Starting phenix.real_space_refine on Tue Jul 7 02:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zdu_60009/07_2026/8zdu_60009.map" } resolution = 4.6 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= 0.005 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 25942 2.51 5 N 7990 2.21 5 O 8534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1252 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1231 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 156, 1231 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 2 bond proxies already assigned to first conformer: 1220 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 Residues with excluded nonbonded symmetry interactions: 68 residue: pdb=" N AHIS A 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 281 " occ=0.50 residue: pdb=" N AARG A 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 373 " occ=0.50 residue: pdb=" N AHIS B 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 281 " occ=0.50 residue: pdb=" N AARG B 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 373 " occ=0.50 residue: pdb=" N AHIS C 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 281 " occ=0.50 residue: pdb=" N AARG C 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 373 " occ=0.50 residue: pdb=" N AHIS D 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 281 " occ=0.50 residue: pdb=" N AARG D 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 373 " occ=0.50 residue: pdb=" N AHIS E 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 281 " occ=0.50 residue: pdb=" N AARG E 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 373 " occ=0.50 residue: pdb=" N AHIS F 281 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 281 " occ=0.50 residue: pdb=" N AARG F 373 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 373 " occ=0.50 ... (remaining 56 not shown) Time building chain proxies: 4.42, per 1000 atoms: 0.10 Number of scatterers: 42568 At special positions: 0 Unit cell: (261, 263, 100, 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 8534 8.00 N 7990 7.00 C 25942 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: 3.48 Conformation dependent library (CDL) restraints added in 3.3 seconds 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10336 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 36 sheets defined 29.5% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 229 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 230 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 230 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'D' and resid 230 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 Processing helix chain 'E' and resid 230 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 Processing helix chain 'F' and resid 230 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 Processing helix chain 'G' and resid 230 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 Processing helix chain 'H' and resid 230 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 Processing helix chain 'I' and resid 230 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'J' and resid 230 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 Processing helix chain 'K' and resid 230 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 Processing helix chain 'L' and resid 230 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 Processing helix chain 'M' and resid 230 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 Processing helix chain 'N' and resid 230 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 Processing helix chain 'O' and resid 230 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 Processing helix chain 'P' and resid 230 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 Processing helix chain 'Q' and resid 230 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 Processing helix chain 'R' and resid 230 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 Processing helix chain 'S' and resid 230 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 Processing helix chain 'T' and resid 230 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 230 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 Processing helix chain 'V' and resid 230 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 Processing helix chain 'W' and resid 230 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 Processing helix chain 'X' and resid 230 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 Processing helix chain 'Y' and resid 230 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 Processing helix chain 'Z' and resid 230 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 Processing helix chain 'a' and resid 230 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 Processing helix chain 'b' and resid 230 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 Processing helix chain 'c' and resid 230 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 Processing helix chain 'd' and resid 230 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 Processing helix chain 'e' and resid 230 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 Processing helix chain 'f' and resid 230 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 Processing helix chain 'g' and resid 230 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 Processing helix chain 'h' and resid 230 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR A 429 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 385 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN A 431 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 387 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL A 433 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 389 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 303 removed outlier: 3.898A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR B 429 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 385 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN B 431 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 387 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL B 433 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 389 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 429 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU C 385 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN C 431 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 387 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL C 433 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 389 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR D 429 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU D 385 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN D 431 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 387 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL D 433 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 389 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR E 429 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU E 385 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN E 431 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 387 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL E 433 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 389 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR F 429 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU F 385 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN F 431 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 387 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL F 433 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 389 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR G 429 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU G 385 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN G 431 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL G 387 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL G 433 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL G 389 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR H 429 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU H 385 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN H 431 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL H 387 " --> pdb=" O ASN H 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL H 433 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL H 389 " --> pdb=" O VAL H 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR I 429 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU I 385 " --> pdb=" O THR I 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN I 431 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL I 387 " --> pdb=" O ASN I 431 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL I 433 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL I 389 " --> pdb=" O VAL I 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR J 429 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU J 385 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN J 431 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL J 387 " --> pdb=" O ASN J 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL J 433 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL J 389 " --> pdb=" O VAL J 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR K 429 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU K 385 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN K 431 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL K 387 " --> pdb=" O ASN K 431 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL K 433 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL K 389 " --> pdb=" O VAL K 433 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR L 429 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU L 385 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN L 431 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL L 387 " --> pdb=" O ASN L 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL L 433 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL L 389 " --> pdb=" O VAL L 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR M 429 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU M 385 " --> pdb=" O THR M 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN M 431 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL M 387 " --> pdb=" O ASN M 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL M 433 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL M 389 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR N 429 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU N 385 " --> pdb=" O THR N 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN N 431 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL N 387 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL N 433 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL N 389 " --> pdb=" O VAL N 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR O 429 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU O 385 " --> pdb=" O THR O 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN O 431 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL O 387 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL O 433 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL O 389 " --> pdb=" O VAL O 433 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR P 429 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU P 385 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN P 431 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL P 387 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL P 433 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL P 389 " --> pdb=" O VAL P 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR Q 429 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU Q 385 " --> pdb=" O THR Q 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN Q 431 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL Q 387 " --> pdb=" O ASN Q 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL Q 433 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL Q 389 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR R 429 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU R 385 " --> pdb=" O THR R 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN R 431 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL R 387 " --> pdb=" O ASN R 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL R 433 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL R 389 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR S 429 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU S 385 " --> pdb=" O THR S 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN S 431 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL S 387 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL S 433 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL S 389 " --> pdb=" O VAL S 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR T 429 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU T 385 " --> pdb=" O THR T 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN T 431 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL T 387 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL T 433 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL T 389 " --> pdb=" O VAL T 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR U 429 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU U 385 " --> pdb=" O THR U 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN U 431 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL U 387 " --> pdb=" O ASN U 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL U 433 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL U 389 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR V 429 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU V 385 " --> pdb=" O THR V 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN V 431 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL V 387 " --> pdb=" O ASN V 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL V 433 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL V 389 " --> pdb=" O VAL V 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR W 429 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU W 385 " --> pdb=" O THR W 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN W 431 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL W 387 " --> pdb=" O ASN W 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL W 433 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL W 389 " --> pdb=" O VAL W 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR X 429 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 385 " --> pdb=" O THR X 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN X 431 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL X 387 " --> pdb=" O ASN X 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL X 433 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL X 389 " --> pdb=" O VAL X 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR Y 429 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU Y 385 " --> pdb=" O THR Y 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN Y 431 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL Y 387 " --> pdb=" O ASN Y 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL Y 433 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL Y 389 " --> pdb=" O VAL Y 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR Z 429 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU Z 385 " --> pdb=" O THR Z 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN Z 431 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL Z 387 " --> pdb=" O ASN Z 431 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL Z 433 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL Z 389 " --> pdb=" O VAL Z 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR a 429 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU a 385 " --> pdb=" O THR a 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN a 431 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL a 387 " --> pdb=" O ASN a 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL a 433 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL a 389 " --> pdb=" O VAL a 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR b 429 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU b 385 " --> pdb=" O THR b 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN b 431 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL b 387 " --> pdb=" O ASN b 431 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL b 433 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL b 389 " --> pdb=" O VAL b 433 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR c 429 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU c 385 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN c 431 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL c 387 " --> pdb=" O ASN c 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL c 433 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL c 389 " --> pdb=" O VAL c 433 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR d 429 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU d 385 " --> pdb=" O THR d 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN d 431 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL d 387 " --> pdb=" O ASN d 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL d 433 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL d 389 " --> pdb=" O VAL d 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR e 429 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU e 385 " --> pdb=" O THR e 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN e 431 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL e 387 " --> pdb=" O ASN e 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL e 433 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL e 389 " --> pdb=" O VAL e 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR f 429 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU f 385 " --> pdb=" O THR f 429 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN f 431 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL f 387 " --> pdb=" O ASN f 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL f 433 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL f 389 " --> pdb=" O VAL f 433 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR g 429 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU g 385 " --> pdb=" O THR g 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN g 431 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL g 387 " --> pdb=" O ASN g 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL g 433 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL g 389 " --> pdb=" O VAL g 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.875A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP h 381 " --> pdb=" O ASP h 271 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR h 429 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU h 385 " --> pdb=" O THR h 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN h 431 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL h 387 " --> pdb=" O ASN h 431 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL h 433 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL h 389 " --> pdb=" O VAL h 433 " (cutoff:3.500A) 2483 hydrogen bonds defined for protein. 7177 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: 10.19 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15368 1.34 - 1.46: 5862 1.46 - 1.57: 21678 1.57 - 1.69: 0 1.69 - 1.80: 204 Bond restraints: 43112 Sorted by residual: bond pdb=" C VAL d 257 " pdb=" N GLY d 258 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.91e-01 bond pdb=" C VAL M 257 " pdb=" N GLY M 258 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.91e-01 bond pdb=" C VAL Y 257 " pdb=" N GLY Y 258 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.89e-01 bond pdb=" C VAL H 257 " pdb=" N GLY H 258 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.89e-01 bond pdb=" C VAL B 257 " pdb=" N GLY B 258 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.72e-01 ... (remaining 43107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 57274 1.21 - 2.42: 667 2.42 - 3.63: 199 3.63 - 4.84: 34 4.84 - 6.05: 68 Bond angle restraints: 58242 Sorted by residual: angle pdb=" CA LYS Z 236 " pdb=" CB LYS Z 236 " pdb=" CG LYS Z 236 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 angle pdb=" CA LYS C 236 " pdb=" CB LYS C 236 " pdb=" CG LYS C 236 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA LYS T 236 " pdb=" CB LYS T 236 " pdb=" CG LYS T 236 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA LYS Q 236 " pdb=" CB LYS Q 236 " pdb=" CG LYS Q 236 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA LYS h 236 " pdb=" CB LYS h 236 " pdb=" CG LYS h 236 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 ... (remaining 58237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 23392 17.08 - 34.17: 2180 34.17 - 51.25: 1084 51.25 - 68.34: 272 68.34 - 85.42: 34 Dihedral angle restraints: 26962 sinusoidal: 11186 harmonic: 15776 Sorted by residual: dihedral pdb=" CA ASN e 361 " pdb=" CB ASN e 361 " pdb=" CG ASN e 361 " pdb=" OD1 ASN e 361 " ideal model delta sinusoidal sigma weight residual 120.00 -173.04 -66.96 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN N 361 " pdb=" CB ASN N 361 " pdb=" CG ASN N 361 " pdb=" OD1 ASN N 361 " ideal model delta sinusoidal sigma weight residual 120.00 -173.04 -66.96 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN F 361 " pdb=" CB ASN F 361 " pdb=" CG ASN F 361 " pdb=" OD1 ASN F 361 " ideal model delta sinusoidal sigma weight residual 120.00 -173.05 -66.95 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 26959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 4030 0.024 - 0.049: 1622 0.049 - 0.073: 504 0.073 - 0.098: 144 0.098 - 0.122: 364 Chirality restraints: 6664 Sorted by residual: chirality pdb=" CA ILE D 372 " pdb=" N ILE D 372 " pdb=" C ILE D 372 " pdb=" CB ILE D 372 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE U 372 " pdb=" N ILE U 372 " pdb=" C ILE U 372 " pdb=" CB ILE U 372 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE E 372 " pdb=" N ILE E 372 " pdb=" C ILE E 372 " pdb=" CB ILE E 372 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 6661 not shown) Planarity restraints: 7820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER X 254 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.14e-01 pdb=" N PRO X 255 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 254 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO F 255 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO F 255 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 255 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 254 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.13e-01 pdb=" N PRO W 255 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO W 255 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO W 255 " 0.012 5.00e-02 4.00e+02 ... (remaining 7817 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 15912 2.91 - 3.41: 36011 3.41 - 3.90: 66590 3.90 - 4.40: 72363 4.40 - 4.90: 133956 Nonbonded interactions: 324832 Sorted by model distance: nonbonded pdb=" OD1 ASN F 392 " pdb=" N TYR F 393 " model vdw 2.411 3.120 nonbonded pdb=" OD1 ASN W 392 " pdb=" N TYR W 393 " model vdw 2.411 3.120 nonbonded pdb=" OD1 ASN Y 392 " pdb=" N TYR Y 393 " model vdw 2.411 3.120 nonbonded pdb=" OD1 ASN L 392 " pdb=" N TYR L 393 " model vdw 2.411 3.120 nonbonded pdb=" OD1 ASN c 392 " pdb=" N TYR c 393 " model vdw 2.411 3.120 ... (remaining 324827 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: 0.17 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 Number of NCS constrained groups: 1 pdb_interpretation.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 refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 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: 6.320 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: 0.060 Extract box with map and model: 0.990 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 38.370 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 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 : 0.001 0.012 43112 Z= 0.085 Angle : 0.447 6.052 58242 Z= 0.247 Chirality : 0.037 0.122 6664 Planarity : 0.002 0.021 7820 Dihedral : 17.005 85.423 16626 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.04 % Allowed : 22.65 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.12), residues: 5304 helix: 4.68 (0.12), residues: 1428 sheet: 2.75 (0.10), residues: 2686 loop : -1.10 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG e 244 TYR 0.004 0.001 TYR g 282 PHE 0.007 0.001 PHE S 237 HIS 0.001 0.000 HIS f 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00145 / 0.09 (43112) covalent geometry : angle 0.44698 / 0.25 (58242) hydrogen bonds : bond 0.15924 / 10.72 ( 2483) hydrogen bonds : angle 4.97585 / 3.66 ( 7177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.062 Fit side-chains REVERT: A 276 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7599 (mt-10) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0843 time to fit residues: 2.7586 Evaluate side-chains 30 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.0770 chunk 388 optimal weight: 0.4980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 494 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 ASN A 361 ASN A 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103288 restraints weight = 99780.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107294 restraints weight = 13577.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.100157 restraints weight = 42427.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100052 restraints weight = 19128.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099673 restraints weight = 51715.692| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 43112 Z= 0.099 Angle : 0.450 4.915 58242 Z= 0.250 Chirality : 0.038 0.118 6664 Planarity : 0.002 0.017 7820 Dihedral : 3.448 12.407 5882 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.09 (0.12), residues: 5304 helix: 5.02 (0.13), residues: 1428 sheet: 2.80 (0.10), residues: 2686 loop : -0.98 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 426 TYR 0.014 0.002 TYR K 393 PHE 0.009 0.001 PHE O 422 HIS 0.005 0.002 HIS J 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.10 (43112) covalent geometry : angle 0.45039 / 0.25 (58242) hydrogen bonds : bond 0.04642 / 3.14 ( 2483) hydrogen bonds : angle 3.85634 / 2.83 ( 7177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0797 time to fit residues: 2.8788 Evaluate side-chains 28 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 470 optimal weight: 5.9990 chunk 401 optimal weight: 0.0980 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 495 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 0.6980 chunk 456 optimal weight: 1.9990 chunk 464 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.097886 restraints weight = 65843.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097875 restraints weight = 84339.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097576 restraints weight = 35776.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098130 restraints weight = 20949.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.097123 restraints weight = 74101.026| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 43112 Z= 0.091 Angle : 0.419 4.830 58242 Z= 0.233 Chirality : 0.037 0.115 6664 Planarity : 0.002 0.017 7820 Dihedral : 3.397 12.723 5882 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 3.97 (0.11), residues: 5304 helix: 4.82 (0.12), residues: 1428 sheet: 2.72 (0.09), residues: 2686 loop : -0.87 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG h 247 TYR 0.005 0.001 TYR O 282 PHE 0.007 0.001 PHE e 422 HIS 0.003 0.001 HIS O 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00152 / 0.09 (43112) covalent geometry : angle 0.41865 / 0.23 (58242) hydrogen bonds : bond 0.04524 / 3.06 ( 2483) hydrogen bonds : angle 3.64179 / 2.67 ( 7177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.050 Fit side-chains REVERT: g 279 GLU cc_start: 0.5464 (mt-10) cc_final: 0.4834 (mt-10) REVERT: g 297 GLN cc_start: 0.6777 (tt0) cc_final: 0.6335 (tt0) REVERT: g 362 GLU cc_start: 0.7192 (tt0) cc_final: 0.6898 (tt0) REVERT: g 420 MET cc_start: 0.4210 (ptm) cc_final: 0.3940 (ptm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0873 time to fit residues: 3.1196 Evaluate side-chains 31 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 258 optimal weight: 0.0970 chunk 71 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 386 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 409 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 505 optimal weight: 8.9990 chunk 465 optimal weight: 10.0000 chunk 272 optimal weight: 0.2980 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103464 restraints weight = 103341.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102934 restraints weight = 14750.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.099849 restraints weight = 44433.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100057 restraints weight = 38444.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.099890 restraints weight = 30712.364| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 43112 Z= 0.081 Angle : 0.403 4.736 58242 Z= 0.223 Chirality : 0.037 0.118 6664 Planarity : 0.002 0.016 7820 Dihedral : 3.330 11.462 5882 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 4.03 (0.11), residues: 5304 helix: 4.90 (0.12), residues: 1428 sheet: 2.77 (0.10), residues: 2686 loop : -0.90 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 294 TYR 0.004 0.001 TYR I 282 PHE 0.007 0.001 PHE J 422 HIS 0.001 0.000 HIS Q 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00134 / 0.08 (43112) covalent geometry : angle 0.40346 / 0.22 (58242) hydrogen bonds : bond 0.03703 / 2.51 ( 2483) hydrogen bonds : angle 3.46502 / 2.53 ( 7177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.055 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0890 time to fit residues: 2.9907 Evaluate side-chains 24 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 503 optimal weight: 2.9990 chunk 361 optimal weight: 0.9980 chunk 414 optimal weight: 2.9990 chunk 308 optimal weight: 0.0570 chunk 461 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 373 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 460 optimal weight: 6.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099181 restraints weight = 82370.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.097712 restraints weight = 19806.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096839 restraints weight = 98294.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.096615 restraints weight = 20172.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.095838 restraints weight = 91231.285| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5611 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 43112 Z= 0.086 Angle : 0.402 4.808 58242 Z= 0.222 Chirality : 0.037 0.110 6664 Planarity : 0.002 0.015 7820 Dihedral : 3.315 11.755 5882 Min Nonbonded Distance : 2.704 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.08 (0.11), residues: 5304 helix: 4.88 (0.12), residues: 1428 sheet: 2.80 (0.09), residues: 2686 loop : -0.81 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 247 TYR 0.005 0.001 TYR W 282 PHE 0.007 0.001 PHE S 422 HIS 0.000 0.000 HIS M 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00143 / 0.09 (43112) covalent geometry : angle 0.40181 / 0.22 (58242) hydrogen bonds : bond 0.04040 / 2.73 ( 2483) hydrogen bonds : angle 3.47479 / 2.55 ( 7177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.051 Fit side-chains REVERT: P 420 MET cc_start: 0.4467 (ptm) cc_final: 0.4156 (ptm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0920 time to fit residues: 2.9878 Evaluate side-chains 28 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 435 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 169 optimal weight: 0.0770 chunk 241 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 312 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098861 restraints weight = 101468.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.099051 restraints weight = 29569.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.097435 restraints weight = 14601.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094958 restraints weight = 41198.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095377 restraints weight = 34363.995| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 43112 Z= 0.105 Angle : 0.438 4.770 58242 Z= 0.245 Chirality : 0.037 0.108 6664 Planarity : 0.002 0.016 7820 Dihedral : 3.526 13.579 5882 Min Nonbonded Distance : 2.701 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.07 (0.11), residues: 5304 helix: 4.84 (0.12), residues: 1428 sheet: 2.78 (0.09), residues: 2686 loop : -0.72 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 426 TYR 0.013 0.002 TYR b 393 PHE 0.008 0.001 PHE J 422 HIS 0.001 0.000 HIS Y 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.11 (43112) covalent geometry : angle 0.43755 / 0.25 (58242) hydrogen bonds : bond 0.04970 / 3.36 ( 2483) hydrogen bonds : angle 3.52975 / 2.59 ( 7177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.052 Fit side-chains REVERT: g 279 GLU cc_start: 0.5739 (mt-10) cc_final: 0.5369 (mt-10) REVERT: g 297 GLN cc_start: 0.6712 (tt0) cc_final: 0.6479 (tp40) REVERT: g 381 ASP cc_start: 0.6949 (m-30) cc_final: 0.6647 (m-30) REVERT: g 420 MET cc_start: 0.3915 (ptm) cc_final: 0.3547 (ptm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0823 time to fit residues: 2.8695 Evaluate side-chains 32 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 467 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 494 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 443 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097867 restraints weight = 114253.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098257 restraints weight = 14343.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096037 restraints weight = 81431.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.095314 restraints weight = 36102.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.094870 restraints weight = 21701.904| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 43112 Z= 0.097 Angle : 0.423 4.743 58242 Z= 0.237 Chirality : 0.037 0.111 6664 Planarity : 0.002 0.017 7820 Dihedral : 3.495 13.189 5882 Min Nonbonded Distance : 2.700 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 4.01 (0.11), residues: 5304 helix: 4.86 (0.12), residues: 1428 sheet: 2.72 (0.09), residues: 2686 loop : -0.77 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 247 TYR 0.006 0.001 TYR h 282 PHE 0.008 0.001 PHE A 422 HIS 0.001 0.000 HIS O 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.10 (43112) covalent geometry : angle 0.42278 / 0.24 (58242) hydrogen bonds : bond 0.04741 / 3.20 ( 2483) hydrogen bonds : angle 3.50117 / 2.56 ( 7177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.049 Fit side-chains REVERT: M 362 GLU cc_start: 0.6943 (tt0) cc_final: 0.6667 (tt0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1044 time to fit residues: 2.9178 Evaluate side-chains 23 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 470 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 468 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 368 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 204 optimal weight: 0.0270 chunk 363 optimal weight: 0.0030 chunk 422 optimal weight: 0.0170 chunk 401 optimal weight: 0.0770 overall best weight: 0.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100725 restraints weight = 101367.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102025 restraints weight = 15364.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098393 restraints weight = 36197.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098024 restraints weight = 82136.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.097770 restraints weight = 30834.246| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 43112 Z= 0.076 Angle : 0.390 4.682 58242 Z= 0.214 Chirality : 0.037 0.115 6664 Planarity : 0.002 0.020 7820 Dihedral : 3.377 11.414 5882 Min Nonbonded Distance : 2.702 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.12 (0.11), residues: 5304 helix: 4.92 (0.12), residues: 1428 sheet: 2.82 (0.09), residues: 2686 loop : -0.76 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 247 TYR 0.003 0.001 TYR J 282 PHE 0.009 0.001 PHE H 422 HIS 0.000 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00128 / 0.08 (43112) covalent geometry : angle 0.39047 / 0.21 (58242) hydrogen bonds : bond 0.03303 / 2.24 ( 2483) hydrogen bonds : angle 3.33076 / 2.43 ( 7177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1136 time to fit residues: 3.5210 Evaluate side-chains 24 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 342 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 423 optimal weight: 3.9990 chunk 444 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 373 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101177 restraints weight = 115377.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100839 restraints weight = 17843.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100582 restraints weight = 75621.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100743 restraints weight = 13653.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.099759 restraints weight = 74997.900| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43112 Z= 0.116 Angle : 0.470 4.788 58242 Z= 0.259 Chirality : 0.038 0.129 6664 Planarity : 0.002 0.016 7820 Dihedral : 3.558 13.618 5882 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.11 (0.11), residues: 5304 helix: 5.03 (0.12), residues: 1428 sheet: 2.75 (0.09), residues: 2686 loop : -0.78 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 426 TYR 0.004 0.001 TYR P 282 PHE 0.009 0.001 PHE H 422 HIS 0.001 0.000 HIS T 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (43112) covalent geometry : angle 0.47014 / 0.26 (58242) hydrogen bonds : bond 0.05249 / 3.55 ( 2483) hydrogen bonds : angle 3.48636 / 2.56 ( 7177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.052 Fit side-chains REVERT: A 276 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 356 ARG cc_start: 0.6218 (mtm110) cc_final: 0.5959 (ttp80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0966 time to fit residues: 2.7249 Evaluate side-chains 24 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 360 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 469 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 113 optimal weight: 0.0970 chunk 122 optimal weight: 0.5980 chunk 411 optimal weight: 2.9990 chunk 495 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098413 restraints weight = 99979.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098187 restraints weight = 49526.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100097 restraints weight = 19895.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097223 restraints weight = 48060.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096591 restraints weight = 121554.443| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 43112 Z= 0.100 Angle : 0.447 4.741 58242 Z= 0.247 Chirality : 0.038 0.126 6664 Planarity : 0.002 0.017 7820 Dihedral : 3.571 12.906 5882 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 4.04 (0.11), residues: 5304 helix: 4.91 (0.12), residues: 1428 sheet: 2.72 (0.09), residues: 2686 loop : -0.75 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 426 TYR 0.005 0.001 TYR N 282 PHE 0.008 0.001 PHE M 422 HIS 0.001 0.000 HIS M 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.10 (43112) covalent geometry : angle 0.44693 / 0.25 (58242) hydrogen bonds : bond 0.04825 / 3.26 ( 2483) hydrogen bonds : angle 3.47298 / 2.54 ( 7177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10608 Ramachandran restraints generated. 5304 Oldfield, 0 Emsley, 5304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.062 Fit side-chains REVERT: d 279 GLU cc_start: 0.5225 (mt-10) cc_final: 0.5009 (mt-10) REVERT: d 356 ARG cc_start: 0.5981 (mtm110) cc_final: 0.5564 (ttp80) REVERT: d 362 GLU cc_start: 0.6884 (tt0) cc_final: 0.6678 (tt0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0881 time to fit residues: 2.7879 Evaluate side-chains 25 residues out of total 137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 411 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 508 optimal weight: 6.9990 chunk 163 optimal weight: 0.0170 chunk 448 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 477 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094730 restraints weight = 72161.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.094730 restraints weight = 23853.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093729 restraints weight = 85007.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.093426 restraints weight = 27709.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.093398 restraints weight = 37624.228| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 43112 Z= 0.136 Angle : 0.505 4.825 58242 Z= 0.280 Chirality : 0.038 0.111 6664 Planarity : 0.002 0.018 7820 Dihedral : 3.731 13.588 5882 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.72 (0.11), residues: 5304 helix: 4.73 (0.12), residues: 1428 sheet: 2.46 (0.09), residues: 2686 loop : -0.85 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 426 TYR 0.006 0.001 TYR P 282 PHE 0.009 0.002 PHE J 422 HIS 0.001 0.000 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (43112) covalent geometry : angle 0.50504 / 0.28 (58242) hydrogen bonds : bond 0.06166 / 4.16 ( 2483) hydrogen bonds : angle 3.56740 / 2.61 ( 7177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.45 seconds wall clock time: 52 minutes 36.75 seconds (3156.75 seconds total)