) cc_final: 0.8265 (t) REVERT: P 409 MET cc_start: 0.8584 (mmm) cc_final: 0.8240 (mmm) REVERT: P 413 GLU cc_start: 0.8339 (tt0) cc_final: 0.7747 (mt-10) REVERT: P 418 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7699 (mm-30) REVERT: Q 386 SER cc_start: 0.9198 (m) cc_final: 0.8193 (t) REVERT: Q 435 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8527 (m) REVERT: R 377 MET cc_start: 0.8337 (mmm) cc_final: 0.8046 (mmm) REVERT: R 423 SER cc_start: 0.7883 (t) cc_final: 0.7667 (t) REVERT: S 412 ILE cc_start: 0.8265 (tt) cc_final: 0.8047 (mp) REVERT: S 413 GLU cc_start: 0.8300 (tp30) cc_final: 0.8047 (tp30) REVERT: T 237 PHE cc_start: 0.8029 (t80) cc_final: 0.7466 (t80) REVERT: T 377 MET cc_start: 0.8407 (mmm) cc_final: 0.8057 (mmm) REVERT: T 386 SER cc_start: 0.9165 (m) cc_final: 0.8263 (t) REVERT: V 386 SER cc_start: 0.9116 (m) cc_final: 0.8189 (t) REVERT: V 417 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8071 (ttm110) REVERT: W 242 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: W 377 MET cc_start: 0.8374 (mmm) cc_final: 0.8076 (mmm) REVERT: W 413 GLU cc_start: 0.8263 (tt0) cc_final: 0.7983 (mt-10) REVERT: X 386 SER cc_start: 0.9272 (m) cc_final: 0.8318 (t) REVERT: X 413 GLU cc_start: 0.8288 (tt0) cc_final: 0.7774 (mt-10) REVERT: Y 386 SER cc_start: 0.9194 (m) cc_final: 0.8260 (t) REVERT: Y 393 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: Y 413 GLU cc_start: 0.8215 (tt0) cc_final: 0.7954 (mt-10) REVERT: Z 377 MET cc_start: 0.8365 (mmm) cc_final: 0.8104 (mmm) REVERT: Z 386 SER cc_start: 0.9099 (m) cc_final: 0.8127 (p) REVERT: Z 414 ASP cc_start: 0.7743 (t0) cc_final: 0.7512 (p0) REVERT: 1 409 MET cc_start: 0.8478 (mmm) cc_final: 0.8192 (mmm) REVERT: 1 413 GLU cc_start: 0.8352 (tt0) cc_final: 0.7922 (mt-10) REVERT: 1 431 ASN cc_start: 0.8535 (t0) cc_final: 0.8248 (t0) REVERT: 2 377 MET cc_start: 0.8346 (mmm) cc_final: 0.8033 (mmm) REVERT: 2 393 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: 3 377 MET cc_start: 0.8317 (mmm) cc_final: 0.8058 (mmm) REVERT: 3 409 MET cc_start: 0.8355 (tpp) cc_final: 0.8021 (tpp) REVERT: 3 413 GLU cc_start: 0.8339 (tt0) cc_final: 0.7663 (mt-10) REVERT: 4 409 MET cc_start: 0.8569 (mmm) cc_final: 0.8017 (mmm) REVERT: 4 413 GLU cc_start: 0.8360 (tt0) cc_final: 0.7855 (mt-10) REVERT: 5 356 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6986 (ttm-80) REVERT: 5 377 MET cc_start: 0.8277 (mmm) cc_final: 0.7961 (mmm) REVERT: 5 413 GLU cc_start: 0.8348 (tt0) cc_final: 0.7713 (mt-10) REVERT: 6 356 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6965 (ttm-80) REVERT: 6 386 SER cc_start: 0.9200 (m) cc_final: 0.8185 (t) REVERT: 6 404 LEU cc_start: 0.6345 (mp) cc_final: 0.6059 (mp) REVERT: 6 409 MET cc_start: 0.8352 (tpp) cc_final: 0.7733 (tpp) outliers start: 145 outliers final: 69 residues processed: 956 average time/residue: 0.2236 time to fit residues: 361.2747 Evaluate side-chains 946 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 863 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain N residue 415 LEU Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 6 residue 231 ASN Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 262 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 45 optimal weight: 4.9990 chunk 357 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 467 optimal weight: 0.0870 chunk 195 optimal weight: 0.8980 chunk 216 optimal weight: 0.3980 chunk 44 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 356 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN D 239 ASN E 239 ASN F 239 ASN G 239 ASN G 261 ASN H 239 ASN I 239 ASN I 261 ASN K 239 ASN L 239 ASN M 239 ASN M 411 GLN N 239 ASN N 261 ASN O 261 ASN P 239 ASN R 239 ASN R 261 ASN S 239 ASN S 261 ASN T 239 ASN U 239 ASN U 261 ASN V 239 ASN X 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 1 261 ASN 2 239 ASN 3 239 ASN 4 239 ASN 4 261 ASN 5 263 HIS 6 239 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.148561 restraints weight = 38521.152| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.73 r_work: 0.3811 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38560 Z= 0.116 Angle : 0.570 8.771 51968 Z= 0.297 Chirality : 0.040 0.217 5952 Planarity : 0.003 0.039 6976 Dihedral : 4.613 17.240 5216 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.96 % Allowed : 24.44 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.13), residues: 4640 helix: 2.42 (0.14), residues: 1280 sheet: -1.74 (0.12), residues: 2208 loop : -2.07 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 247 TYR 0.017 0.001 TYR O 393 PHE 0.023 0.001 PHE 1 237 HIS 0.001 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (38560) covalent geometry : angle 0.57049 (51968) hydrogen bonds : bond 0.03109 ( 1668) hydrogen bonds : angle 4.26559 ( 4770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 904 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7720 (t0) cc_final: 0.7469 (t0) REVERT: A 276 GLU cc_start: 0.7529 (mp0) cc_final: 0.7280 (mp0) REVERT: A 386 SER cc_start: 0.9175 (m) cc_final: 0.8239 (p) REVERT: A 393 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: B 276 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: B 377 MET cc_start: 0.8349 (mmm) cc_final: 0.8026 (mmm) REVERT: B 386 SER cc_start: 0.9106 (m) cc_final: 0.8079 (p) REVERT: B 393 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.6493 (m-10) REVERT: B 413 GLU cc_start: 0.8184 (tt0) cc_final: 0.7907 (mt-10) REVERT: C 393 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: C 409 MET cc_start: 0.8363 (mmm) cc_final: 0.7840 (tpt) REVERT: C 413 GLU cc_start: 0.8240 (tt0) cc_final: 0.7664 (mt-10) REVERT: D 237 PHE cc_start: 0.7988 (t80) cc_final: 0.7344 (t80) REVERT: D 377 MET cc_start: 0.8330 (mmm) cc_final: 0.7979 (mmm) REVERT: D 393 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7232 (m-10) REVERT: D 413 GLU cc_start: 0.8287 (tt0) cc_final: 0.7917 (mt-10) REVERT: E 413 GLU cc_start: 0.8328 (tt0) cc_final: 0.7953 (mt-10) REVERT: E 414 ASP cc_start: 0.7831 (t0) cc_final: 0.7537 (p0) REVERT: F 232 ASP cc_start: 0.7855 (t0) cc_final: 0.7634 (t0) REVERT: F 376 LYS cc_start: 0.7262 (tttt) cc_final: 0.6766 (tttp) REVERT: F 386 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.7987 (p) REVERT: F 404 LEU cc_start: 0.6737 (mp) cc_final: 0.6520 (mp) REVERT: F 413 GLU cc_start: 0.8291 (tt0) cc_final: 0.7909 (mt-10) REVERT: G 356 ARG cc_start: 0.7056 (ttt180) cc_final: 0.6790 (ttm-80) REVERT: G 377 MET cc_start: 0.8259 (mmm) cc_final: 0.7909 (mmm) REVERT: G 386 SER cc_start: 0.9057 (m) cc_final: 0.8033 (p) REVERT: G 393 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: G 413 GLU cc_start: 0.8371 (tt0) cc_final: 0.7771 (mt-10) REVERT: H 276 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: H 377 MET cc_start: 0.8332 (mmm) cc_final: 0.8051 (mmm) REVERT: H 418 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7444 (mm-30) REVERT: I 276 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: I 386 SER cc_start: 0.9046 (m) cc_final: 0.7994 (t) REVERT: I 393 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: J 413 GLU cc_start: 0.8103 (tt0) cc_final: 0.7670 (mt-10) REVERT: K 276 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: K 386 SER cc_start: 0.9140 (m) cc_final: 0.8138 (t) REVERT: K 410 LYS cc_start: 0.9095 (tptt) cc_final: 0.8806 (tptt) REVERT: K 413 GLU cc_start: 0.8260 (tt0) cc_final: 0.7809 (mt-10) REVERT: K 414 ASP cc_start: 0.7675 (t0) cc_final: 0.7442 (p0) REVERT: K 435 SER cc_start: 0.8228 (t) cc_final: 0.7833 (m) REVERT: L 237 PHE cc_start: 0.7938 (t80) cc_final: 0.7362 (t80) REVERT: L 377 MET cc_start: 0.8337 (mmm) cc_final: 0.7980 (mmm) REVERT: L 386 SER cc_start: 0.9098 (m) cc_final: 0.8071 (t) REVERT: M 356 ARG cc_start: 0.7149 (ttt180) cc_final: 0.6925 (ttm-80) REVERT: M 413 GLU cc_start: 0.8275 (tt0) cc_final: 0.7880 (mt-10) REVERT: M 414 ASP cc_start: 0.7694 (t0) cc_final: 0.7460 (p0) REVERT: N 376 LYS cc_start: 0.7289 (tttt) cc_final: 0.6807 (tttp) REVERT: N 414 ASP cc_start: 0.7760 (t0) cc_final: 0.7496 (p0) REVERT: O 386 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8222 (t) REVERT: O 409 MET cc_start: 0.8678 (mmm) cc_final: 0.8407 (mmm) REVERT: O 410 LYS cc_start: 0.9098 (tptt) cc_final: 0.8885 (tptt) REVERT: P 276 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: P 386 SER cc_start: 0.9139 (m) cc_final: 0.8138 (p) REVERT: P 409 MET cc_start: 0.8590 (mmm) cc_final: 0.8196 (mmm) REVERT: P 413 GLU cc_start: 0.8370 (tt0) cc_final: 0.7746 (mt-10) REVERT: P 418 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7702 (mm-30) REVERT: Q 386 SER cc_start: 0.9156 (m) cc_final: 0.8119 (t) REVERT: Q 435 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8390 (m) REVERT: R 377 MET cc_start: 0.8303 (mmm) cc_final: 0.8005 (mmm) REVERT: R 413 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8358 (tm-30) REVERT: T 237 PHE cc_start: 0.7972 (t80) cc_final: 0.7420 (t80) REVERT: T 377 MET cc_start: 0.8347 (mmm) cc_final: 0.7989 (mmm) REVERT: T 386 SER cc_start: 0.9115 (m) cc_final: 0.8152 (t) REVERT: V 376 LYS cc_start: 0.7276 (tttt) cc_final: 0.6794 (tttp) REVERT: V 417 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7278 (ttm110) REVERT: W 242 GLU cc_start: 0.7072 (pt0) cc_final: 0.6748 (tt0) REVERT: W 377 MET cc_start: 0.8371 (mmm) cc_final: 0.8073 (mmm) REVERT: W 386 SER cc_start: 0.9179 (m) cc_final: 0.8234 (t) REVERT: W 409 MET cc_start: 0.8591 (mmm) cc_final: 0.8254 (tpp) REVERT: X 386 SER cc_start: 0.9200 (m) cc_final: 0.8233 (t) REVERT: X 413 GLU cc_start: 0.8053 (tt0) cc_final: 0.7696 (mt-10) REVERT: X 418 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7402 (mm-30) REVERT: X 431 ASN cc_start: 0.8451 (t0) cc_final: 0.8135 (t0) REVERT: Y 386 SER cc_start: 0.9154 (m) cc_final: 0.8157 (t) REVERT: Y 393 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: Z 377 MET cc_start: 0.8308 (mmm) cc_final: 0.8062 (mmm) REVERT: Z 386 SER cc_start: 0.9037 (m) cc_final: 0.8026 (p) REVERT: Z 414 ASP cc_start: 0.7617 (t0) cc_final: 0.7406 (p0) REVERT: 1 409 MET cc_start: 0.8384 (mmm) cc_final: 0.8183 (mmm) REVERT: 1 413 GLU cc_start: 0.8339 (tt0) cc_final: 0.7956 (mt-10) REVERT: 1 431 ASN cc_start: 0.8494 (t0) cc_final: 0.8130 (t0) REVERT: 2 377 MET cc_start: 0.8324 (mmm) cc_final: 0.7994 (mmm) REVERT: 2 386 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8019 (p) REVERT: 2 393 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: 2 413 GLU cc_start: 0.8326 (tt0) cc_final: 0.7828 (mp0) REVERT: 3 377 MET cc_start: 0.8290 (mmm) cc_final: 0.8025 (mmm) REVERT: 3 409 MET cc_start: 0.8321 (tpp) cc_final: 0.7838 (tpp) REVERT: 3 413 GLU cc_start: 0.8357 (tt0) cc_final: 0.7643 (mt-10) REVERT: 4 376 LYS cc_start: 0.7227 (tttt) cc_final: 0.6749 (tttp) REVERT: 4 409 MET cc_start: 0.8504 (mmm) cc_final: 0.7536 (tpt) REVERT: 4 413 GLU cc_start: 0.8341 (tt0) cc_final: 0.7748 (mt-10) REVERT: 4 414 ASP cc_start: 0.7772 (t0) cc_final: 0.7542 (p0) REVERT: 5 356 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6866 (ttm-80) REVERT: 5 377 MET cc_start: 0.8269 (mmm) cc_final: 0.7972 (mmm) REVERT: 5 386 SER cc_start: 0.9136 (m) cc_final: 0.8114 (p) REVERT: 5 413 GLU cc_start: 0.8356 (tt0) cc_final: 0.7692 (mt-10) REVERT: 6 243 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.7950 (m) REVERT: 6 356 ARG cc_start: 0.7072 (ttt180) cc_final: 0.6827 (ttm-80) REVERT: 6 386 SER cc_start: 0.9155 (m) cc_final: 0.8132 (t) REVERT: 6 404 LEU cc_start: 0.6291 (mp) cc_final: 0.6049 (mp) REVERT: 6 409 MET cc_start: 0.8344 (tpp) cc_final: 0.7603 (tpp) REVERT: 6 412 ILE cc_start: 0.8362 (mm) cc_final: 0.8135 (tt) outliers start: 127 outliers final: 60 residues processed: 963 average time/residue: 0.2202 time to fit residues: 361.1133 Evaluate side-chains 959 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 881 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 415 LEU Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain V residue 430 LEU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 386 SER Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 386 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 6 residue 243 SER Chi-restraints excluded: chain 6 residue 262 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 2.9990 chunk 386 optimal weight: 0.0050 chunk 228 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 380 optimal weight: 0.5980 chunk 410 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 420 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN C 261 ASN D 239 ASN E 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN K 261 ASN L 239 ASN M 239 ASN N 239 ASN P 239 ASN Q 239 ASN R 239 ASN S 239 ASN T 239 ASN U 239 ASN V 239 ASN X 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 2 239 ASN 3 239 ASN 4 239 ASN 6 239 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.186052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.149661 restraints weight = 38846.638| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.79 r_work: 0.3814 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38560 Z= 0.122 Angle : 0.575 9.838 51968 Z= 0.300 Chirality : 0.040 0.265 5952 Planarity : 0.003 0.035 6976 Dihedral : 4.550 16.593 5216 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.85 % Allowed : 24.51 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 4640 helix: 2.36 (0.14), residues: 1280 sheet: -1.68 (0.12), residues: 2208 loop : -2.06 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 417 TYR 0.009 0.001 TYR 4 393 PHE 0.023 0.001 PHE 1 237 HIS 0.001 0.000 HIS 6 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (38560) covalent geometry : angle 0.57512 (51968) hydrogen bonds : bond 0.03108 ( 1668) hydrogen bonds : angle 4.37838 ( 4770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 893 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7737 (t0) cc_final: 0.7487 (t0) REVERT: A 271 ASP cc_start: 0.7770 (t0) cc_final: 0.7358 (t0) REVERT: A 276 GLU cc_start: 0.7475 (mp0) cc_final: 0.7236 (mp0) REVERT: A 386 SER cc_start: 0.9191 (m) cc_final: 0.8257 (p) REVERT: A 393 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 404 LEU cc_start: 0.6744 (mp) cc_final: 0.6543 (mp) REVERT: A 409 MET cc_start: 0.8214 (tpp) cc_final: 0.7766 (tpt) REVERT: B 232 ASP cc_start: 0.7768 (t0) cc_final: 0.7524 (t0) REVERT: B 276 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 377 MET cc_start: 0.8339 (mmm) cc_final: 0.8023 (mmm) REVERT: B 386 SER cc_start: 0.9152 (m) cc_final: 0.8145 (p) REVERT: B 393 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6545 (m-10) REVERT: C 386 SER cc_start: 0.9151 (m) cc_final: 0.8118 (t) REVERT: C 393 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6541 (m-10) REVERT: D 237 PHE cc_start: 0.7997 (t80) cc_final: 0.7379 (t80) REVERT: D 377 MET cc_start: 0.8298 (mmm) cc_final: 0.7946 (mmm) REVERT: D 393 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: E 413 GLU cc_start: 0.8294 (tt0) cc_final: 0.7958 (mt-10) REVERT: E 414 ASP cc_start: 0.7804 (t0) cc_final: 0.7541 (p0) REVERT: F 232 ASP cc_start: 0.7843 (t0) cc_final: 0.7634 (t0) REVERT: F 376 LYS cc_start: 0.7222 (tttt) cc_final: 0.6718 (tttp) REVERT: F 386 SER cc_start: 0.9121 (m) cc_final: 0.7971 (p) REVERT: F 409 MET cc_start: 0.8292 (tpp) cc_final: 0.7553 (tpp) REVERT: F 413 GLU cc_start: 0.8238 (tt0) cc_final: 0.7909 (mt-10) REVERT: G 356 ARG cc_start: 0.7093 (ttt180) cc_final: 0.6819 (ttm-80) REVERT: G 377 MET cc_start: 0.8223 (mmm) cc_final: 0.7867 (mmm) REVERT: G 386 SER cc_start: 0.9027 (m) cc_final: 0.8002 (p) REVERT: G 393 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: G 413 GLU cc_start: 0.8395 (tt0) cc_final: 0.7774 (mt-10) REVERT: H 276 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: H 377 MET cc_start: 0.8298 (mmm) cc_final: 0.8019 (mmm) REVERT: H 418 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7490 (mm-30) REVERT: I 276 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: I 393 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7471 (m-10) REVERT: I 409 MET cc_start: 0.8448 (mmm) cc_final: 0.8194 (tpt) REVERT: K 276 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: K 410 LYS cc_start: 0.9069 (tptt) cc_final: 0.8792 (tptt) REVERT: K 413 GLU cc_start: 0.8275 (tt0) cc_final: 0.7817 (mt-10) REVERT: K 414 ASP cc_start: 0.7651 (t0) cc_final: 0.7414 (p0) REVERT: K 435 SER cc_start: 0.8194 (t) cc_final: 0.7794 (m) REVERT: L 237 PHE cc_start: 0.7928 (t80) cc_final: 0.7389 (t80) REVERT: L 377 MET cc_start: 0.8302 (mmm) cc_final: 0.7939 (mmm) REVERT: L 386 SER cc_start: 0.9118 (m) cc_final: 0.8092 (t) REVERT: L 413 GLU cc_start: 0.8169 (tt0) cc_final: 0.7756 (mp0) REVERT: M 356 ARG cc_start: 0.7114 (ttt180) cc_final: 0.6909 (ttm-80) REVERT: M 413 GLU cc_start: 0.8229 (tt0) cc_final: 0.7895 (mt-10) REVERT: N 376 LYS cc_start: 0.7234 (tttt) cc_final: 0.6752 (tttp) REVERT: N 413 GLU cc_start: 0.8208 (tt0) cc_final: 0.7934 (mt-10) REVERT: N 414 ASP cc_start: 0.7738 (t0) cc_final: 0.7471 (p0) REVERT: O 386 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8171 (p) REVERT: O 409 MET cc_start: 0.8703 (mmm) cc_final: 0.8442 (mmm) REVERT: O 410 LYS cc_start: 0.9103 (tptt) cc_final: 0.8888 (tptt) REVERT: P 276 GLU cc_start: 0.7682 (mp0) cc_final: 0.7355 (mp0) REVERT: P 386 SER cc_start: 0.9164 (m) cc_final: 0.8158 (t) REVERT: P 409 MET cc_start: 0.8579 (mmm) cc_final: 0.8204 (mmm) REVERT: P 413 GLU cc_start: 0.8374 (tt0) cc_final: 0.7712 (mt-10) REVERT: P 418 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7733 (mm-30) REVERT: Q 303 GLN cc_start: 0.7094 (mt0) cc_final: 0.6642 (mp10) REVERT: Q 376 LYS cc_start: 0.7378 (tttt) cc_final: 0.7093 (ttpt) REVERT: Q 386 SER cc_start: 0.9129 (m) cc_final: 0.8102 (t) REVERT: Q 435 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8331 (m) REVERT: R 377 MET cc_start: 0.8291 (mmm) cc_final: 0.7995 (mmm) REVERT: R 413 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8343 (tm-30) REVERT: S 386 SER cc_start: 0.9133 (m) cc_final: 0.8056 (t) REVERT: T 237 PHE cc_start: 0.8036 (t80) cc_final: 0.7468 (t80) REVERT: T 377 MET cc_start: 0.8327 (mmm) cc_final: 0.7958 (mmm) REVERT: U 386 SER cc_start: 0.9276 (m) cc_final: 0.8240 (t) REVERT: V 376 LYS cc_start: 0.7210 (tttt) cc_final: 0.6720 (tttp) REVERT: W 242 GLU cc_start: 0.7045 (pt0) cc_final: 0.6696 (tt0) REVERT: W 377 MET cc_start: 0.8359 (mmm) cc_final: 0.8057 (mmm) REVERT: W 386 SER cc_start: 0.9173 (m) cc_final: 0.8232 (t) REVERT: W 409 MET cc_start: 0.8579 (mmm) cc_final: 0.8282 (tpp) REVERT: X 386 SER cc_start: 0.9206 (m) cc_final: 0.8265 (t) REVERT: X 418 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7478 (mm-30) REVERT: Y 386 SER cc_start: 0.9095 (m) cc_final: 0.8098 (t) REVERT: Y 393 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: Y 409 MET cc_start: 0.8496 (mmm) cc_final: 0.8278 (tpt) REVERT: Z 377 MET cc_start: 0.8278 (mmm) cc_final: 0.8037 (mmm) REVERT: Z 386 SER cc_start: 0.9036 (m) cc_final: 0.8010 (p) REVERT: 1 413 GLU cc_start: 0.8257 (tt0) cc_final: 0.7974 (mt-10) REVERT: 1 414 ASP cc_start: 0.7664 (t0) cc_final: 0.7439 (p0) REVERT: 1 431 ASN cc_start: 0.8471 (t0) cc_final: 0.8097 (t0) REVERT: 2 377 MET cc_start: 0.8282 (mmm) cc_final: 0.7963 (mmm) REVERT: 2 393 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: 2 413 GLU cc_start: 0.8318 (tt0) cc_final: 0.7814 (mp0) REVERT: 3 377 MET cc_start: 0.8299 (mmm) cc_final: 0.8056 (mmm) REVERT: 3 413 GLU cc_start: 0.8357 (tt0) cc_final: 0.7719 (mt-10) REVERT: 4 376 LYS cc_start: 0.7278 (tttt) cc_final: 0.6787 (tttp) REVERT: 4 409 MET cc_start: 0.8470 (mmm) cc_final: 0.7612 (tpt) REVERT: 4 413 GLU cc_start: 0.8337 (tt0) cc_final: 0.7882 (mt-10) REVERT: 4 414 ASP cc_start: 0.7724 (t0) cc_final: 0.7493 (p0) REVERT: 5 356 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6868 (ttm-80) REVERT: 5 377 MET cc_start: 0.8249 (mmm) cc_final: 0.7949 (mmm) REVERT: 5 386 SER cc_start: 0.9138 (m) cc_final: 0.8128 (p) REVERT: 5 413 GLU cc_start: 0.8379 (tt0) cc_final: 0.7705 (mt-10) REVERT: 6 356 ARG cc_start: 0.7084 (ttt180) cc_final: 0.6813 (ttm-80) REVERT: 6 404 LEU cc_start: 0.6299 (mp) cc_final: 0.6075 (mp) REVERT: 6 409 MET cc_start: 0.8306 (tpp) cc_final: 0.7554 (tpp) outliers start: 122 outliers final: 65 residues processed: 945 average time/residue: 0.2193 time to fit residues: 352.0745 Evaluate side-chains 960 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 881 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 410 LYS Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 430 LEU Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 243 SER Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 6 residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 168 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 299 optimal weight: 1.9990 chunk 450 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 382 optimal weight: 0.3980 chunk 205 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 436 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN D 239 ASN E 239 ASN G 239 ASN H 239 ASN I 239 ASN J 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN P 239 ASN Q 239 ASN R 239 ASN S 239 ASN T 239 ASN U 239 ASN V 239 ASN V 261 ASN X 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 2 239 ASN 3 239 ASN 4 239 ASN 6 239 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143534 restraints weight = 39371.940| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.76 r_work: 0.3804 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 38560 Z= 0.124 Angle : 0.581 9.023 51968 Z= 0.302 Chirality : 0.041 0.278 5952 Planarity : 0.003 0.041 6976 Dihedral : 4.514 16.601 5216 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.78 % Allowed : 24.86 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.13), residues: 4640 helix: 2.44 (0.14), residues: 1280 sheet: -1.62 (0.12), residues: 2208 loop : -2.03 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 417 TYR 0.009 0.001 TYR F 393 PHE 0.022 0.001 PHE 1 237 HIS 0.001 0.000 HIS O 374 Details of bonding type rmsd covalent geometry : bond 0.00290 (38560) covalent geometry : angle 0.58072 (51968) hydrogen bonds : bond 0.03102 ( 1668) hydrogen bonds : angle 4.36381 ( 4770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9280 Ramachandran restraints generated. 4640 Oldfield, 0 Emsley, 4640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 900 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7759 (t0) cc_final: 0.7449 (t0) REVERT: A 271 ASP cc_start: 0.7748 (t0) cc_final: 0.7378 (t0) REVERT: A 276 GLU cc_start: 0.7518 (mp0) cc_final: 0.7293 (mp0) REVERT: A 386 SER cc_start: 0.9166 (m) cc_final: 0.8276 (p) REVERT: A 393 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: A 409 MET cc_start: 0.8299 (tpp) cc_final: 0.7952 (tpt) REVERT: A 414 ASP cc_start: 0.7846 (t0) cc_final: 0.7475 (p0) REVERT: B 232 ASP cc_start: 0.7776 (t0) cc_final: 0.7543 (t0) REVERT: B 276 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 377 MET cc_start: 0.8309 (mmm) cc_final: 0.8034 (mmm) REVERT: B 386 SER cc_start: 0.9107 (m) cc_final: 0.8166 (p) REVERT: B 393 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: C 253 LEU cc_start: 0.8273 (mt) cc_final: 0.7969 (mt) REVERT: C 393 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: C 413 GLU cc_start: 0.8714 (tp30) cc_final: 0.8453 (tp30) REVERT: C 414 ASP cc_start: 0.7861 (t0) cc_final: 0.7550 (p0) REVERT: D 237 PHE cc_start: 0.7972 (t80) cc_final: 0.7356 (t80) REVERT: D 377 MET cc_start: 0.8299 (mmm) cc_final: 0.8003 (mmm) REVERT: D 393 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: E 413 GLU cc_start: 0.8302 (tt0) cc_final: 0.8031 (mt-10) REVERT: E 414 ASP cc_start: 0.7798 (t0) cc_final: 0.7542 (p0) REVERT: F 232 ASP cc_start: 0.7819 (t0) cc_final: 0.7598 (t0) REVERT: F 376 LYS cc_start: 0.7335 (tttt) cc_final: 0.6867 (tttp) REVERT: F 386 SER cc_start: 0.9083 (m) cc_final: 0.8005 (p) REVERT: F 409 MET cc_start: 0.8393 (tpp) cc_final: 0.7938 (tpp) REVERT: G 356 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6941 (ttm-80) REVERT: G 377 MET cc_start: 0.8220 (mmm) cc_final: 0.7916 (mmm) REVERT: G 393 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: G 413 GLU cc_start: 0.8362 (tt0) cc_final: 0.7796 (mt-10) REVERT: H 276 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: H 377 MET cc_start: 0.8249 (mmm) cc_final: 0.8023 (mmm) REVERT: H 418 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7541 (mm-30) REVERT: I 276 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: I 393 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7611 (m-10) REVERT: K 276 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: K 386 SER cc_start: 0.9097 (m) cc_final: 0.8105 (t) REVERT: K 409 MET cc_start: 0.8711 (mmm) cc_final: 0.8388 (tpp) REVERT: K 413 GLU cc_start: 0.8246 (tt0) cc_final: 0.7776 (mt-10) REVERT: K 429 THR cc_start: 0.8504 (t) cc_final: 0.8275 (t) REVERT: L 237 PHE cc_start: 0.7960 (t80) cc_final: 0.7410 (t80) REVERT: L 377 MET cc_start: 0.8265 (mmm) cc_final: 0.7963 (mmm) REVERT: L 386 SER cc_start: 0.9077 (m) cc_final: 0.8140 (t) REVERT: L 413 GLU cc_start: 0.8165 (tt0) cc_final: 0.7832 (mp0) REVERT: M 253 LEU cc_start: 0.8346 (mt) cc_final: 0.8122 (mt) REVERT: M 409 MET cc_start: 0.8363 (mmm) cc_final: 0.8102 (tpt) REVERT: N 376 LYS cc_start: 0.7367 (tttt) cc_final: 0.6904 (tttp) REVERT: N 414 ASP cc_start: 0.7783 (t0) cc_final: 0.7583 (p0) REVERT: N 431 ASN cc_start: 0.8371 (t0) cc_final: 0.8128 (t0) REVERT: O 386 SER cc_start: 0.9199 (m) cc_final: 0.8216 (p) REVERT: O 410 LYS cc_start: 0.9100 (tptt) cc_final: 0.8899 (tptt) REVERT: P 276 GLU cc_start: 0.7659 (mp0) cc_final: 0.7377 (mp0) REVERT: P 409 MET cc_start: 0.8588 (mmm) cc_final: 0.8229 (mmm) REVERT: P 413 GLU cc_start: 0.8396 (tt0) cc_final: 0.7763 (mt-10) REVERT: P 418 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7729 (mm-30) REVERT: Q 303 GLN cc_start: 0.7158 (mt0) cc_final: 0.6794 (mp10) REVERT: Q 376 LYS cc_start: 0.7467 (tttt) cc_final: 0.7177 (ttpt) REVERT: Q 386 SER cc_start: 0.9153 (m) cc_final: 0.8198 (t) REVERT: Q 435 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8357 (m) REVERT: R 377 MET cc_start: 0.8303 (mmm) cc_final: 0.8053 (mmm) REVERT: R 413 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8404 (tm-30) REVERT: R 414 ASP cc_start: 0.7854 (m-30) cc_final: 0.7579 (p0) REVERT: T 237 PHE cc_start: 0.7997 (t80) cc_final: 0.7467 (t80) REVERT: T 377 MET cc_start: 0.8308 (mmm) cc_final: 0.7984 (mmm) REVERT: U 386 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8262 (t) REVERT: V 376 LYS cc_start: 0.7323 (tttt) cc_final: 0.6872 (tttp) REVERT: V 409 MET cc_start: 0.8722 (mmm) cc_final: 0.8500 (tpt) REVERT: V 414 ASP cc_start: 0.7938 (t0) cc_final: 0.7539 (p0) REVERT: W 242 GLU cc_start: 0.7068 (pt0) cc_final: 0.6759 (tt0) REVERT: W 377 MET cc_start: 0.8389 (mmm) cc_final: 0.8136 (mmm) REVERT: W 386 SER cc_start: 0.9165 (m) cc_final: 0.8255 (t) REVERT: W 409 MET cc_start: 0.8653 (mmm) cc_final: 0.8311 (tpp) REVERT: W 414 ASP cc_start: 0.7861 (t0) cc_final: 0.7466 (p0) REVERT: X 386 SER cc_start: 0.9200 (m) cc_final: 0.8283 (t) REVERT: X 414 ASP cc_start: 0.7843 (t0) cc_final: 0.7454 (p0) REVERT: X 418 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7503 (mm-30) REVERT: Y 386 SER cc_start: 0.9063 (m) cc_final: 0.8148 (t) REVERT: Y 393 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: Y 409 MET cc_start: 0.8536 (mmm) cc_final: 0.8281 (tpt) REVERT: Z 377 MET cc_start: 0.8271 (mmm) cc_final: 0.8063 (mmm) REVERT: Z 409 MET cc_start: 0.8700 (mmm) cc_final: 0.8492 (tpp) REVERT: 1 253 LEU cc_start: 0.8164 (mt) cc_final: 0.7192 (mt) REVERT: 1 413 GLU cc_start: 0.8162 (tt0) cc_final: 0.7954 (mt-10) REVERT: 1 431 ASN cc_start: 0.8457 (t0) cc_final: 0.8177 (t0) REVERT: 2 377 MET cc_start: 0.8246 (mmm) cc_final: 0.7984 (mmm) REVERT: 2 393 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: 2 413 GLU cc_start: 0.8301 (tt0) cc_final: 0.7889 (mp0) REVERT: 3 409 MET cc_start: 0.8405 (tpp) cc_final: 0.8067 (tpp) REVERT: 3 413 GLU cc_start: 0.8390 (tt0) cc_final: 0.7637 (mt-10) REVERT: 4 376 LYS cc_start: 0.7398 (tttt) cc_final: 0.6941 (tttp) REVERT: 4 386 SER cc_start: 0.9106 (m) cc_final: 0.8034 (p) REVERT: 4 409 MET cc_start: 0.8463 (mmm) cc_final: 0.7632 (tpt) REVERT: 4 413 GLU cc_start: 0.8310 (tt0) cc_final: 0.7922 (mt-10) REVERT: 5 356 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6965 (ttm-80) REVERT: 5 377 MET cc_start: 0.8229 (mmm) cc_final: 0.7994 (mmm) REVERT: 5 386 SER cc_start: 0.9112 (m) cc_final: 0.8143 (p) REVERT: 5 413 GLU cc_start: 0.8351 (tt0) cc_final: 0.7715 (mt-10) REVERT: 6 356 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6941 (ttm-80) outliers start: 119 outliers final: 71 residues processed: 943 average time/residue: 0.2205 time to fit residues: 355.7959 Evaluate side-chains 966 residues out of total 4288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 881 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 393 TYR Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 391 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 393 TYR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 430 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 243 SER Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 289 SER Chi-restraints excluded: chain M residue 393 TYR Chi-restraints excluded: chain M residue 430 LEU Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 375 THR Chi-restraints excluded: chain O residue 391 VAL Chi-restraints excluded: chain P residue 242 GLU Chi-restraints excluded: chain P residue 381 ASP Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 391 VAL Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain R residue 429 THR Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 386 SER Chi-restraints excluded: chain U residue 414 ASP Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 242 GLU Chi-restraints excluded: chain V residue 375 THR Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 391 VAL Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 243 SER Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 393 TYR Chi-restraints excluded: chain Y residue 410 LYS Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain 1 residue 242 GLU Chi-restraints excluded: chain 1 residue 430 LEU Chi-restraints excluded: chain 2 residue 393 TYR Chi-restraints excluded: chain 2 residue 430 LEU Chi-restraints excluded: chain 3 residue 242 GLU Chi-restraints excluded: chain 3 residue 393 TYR Chi-restraints excluded: chain 3 residue 430 LEU Chi-restraints excluded: chain 4 residue 242 GLU Chi-restraints excluded: chain 4 residue 243 SER Chi-restraints excluded: chain 5 residue 289 SER Chi-restraints excluded: chain 5 residue 411 GLN Chi-restraints excluded: chain 6 residue 262 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 28 optimal weight: 1.9990 chunk 131 optimal weight: 0.1980 chunk 218 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 452 optimal weight: 2.9990 chunk 323 optimal weight: 0.0770 chunk 77 optimal weight: 0.5980 chunk 293 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 239 ASN C 239 ASN D 239 ASN E 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN L 239 ASN M 239 ASN N 239 ASN P 239 ASN Q 239 ASN R 239 ASN S 239 ASN T 239 ASN U 239 ASN V 239 ASN X 239 ASN Y 239 ASN Z 239 ASN 1 239 ASN 2 239 ASN 4 239 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.142532 restraints weight = 39722.072| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.86 r_work: 0.3748 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 38560 Z= 0.137 Angle : 0.599 8.933 51968 Z= 0.309 Chirality : 0.041 0.283 5952 Planarity : 0.003 0.039 6976 Dihedral : 4.578 17.051 5216 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.82 % Allowed : 24.79 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 4640 helix: 2.44 (0.14), residues: 1280 sheet: -1.59 (0.12), residues: 2208 loop : -2.01 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 417 TYR 0.012 0.001 TYR H 393 PHE 0.022 0.001 PHE 1 237 HIS 0.002 0.000 HIS 6 374 Details of bonding type rmsd covalent geometry : bond 0.00320 (38560) covalent geometry : angle 0.59854 (51968) hydrogen bonds : bond 0.03153 ( 1668) hydrogen bonds : angle 4.41018 ( 4770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12059.00 seconds wall clock time: 206 minutes 30.29 seconds (12390.29 seconds total)