Starting phenix.real_space_refine on Sat Mar 7 08:17:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.map" model { file = "/net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sd4_10148/03_2026/6sd4_10148.cif" } resolution = 2.8 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 102 5.16 5 C 24684 2.51 5 N 7582 2.21 5 O 8194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40562 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, a, b, c, d, e, f, g, h Time building chain proxies: 2.95, per 1000 atoms: 0.07 Number of scatterers: 40562 At special positions: 0 Unit cell: (247.422, 247.422, 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 102 16.00 O 8194 8.00 N 7582 7.00 C 24684 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9860 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 101 sheets defined 31.8% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 415 " --> pdb=" O GLN C 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE G 412 " --> pdb=" O GLN G 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 415 " --> pdb=" O GLN G 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU H 415 " --> pdb=" O GLN H 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE I 412 " --> pdb=" O GLN I 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU I 415 " --> pdb=" O GLN I 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE J 412 " --> pdb=" O GLN J 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 415 " --> pdb=" O GLN J 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE K 412 " --> pdb=" O GLN K 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU K 415 " --> pdb=" O GLN K 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS L 236 " --> pdb=" O ASP L 232 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE L 412 " --> pdb=" O GLN L 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU L 415 " --> pdb=" O GLN L 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS M 236 " --> pdb=" O ASP M 232 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE M 412 " --> pdb=" O GLN M 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU M 415 " --> pdb=" O GLN M 411 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS N 236 " --> pdb=" O ASP N 232 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE N 412 " --> pdb=" O GLN N 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU N 415 " --> pdb=" O GLN N 411 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS O 236 " --> pdb=" O ASP O 232 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE O 412 " --> pdb=" O GLN O 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU O 415 " --> pdb=" O GLN O 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS P 236 " --> pdb=" O ASP P 232 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA P 291 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE P 412 " --> pdb=" O GLN P 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 415 " --> pdb=" O GLN P 411 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Q 291 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Q 412 " --> pdb=" O GLN Q 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU Q 415 " --> pdb=" O GLN Q 411 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS R 236 " --> pdb=" O ASP R 232 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA R 291 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE R 412 " --> pdb=" O GLN R 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU R 415 " --> pdb=" O GLN R 411 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS S 236 " --> pdb=" O ASP S 232 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 removed outlier: 3.591A pdb=" N ALA S 291 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE S 412 " --> pdb=" O GLN S 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU S 415 " --> pdb=" O GLN S 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS T 236 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA T 291 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE T 412 " --> pdb=" O GLN T 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU T 415 " --> pdb=" O GLN T 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS U 236 " --> pdb=" O ASP U 232 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE U 412 " --> pdb=" O GLN U 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU U 415 " --> pdb=" O GLN U 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS V 236 " --> pdb=" O ASP V 232 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA V 291 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE V 412 " --> pdb=" O GLN V 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU V 415 " --> pdb=" O GLN V 411 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS W 236 " --> pdb=" O ASP W 232 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU W 415 " --> pdb=" O GLN W 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS X 236 " --> pdb=" O ASP X 232 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA X 291 " --> pdb=" O ALA X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE X 412 " --> pdb=" O GLN X 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU X 415 " --> pdb=" O GLN X 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS Y 236 " --> pdb=" O ASP Y 232 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Y 291 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU Y 415 " --> pdb=" O GLN Y 411 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Z 291 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU Z 415 " --> pdb=" O GLN Z 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS a 236 " --> pdb=" O ASP a 232 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE a 412 " --> pdb=" O GLN a 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a 415 " --> pdb=" O GLN a 411 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS b 236 " --> pdb=" O ASP b 232 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA b 291 " --> pdb=" O ALA b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE b 412 " --> pdb=" O GLN b 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU b 415 " --> pdb=" O GLN b 411 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS c 236 " --> pdb=" O ASP c 232 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA c 291 " --> pdb=" O ALA c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE c 412 " --> pdb=" O GLN c 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU c 415 " --> pdb=" O GLN c 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS d 236 " --> pdb=" O ASP d 232 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA d 291 " --> pdb=" O ALA d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE d 412 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU d 415 " --> pdb=" O GLN d 411 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS e 236 " --> pdb=" O ASP e 232 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA e 291 " --> pdb=" O ALA e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE e 412 " --> pdb=" O GLN e 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU e 415 " --> pdb=" O GLN e 411 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS f 236 " --> pdb=" O ASP f 232 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA f 291 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE f 412 " --> pdb=" O GLN f 408 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU f 415 " --> pdb=" O GLN f 411 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS g 236 " --> pdb=" O ASP g 232 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA g 291 " --> pdb=" O ALA g 288 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE g 412 " --> pdb=" O GLN g 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU g 415 " --> pdb=" O GLN g 411 " (cutoff:3.500A) Processing helix chain 'h' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS h 236 " --> pdb=" O ASP h 232 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE h 412 " --> pdb=" O GLN h 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU h 415 " --> pdb=" O GLN h 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR B 292 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR C 292 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 374 through 376 Processing sheet with id=AB2, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR D 292 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 374 through 376 Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR E 292 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 374 through 376 Processing sheet with id=AB8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR F 292 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 374 through 376 Processing sheet with id=AC2, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR G 292 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 374 through 376 Processing sheet with id=AC5, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR H 292 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 374 through 376 Processing sheet with id=AC8, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR I 292 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 374 through 376 Processing sheet with id=AD2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR J 292 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 374 through 376 Processing sheet with id=AD5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR K 292 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 374 through 376 Processing sheet with id=AD8, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR L 292 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 374 through 376 Processing sheet with id=AE2, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 362 through 367 removed outlier: 6.613A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR M 292 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG M 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR N 292 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 374 through 376 Processing sheet with id=AE5, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 374 through 376 Processing sheet with id=AE7, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR O 292 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 374 through 376 Processing sheet with id=AF1, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR P 292 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 374 through 376 Processing sheet with id=AF4, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Q 292 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 374 through 376 Processing sheet with id=AF7, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 374 through 376 Processing sheet with id=AG1, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR S 292 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 374 through 376 Processing sheet with id=AG4, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR T 292 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 374 through 376 Processing sheet with id=AG7, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR U 292 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 374 through 376 Processing sheet with id=AH1, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR V 292 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 374 through 376 Processing sheet with id=AH4, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR W 292 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 374 through 376 Processing sheet with id=AH7, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR X 292 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 374 through 376 Processing sheet with id=AI1, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Y 292 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 374 through 376 Processing sheet with id=AI4, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Z 292 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 374 through 376 Processing sheet with id=AI7, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR a 292 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'a' and resid 374 through 376 Processing sheet with id=AJ1, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'b' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR b 292 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'b' and resid 374 through 376 Processing sheet with id=AJ4, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'c' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR c 292 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'c' and resid 374 through 376 Processing sheet with id=AJ7, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'd' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR d 292 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 374 through 376 Processing sheet with id=AK1, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'e' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR e 292 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'e' and resid 374 through 376 Processing sheet with id=AK4, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'f' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR f 292 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'f' and resid 374 through 376 Processing sheet with id=AK7, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'g' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR g 292 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'g' and resid 374 through 376 Processing sheet with id=AL1, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP h 381 " --> pdb=" O ASP h 271 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'h' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR h 292 " --> pdb=" O GLU h 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) 1501 hydrogen bonds defined for protein. 4092 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: 6.82 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13655 1.33 - 1.45: 3994 1.45 - 1.57: 23117 1.57 - 1.68: 0 1.68 - 1.80: 204 Bond restraints: 40970 Sorted by residual: bond pdb=" C TYR f 282 " pdb=" N SER f 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.46e+00 bond pdb=" C TYR T 282 " pdb=" N SER T 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.45e+00 bond pdb=" C TYR E 282 " pdb=" N SER E 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.39e+00 bond pdb=" C TYR W 282 " pdb=" N SER W 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.39e+00 bond pdb=" C TYR H 282 " pdb=" N SER H 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.38e+00 ... (remaining 40965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 52824 1.60 - 3.21: 2154 3.21 - 4.81: 170 4.81 - 6.42: 0 6.42 - 8.02: 68 Bond angle restraints: 55216 Sorted by residual: angle pdb=" N GLY F 421 " pdb=" CA GLY F 421 " pdb=" C GLY F 421 " ideal model delta sigma weight residual 115.08 107.06 8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY V 421 " pdb=" CA GLY V 421 " pdb=" C GLY V 421 " ideal model delta sigma weight residual 115.08 107.06 8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY U 421 " pdb=" CA GLY U 421 " pdb=" C GLY U 421 " ideal model delta sigma weight residual 115.08 107.07 8.01 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY b 421 " pdb=" CA GLY b 421 " pdb=" C GLY b 421 " ideal model delta sigma weight residual 115.08 107.07 8.01 1.64e+00 3.72e-01 2.38e+01 angle pdb=" N GLY a 421 " pdb=" CA GLY a 421 " pdb=" C GLY a 421 " ideal model delta sigma weight residual 115.08 107.08 8.00 1.64e+00 3.72e-01 2.38e+01 ... (remaining 55211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.43: 20546 10.43 - 20.86: 3661 20.86 - 31.28: 1055 31.28 - 41.71: 208 41.71 - 52.14: 132 Dihedral angle restraints: 25602 sinusoidal: 10608 harmonic: 14994 Sorted by residual: dihedral pdb=" CA MET c 420 " pdb=" C MET c 420 " pdb=" N GLY c 421 " pdb=" CA GLY c 421 " ideal model delta harmonic sigma weight residual 180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET O 420 " pdb=" C MET O 420 " pdb=" N GLY O 421 " pdb=" CA GLY O 421 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET N 420 " pdb=" C MET N 420 " pdb=" N GLY N 421 " pdb=" CA GLY N 421 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 25599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2747 0.023 - 0.045: 1834 0.045 - 0.068: 1120 0.068 - 0.091: 369 0.091 - 0.114: 254 Chirality restraints: 6324 Sorted by residual: chirality pdb=" CA VAL a 432 " pdb=" N VAL a 432 " pdb=" C VAL a 432 " pdb=" CB VAL a 432 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 chirality pdb=" CA ILE W 382 " pdb=" N ILE W 382 " pdb=" C ILE W 382 " pdb=" CB ILE W 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL e 432 " pdb=" N VAL e 432 " pdb=" C VAL e 432 " pdb=" CB VAL e 432 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.13e-01 ... (remaining 6321 not shown) Planarity restraints: 7412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 254 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 254 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO H 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 255 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 254 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO P 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO P 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 255 " 0.019 5.00e-02 4.00e+02 ... (remaining 7409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8537 2.77 - 3.30: 35634 3.30 - 3.83: 63593 3.83 - 4.37: 84356 4.37 - 4.90: 145833 Nonbonded interactions: 337953 Sorted by model distance: nonbonded pdb=" O GLU A 250 " pdb=" OG SER A 254 " model vdw 2.235 3.040 nonbonded pdb=" O GLU C 250 " pdb=" OG SER C 254 " model vdw 2.235 3.040 nonbonded pdb=" O GLU G 250 " pdb=" OG SER G 254 " model vdw 2.235 3.040 nonbonded pdb=" O GLU E 250 " pdb=" OG SER E 254 " model vdw 2.235 3.040 nonbonded pdb=" O GLU O 250 " pdb=" OG SER O 254 " model vdw 2.235 3.040 ... (remaining 337948 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: 0.10 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 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 27.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.010 0.045 40970 Z= 0.443 Angle : 0.782 8.022 55216 Z= 0.475 Chirality : 0.041 0.114 6324 Planarity : 0.004 0.034 7412 Dihedral : 12.269 52.140 15742 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.66 % Favored : 89.66 % Rotamer: Outliers : 0.75 % Allowed : 7.11 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.10), residues: 4930 helix: -3.62 (0.09), residues: 1326 sheet: -2.64 (0.10), residues: 2380 loop : -2.46 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 426 TYR 0.022 0.003 TYR P 393 PHE 0.014 0.002 PHE Z 422 HIS 0.003 0.001 HIS b 281 Details of bonding type rmsd covalent geometry : bond 0.00959 (40970) covalent geometry : angle 0.78236 (55216) hydrogen bonds : bond 0.23577 ( 1501) hydrogen bonds : angle 10.48640 ( 4092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1292 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 408 GLN cc_start: 0.7670 (tt0) cc_final: 0.7423 (tt0) REVERT: C 414 ASP cc_start: 0.7688 (m-30) cc_final: 0.6939 (m-30) REVERT: C 418 GLU cc_start: 0.8841 (mm-30) cc_final: 0.7597 (mp0) REVERT: D 383 GLU cc_start: 0.7850 (tt0) cc_final: 0.7614 (tm-30) REVERT: F 267 THR cc_start: 0.8776 (m) cc_final: 0.8569 (m) REVERT: H 418 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8620 (mm-30) REVERT: I 408 GLN cc_start: 0.7800 (tt0) cc_final: 0.7503 (tm-30) REVERT: I 417 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7330 (mtt90) REVERT: J 367 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8353 (mm-30) REVERT: J 408 GLN cc_start: 0.7589 (tt0) cc_final: 0.7330 (tm-30) REVERT: K 408 GLN cc_start: 0.7667 (tt0) cc_final: 0.7429 (tm-30) REVERT: M 418 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8408 (mp0) REVERT: N 417 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7688 (mtm-85) REVERT: O 367 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8566 (mm-30) REVERT: Q 394 LYS cc_start: 0.7224 (tttt) cc_final: 0.6908 (tttm) REVERT: R 408 GLN cc_start: 0.7574 (tt0) cc_final: 0.7317 (tt0) REVERT: T 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.6792 (m-30) REVERT: T 417 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7620 (ttm-80) REVERT: T 418 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7533 (mp0) REVERT: U 383 GLU cc_start: 0.7809 (tt0) cc_final: 0.7553 (tm-30) REVERT: V 417 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7605 (mtt-85) REVERT: X 296 ARG cc_start: 0.7302 (ttt90) cc_final: 0.7083 (ttm170) REVERT: Y 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.6686 (m-30) REVERT: Y 418 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7432 (mp0) REVERT: a 408 GLN cc_start: 0.7641 (tt0) cc_final: 0.7361 (tm-30) REVERT: a 417 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7354 (mtt90) REVERT: c 276 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7045 (mt-10) REVERT: c 414 ASP cc_start: 0.7628 (m-30) cc_final: 0.6941 (m-30) REVERT: d 429 THR cc_start: 0.8560 (m) cc_final: 0.8353 (p) REVERT: e 417 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7669 (mtm-85) REVERT: e 418 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8129 (mm-30) REVERT: f 367 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8564 (mm-30) REVERT: g 418 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 34 outliers final: 26 residues processed: 1320 average time/residue: 0.9777 time to fit residues: 1486.8537 Evaluate side-chains 1185 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 1159 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 494 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 269 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 408 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 269 GLN D 408 GLN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 HIS G 365 ASN ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 HIS H 365 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 HIS I 365 ASN ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 HIS J 365 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 HIS K 365 ASN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 263 HIS L 365 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 HIS M 365 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 HIS ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN O 263 HIS ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 HIS ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 HIS ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS ** R 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 263 HIS S 269 GLN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 HIS T 365 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 HIS U 303 GLN U 365 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 263 HIS V 365 ASN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 HIS W 365 ASN ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 HIS X 303 GLN X 365 ASN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 263 HIS Y 269 GLN ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 HIS ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 HIS a 365 ASN ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 HIS b 365 ASN ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 HIS ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 263 HIS ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 263 HIS ** e 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 246 GLN f 263 HIS f 303 GLN f 365 ASN ** f 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 263 HIS g 269 GLN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 263 HIS h 408 GLN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121976 restraints weight = 45536.033| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.58 r_work: 0.3455 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 40970 Z= 0.131 Angle : 0.520 4.735 55216 Z= 0.285 Chirality : 0.040 0.125 6324 Planarity : 0.004 0.054 7412 Dihedral : 5.168 22.401 5594 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.97 % Allowed : 14.35 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.12), residues: 4930 helix: -0.49 (0.15), residues: 1326 sheet: -1.89 (0.10), residues: 2380 loop : -2.04 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 417 TYR 0.010 0.001 TYR d 393 PHE 0.010 0.002 PHE d 237 HIS 0.003 0.000 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00280 (40970) covalent geometry : angle 0.52038 (55216) hydrogen bonds : bond 0.03900 ( 1501) hydrogen bonds : angle 5.34783 ( 4092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 1240 time to evaluate : 1.492 Fit side-chains REVERT: A 376 LYS cc_start: 0.8104 (tttt) cc_final: 0.7890 (tttp) REVERT: B 276 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7837 (mp0) REVERT: B 297 GLN cc_start: 0.8118 (tt0) cc_final: 0.7903 (tp40) REVERT: B 302 GLU cc_start: 0.7523 (tt0) cc_final: 0.7159 (tp30) REVERT: C 302 GLU cc_start: 0.7342 (tt0) cc_final: 0.6942 (tp30) REVERT: C 383 GLU cc_start: 0.8096 (tt0) cc_final: 0.7868 (tt0) REVERT: C 410 LYS cc_start: 0.8142 (tttp) cc_final: 0.7490 (tppt) REVERT: C 414 ASP cc_start: 0.7510 (m-30) cc_final: 0.6944 (m-30) REVERT: C 429 THR cc_start: 0.8821 (m) cc_final: 0.8536 (p) REVERT: D 276 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7906 (mt-10) REVERT: D 290 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8325 (ptpt) REVERT: E 394 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7077 (mtpt) REVERT: G 429 THR cc_start: 0.8664 (m) cc_final: 0.8198 (p) REVERT: H 386 SER cc_start: 0.8955 (m) cc_final: 0.8726 (m) REVERT: I 276 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7785 (mp0) REVERT: J 276 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7847 (mp0) REVERT: J 297 GLN cc_start: 0.8094 (tt0) cc_final: 0.7886 (tp40) REVERT: J 418 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8067 (tp30) REVERT: L 297 GLN cc_start: 0.8014 (tt0) cc_final: 0.7795 (tp40) REVERT: L 414 ASP cc_start: 0.7566 (m-30) cc_final: 0.7284 (m-30) REVERT: M 276 GLU cc_start: 0.7547 (mp0) cc_final: 0.7271 (mp0) REVERT: N 303 GLN cc_start: 0.7361 (mt0) cc_final: 0.6714 (mp10) REVERT: O 246 GLN cc_start: 0.8733 (tt0) cc_final: 0.8476 (tt0) REVERT: O 297 GLN cc_start: 0.8186 (tt0) cc_final: 0.7935 (tp40) REVERT: O 367 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8784 (mm-30) REVERT: O 418 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: P 276 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7675 (mp0) REVERT: P 418 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: Q 276 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7898 (mm-30) REVERT: R 377 MET cc_start: 0.8436 (mpt) cc_final: 0.8089 (mpt) REVERT: S 276 GLU cc_start: 0.7811 (mp0) cc_final: 0.7527 (mp0) REVERT: T 377 MET cc_start: 0.8494 (mpt) cc_final: 0.7824 (mpt) REVERT: T 383 GLU cc_start: 0.8002 (tt0) cc_final: 0.7766 (tt0) REVERT: T 429 THR cc_start: 0.8818 (m) cc_final: 0.8490 (p) REVERT: U 276 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7886 (mt-10) REVERT: U 290 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8418 (ptpt) REVERT: U 303 GLN cc_start: 0.7210 (mt0) cc_final: 0.6978 (mp10) REVERT: W 246 GLN cc_start: 0.8725 (tt0) cc_final: 0.8408 (tt0) REVERT: W 417 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7835 (mtm-85) REVERT: X 376 LYS cc_start: 0.8176 (tttt) cc_final: 0.7953 (tmtt) REVERT: X 418 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: Y 269 GLN cc_start: 0.8758 (mm110) cc_final: 0.8501 (mp-120) REVERT: Y 290 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8127 (pttm) REVERT: Y 303 GLN cc_start: 0.7391 (mt0) cc_final: 0.7080 (mp10) REVERT: Y 414 ASP cc_start: 0.7641 (m-30) cc_final: 0.7342 (m-30) REVERT: Z 302 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7375 (tm-30) REVERT: Z 410 LYS cc_start: 0.8211 (tttm) cc_final: 0.7921 (tptt) REVERT: a 408 GLN cc_start: 0.7630 (tt0) cc_final: 0.6779 (tm-30) REVERT: c 290 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8498 (ptpp) REVERT: c 414 ASP cc_start: 0.7623 (m-30) cc_final: 0.7389 (m-30) REVERT: e 303 GLN cc_start: 0.7383 (mt0) cc_final: 0.6735 (mp10) REVERT: e 367 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8613 (mm-30) REVERT: e 417 ARG cc_start: 0.7930 (ttm110) cc_final: 0.7680 (mtm-85) REVERT: f 246 GLN cc_start: 0.8757 (tt0) cc_final: 0.8502 (tt0) REVERT: f 275 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (mtpp) REVERT: f 367 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8718 (mm-30) REVERT: f 413 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7443 (tt0) REVERT: f 418 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: g 290 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8303 (pttp) REVERT: g 417 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7553 (mtt90) REVERT: g 429 THR cc_start: 0.8622 (m) cc_final: 0.8097 (p) REVERT: h 246 GLN cc_start: 0.8685 (tt0) cc_final: 0.8449 (tt0) REVERT: h 276 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7852 (mm-30) REVERT: h 297 GLN cc_start: 0.8180 (tt0) cc_final: 0.7976 (tp40) outliers start: 44 outliers final: 9 residues processed: 1254 average time/residue: 0.9837 time to fit residues: 1420.0144 Evaluate side-chains 1157 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1142 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain O residue 418 GLU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain Q residue 412 ILE Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 394 LYS Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain e residue 383 GLU Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain h residue 412 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 183 optimal weight: 10.0000 chunk 441 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 392 optimal weight: 0.6980 chunk 500 optimal weight: 0.4980 chunk 414 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 453 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 chunk 356 optimal weight: 10.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN B 365 ASN B 434 ASN C 239 ASN C 269 GLN C 365 ASN C 434 ASN D 434 ASN E 239 ASN E 434 ASN F 365 ASN F 434 ASN G 434 ASN H 411 GLN H 434 ASN I 411 GLN I 434 ASN J 434 ASN K 434 ASN L 434 ASN M 434 ASN N 365 ASN N 434 ASN O 365 ASN O 434 ASN P 269 GLN P 365 ASN P 434 ASN Q 408 GLN Q 434 ASN R 434 ASN S 269 GLN S 365 ASN S 434 ASN T 239 ASN T 434 ASN U 434 ASN V 434 ASN W 434 ASN X 434 ASN Y 365 ASN Y 411 GLN Y 434 ASN Z 365 ASN Z 434 ASN a 434 ASN b 434 ASN c 434 ASN d 434 ASN e 434 ASN f 434 ASN g 269 GLN g 434 ASN h 434 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114874 restraints weight = 45292.987| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.68 r_work: 0.3354 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 40970 Z= 0.331 Angle : 0.617 5.732 55216 Z= 0.332 Chirality : 0.044 0.127 6324 Planarity : 0.005 0.071 7412 Dihedral : 5.446 22.087 5542 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.19 % Allowed : 16.29 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.12), residues: 4930 helix: 0.85 (0.15), residues: 1326 sheet: -1.69 (0.10), residues: 2380 loop : -1.71 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 417 TYR 0.015 0.001 TYR b 393 PHE 0.016 0.001 PHE g 422 HIS 0.009 0.002 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00732 (40970) covalent geometry : angle 0.61748 (55216) hydrogen bonds : bond 0.05188 ( 1501) hydrogen bonds : angle 5.27538 ( 4092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1102 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 376 LYS cc_start: 0.8200 (tttt) cc_final: 0.7937 (tttp) REVERT: A 408 GLN cc_start: 0.7529 (tt0) cc_final: 0.7276 (tt0) REVERT: B 414 ASP cc_start: 0.7643 (m-30) cc_final: 0.7398 (m-30) REVERT: B 418 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 303 GLN cc_start: 0.7399 (mt0) cc_final: 0.7034 (mp10) REVERT: C 377 MET cc_start: 0.8369 (mpt) cc_final: 0.7937 (mpt) REVERT: C 410 LYS cc_start: 0.8318 (tttp) cc_final: 0.7606 (tppt) REVERT: C 414 ASP cc_start: 0.7663 (m-30) cc_final: 0.6508 (m-30) REVERT: C 418 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: D 290 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8330 (ptpt) REVERT: D 297 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: D 410 LYS cc_start: 0.8227 (tttp) cc_final: 0.7733 (tppt) REVERT: D 414 ASP cc_start: 0.7641 (m-30) cc_final: 0.6639 (m-30) REVERT: D 418 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 429 THR cc_start: 0.8611 (m) cc_final: 0.8210 (p) REVERT: E 276 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: E 297 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: E 410 LYS cc_start: 0.8318 (tttp) cc_final: 0.7788 (tppt) REVERT: F 297 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: G 297 GLN cc_start: 0.8342 (tt0) cc_final: 0.8117 (tp40) REVERT: H 290 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8161 (pttm) REVERT: H 297 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: H 303 GLN cc_start: 0.7262 (mt0) cc_final: 0.6884 (mp10) REVERT: I 276 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7937 (mp0) REVERT: I 290 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8194 (pttm) REVERT: L 303 GLN cc_start: 0.7317 (mt0) cc_final: 0.6831 (mp10) REVERT: L 414 ASP cc_start: 0.7541 (m-30) cc_final: 0.7291 (m-30) REVERT: M 276 GLU cc_start: 0.7652 (mp0) cc_final: 0.7346 (mp0) REVERT: M 297 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: N 303 GLN cc_start: 0.7377 (mt0) cc_final: 0.6684 (mp10) REVERT: O 296 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7279 (tpp-160) REVERT: O 297 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: O 367 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8880 (mm-30) REVERT: O 410 LYS cc_start: 0.8340 (tttp) cc_final: 0.7704 (tppt) REVERT: O 414 ASP cc_start: 0.7525 (m-30) cc_final: 0.7149 (m-30) REVERT: O 418 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: O 429 THR cc_start: 0.8645 (m) cc_final: 0.8177 (p) REVERT: P 290 LYS cc_start: 0.8484 (ptpt) cc_final: 0.8071 (pttp) REVERT: P 410 LYS cc_start: 0.8290 (tttp) cc_final: 0.7840 (tppt) REVERT: Q 276 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7843 (mm-30) REVERT: Q 296 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7709 (ttp-170) REVERT: Q 410 LYS cc_start: 0.8333 (tttp) cc_final: 0.7881 (tppt) REVERT: Q 429 THR cc_start: 0.8646 (m) cc_final: 0.8223 (p) REVERT: R 297 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: R 377 MET cc_start: 0.8553 (mpt) cc_final: 0.8047 (mpt) REVERT: R 408 GLN cc_start: 0.7526 (tt0) cc_final: 0.7285 (tt0) REVERT: S 376 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8076 (tttt) REVERT: S 418 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: T 297 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: T 303 GLN cc_start: 0.7350 (mt0) cc_final: 0.6931 (mp10) REVERT: T 377 MET cc_start: 0.8380 (mpt) cc_final: 0.7976 (mpt) REVERT: T 429 THR cc_start: 0.8744 (m) cc_final: 0.8322 (p) REVERT: U 290 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8365 (ptpt) REVERT: U 297 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: U 303 GLN cc_start: 0.7295 (mt0) cc_final: 0.6978 (mp10) REVERT: W 297 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: W 303 GLN cc_start: 0.7604 (mp10) cc_final: 0.7297 (mp10) REVERT: W 417 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7703 (mtt90) REVERT: X 297 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: X 418 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: Y 290 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8161 (pttm) REVERT: Y 414 ASP cc_start: 0.7647 (m-30) cc_final: 0.7434 (m-30) REVERT: Z 290 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8202 (pttm) REVERT: Z 410 LYS cc_start: 0.8146 (tttm) cc_final: 0.7891 (tptt) REVERT: a 297 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: c 290 LYS cc_start: 0.8668 (ptpp) cc_final: 0.8437 (ptpp) REVERT: c 297 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: c 303 GLN cc_start: 0.7400 (mt0) cc_final: 0.6977 (mp10) REVERT: c 414 ASP cc_start: 0.7590 (m-30) cc_final: 0.7316 (m-30) REVERT: d 297 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: e 303 GLN cc_start: 0.7458 (mt0) cc_final: 0.6688 (mp10) REVERT: e 414 ASP cc_start: 0.7601 (m-30) cc_final: 0.7028 (m-30) REVERT: e 417 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7607 (ttm-80) REVERT: e 418 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: f 275 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8290 (mtpp) REVERT: f 297 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: f 303 GLN cc_start: 0.7481 (mt0) cc_final: 0.7031 (mp10) REVERT: f 367 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8901 (mm-30) REVERT: f 410 LYS cc_start: 0.8353 (tttp) cc_final: 0.7691 (tppt) REVERT: f 413 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7344 (tt0) REVERT: f 414 ASP cc_start: 0.7423 (m-30) cc_final: 0.7058 (m-30) REVERT: f 429 THR cc_start: 0.8660 (m) cc_final: 0.8217 (p) REVERT: g 290 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8210 (pttp) REVERT: g 418 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: h 297 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8021 (tp40) outliers start: 100 outliers final: 28 residues processed: 1147 average time/residue: 1.0295 time to fit residues: 1353.4388 Evaluate side-chains 1126 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1067 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 297 GLN Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain H residue 290 LYS Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain M residue 412 ILE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain O residue 296 ARG Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 418 GLU Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 412 ILE Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 297 GLN Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 275 LYS Chi-restraints excluded: chain S residue 376 LYS Chi-restraints excluded: chain S residue 418 GLU Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain X residue 297 GLN Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain a residue 297 GLN Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 418 GLU Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 441 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 320 optimal weight: 0.3980 chunk 216 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 239 ASN E 239 ASN H 411 GLN I 411 GLN P 269 GLN Q 408 GLN S 269 GLN T 239 ASN X 374 HIS g 269 GLN h 408 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120489 restraints weight = 44552.971| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.66 r_work: 0.3403 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 40970 Z= 0.149 Angle : 0.492 5.293 55216 Z= 0.266 Chirality : 0.040 0.128 6324 Planarity : 0.004 0.055 7412 Dihedral : 4.887 21.097 5542 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.04 % Allowed : 16.79 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4930 helix: 1.80 (0.16), residues: 1326 sheet: -1.30 (0.11), residues: 2380 loop : -1.43 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 247 TYR 0.008 0.001 TYR b 393 PHE 0.011 0.001 PHE G 422 HIS 0.006 0.001 HIS H 281 Details of bonding type rmsd covalent geometry : bond 0.00326 (40970) covalent geometry : angle 0.49197 (55216) hydrogen bonds : bond 0.03819 ( 1501) hydrogen bonds : angle 4.74217 ( 4092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1077 time to evaluate : 1.329 Fit side-chains REVERT: A 302 GLU cc_start: 0.7110 (tt0) cc_final: 0.6765 (mt-10) REVERT: A 376 LYS cc_start: 0.8104 (tttt) cc_final: 0.7836 (tttp) REVERT: B 276 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7771 (mp0) REVERT: B 297 GLN cc_start: 0.8122 (tt0) cc_final: 0.7885 (tp40) REVERT: C 303 GLN cc_start: 0.7239 (mt0) cc_final: 0.6858 (mp10) REVERT: C 377 MET cc_start: 0.8360 (mpt) cc_final: 0.7836 (mpt) REVERT: C 414 ASP cc_start: 0.7592 (m-30) cc_final: 0.7386 (m-30) REVERT: C 418 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8349 (mm-30) REVERT: C 429 THR cc_start: 0.8705 (m) cc_final: 0.8311 (p) REVERT: D 290 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8300 (ptpt) REVERT: D 297 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: D 418 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: D 429 THR cc_start: 0.8572 (m) cc_final: 0.8109 (p) REVERT: E 290 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8096 (pttm) REVERT: E 417 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7609 (mtt90) REVERT: F 297 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: G 276 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7756 (mp0) REVERT: H 297 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: I 276 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7844 (mp0) REVERT: I 290 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8139 (pttm) REVERT: K 429 THR cc_start: 0.8636 (m) cc_final: 0.8235 (p) REVERT: L 276 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: L 414 ASP cc_start: 0.7499 (m-30) cc_final: 0.7246 (m-30) REVERT: M 276 GLU cc_start: 0.7603 (mp0) cc_final: 0.7319 (mp0) REVERT: M 297 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: N 303 GLN cc_start: 0.7290 (mt0) cc_final: 0.6608 (mp10) REVERT: N 418 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: O 410 LYS cc_start: 0.8332 (tttp) cc_final: 0.7706 (tppt) REVERT: O 414 ASP cc_start: 0.7390 (m-30) cc_final: 0.6986 (m-30) REVERT: O 418 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: P 290 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8069 (pttp) REVERT: P 410 LYS cc_start: 0.8254 (tttp) cc_final: 0.7805 (tppt) REVERT: Q 276 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7785 (mm-30) REVERT: Q 296 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7655 (ttp-170) REVERT: Q 297 GLN cc_start: 0.8252 (tt0) cc_final: 0.8018 (tp40) REVERT: Q 429 THR cc_start: 0.8592 (m) cc_final: 0.8268 (p) REVERT: R 276 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7743 (mp0) REVERT: R 377 MET cc_start: 0.8507 (mpt) cc_final: 0.7919 (mpt) REVERT: S 276 GLU cc_start: 0.7805 (mp0) cc_final: 0.7509 (mp0) REVERT: T 377 MET cc_start: 0.8371 (mpt) cc_final: 0.7882 (mpt) REVERT: T 429 THR cc_start: 0.8721 (m) cc_final: 0.8336 (p) REVERT: U 297 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: U 303 GLN cc_start: 0.7179 (mt0) cc_final: 0.6852 (mp10) REVERT: U 429 THR cc_start: 0.8583 (m) cc_final: 0.8128 (p) REVERT: V 290 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8129 (pttm) REVERT: W 275 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8344 (ttmm) REVERT: W 297 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7962 (tp40) REVERT: W 303 GLN cc_start: 0.7453 (mp10) cc_final: 0.7133 (mp10) REVERT: X 276 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7756 (mp0) REVERT: X 297 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: X 376 LYS cc_start: 0.8077 (tttt) cc_final: 0.7862 (tmtt) REVERT: X 418 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: Y 290 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8081 (pttm) REVERT: Y 414 ASP cc_start: 0.7542 (m-30) cc_final: 0.7289 (m-30) REVERT: Z 290 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8152 (pttm) REVERT: Z 410 LYS cc_start: 0.8151 (tttm) cc_final: 0.7894 (tptt) REVERT: a 429 THR cc_start: 0.8528 (m) cc_final: 0.8135 (p) REVERT: b 429 THR cc_start: 0.8652 (m) cc_final: 0.8269 (p) REVERT: c 276 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7726 (mp0) REVERT: c 290 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8393 (ptpp) REVERT: c 303 GLN cc_start: 0.7271 (mt0) cc_final: 0.6875 (mp10) REVERT: c 414 ASP cc_start: 0.7486 (m-30) cc_final: 0.7226 (m-30) REVERT: d 297 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: d 302 GLU cc_start: 0.7118 (tt0) cc_final: 0.6674 (tp30) REVERT: e 303 GLN cc_start: 0.7376 (mt0) cc_final: 0.6629 (mp10) REVERT: e 418 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: f 275 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (mtpp) REVERT: f 297 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: f 367 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8840 (mm-30) REVERT: f 413 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7344 (tt0) REVERT: g 290 LYS cc_start: 0.8530 (ptpp) cc_final: 0.8158 (pttp) REVERT: g 417 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7480 (mtt90) REVERT: g 429 THR cc_start: 0.8551 (m) cc_final: 0.8204 (p) REVERT: h 246 GLN cc_start: 0.8722 (tt0) cc_final: 0.8277 (tt0) REVERT: h 276 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7773 (mm-30) REVERT: h 297 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: h 429 THR cc_start: 0.8611 (m) cc_final: 0.8295 (p) outliers start: 93 outliers final: 37 residues processed: 1128 average time/residue: 1.0325 time to fit residues: 1334.7622 Evaluate side-chains 1070 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1013 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain N residue 418 GLU Chi-restraints excluded: chain O residue 418 GLU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 275 LYS Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 275 LYS Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain X residue 297 GLN Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 394 LYS Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 297 GLN Chi-restraints excluded: chain e residue 275 LYS Chi-restraints excluded: chain e residue 394 LYS Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 262 optimal weight: 0.0370 chunk 200 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 387 optimal weight: 4.9990 chunk 381 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 406 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 420 optimal weight: 0.7980 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN Q 408 GLN S 269 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN g 269 GLN h 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.152741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122053 restraints weight = 44427.186| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.66 r_work: 0.3430 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 40970 Z= 0.107 Angle : 0.455 6.193 55216 Z= 0.244 Chirality : 0.039 0.127 6324 Planarity : 0.003 0.051 7412 Dihedral : 4.556 20.775 5542 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.51 % Allowed : 18.74 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4930 helix: 2.31 (0.16), residues: 1326 sheet: -0.98 (0.11), residues: 2380 loop : -1.05 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 370 TYR 0.006 0.001 TYR b 393 PHE 0.011 0.001 PHE G 422 HIS 0.005 0.001 HIS c 281 Details of bonding type rmsd covalent geometry : bond 0.00231 (40970) covalent geometry : angle 0.45505 (55216) hydrogen bonds : bond 0.03485 ( 1501) hydrogen bonds : angle 4.51093 ( 4092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1038 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 GLU cc_start: 0.7019 (tt0) cc_final: 0.6710 (mt-10) REVERT: A 376 LYS cc_start: 0.8093 (tttt) cc_final: 0.7819 (tttp) REVERT: B 276 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7727 (mp0) REVERT: B 297 GLN cc_start: 0.8078 (tt0) cc_final: 0.7867 (tp40) REVERT: B 302 GLU cc_start: 0.7482 (tt0) cc_final: 0.6965 (tp30) REVERT: C 296 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7571 (tpp-160) REVERT: C 302 GLU cc_start: 0.7138 (tt0) cc_final: 0.6678 (tp30) REVERT: C 377 MET cc_start: 0.8334 (mpt) cc_final: 0.7813 (mpt) REVERT: C 429 THR cc_start: 0.8639 (m) cc_final: 0.8329 (p) REVERT: D 418 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: D 429 THR cc_start: 0.8627 (m) cc_final: 0.8162 (p) REVERT: E 290 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8070 (pttm) REVERT: F 297 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: G 276 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7701 (mp0) REVERT: G 376 LYS cc_start: 0.8088 (tttt) cc_final: 0.7849 (tmtt) REVERT: H 290 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8112 (pttm) REVERT: H 297 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: I 276 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7764 (mp0) REVERT: I 290 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8085 (pttm) REVERT: J 276 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7690 (mp0) REVERT: J 290 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8005 (pttm) REVERT: J 413 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7417 (tt0) REVERT: K 429 THR cc_start: 0.8643 (m) cc_final: 0.8232 (p) REVERT: L 276 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: L 414 ASP cc_start: 0.7520 (m-30) cc_final: 0.7211 (m-30) REVERT: M 276 GLU cc_start: 0.7520 (mp0) cc_final: 0.7316 (mp0) REVERT: O 410 LYS cc_start: 0.8348 (tttp) cc_final: 0.7735 (tppt) REVERT: O 414 ASP cc_start: 0.7347 (m-30) cc_final: 0.6905 (m-30) REVERT: O 429 THR cc_start: 0.8645 (m) cc_final: 0.8362 (p) REVERT: P 290 LYS cc_start: 0.8444 (ptpt) cc_final: 0.8082 (pttp) REVERT: P 302 GLU cc_start: 0.7128 (tt0) cc_final: 0.6746 (tp30) REVERT: P 370 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8022 (ttt180) REVERT: P 410 LYS cc_start: 0.8251 (tttp) cc_final: 0.7808 (tppt) REVERT: P 414 ASP cc_start: 0.7287 (m-30) cc_final: 0.6917 (m-30) REVERT: P 418 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: Q 276 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7700 (mm-30) REVERT: Q 290 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8152 (pttm) REVERT: Q 297 GLN cc_start: 0.8177 (tt0) cc_final: 0.7960 (tp40) REVERT: Q 370 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.8047 (ttt180) REVERT: R 276 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7691 (mp0) REVERT: R 302 GLU cc_start: 0.7268 (tt0) cc_final: 0.6618 (mt-10) REVERT: R 377 MET cc_start: 0.8554 (mpt) cc_final: 0.7951 (mpt) REVERT: S 276 GLU cc_start: 0.7713 (mp0) cc_final: 0.7429 (mp0) REVERT: S 302 GLU cc_start: 0.7505 (tt0) cc_final: 0.6693 (mt-10) REVERT: T 290 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8164 (pttp) REVERT: T 377 MET cc_start: 0.8385 (mpt) cc_final: 0.7874 (mpt) REVERT: T 429 THR cc_start: 0.8627 (m) cc_final: 0.8336 (p) REVERT: V 290 LYS cc_start: 0.8484 (ptpt) cc_final: 0.8107 (pttm) REVERT: W 303 GLN cc_start: 0.7406 (mp10) cc_final: 0.7192 (mp10) REVERT: X 276 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7677 (mp0) REVERT: Y 290 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8069 (pttm) REVERT: Y 414 ASP cc_start: 0.7557 (m-30) cc_final: 0.7303 (m-30) REVERT: Z 276 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7876 (mp0) REVERT: Z 290 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8087 (pttm) REVERT: Z 410 LYS cc_start: 0.8165 (tttm) cc_final: 0.7907 (tptp) REVERT: a 290 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8010 (pttm) REVERT: a 429 THR cc_start: 0.8575 (m) cc_final: 0.8188 (p) REVERT: b 429 THR cc_start: 0.8609 (m) cc_final: 0.8225 (p) REVERT: c 276 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7676 (mp0) REVERT: c 303 GLN cc_start: 0.7273 (mt0) cc_final: 0.6821 (mp10) REVERT: c 414 ASP cc_start: 0.7479 (m-30) cc_final: 0.7228 (m-30) REVERT: d 302 GLU cc_start: 0.7100 (tt0) cc_final: 0.6685 (tp30) REVERT: e 290 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8197 (pttp) REVERT: f 275 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8231 (mtpp) REVERT: f 302 GLU cc_start: 0.7037 (tt0) cc_final: 0.6606 (tp30) REVERT: f 367 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8838 (mm-30) REVERT: f 410 LYS cc_start: 0.8320 (tttp) cc_final: 0.7721 (tppt) REVERT: f 414 ASP cc_start: 0.7304 (m-30) cc_final: 0.6962 (m-30) REVERT: f 418 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: f 429 THR cc_start: 0.8678 (m) cc_final: 0.8380 (p) REVERT: g 290 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8180 (pttp) REVERT: g 302 GLU cc_start: 0.7287 (tt0) cc_final: 0.6597 (mt-10) REVERT: g 410 LYS cc_start: 0.8276 (tttp) cc_final: 0.7750 (tppt) REVERT: g 414 ASP cc_start: 0.7343 (m-30) cc_final: 0.6892 (m-30) REVERT: g 417 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7546 (mtt90) REVERT: g 429 THR cc_start: 0.8577 (m) cc_final: 0.8005 (p) REVERT: h 276 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7700 (mm-30) REVERT: h 297 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7933 (tp40) REVERT: h 429 THR cc_start: 0.8622 (m) cc_final: 0.8324 (p) outliers start: 69 outliers final: 29 residues processed: 1078 average time/residue: 1.0064 time to fit residues: 1245.8517 Evaluate side-chains 1014 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 977 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 394 LYS Chi-restraints excluded: chain d residue 433 VAL Chi-restraints excluded: chain e residue 275 LYS Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 376 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 468 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 377 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 391 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN N 281 HIS Q 408 GLN R 239 ASN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN e 281 HIS h 408 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122087 restraints weight = 44537.922| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.67 r_work: 0.3433 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 40970 Z= 0.116 Angle : 0.457 6.585 55216 Z= 0.243 Chirality : 0.039 0.125 6324 Planarity : 0.003 0.048 7412 Dihedral : 4.462 20.373 5542 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.58 % Allowed : 19.80 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4930 helix: 2.54 (0.16), residues: 1326 sheet: -0.70 (0.11), residues: 2380 loop : -0.77 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 370 TYR 0.006 0.001 TYR h 282 PHE 0.011 0.001 PHE N 422 HIS 0.005 0.001 HIS c 281 Details of bonding type rmsd covalent geometry : bond 0.00253 (40970) covalent geometry : angle 0.45734 (55216) hydrogen bonds : bond 0.03511 ( 1501) hydrogen bonds : angle 4.40170 ( 4092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1007 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 290 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8149 (pttt) REVERT: A 302 GLU cc_start: 0.7011 (tt0) cc_final: 0.6697 (mt-10) REVERT: A 376 LYS cc_start: 0.8057 (tttt) cc_final: 0.7783 (tttp) REVERT: B 275 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8347 (mtpm) REVERT: B 276 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7683 (mp0) REVERT: B 297 GLN cc_start: 0.8049 (tt0) cc_final: 0.7842 (tp40) REVERT: B 302 GLU cc_start: 0.7482 (tt0) cc_final: 0.6952 (tp30) REVERT: B 413 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7302 (tt0) REVERT: C 290 LYS cc_start: 0.8591 (ptpt) cc_final: 0.8188 (pttp) REVERT: C 296 ARG cc_start: 0.7780 (ttt90) cc_final: 0.7549 (tpp-160) REVERT: C 302 GLU cc_start: 0.7109 (tt0) cc_final: 0.6652 (tp30) REVERT: C 377 MET cc_start: 0.8328 (mpt) cc_final: 0.7815 (mpt) REVERT: C 429 THR cc_start: 0.8644 (m) cc_final: 0.8313 (p) REVERT: D 276 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7931 (mt-10) REVERT: D 297 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: D 410 LYS cc_start: 0.8299 (tttp) cc_final: 0.7828 (tppt) REVERT: D 414 ASP cc_start: 0.7433 (m-30) cc_final: 0.7074 (m-30) REVERT: D 418 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8046 (tp30) REVERT: E 290 LYS cc_start: 0.8463 (ptpt) cc_final: 0.8037 (pttm) REVERT: E 417 ARG cc_start: 0.7809 (mtt-85) cc_final: 0.7429 (mtt90) REVERT: F 297 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: G 276 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7691 (mp0) REVERT: G 376 LYS cc_start: 0.8079 (tttt) cc_final: 0.7833 (tmtt) REVERT: H 290 LYS cc_start: 0.8510 (ptpt) cc_final: 0.8105 (pttm) REVERT: H 297 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: H 429 THR cc_start: 0.8660 (m) cc_final: 0.8261 (p) REVERT: I 276 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7764 (mp0) REVERT: I 290 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8064 (pttm) REVERT: J 290 LYS cc_start: 0.8490 (ptpt) cc_final: 0.8041 (pttm) REVERT: J 413 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7385 (tt0) REVERT: K 290 LYS cc_start: 0.8343 (ptpp) cc_final: 0.7963 (pttp) REVERT: K 296 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7651 (tpp-160) REVERT: K 429 THR cc_start: 0.8637 (m) cc_final: 0.8263 (p) REVERT: L 276 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: L 414 ASP cc_start: 0.7480 (m-30) cc_final: 0.7183 (m-30) REVERT: M 276 GLU cc_start: 0.7499 (mp0) cc_final: 0.7213 (mp0) REVERT: N 290 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8166 (pttp) REVERT: O 276 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7681 (mt-10) REVERT: O 410 LYS cc_start: 0.8352 (tttp) cc_final: 0.7752 (tppt) REVERT: O 414 ASP cc_start: 0.7348 (m-30) cc_final: 0.6911 (m-30) REVERT: O 429 THR cc_start: 0.8654 (m) cc_final: 0.8320 (p) REVERT: P 290 LYS cc_start: 0.8427 (ptpt) cc_final: 0.8048 (pttp) REVERT: P 370 ARG cc_start: 0.8280 (ttp80) cc_final: 0.8021 (ttt180) REVERT: P 410 LYS cc_start: 0.8266 (tttp) cc_final: 0.7845 (tppt) REVERT: Q 297 GLN cc_start: 0.8182 (tt0) cc_final: 0.7945 (tp40) REVERT: Q 370 ARG cc_start: 0.8273 (ttp-170) cc_final: 0.8022 (ttt180) REVERT: R 302 GLU cc_start: 0.7240 (tt0) cc_final: 0.6592 (mt-10) REVERT: R 377 MET cc_start: 0.8539 (mpt) cc_final: 0.7925 (mpt) REVERT: S 302 GLU cc_start: 0.7497 (tt0) cc_final: 0.6682 (mt-10) REVERT: T 290 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8147 (pttp) REVERT: T 377 MET cc_start: 0.8395 (mpt) cc_final: 0.7870 (mpt) REVERT: T 429 THR cc_start: 0.8657 (m) cc_final: 0.8329 (p) REVERT: U 303 GLN cc_start: 0.7177 (mt0) cc_final: 0.6854 (mp10) REVERT: V 290 LYS cc_start: 0.8480 (ptpt) cc_final: 0.8069 (pttm) REVERT: W 296 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: W 303 GLN cc_start: 0.7453 (mp10) cc_final: 0.7201 (mp10) REVERT: X 276 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7649 (mp0) REVERT: Y 290 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8062 (pttm) REVERT: Y 414 ASP cc_start: 0.7551 (m-30) cc_final: 0.7311 (m-30) REVERT: Z 276 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7822 (mp0) REVERT: Z 290 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8077 (pttm) REVERT: Z 410 LYS cc_start: 0.8163 (tttm) cc_final: 0.7924 (tptp) REVERT: Z 413 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7541 (tt0) REVERT: a 290 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8010 (pttm) REVERT: a 429 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8202 (p) REVERT: b 290 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8018 (pttp) REVERT: b 429 THR cc_start: 0.8597 (m) cc_final: 0.8195 (p) REVERT: c 276 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7679 (mp0) REVERT: c 303 GLN cc_start: 0.7224 (mt0) cc_final: 0.6813 (mp10) REVERT: c 414 ASP cc_start: 0.7497 (m-30) cc_final: 0.7239 (m-30) REVERT: d 302 GLU cc_start: 0.7082 (tt0) cc_final: 0.6603 (tp30) REVERT: e 290 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8181 (pttp) REVERT: e 296 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7227 (tpp-160) REVERT: f 275 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: f 302 GLU cc_start: 0.7010 (tt0) cc_final: 0.6568 (tp30) REVERT: f 367 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8804 (mm-30) REVERT: f 418 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: f 429 THR cc_start: 0.8683 (m) cc_final: 0.8341 (p) REVERT: g 290 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8183 (pttp) REVERT: g 302 GLU cc_start: 0.7233 (tt0) cc_final: 0.6623 (mt-10) REVERT: g 410 LYS cc_start: 0.8267 (tttp) cc_final: 0.7753 (tppt) REVERT: g 414 ASP cc_start: 0.7373 (m-30) cc_final: 0.6901 (m-30) REVERT: g 417 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7523 (mtt90) REVERT: g 429 THR cc_start: 0.8582 (m) cc_final: 0.8012 (p) REVERT: h 297 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7920 (tp40) REVERT: h 370 ARG cc_start: 0.8396 (tmm-80) cc_final: 0.8082 (ttt180) REVERT: h 402 LEU cc_start: 0.7447 (mt) cc_final: 0.7219 (mm) REVERT: h 429 THR cc_start: 0.8582 (m) cc_final: 0.8290 (p) outliers start: 72 outliers final: 34 residues processed: 1053 average time/residue: 0.9973 time to fit residues: 1208.3792 Evaluate side-chains 1017 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 970 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 394 LYS Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain d residue 433 VAL Chi-restraints excluded: chain e residue 296 ARG Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 462 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 424 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 438 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 410 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 269 GLN C 239 ASN D 411 GLN E 239 ASN F 239 ASN G 239 ASN G 281 HIS H 239 ASN H 411 GLN I 239 ASN I 411 GLN N 281 HIS N 411 GLN P 411 GLN Q 374 HIS R 239 ASN S 269 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN X 281 HIS Y 239 ASN Z 239 ASN b 239 ASN d 239 ASN e 281 HIS e 411 GLN h 374 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118984 restraints weight = 44787.679| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.67 r_work: 0.3392 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 40970 Z= 0.223 Angle : 0.524 6.534 55216 Z= 0.278 Chirality : 0.041 0.123 6324 Planarity : 0.004 0.056 7412 Dihedral : 4.788 21.004 5542 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.89 % Allowed : 20.83 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4930 helix: 2.38 (0.16), residues: 1326 sheet: -0.71 (0.11), residues: 2380 loop : -0.61 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 370 TYR 0.009 0.001 TYR R 393 PHE 0.013 0.001 PHE g 422 HIS 0.007 0.001 HIS c 281 Details of bonding type rmsd covalent geometry : bond 0.00495 (40970) covalent geometry : angle 0.52367 (55216) hydrogen bonds : bond 0.04193 ( 1501) hydrogen bonds : angle 4.57126 ( 4092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1000 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 290 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8156 (pttt) REVERT: A 302 GLU cc_start: 0.6995 (tt0) cc_final: 0.6665 (mt-10) REVERT: A 376 LYS cc_start: 0.8113 (tttt) cc_final: 0.7831 (tttp) REVERT: B 275 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8373 (mtpm) REVERT: B 276 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 297 GLN cc_start: 0.8132 (tt0) cc_final: 0.7888 (tp40) REVERT: B 418 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: C 290 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8215 (pttp) REVERT: C 302 GLU cc_start: 0.7178 (tt0) cc_final: 0.6685 (tp30) REVERT: C 303 GLN cc_start: 0.7319 (mt0) cc_final: 0.6807 (mp10) REVERT: C 377 MET cc_start: 0.8332 (mpt) cc_final: 0.7905 (mpt) REVERT: C 429 THR cc_start: 0.8703 (m) cc_final: 0.8271 (p) REVERT: D 276 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7733 (mp0) REVERT: D 297 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: D 410 LYS cc_start: 0.8340 (tttp) cc_final: 0.7898 (tppt) REVERT: D 414 ASP cc_start: 0.7544 (m-30) cc_final: 0.7213 (m-30) REVERT: D 418 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: E 276 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: E 290 LYS cc_start: 0.8488 (ptpt) cc_final: 0.8026 (pttm) REVERT: F 297 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: F 303 GLN cc_start: 0.7377 (mt0) cc_final: 0.6842 (mp10) REVERT: G 376 LYS cc_start: 0.8155 (tttt) cc_final: 0.7895 (tmtt) REVERT: H 290 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8088 (pttm) REVERT: H 297 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: H 303 GLN cc_start: 0.7264 (mt0) cc_final: 0.6917 (mp10) REVERT: I 290 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8137 (pttm) REVERT: J 290 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8047 (pttm) REVERT: J 297 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: K 290 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8017 (pttp) REVERT: K 429 THR cc_start: 0.8739 (m) cc_final: 0.8463 (p) REVERT: L 303 GLN cc_start: 0.7261 (mt0) cc_final: 0.6784 (mp10) REVERT: L 414 ASP cc_start: 0.7526 (m-30) cc_final: 0.7263 (m-30) REVERT: M 276 GLU cc_start: 0.7523 (mp0) cc_final: 0.7223 (mp0) REVERT: N 290 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8138 (pttp) REVERT: N 303 GLN cc_start: 0.7367 (mt0) cc_final: 0.6665 (mp10) REVERT: O 410 LYS cc_start: 0.8385 (tttp) cc_final: 0.7771 (tppt) REVERT: O 414 ASP cc_start: 0.7448 (m-30) cc_final: 0.7015 (m-30) REVERT: O 429 THR cc_start: 0.8663 (m) cc_final: 0.8253 (p) REVERT: P 290 LYS cc_start: 0.8482 (ptpt) cc_final: 0.8110 (pttp) REVERT: P 302 GLU cc_start: 0.7153 (tt0) cc_final: 0.6670 (tm-30) REVERT: P 410 LYS cc_start: 0.8297 (tttp) cc_final: 0.7868 (tppt) REVERT: Q 276 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7728 (mp0) REVERT: Q 290 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8135 (pttp) REVERT: Q 296 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: R 290 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8144 (pttt) REVERT: R 377 MET cc_start: 0.8541 (mpt) cc_final: 0.7997 (mpt) REVERT: T 290 LYS cc_start: 0.8577 (ptpt) cc_final: 0.8178 (pttp) REVERT: T 296 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7198 (tpp-160) REVERT: T 297 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: T 303 GLN cc_start: 0.7292 (mt0) cc_final: 0.6852 (mp10) REVERT: T 377 MET cc_start: 0.8340 (mpt) cc_final: 0.7900 (mpt) REVERT: T 429 THR cc_start: 0.8653 (m) cc_final: 0.8201 (p) REVERT: U 303 GLN cc_start: 0.7253 (mt0) cc_final: 0.6931 (mp10) REVERT: U 410 LYS cc_start: 0.8333 (tttp) cc_final: 0.7867 (tppt) REVERT: U 414 ASP cc_start: 0.7445 (m-30) cc_final: 0.7101 (m-30) REVERT: V 290 LYS cc_start: 0.8501 (ptpt) cc_final: 0.8066 (pttm) REVERT: W 296 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7587 (ttt180) REVERT: W 303 GLN cc_start: 0.7614 (mp10) cc_final: 0.7327 (mp10) REVERT: W 376 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7969 (tmtp) REVERT: X 276 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7711 (mp0) REVERT: Y 290 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8128 (pttm) REVERT: Y 370 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8142 (ttt180) REVERT: Y 414 ASP cc_start: 0.7604 (m-30) cc_final: 0.7364 (m-30) REVERT: Z 290 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8125 (pttm) REVERT: Z 410 LYS cc_start: 0.8148 (tttm) cc_final: 0.7902 (tptt) REVERT: Z 413 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7559 (tt0) REVERT: Z 417 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7480 (mtp85) REVERT: a 276 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: a 290 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8010 (pttm) REVERT: a 429 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8142 (p) REVERT: b 290 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8028 (pttp) REVERT: b 429 THR cc_start: 0.8660 (m) cc_final: 0.8172 (p) REVERT: c 297 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: c 303 GLN cc_start: 0.7314 (mt0) cc_final: 0.6933 (mp10) REVERT: c 414 ASP cc_start: 0.7579 (m-30) cc_final: 0.7296 (m-30) REVERT: e 290 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8127 (pttp) REVERT: e 296 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7260 (tpp-160) REVERT: e 303 GLN cc_start: 0.7423 (mt0) cc_final: 0.6694 (mp10) REVERT: f 275 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8242 (mtpp) REVERT: f 303 GLN cc_start: 0.7422 (mt0) cc_final: 0.6900 (mp10) REVERT: f 367 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8828 (mm-30) REVERT: f 381 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: f 429 THR cc_start: 0.8688 (m) cc_final: 0.8256 (p) REVERT: g 290 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8156 (pttp) REVERT: g 410 LYS cc_start: 0.8274 (tttp) cc_final: 0.7772 (tppt) REVERT: g 414 ASP cc_start: 0.7455 (m-30) cc_final: 0.7044 (m-30) REVERT: g 417 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7503 (mtt90) REVERT: g 418 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: g 429 THR cc_start: 0.8658 (m) cc_final: 0.8200 (p) REVERT: h 276 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7741 (mp0) REVERT: h 297 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7938 (tp40) REVERT: h 402 LEU cc_start: 0.7533 (mt) cc_final: 0.7317 (mm) outliers start: 86 outliers final: 41 residues processed: 1057 average time/residue: 1.0104 time to fit residues: 1226.0216 Evaluate side-chains 1047 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 984 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 297 GLN Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 376 LYS Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 276 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain e residue 296 ARG Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 381 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 418 GLU Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 9 optimal weight: 1.9990 chunk 419 optimal weight: 7.9990 chunk 195 optimal weight: 0.3980 chunk 188 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 chunk 509 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN Q 374 HIS T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN h 374 HIS h 408 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124733 restraints weight = 43779.881| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.76 r_work: 0.3443 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 40970 Z= 0.107 Angle : 0.454 6.344 55216 Z= 0.242 Chirality : 0.039 0.124 6324 Planarity : 0.003 0.042 7412 Dihedral : 4.403 20.754 5542 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 1.27 % Allowed : 21.66 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.13), residues: 4930 helix: 2.69 (0.16), residues: 1326 sheet: -0.42 (0.11), residues: 2380 loop : -0.40 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 370 TYR 0.007 0.001 TYR A 393 PHE 0.012 0.001 PHE Y 422 HIS 0.005 0.001 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00233 (40970) covalent geometry : angle 0.45432 (55216) hydrogen bonds : bond 0.03418 ( 1501) hydrogen bonds : angle 4.31532 ( 4092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1004 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.8499 (ptpt) cc_final: 0.8042 (pttt) REVERT: A 302 GLU cc_start: 0.7000 (tt0) cc_final: 0.6633 (mt-10) REVERT: A 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7699 (tttp) REVERT: B 276 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7629 (mp0) REVERT: B 297 GLN cc_start: 0.8113 (tt0) cc_final: 0.7857 (tp40) REVERT: B 302 GLU cc_start: 0.7473 (tt0) cc_final: 0.6868 (tp30) REVERT: C 290 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8097 (pttp) REVERT: C 296 ARG cc_start: 0.7860 (ttt90) cc_final: 0.7628 (tpp-160) REVERT: C 302 GLU cc_start: 0.7099 (tt0) cc_final: 0.6561 (tp30) REVERT: C 377 MET cc_start: 0.8304 (mpt) cc_final: 0.7899 (mpt) REVERT: C 429 THR cc_start: 0.8544 (m) cc_final: 0.8174 (p) REVERT: D 276 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7638 (mp0) REVERT: D 410 LYS cc_start: 0.8305 (tttp) cc_final: 0.7796 (tppt) REVERT: D 414 ASP cc_start: 0.7339 (m-30) cc_final: 0.7009 (m-30) REVERT: E 290 LYS cc_start: 0.8415 (ptpt) cc_final: 0.7904 (pttm) REVERT: E 429 THR cc_start: 0.8596 (m) cc_final: 0.8226 (p) REVERT: F 297 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: G 276 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7558 (mp0) REVERT: G 376 LYS cc_start: 0.7979 (tttt) cc_final: 0.7778 (tmtt) REVERT: H 290 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8025 (pttm) REVERT: H 402 LEU cc_start: 0.7561 (mt) cc_final: 0.7303 (mm) REVERT: H 429 THR cc_start: 0.8520 (m) cc_final: 0.8096 (p) REVERT: I 276 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7748 (mp0) REVERT: I 290 LYS cc_start: 0.8492 (ptpt) cc_final: 0.8008 (pttm) REVERT: J 276 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7576 (mp0) REVERT: J 290 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7925 (pttm) REVERT: J 413 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7320 (tt0) REVERT: K 290 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7891 (pttp) REVERT: K 302 GLU cc_start: 0.7147 (tt0) cc_final: 0.6519 (tp30) REVERT: K 429 THR cc_start: 0.8672 (m) cc_final: 0.8470 (p) REVERT: L 414 ASP cc_start: 0.7403 (m-30) cc_final: 0.7104 (m-30) REVERT: M 276 GLU cc_start: 0.7462 (mp0) cc_final: 0.7157 (mp0) REVERT: M 281 HIS cc_start: 0.7772 (t70) cc_final: 0.7555 (t-170) REVERT: M 402 LEU cc_start: 0.7561 (mt) cc_final: 0.7322 (mm) REVERT: N 290 LYS cc_start: 0.8523 (ptpt) cc_final: 0.8115 (pttp) REVERT: O 276 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7629 (mt-10) REVERT: O 302 GLU cc_start: 0.7273 (tt0) cc_final: 0.6466 (tm-30) REVERT: O 410 LYS cc_start: 0.8352 (tttp) cc_final: 0.7729 (tppt) REVERT: O 414 ASP cc_start: 0.7284 (m-30) cc_final: 0.6839 (m-30) REVERT: O 429 THR cc_start: 0.8557 (m) cc_final: 0.8191 (p) REVERT: P 290 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8017 (pttp) REVERT: P 302 GLU cc_start: 0.7087 (tt0) cc_final: 0.6504 (tp30) REVERT: P 370 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8117 (ttt180) REVERT: P 410 LYS cc_start: 0.8259 (tttp) cc_final: 0.7765 (tppt) REVERT: P 414 ASP cc_start: 0.7187 (m-30) cc_final: 0.6765 (m-30) REVERT: P 429 THR cc_start: 0.8527 (m) cc_final: 0.8169 (p) REVERT: Q 276 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7630 (mp0) REVERT: Q 290 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8003 (pttm) REVERT: Q 297 GLN cc_start: 0.8187 (tt0) cc_final: 0.7892 (tp40) REVERT: Q 302 GLU cc_start: 0.7338 (tt0) cc_final: 0.6574 (mt-10) REVERT: Q 402 LEU cc_start: 0.7525 (mt) cc_final: 0.7278 (mm) REVERT: Q 409 MET cc_start: 0.8101 (mmm) cc_final: 0.7660 (mmm) REVERT: Q 429 THR cc_start: 0.8576 (m) cc_final: 0.8298 (p) REVERT: R 290 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8004 (pttt) REVERT: R 302 GLU cc_start: 0.7288 (tt0) cc_final: 0.6594 (mt-10) REVERT: R 377 MET cc_start: 0.8523 (mpt) cc_final: 0.7958 (mpt) REVERT: T 290 LYS cc_start: 0.8508 (ptpt) cc_final: 0.8074 (pttp) REVERT: T 377 MET cc_start: 0.8336 (mpt) cc_final: 0.7900 (mpt) REVERT: T 429 THR cc_start: 0.8566 (m) cc_final: 0.8201 (p) REVERT: U 303 GLN cc_start: 0.7140 (mt0) cc_final: 0.6751 (mp10) REVERT: U 410 LYS cc_start: 0.8298 (tttp) cc_final: 0.7767 (tppt) REVERT: U 414 ASP cc_start: 0.7275 (m-30) cc_final: 0.6926 (m-30) REVERT: U 429 THR cc_start: 0.8467 (m) cc_final: 0.7998 (p) REVERT: V 290 LYS cc_start: 0.8410 (ptpt) cc_final: 0.7908 (pttm) REVERT: V 402 LEU cc_start: 0.7520 (mt) cc_final: 0.7256 (mm) REVERT: W 296 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7465 (ttt180) REVERT: W 303 GLN cc_start: 0.7382 (mp10) cc_final: 0.7090 (mp10) REVERT: W 376 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7917 (tmtp) REVERT: X 276 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7578 (mp0) REVERT: Y 290 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8020 (pttm) REVERT: Y 414 ASP cc_start: 0.7529 (m-30) cc_final: 0.7247 (m-30) REVERT: Y 429 THR cc_start: 0.8576 (m) cc_final: 0.8269 (p) REVERT: Z 290 LYS cc_start: 0.8560 (ptpt) cc_final: 0.8086 (pttm) REVERT: Z 410 LYS cc_start: 0.8151 (tttm) cc_final: 0.7885 (tptp) REVERT: Z 413 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7479 (tt0) REVERT: Z 418 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8421 (mm-30) REVERT: a 276 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: a 290 LYS cc_start: 0.8405 (ptpp) cc_final: 0.7965 (pttm) REVERT: a 429 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8081 (p) REVERT: b 290 LYS cc_start: 0.8309 (ptpp) cc_final: 0.7928 (pttp) REVERT: b 429 THR cc_start: 0.8572 (m) cc_final: 0.8103 (p) REVERT: c 276 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7592 (mp0) REVERT: c 297 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: c 303 GLN cc_start: 0.7224 (mt0) cc_final: 0.6748 (mp10) REVERT: c 414 ASP cc_start: 0.7430 (m-30) cc_final: 0.7159 (m-30) REVERT: d 302 GLU cc_start: 0.7102 (tt0) cc_final: 0.6554 (tp30) REVERT: e 290 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8078 (pttp) REVERT: e 296 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7268 (tpp-160) REVERT: e 429 THR cc_start: 0.8500 (m) cc_final: 0.8165 (p) REVERT: f 275 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: f 302 GLU cc_start: 0.7010 (tt0) cc_final: 0.6476 (tp30) REVERT: f 367 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8859 (mm-30) REVERT: f 381 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: f 417 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7491 (mtp85) REVERT: f 418 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: f 429 THR cc_start: 0.8567 (m) cc_final: 0.8192 (p) REVERT: g 290 LYS cc_start: 0.8420 (ptpp) cc_final: 0.8042 (pttp) REVERT: g 302 GLU cc_start: 0.7239 (tt0) cc_final: 0.6544 (mt-10) REVERT: g 410 LYS cc_start: 0.8245 (tttp) cc_final: 0.7696 (tppt) REVERT: g 414 ASP cc_start: 0.7273 (m-30) cc_final: 0.6819 (m-30) REVERT: g 417 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7427 (mtt90) REVERT: g 429 THR cc_start: 0.8544 (m) cc_final: 0.7924 (p) REVERT: h 276 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7663 (mp0) REVERT: h 290 LYS cc_start: 0.8470 (ptpt) cc_final: 0.8020 (pttm) REVERT: h 370 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7963 (ttt180) REVERT: h 402 LEU cc_start: 0.7425 (mt) cc_final: 0.7216 (mm) REVERT: h 429 THR cc_start: 0.8493 (m) cc_final: 0.8268 (p) outliers start: 58 outliers final: 34 residues processed: 1043 average time/residue: 1.0062 time to fit residues: 1206.0841 Evaluate side-chains 1005 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 960 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 376 LYS Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 276 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain e residue 296 ARG Chi-restraints excluded: chain e residue 394 LYS Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 381 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 136 optimal weight: 4.9990 chunk 486 optimal weight: 0.7980 chunk 494 optimal weight: 8.9990 chunk 452 optimal weight: 0.7980 chunk 356 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 360 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 374 HIS B 359 GLN B 411 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN Q 374 HIS R 239 ASN R 374 HIS S 359 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN b 239 ASN h 374 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124470 restraints weight = 44077.023| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.77 r_work: 0.3437 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40970 Z= 0.119 Angle : 0.456 6.000 55216 Z= 0.243 Chirality : 0.039 0.125 6324 Planarity : 0.003 0.040 7412 Dihedral : 4.346 21.164 5542 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.29 % Allowed : 22.08 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.13), residues: 4930 helix: 2.76 (0.16), residues: 1326 sheet: -0.25 (0.11), residues: 2380 loop : -0.19 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 370 TYR 0.007 0.001 TYR A 393 PHE 0.011 0.001 PHE N 422 HIS 0.006 0.001 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00258 (40970) covalent geometry : angle 0.45632 (55216) hydrogen bonds : bond 0.03523 ( 1501) hydrogen bonds : angle 4.26097 ( 4092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 970 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8072 (pttt) REVERT: A 302 GLU cc_start: 0.7053 (tt0) cc_final: 0.6658 (mt-10) REVERT: A 376 LYS cc_start: 0.8016 (tttt) cc_final: 0.7720 (tttp) REVERT: B 276 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7676 (mp0) REVERT: B 297 GLN cc_start: 0.8084 (tt0) cc_final: 0.7826 (tp40) REVERT: B 302 GLU cc_start: 0.7487 (tt0) cc_final: 0.6623 (mt-10) REVERT: C 290 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8111 (pttp) REVERT: C 296 ARG cc_start: 0.7862 (ttt90) cc_final: 0.7633 (tpp-160) REVERT: C 302 GLU cc_start: 0.7129 (tt0) cc_final: 0.6624 (tp30) REVERT: C 377 MET cc_start: 0.8315 (mpt) cc_final: 0.7910 (mpt) REVERT: C 429 THR cc_start: 0.8595 (m) cc_final: 0.8187 (p) REVERT: D 276 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7662 (mp0) REVERT: D 410 LYS cc_start: 0.8325 (tttp) cc_final: 0.7812 (tppt) REVERT: D 414 ASP cc_start: 0.7411 (m-30) cc_final: 0.7061 (m-30) REVERT: E 290 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8068 (pttp) REVERT: E 417 ARG cc_start: 0.7663 (mtt-85) cc_final: 0.7425 (mtt90) REVERT: E 429 THR cc_start: 0.8637 (m) cc_final: 0.8261 (p) REVERT: F 297 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: G 276 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7622 (mp0) REVERT: G 376 LYS cc_start: 0.8043 (tttt) cc_final: 0.7842 (tmtt) REVERT: H 290 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8088 (pttm) REVERT: H 402 LEU cc_start: 0.7581 (mt) cc_final: 0.7331 (mm) REVERT: I 290 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8128 (pttm) REVERT: J 290 LYS cc_start: 0.8409 (ptpt) cc_final: 0.7944 (pttm) REVERT: J 413 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7381 (tt0) REVERT: K 290 LYS cc_start: 0.8342 (ptpp) cc_final: 0.7924 (pttp) REVERT: K 302 GLU cc_start: 0.7157 (tt0) cc_final: 0.6560 (tp30) REVERT: L 414 ASP cc_start: 0.7457 (m-30) cc_final: 0.7164 (m-30) REVERT: M 276 GLU cc_start: 0.7501 (mp0) cc_final: 0.7182 (mp0) REVERT: N 290 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8091 (pttp) REVERT: O 276 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7645 (mt-10) REVERT: O 370 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8121 (ttt180) REVERT: O 410 LYS cc_start: 0.8360 (tttp) cc_final: 0.7748 (tppt) REVERT: O 414 ASP cc_start: 0.7343 (m-30) cc_final: 0.6905 (m-30) REVERT: O 429 THR cc_start: 0.8592 (m) cc_final: 0.8223 (p) REVERT: P 290 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8049 (pttp) REVERT: P 302 GLU cc_start: 0.7109 (tt0) cc_final: 0.6571 (tp30) REVERT: P 370 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8068 (ttt180) REVERT: P 410 LYS cc_start: 0.8290 (tttp) cc_final: 0.7760 (tppt) REVERT: P 429 THR cc_start: 0.8526 (m) cc_final: 0.8178 (p) REVERT: Q 276 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7663 (mp0) REVERT: Q 290 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8005 (pttp) REVERT: Q 402 LEU cc_start: 0.7547 (mt) cc_final: 0.7306 (mm) REVERT: Q 409 MET cc_start: 0.8140 (mmm) cc_final: 0.7704 (mmm) REVERT: Q 429 THR cc_start: 0.8570 (m) cc_final: 0.8308 (p) REVERT: R 290 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8053 (pttt) REVERT: R 302 GLU cc_start: 0.7327 (tt0) cc_final: 0.6654 (mt-10) REVERT: R 377 MET cc_start: 0.8537 (mpt) cc_final: 0.7976 (mpt) REVERT: T 276 GLU cc_start: 0.7924 (mp0) cc_final: 0.7685 (mp0) REVERT: T 290 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8093 (pttp) REVERT: T 296 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7152 (tpp-160) REVERT: T 377 MET cc_start: 0.8362 (mpt) cc_final: 0.7925 (mpt) REVERT: T 429 THR cc_start: 0.8595 (m) cc_final: 0.8226 (p) REVERT: U 303 GLN cc_start: 0.7174 (mt0) cc_final: 0.6791 (mp10) REVERT: U 410 LYS cc_start: 0.8342 (tttp) cc_final: 0.7846 (tppt) REVERT: U 414 ASP cc_start: 0.7371 (m-30) cc_final: 0.6998 (m-30) REVERT: V 290 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8050 (pttp) REVERT: V 402 LEU cc_start: 0.7526 (mt) cc_final: 0.7283 (mm) REVERT: W 376 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7928 (tmtp) REVERT: X 276 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7617 (mp0) REVERT: Y 290 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8047 (pttm) REVERT: Y 414 ASP cc_start: 0.7529 (m-30) cc_final: 0.7277 (m-30) REVERT: Y 429 THR cc_start: 0.8608 (m) cc_final: 0.8294 (p) REVERT: Z 276 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7797 (mp0) REVERT: Z 290 LYS cc_start: 0.8569 (ptpt) cc_final: 0.8119 (pttm) REVERT: Z 410 LYS cc_start: 0.8160 (tttm) cc_final: 0.7900 (tptp) REVERT: Z 413 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7528 (tt0) REVERT: Z 418 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8428 (mm-30) REVERT: a 276 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: a 290 LYS cc_start: 0.8433 (ptpp) cc_final: 0.8006 (pttm) REVERT: a 429 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8119 (p) REVERT: b 290 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7987 (pttp) REVERT: b 429 THR cc_start: 0.8611 (m) cc_final: 0.8141 (p) REVERT: c 276 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7611 (mp0) REVERT: c 297 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: c 303 GLN cc_start: 0.7240 (mt0) cc_final: 0.6763 (mp10) REVERT: c 414 ASP cc_start: 0.7469 (m-30) cc_final: 0.7203 (m-30) REVERT: d 302 GLU cc_start: 0.7127 (tt0) cc_final: 0.6550 (tp30) REVERT: d 303 GLN cc_start: 0.7232 (mt0) cc_final: 0.6298 (mp10) REVERT: e 290 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8092 (pttp) REVERT: e 296 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7340 (tpp-160) REVERT: e 429 THR cc_start: 0.8525 (m) cc_final: 0.8216 (p) REVERT: f 275 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8213 (mtpp) REVERT: f 290 LYS cc_start: 0.8475 (ptpt) cc_final: 0.8055 (pttp) REVERT: f 302 GLU cc_start: 0.7057 (tt0) cc_final: 0.6559 (tp30) REVERT: f 367 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8815 (mm-30) REVERT: f 381 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: f 417 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7563 (mtp85) REVERT: f 418 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: f 429 THR cc_start: 0.8606 (m) cc_final: 0.8217 (p) REVERT: g 290 LYS cc_start: 0.8461 (ptpp) cc_final: 0.8086 (pttp) REVERT: g 302 GLU cc_start: 0.7314 (tt0) cc_final: 0.6660 (mt-10) REVERT: g 410 LYS cc_start: 0.8275 (tttp) cc_final: 0.7730 (tppt) REVERT: g 414 ASP cc_start: 0.7320 (m-30) cc_final: 0.6867 (m-30) REVERT: g 417 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7448 (mtt90) REVERT: g 429 THR cc_start: 0.8584 (m) cc_final: 0.7957 (p) REVERT: h 276 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7668 (mp0) REVERT: h 290 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8009 (pttp) REVERT: h 409 MET cc_start: 0.8129 (mmm) cc_final: 0.7709 (mmm) REVERT: h 429 THR cc_start: 0.8547 (m) cc_final: 0.8309 (p) outliers start: 59 outliers final: 39 residues processed: 1013 average time/residue: 0.9968 time to fit residues: 1160.6789 Evaluate side-chains 996 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 945 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 376 LYS Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 276 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 394 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain e residue 296 ARG Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 381 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 436 optimal weight: 2.9990 chunk 482 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 366 optimal weight: 2.9990 chunk 413 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 374 HIS B 269 GLN B 359 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN Q 374 HIS R 239 ASN R 374 HIS S 269 GLN S 359 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN b 239 ASN h 374 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121796 restraints weight = 44361.377| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.66 r_work: 0.3434 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40970 Z= 0.134 Angle : 0.464 6.471 55216 Z= 0.247 Chirality : 0.039 0.126 6324 Planarity : 0.003 0.042 7412 Dihedral : 4.380 21.235 5542 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.23 % Allowed : 22.15 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.13), residues: 4930 helix: 2.77 (0.16), residues: 1326 sheet: -0.19 (0.11), residues: 2380 loop : -0.07 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 370 TYR 0.007 0.001 TYR A 393 PHE 0.012 0.001 PHE Y 422 HIS 0.006 0.001 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00294 (40970) covalent geometry : angle 0.46383 (55216) hydrogen bonds : bond 0.03613 ( 1501) hydrogen bonds : angle 4.26297 ( 4092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 968 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8137 (pttt) REVERT: A 302 GLU cc_start: 0.7026 (tt0) cc_final: 0.6748 (mt-10) REVERT: A 376 LYS cc_start: 0.8046 (tttt) cc_final: 0.7780 (tttp) REVERT: B 276 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7712 (mp0) REVERT: B 290 LYS cc_start: 0.8538 (ptpt) cc_final: 0.8158 (pttp) REVERT: B 297 GLN cc_start: 0.8016 (tt0) cc_final: 0.7797 (tp40) REVERT: B 394 LYS cc_start: 0.7055 (ttpt) cc_final: 0.6855 (ttpt) REVERT: C 290 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8174 (pttp) REVERT: C 302 GLU cc_start: 0.7180 (tt0) cc_final: 0.6747 (tp30) REVERT: C 429 THR cc_start: 0.8673 (m) cc_final: 0.8270 (p) REVERT: D 276 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7700 (mp0) REVERT: D 297 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: D 410 LYS cc_start: 0.8338 (tttp) cc_final: 0.7875 (tppt) REVERT: D 414 ASP cc_start: 0.7497 (m-30) cc_final: 0.7124 (m-30) REVERT: E 290 LYS cc_start: 0.8492 (ptpt) cc_final: 0.8135 (pttp) REVERT: E 417 ARG cc_start: 0.7718 (mtt-85) cc_final: 0.7464 (mtt90) REVERT: E 429 THR cc_start: 0.8666 (m) cc_final: 0.8301 (p) REVERT: F 297 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: F 303 GLN cc_start: 0.7304 (mt0) cc_final: 0.6862 (mp10) REVERT: G 276 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7687 (mp0) REVERT: H 290 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8157 (pttm) REVERT: H 402 LEU cc_start: 0.7610 (mt) cc_final: 0.7372 (mm) REVERT: H 429 THR cc_start: 0.8638 (m) cc_final: 0.8255 (p) REVERT: I 290 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8193 (pttm) REVERT: J 290 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8031 (pttm) REVERT: K 290 LYS cc_start: 0.8373 (ptpp) cc_final: 0.7973 (pttp) REVERT: K 302 GLU cc_start: 0.7223 (tt0) cc_final: 0.6686 (tp30) REVERT: K 402 LEU cc_start: 0.7453 (mp) cc_final: 0.7233 (mm) REVERT: L 414 ASP cc_start: 0.7501 (m-30) cc_final: 0.7215 (m-30) REVERT: M 276 GLU cc_start: 0.7454 (mp0) cc_final: 0.7169 (mp0) REVERT: M 290 LYS cc_start: 0.8464 (ptpt) cc_final: 0.8097 (pttp) REVERT: M 297 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: N 290 LYS cc_start: 0.8515 (ptpt) cc_final: 0.8124 (pttp) REVERT: O 410 LYS cc_start: 0.8401 (tttp) cc_final: 0.7829 (tppt) REVERT: O 414 ASP cc_start: 0.7412 (m-30) cc_final: 0.7010 (m-30) REVERT: O 429 THR cc_start: 0.8663 (m) cc_final: 0.8304 (p) REVERT: P 290 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8132 (pttp) REVERT: P 302 GLU cc_start: 0.7165 (tt0) cc_final: 0.6692 (tp30) REVERT: P 370 ARG cc_start: 0.8259 (ttp80) cc_final: 0.8027 (ttt180) REVERT: P 410 LYS cc_start: 0.8268 (tttp) cc_final: 0.7804 (tppt) REVERT: P 429 THR cc_start: 0.8606 (m) cc_final: 0.8285 (p) REVERT: Q 276 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7686 (mp0) REVERT: Q 290 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8130 (pttp) REVERT: Q 409 MET cc_start: 0.8264 (mmm) cc_final: 0.7832 (mmm) REVERT: Q 429 THR cc_start: 0.8613 (m) cc_final: 0.8366 (p) REVERT: R 290 LYS cc_start: 0.8580 (ptpt) cc_final: 0.8151 (pttt) REVERT: R 302 GLU cc_start: 0.7399 (tt0) cc_final: 0.6761 (mt-10) REVERT: R 377 MET cc_start: 0.8532 (mpt) cc_final: 0.8015 (mpt) REVERT: S 290 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8133 (pttp) REVERT: T 276 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: T 290 LYS cc_start: 0.8559 (ptpt) cc_final: 0.8165 (pttp) REVERT: T 296 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7043 (tpp-160) REVERT: T 429 THR cc_start: 0.8653 (m) cc_final: 0.8304 (p) REVERT: U 303 GLN cc_start: 0.7229 (mt0) cc_final: 0.6920 (mp10) REVERT: U 410 LYS cc_start: 0.8348 (tttp) cc_final: 0.7914 (tppt) REVERT: U 414 ASP cc_start: 0.7444 (m-30) cc_final: 0.7062 (m-30) REVERT: V 290 LYS cc_start: 0.8481 (ptpt) cc_final: 0.8131 (pttp) REVERT: V 402 LEU cc_start: 0.7647 (mt) cc_final: 0.7407 (mm) REVERT: W 297 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: W 303 GLN cc_start: 0.7515 (mp10) cc_final: 0.7219 (mp10) REVERT: W 376 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8010 (tmtp) REVERT: X 276 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7666 (mp0) REVERT: Y 290 LYS cc_start: 0.8539 (ptpt) cc_final: 0.8130 (pttm) REVERT: Y 414 ASP cc_start: 0.7593 (m-30) cc_final: 0.7356 (m-30) REVERT: Y 429 THR cc_start: 0.8677 (m) cc_final: 0.8382 (p) REVERT: Z 290 LYS cc_start: 0.8551 (ptpt) cc_final: 0.8156 (pttm) REVERT: Z 410 LYS cc_start: 0.8186 (tttm) cc_final: 0.7941 (tptp) REVERT: Z 413 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7624 (tt0) REVERT: Z 418 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: a 276 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: a 290 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8076 (pttm) REVERT: a 370 ARG cc_start: 0.8349 (tmm-80) cc_final: 0.8139 (ttt180) REVERT: a 429 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8256 (p) REVERT: b 290 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8053 (pttp) REVERT: b 429 THR cc_start: 0.8686 (m) cc_final: 0.8240 (p) REVERT: c 276 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7644 (mp0) REVERT: c 296 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6945 (tpp-160) REVERT: c 297 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: c 303 GLN cc_start: 0.7262 (mt0) cc_final: 0.6869 (mp10) REVERT: c 414 ASP cc_start: 0.7522 (m-30) cc_final: 0.7263 (m-30) REVERT: d 302 GLU cc_start: 0.7160 (tt0) cc_final: 0.6717 (tp30) REVERT: d 303 GLN cc_start: 0.7274 (mt0) cc_final: 0.6462 (mp10) REVERT: e 290 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8157 (pttp) REVERT: e 296 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7232 (tpp-160) REVERT: e 429 THR cc_start: 0.8568 (m) cc_final: 0.8304 (p) REVERT: f 275 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8257 (mtpp) REVERT: f 290 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8114 (pttp) REVERT: f 302 GLU cc_start: 0.7105 (tt0) cc_final: 0.6665 (tp30) REVERT: f 303 GLN cc_start: 0.7427 (mt0) cc_final: 0.6725 (mp10) REVERT: f 367 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8818 (mm-30) REVERT: f 381 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: f 417 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7603 (mtp85) REVERT: f 418 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: f 429 THR cc_start: 0.8673 (m) cc_final: 0.8307 (p) REVERT: g 290 LYS cc_start: 0.8501 (ptpp) cc_final: 0.8170 (pttp) REVERT: g 302 GLU cc_start: 0.7397 (tt0) cc_final: 0.6787 (mt-10) REVERT: g 410 LYS cc_start: 0.8282 (tttp) cc_final: 0.7794 (tppt) REVERT: g 414 ASP cc_start: 0.7352 (m-30) cc_final: 0.6900 (m-30) REVERT: g 417 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7506 (mtt90) REVERT: g 429 THR cc_start: 0.8641 (m) cc_final: 0.8042 (p) REVERT: h 276 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7699 (mp0) REVERT: h 290 LYS cc_start: 0.8527 (ptpt) cc_final: 0.8154 (pttp) REVERT: h 370 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7970 (ttt180) REVERT: h 409 MET cc_start: 0.8249 (mmm) cc_final: 0.7829 (mmm) REVERT: h 429 THR cc_start: 0.8653 (m) cc_final: 0.8415 (p) outliers start: 56 outliers final: 37 residues processed: 1012 average time/residue: 1.0055 time to fit residues: 1170.5858 Evaluate side-chains 993 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 939 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 297 GLN Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 276 GLU Chi-restraints excluded: chain T residue 296 ARG Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain W residue 376 LYS Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 276 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 296 ARG Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain e residue 296 ARG Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 275 LYS Chi-restraints excluded: chain f residue 381 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 105 optimal weight: 0.6980 chunk 452 optimal weight: 1.9990 chunk 395 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 358 optimal weight: 0.0770 chunk 392 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 374 HIS B 359 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN H 411 GLN I 239 ASN I 411 GLN K 239 ASN Q 374 HIS R 239 ASN R 374 HIS S 359 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN b 239 ASN h 374 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124718 restraints weight = 44480.146| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.66 r_work: 0.3482 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 40970 Z= 0.085 Angle : 0.431 6.467 55216 Z= 0.230 Chirality : 0.038 0.123 6324 Planarity : 0.002 0.033 7412 Dihedral : 4.117 19.689 5542 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Rotamer: Outliers : 1.01 % Allowed : 22.54 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.13), residues: 4930 helix: 2.97 (0.16), residues: 1326 sheet: 0.02 (0.11), residues: 2414 loop : -0.17 (0.20), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 247 TYR 0.007 0.001 TYR B 282 PHE 0.012 0.001 PHE N 422 HIS 0.005 0.001 HIS L 281 Details of bonding type rmsd covalent geometry : bond 0.00180 (40970) covalent geometry : angle 0.43084 (55216) hydrogen bonds : bond 0.03168 ( 1501) hydrogen bonds : angle 4.11284 ( 4092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22724.56 seconds wall clock time: 384 minutes 25.81 seconds (23065.81 seconds total)