Starting phenix.real_space_refine on Thu Dec 26 03:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.map" model { file = "/net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d84_30612/12_2024/7d84_30612.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.093 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 26044 2.51 5 N 7990 2.21 5 O 8568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, h Time building chain proxies: 8.31, per 1000 atoms: 0.19 Number of scatterers: 42704 At special positions: 0 Unit cell: (262.15, 260.01, 96.3, 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 8568 8.00 N 7990 7.00 C 26044 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: 10.53 Conformation dependent library (CDL) restraints added in 5.8 seconds 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10404 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 36 sheets defined 32.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 228 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA P 291 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Q 291 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA R 291 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA S 291 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA T 291 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA V 291 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 229 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA X 291 " --> pdb=" O ALA X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Y 291 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Z 291 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 229 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 229 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA b 291 " --> pdb=" O ALA b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA c 291 " --> pdb=" O ALA c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA d 291 " --> pdb=" O ALA d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA e 291 " --> pdb=" O ALA e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 229 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA f 291 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA g 291 " --> pdb=" O ALA g 288 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 229 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 279 removed outlier: 3.518A pdb=" N GLU B 276 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 274 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 276 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 274 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 276 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 276 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN E 274 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 276 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN F 274 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 276 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 274 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 276 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU I 276 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 274 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 276 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 274 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 276 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN K 274 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU L 276 " --> pdb=" O HIS K 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN L 274 " --> pdb=" O LYS K 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU M 276 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 274 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 276 " --> pdb=" O HIS M 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN N 274 " --> pdb=" O LYS M 376 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 276 " --> pdb=" O HIS O 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN P 274 " --> pdb=" O LYS O 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 276 " --> pdb=" O HIS P 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN Q 274 " --> pdb=" O LYS P 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 276 " --> pdb=" O HIS Q 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 274 " --> pdb=" O LYS Q 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU S 276 " --> pdb=" O HIS R 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN S 274 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU T 276 " --> pdb=" O HIS S 374 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN T 274 " --> pdb=" O LYS S 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN U 274 " --> pdb=" O LYS T 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU V 276 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN V 274 " --> pdb=" O LYS U 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU W 276 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU X 276 " --> pdb=" O HIS W 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN X 274 " --> pdb=" O LYS W 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU Y 276 " --> pdb=" O HIS X 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Y 274 " --> pdb=" O LYS X 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Z 276 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN Z 274 " --> pdb=" O LYS Y 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU a 276 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN a 274 " --> pdb=" O LYS Z 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU b 276 " --> pdb=" O HIS a 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN b 274 " --> pdb=" O LYS a 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 276 " --> pdb=" O HIS b 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN c 274 " --> pdb=" O LYS b 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU d 276 " --> pdb=" O HIS c 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN d 274 " --> pdb=" O LYS c 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU e 276 " --> pdb=" O HIS d 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN e 274 " --> pdb=" O LYS d 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU f 276 " --> pdb=" O HIS e 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN f 274 " --> pdb=" O LYS e 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 276 " --> pdb=" O HIS f 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN g 274 " --> pdb=" O LYS f 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU h 276 " --> pdb=" O HIS g 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN h 274 " --> pdb=" O LYS g 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 276 " --> pdb=" O HIS h 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 274 " --> pdb=" O LYS h 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 302 removed outlier: 3.787A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 365 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 301 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 359 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG h 296 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN h 365 " --> pdb=" O SER h 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER h 301 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN h 359 " --> pdb=" O SER h 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG g 296 " --> pdb=" O SER h 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN g 365 " --> pdb=" O SER g 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER g 301 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN g 359 " --> pdb=" O SER g 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG f 296 " --> pdb=" O SER g 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN f 365 " --> pdb=" O SER f 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 301 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN f 359 " --> pdb=" O SER f 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG e 296 " --> pdb=" O SER f 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN e 365 " --> pdb=" O SER e 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER e 301 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN e 359 " --> pdb=" O SER e 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG d 296 " --> pdb=" O SER e 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN d 365 " --> pdb=" O SER d 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER d 301 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN d 359 " --> pdb=" O SER d 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG c 296 " --> pdb=" O SER d 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN c 365 " --> pdb=" O SER c 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 301 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 359 " --> pdb=" O SER c 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG b 296 " --> pdb=" O SER c 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN b 365 " --> pdb=" O SER b 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER b 301 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN b 359 " --> pdb=" O SER b 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG a 296 " --> pdb=" O SER b 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN a 365 " --> pdb=" O SER a 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER a 301 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN a 359 " --> pdb=" O SER a 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Z 296 " --> pdb=" O SER a 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Z 365 " --> pdb=" O SER Z 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Z 301 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Z 359 " --> pdb=" O SER Z 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Y 296 " --> pdb=" O SER Z 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN Y 365 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER Y 301 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN Y 359 " --> pdb=" O SER Y 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG X 296 " --> pdb=" O SER Y 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN X 365 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER X 301 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN X 359 " --> pdb=" O SER X 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 296 " --> pdb=" O SER X 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN W 365 " --> pdb=" O SER W 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER W 301 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN W 359 " --> pdb=" O SER W 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG V 296 " --> pdb=" O SER W 364 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN V 365 " --> pdb=" O SER V 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER V 301 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN V 359 " --> pdb=" O SER V 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 296 " --> pdb=" O SER V 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN U 365 " --> pdb=" O SER U 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER U 301 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN U 359 " --> pdb=" O SER U 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG T 296 " --> pdb=" O SER U 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN T 365 " --> pdb=" O SER T 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER T 301 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN T 359 " --> pdb=" O SER T 301 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG S 296 " --> pdb=" O SER T 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN S 365 " --> pdb=" O SER S 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S 301 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN S 359 " --> pdb=" O SER S 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG R 296 " --> pdb=" O SER S 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN R 365 " --> pdb=" O SER R 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 301 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN R 359 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Q 296 " --> pdb=" O SER R 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Q 365 " --> pdb=" O SER Q 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Q 301 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Q 359 " --> pdb=" O SER Q 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG P 296 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN P 365 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER P 301 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN P 359 " --> pdb=" O SER P 301 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 302 " --> pdb=" O THR P 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG O 296 " --> pdb=" O SER P 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN O 365 " --> pdb=" O SER O 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER O 301 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN O 359 " --> pdb=" O SER O 301 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG N 296 " --> pdb=" O SER O 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN N 365 " --> pdb=" O SER N 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER N 301 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN N 359 " --> pdb=" O SER N 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG M 296 " --> pdb=" O SER N 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN M 365 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER M 301 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN M 359 " --> pdb=" O SER M 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG L 296 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN L 365 " --> pdb=" O SER L 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 301 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 359 " --> pdb=" O SER L 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 296 " --> pdb=" O SER L 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN K 365 " --> pdb=" O SER K 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER K 301 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN K 359 " --> pdb=" O SER K 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG J 296 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN J 365 " --> pdb=" O SER J 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER J 301 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN J 359 " --> pdb=" O SER J 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG I 296 " --> pdb=" O SER J 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN I 365 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER I 301 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN I 359 " --> pdb=" O SER I 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG H 296 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 365 " --> pdb=" O SER H 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 301 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 359 " --> pdb=" O SER H 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 296 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN G 365 " --> pdb=" O SER G 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER G 301 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 359 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 296 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN F 365 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 301 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 359 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 296 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN E 365 " --> pdb=" O SER E 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 301 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 359 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 296 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 365 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 301 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 359 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 296 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 365 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 301 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 359 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 296 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 365 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 301 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 359 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 296 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) 2043 hydrogen bonds defined for protein. 5718 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: 18.46 Time building geometry restraints manager: 12.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15229 1.34 - 1.45: 5119 1.45 - 1.57: 22594 1.57 - 1.68: 0 1.68 - 1.80: 204 Bond restraints: 43146 Sorted by residual: bond pdb=" CG ARG F 294 " pdb=" CD ARG F 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG W 294 " pdb=" CD ARG W 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG B 294 " pdb=" CD ARG B 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG S 294 " pdb=" CD ARG S 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG L 294 " pdb=" CD ARG L 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.62e+00 ... (remaining 43141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 56222 2.00 - 3.99: 1682 3.99 - 5.99: 202 5.99 - 7.98: 0 7.98 - 9.98: 68 Bond angle restraints: 58174 Sorted by residual: angle pdb=" N GLY P 421 " pdb=" CA GLY P 421 " pdb=" C GLY P 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY g 421 " pdb=" CA GLY g 421 " pdb=" C GLY g 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY H 421 " pdb=" CA GLY H 421 " pdb=" C GLY H 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " pdb=" C GLY Y 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY U 421 " pdb=" CA GLY U 421 " pdb=" C GLY U 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 ... (remaining 58169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.27: 21963 11.27 - 22.54: 2925 22.54 - 33.81: 1428 33.81 - 45.08: 374 45.08 - 56.35: 374 Dihedral angle restraints: 27064 sinusoidal: 11254 harmonic: 15810 Sorted by residual: dihedral pdb=" CA MET E 420 " pdb=" C MET E 420 " pdb=" N GLY E 421 " pdb=" CA GLY E 421 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET K 420 " pdb=" C MET K 420 " pdb=" N GLY K 421 " pdb=" CA GLY K 421 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET b 420 " pdb=" C MET b 420 " pdb=" N GLY b 421 " pdb=" CA GLY b 421 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 27061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3464 0.030 - 0.059: 2165 0.059 - 0.089: 640 0.089 - 0.118: 221 0.118 - 0.148: 208 Chirality restraints: 6698 Sorted by residual: chirality pdb=" CA PRO A 255 " pdb=" N PRO A 255 " pdb=" C PRO A 255 " pdb=" CB PRO A 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO R 255 " pdb=" N PRO R 255 " pdb=" C PRO R 255 " pdb=" CB PRO R 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO O 255 " pdb=" N PRO O 255 " pdb=" C PRO O 255 " pdb=" CB PRO O 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 6695 not shown) Planarity restraints: 7786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER d 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO d 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO d 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO d 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO M 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO M 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Y 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO Y 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 255 " -0.040 5.00e-02 4.00e+02 ... (remaining 7783 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 11711 2.80 - 3.32: 36254 3.32 - 3.85: 68608 3.85 - 4.37: 76405 4.37 - 4.90: 137058 Nonbonded interactions: 330036 Sorted by model distance: nonbonded pdb=" N ASP D 369 " pdb=" OD1 ASP D 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP U 369 " pdb=" OD1 ASP U 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP f 369 " pdb=" OD1 ASP f 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP C 369 " pdb=" OD1 ASP C 369 " model vdw 2.271 3.120 nonbonded pdb=" N ASP F 369 " pdb=" OD1 ASP F 369 " model vdw 2.271 3.120 ... (remaining 330031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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 group one per residue 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.640 Check model and map are aligned: 0.320 Set scattering table: 0.340 Process input model: 76.090 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.640 ------------------------------------------------------------------------------- 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 : 0.009 0.074 43146 Z= 0.595 Angle : 0.897 9.977 58174 Z= 0.496 Chirality : 0.047 0.148 6698 Planarity : 0.007 0.070 7786 Dihedral : 15.250 56.353 16660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 7.78 % Allowed : 7.24 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 5202 helix: -0.63 (0.11), residues: 1462 sheet: -1.79 (0.10), residues: 2550 loop : -2.59 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 263 PHE 0.015 0.003 PHE S 422 TYR 0.005 0.002 TYR I 366 ARG 0.003 0.001 ARG T 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 1332 time to evaluate : 5.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8295 (mt-10) REVERT: A 429 THR cc_start: 0.7766 (p) cc_final: 0.6995 (p) REVERT: B 246 GLN cc_start: 0.9040 (tt0) cc_final: 0.8758 (pt0) REVERT: B 267 THR cc_start: 0.9090 (m) cc_final: 0.8809 (p) REVERT: B 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8329 (mt-10) REVERT: C 267 THR cc_start: 0.9084 (m) cc_final: 0.8728 (p) REVERT: C 280 GLU cc_start: 0.7726 (tt0) cc_final: 0.7521 (tt0) REVERT: C 418 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8348 (mt-10) REVERT: D 250 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8088 (mt-10) REVERT: D 267 THR cc_start: 0.9076 (m) cc_final: 0.8837 (p) REVERT: D 409 MET cc_start: 0.8486 (mmm) cc_final: 0.8251 (tpp) REVERT: D 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8297 (mt-10) REVERT: E 246 GLN cc_start: 0.9072 (tt0) cc_final: 0.8754 (pt0) REVERT: E 267 THR cc_start: 0.9225 (m) cc_final: 0.8964 (p) REVERT: E 382 ILE cc_start: 0.9234 (mt) cc_final: 0.9033 (mt) REVERT: E 418 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8416 (mt-10) REVERT: F 246 GLN cc_start: 0.9024 (tt0) cc_final: 0.8730 (pt0) REVERT: F 267 THR cc_start: 0.9079 (m) cc_final: 0.8871 (p) REVERT: F 269 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8647 (mm-40) REVERT: F 302 GLU cc_start: 0.7877 (tt0) cc_final: 0.7473 (tm-30) REVERT: F 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8297 (mt-10) REVERT: G 267 THR cc_start: 0.9084 (m) cc_final: 0.8778 (p) REVERT: G 418 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8398 (mt-10) REVERT: H 267 THR cc_start: 0.9103 (m) cc_final: 0.8887 (p) REVERT: H 418 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8336 (mt-10) REVERT: I 267 THR cc_start: 0.9090 (m) cc_final: 0.8887 (p) REVERT: I 299 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: I 418 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8216 (mt-10) REVERT: J 267 THR cc_start: 0.9059 (m) cc_final: 0.8853 (p) REVERT: K 246 GLN cc_start: 0.9122 (tt0) cc_final: 0.8851 (pt0) REVERT: K 252 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9062 (tp) REVERT: K 267 THR cc_start: 0.9167 (m) cc_final: 0.8870 (p) REVERT: K 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7878 (tt0) REVERT: K 418 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8284 (mt-10) REVERT: L 246 GLN cc_start: 0.9035 (tt0) cc_final: 0.8777 (pt0) REVERT: L 267 THR cc_start: 0.9097 (m) cc_final: 0.8836 (p) REVERT: L 302 GLU cc_start: 0.7788 (tt0) cc_final: 0.7545 (tm-30) REVERT: L 418 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8253 (mt-10) REVERT: M 267 THR cc_start: 0.9115 (m) cc_final: 0.8868 (p) REVERT: M 418 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8258 (mt-10) REVERT: N 267 THR cc_start: 0.9104 (m) cc_final: 0.8861 (p) REVERT: N 418 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8227 (mt-10) REVERT: O 267 THR cc_start: 0.9091 (m) cc_final: 0.8843 (p) REVERT: O 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8162 (mt-10) REVERT: P 246 GLN cc_start: 0.9013 (tt0) cc_final: 0.8672 (pt0) REVERT: P 252 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9186 (tp) REVERT: P 267 THR cc_start: 0.9110 (m) cc_final: 0.8837 (p) REVERT: P 382 ILE cc_start: 0.9181 (mt) cc_final: 0.8953 (mm) REVERT: P 418 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8421 (mt-10) REVERT: Q 246 GLN cc_start: 0.9087 (tt0) cc_final: 0.8809 (pt0) REVERT: Q 252 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9132 (tp) REVERT: Q 267 THR cc_start: 0.9119 (m) cc_final: 0.8874 (p) REVERT: Q 302 GLU cc_start: 0.7770 (tt0) cc_final: 0.7470 (tm-30) REVERT: Q 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8371 (mt-10) REVERT: R 267 THR cc_start: 0.9039 (m) cc_final: 0.8826 (p) REVERT: R 418 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8295 (mt-10) REVERT: S 246 GLN cc_start: 0.9038 (tt0) cc_final: 0.8752 (pt0) REVERT: S 267 THR cc_start: 0.9094 (m) cc_final: 0.8810 (p) REVERT: S 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7148 (mm-30) REVERT: T 267 THR cc_start: 0.9068 (m) cc_final: 0.8718 (p) REVERT: T 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8401 (mt-10) REVERT: T 429 THR cc_start: 0.7972 (p) cc_final: 0.7719 (p) REVERT: U 250 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8088 (mt-10) REVERT: U 267 THR cc_start: 0.9075 (m) cc_final: 0.8833 (p) REVERT: U 409 MET cc_start: 0.8482 (mmm) cc_final: 0.8243 (tpp) REVERT: U 418 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8298 (mt-10) REVERT: V 246 GLN cc_start: 0.9075 (tt0) cc_final: 0.8745 (pt0) REVERT: V 252 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9049 (tp) REVERT: V 267 THR cc_start: 0.9222 (m) cc_final: 0.8969 (p) REVERT: V 382 ILE cc_start: 0.9229 (mt) cc_final: 0.9029 (mt) REVERT: V 418 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8399 (mt-10) REVERT: W 246 GLN cc_start: 0.9029 (tt0) cc_final: 0.8719 (pt0) REVERT: W 269 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8634 (mm-40) REVERT: W 302 GLU cc_start: 0.7879 (tt0) cc_final: 0.7485 (tm-30) REVERT: W 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8286 (mt-10) REVERT: X 267 THR cc_start: 0.9084 (m) cc_final: 0.8775 (p) REVERT: X 418 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8399 (mt-10) REVERT: Y 267 THR cc_start: 0.9107 (m) cc_final: 0.8889 (p) REVERT: Y 418 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8336 (mt-10) REVERT: Z 267 THR cc_start: 0.9088 (m) cc_final: 0.8886 (p) REVERT: Z 299 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: Z 418 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8208 (mt-10) REVERT: a 267 THR cc_start: 0.9063 (m) cc_final: 0.8856 (p) REVERT: b 246 GLN cc_start: 0.9125 (tt0) cc_final: 0.8853 (pt0) REVERT: b 252 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9067 (tp) REVERT: b 267 THR cc_start: 0.9170 (m) cc_final: 0.8873 (p) REVERT: b 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7873 (tt0) REVERT: b 418 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8279 (mt-10) REVERT: c 246 GLN cc_start: 0.9033 (tt0) cc_final: 0.8773 (pt0) REVERT: c 267 THR cc_start: 0.9100 (m) cc_final: 0.8841 (p) REVERT: c 302 GLU cc_start: 0.7795 (tt0) cc_final: 0.7548 (tm-30) REVERT: c 418 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8253 (mt-10) REVERT: d 267 THR cc_start: 0.9114 (m) cc_final: 0.8871 (p) REVERT: d 418 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8248 (mt-10) REVERT: e 267 THR cc_start: 0.9108 (m) cc_final: 0.8858 (p) REVERT: e 418 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8213 (mt-10) REVERT: f 267 THR cc_start: 0.9136 (m) cc_final: 0.8875 (p) REVERT: f 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8221 (mt-10) REVERT: g 246 GLN cc_start: 0.9009 (tt0) cc_final: 0.8676 (pt0) REVERT: g 252 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9181 (tp) REVERT: g 267 THR cc_start: 0.9105 (m) cc_final: 0.8844 (p) REVERT: g 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8421 (mt-10) REVERT: h 246 GLN cc_start: 0.9088 (tt0) cc_final: 0.8805 (pt0) REVERT: h 252 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9129 (tp) REVERT: h 267 THR cc_start: 0.9113 (m) cc_final: 0.8870 (p) REVERT: h 302 GLU cc_start: 0.7769 (tt0) cc_final: 0.7458 (tm-30) REVERT: h 418 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 373 outliers final: 138 residues processed: 1570 average time/residue: 0.5706 time to fit residues: 1454.3072 Evaluate side-chains 1290 residues out of total 4794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1143 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 274 ASN Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 435 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 252 ILE Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 435 SER Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 252 ILE Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 274 ASN Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 435 SER Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 299 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 435 SER Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6673 > 50: distance: 47 - 152: 14.560 distance: 109 - 110: 7.179 distance: 110 - 111: 9.355 distance: 110 - 113: 18.288 distance: 111 - 112: 19.709 distance: 111 - 117: 6.208 distance: 113 - 114: 28.578 distance: 114 - 115: 11.261 distance: 115 - 116: 8.704 distance: 117 - 118: 21.955 distance: 118 - 121: 12.459 distance: 119 - 120: 3.112 distance: 119 - 125: 9.481 distance: 121 - 122: 16.701 distance: 122 - 123: 18.860 distance: 122 - 124: 12.970 distance: 125 - 126: 3.933 distance: 126 - 127: 5.094 distance: 126 - 129: 8.763 distance: 127 - 128: 5.971 distance: 127 - 132: 8.829 distance: 129 - 130: 10.467 distance: 129 - 131: 18.236 distance: 132 - 133: 26.604 distance: 134 - 135: 20.742 distance: 134 - 136: 16.012 distance: 136 - 137: 14.745 distance: 137 - 138: 12.020 distance: 137 - 140: 5.681 distance: 138 - 139: 24.315 distance: 138 - 144: 14.758 distance: 140 - 141: 24.570 distance: 141 - 142: 17.501 distance: 141 - 143: 4.378 distance: 144 - 145: 18.304 distance: 145 - 146: 24.621 distance: 145 - 148: 11.526 distance: 146 - 147: 7.184 distance: 146 - 152: 29.719 distance: 148 - 149: 18.259 distance: 148 - 150: 12.128 distance: 149 - 151: 25.689 distance: 152 - 153: 13.642 distance: 153 - 154: 33.000 distance: 153 - 156: 26.007 distance: 154 - 155: 18.994 distance: 154 - 161: 25.202 distance: 157 - 158: 36.468 distance: 158 - 159: 34.145 distance: 158 - 160: 4.359 distance: 161 - 162: 9.222 distance: 162 - 163: 9.333 distance: 162 - 165: 9.836 distance: 163 - 164: 25.608 distance: 163 - 172: 9.711 distance: 165 - 166: 23.679 distance: 166 - 167: 5.270 distance: 167 - 168: 5.663 distance: 168 - 169: 24.863 distance: 169 - 170: 16.157 distance: 169 - 171: 13.324 distance: 172 - 173: 10.108 distance: 173 - 174: 13.766 distance: 173 - 176: 12.478 distance: 174 - 175: 8.300 distance: 174 - 180: 14.068 distance: 175 - 222: 33.005 distance: 176 - 177: 12.938 distance: 177 - 178: 7.730 distance: 177 - 179: 17.668 distance: 180 - 181: 14.473 distance: 181 - 182: 7.945 distance: 181 - 184: 8.230 distance: 182 - 183: 12.052 distance: 182 - 186: 13.315 distance: 184 - 185: 16.358