Starting phenix.real_space_refine on Tue Aug 26 21:10:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdz_17627/08_2025/8pdz_17627.map" } resolution = 3.32 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= 0.004 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 252 5.16 5 C 13804 2.51 5 N 3640 2.21 5 O 4592 1.98 5 H 20272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42560 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1520 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Restraints were copied for chains: Q, P, O, U, T, S, V, W, X, Y, Z, a, b, H, I, J, K, L, M, N, A, B, C, D, E, F, G Time building chain proxies: 3.34, per 1000 atoms: 0.08 Number of scatterers: 42560 At special positions: 0 Unit cell: (87.86, 89.388, 220.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 252 16.00 O 4592 8.00 N 3640 7.00 C 13804 6.00 H 20272 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=77, symmetry=0 Simple disulfide: pdb=" SG CYS R 8 " - pdb=" SG CYS L 21 " distance=2.01 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS S 15 " distance=2.18 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS Q 14 " distance=1.83 Simple disulfide: pdb=" SG CYS R 21 " - pdb=" SG CYS X 8 " distance=2.43 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS S 82 " distance=2.05 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS Q 22 " distance=2.26 Simple disulfide: pdb=" SG CYS Q 8 " - pdb=" SG CYS K 21 " distance=2.27 Simple disulfide: pdb=" SG CYS P 8 " - pdb=" SG CYS J 21 " distance=1.90 Simple disulfide: pdb=" SG CYS O 8 " - pdb=" SG CYS I 21 " distance=2.16 Simple disulfide: pdb=" SG CYS U 8 " - pdb=" SG CYS H 21 " distance=2.25 Simple disulfide: pdb=" SG CYS T 8 " - pdb=" SG CYS N 21 " distance=1.76 Simple disulfide: pdb=" SG CYS S 8 " - pdb=" SG CYS M 21 " distance=2.07 Simple disulfide: pdb=" SG CYS V 8 " - pdb=" SG CYS P 21 " distance=1.98 Simple disulfide: pdb=" SG CYS W 8 " - pdb=" SG CYS Q 21 " distance=1.86 Simple disulfide: pdb=" SG CYS Y 8 " - pdb=" SG CYS S 21 " distance=2.14 Simple disulfide: pdb=" SG CYS Z 8 " - pdb=" SG CYS T 21 " distance=2.00 Simple disulfide: pdb=" SG CYS a 8 " - pdb=" SG CYS U 21 " distance=2.12 Simple disulfide: pdb=" SG CYS b 8 " - pdb=" SG CYS O 21 " distance=2.09 Simple disulfide: pdb=" SG CYS H 8 " - pdb=" SG CYS B 21 " distance=1.91 Simple disulfide: pdb=" SG CYS I 8 " - pdb=" SG CYS C 21 " distance=2.19 Simple disulfide: pdb=" SG CYS J 8 " - pdb=" SG CYS D 21 " distance=1.89 Simple disulfide: pdb=" SG CYS K 8 " - pdb=" SG CYS E 21 " distance=1.92 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS F 21 " distance=2.20 Simple disulfide: pdb=" SG CYS M 8 " - pdb=" SG CYS G 21 " distance=1.64 Simple disulfide: pdb=" SG CYS N 8 " - pdb=" SG CYS A 21 " distance=1.89 Simple disulfide: pdb=" SG CYS P 14 " - pdb=" SG CYS Q 15 " distance=2.06 Simple disulfide: pdb=" SG CYS O 14 " - pdb=" SG CYS P 15 " distance=2.19 Simple disulfide: pdb=" SG CYS U 14 " - pdb=" SG CYS O 15 " distance=1.97 Simple disulfide: pdb=" SG CYS T 14 " - pdb=" SG CYS U 15 " distance=1.97 Simple disulfide: pdb=" SG CYS S 14 " - pdb=" SG CYS T 15 " distance=2.07 Simple disulfide: pdb=" SG CYS V 14 " - pdb=" SG CYS W 15 " distance=2.03 Simple disulfide: pdb=" SG CYS W 14 " - pdb=" SG CYS X 15 " distance=2.04 Simple disulfide: pdb=" SG CYS X 14 " - pdb=" SG CYS Y 15 " distance=2.18 Simple disulfide: pdb=" SG CYS Y 14 " - pdb=" SG CYS Z 15 " distance=1.86 Simple disulfide: pdb=" SG CYS Z 14 " - pdb=" SG CYS a 15 " distance=1.80 Simple disulfide: pdb=" SG CYS a 14 " - pdb=" SG CYS b 15 " distance=1.84 Simple disulfide: pdb=" SG CYS b 14 " - pdb=" SG CYS V 15 " distance=1.93 Simple disulfide: pdb=" SG CYS H 14 " - pdb=" SG CYS I 15 " distance=2.11 Simple disulfide: pdb=" SG CYS I 14 " - pdb=" SG CYS J 15 " distance=2.36 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS K 15 " distance=2.00 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS L 15 " distance=2.26 Simple disulfide: pdb=" SG CYS L 14 " - pdb=" SG CYS M 15 " distance=1.99 Simple disulfide: pdb=" SG CYS M 14 " - pdb=" SG CYS N 15 " distance=1.74 Simple disulfide: pdb=" SG CYS N 14 " - pdb=" SG CYS H 15 " distance=1.95 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 15 " distance=1.98 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS C 15 " distance=2.28 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 15 " distance=2.66 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS E 15 " distance=2.05 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 15 " distance=1.73 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS G 15 " distance=2.05 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS A 15 " distance=1.84 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS Q 82 " distance=1.92 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS P 82 " distance=1.82 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS O 82 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS U 82 " distance=2.12 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS T 82 " distance=1.84 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS W 82 " distance=1.86 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS X 82 " distance=2.08 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS Y 82 " distance=2.06 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Z 82 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS a 82 " distance=2.13 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS b 82 " distance=2.27 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS V 82 " distance=1.94 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS I 82 " distance=1.77 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS J 82 " distance=1.71 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS K 82 " distance=2.18 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS L 82 " distance=1.71 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS M 82 " distance=1.93 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS N 82 " distance=2.46 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS H 82 " distance=2.28 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS B 82 " distance=2.16 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS C 82 " distance=1.87 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS D 82 " distance=1.80 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS E 82 " distance=1.95 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS F 82 " distance=2.33 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS G 82 " distance=1.87 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS A 82 " distance=2.49 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: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 54.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'R' and resid 4 through 5 removed outlier: 3.767A pdb=" N THR L 48 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU L 81 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N LEU K 34 " --> pdb=" O CYS L 82 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N SER L 84 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE K 36 " --> pdb=" O SER L 84 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR L 86 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP K 38 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N ASN L 88 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE K 93 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 65 " --> pdb=" O PHE K 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE K 75 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL K 67 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 73 " --> pdb=" O VAL K 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY Q 73 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL Q 67 " --> pdb=" O GLY Q 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE Q 75 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 65 " --> pdb=" O PHE Q 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Q 93 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS R 82 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE Q 36 " --> pdb=" O CYS R 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU R 81 " --> pdb=" O ASN R 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR R 48 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE X 5 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA R 19 " --> pdb=" O ILE X 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY R 73 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL R 67 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE R 75 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 65 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE R 93 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N LEU R 34 " --> pdb=" O CYS S 82 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N SER S 84 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE R 36 " --> pdb=" O SER S 84 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR S 86 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP R 38 " --> pdb=" O THR S 86 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N ASN S 88 " --> pdb=" O ASP R 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU S 81 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR S 48 " --> pdb=" O SER S 110 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE Y 5 " --> pdb=" O ASN S 17 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA S 19 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.700A pdb=" N CYS K 21 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR K 48 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU K 81 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU J 34 " --> pdb=" O CYS K 82 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N SER K 84 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE J 36 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR K 86 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP J 38 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N ASN K 88 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE J 93 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 65 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE J 75 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL J 67 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY J 73 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY P 73 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL P 67 " --> pdb=" O GLY P 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE P 75 " --> pdb=" O LEU P 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU P 65 " --> pdb=" O PHE P 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE P 93 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N CYS Q 82 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE P 36 " --> pdb=" O CYS Q 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 81 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR Q 48 " --> pdb=" O SER Q 110 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE W 5 " --> pdb=" O ASN Q 17 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA Q 19 " --> pdb=" O ILE W 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 4 through 5 removed outlier: 3.556A pdb=" N CYS J 21 " --> pdb=" O ILE P 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR J 48 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU J 81 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU I 34 " --> pdb=" O CYS J 82 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER J 84 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE I 36 " --> pdb=" O SER J 84 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR J 86 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP I 38 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN J 88 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE I 93 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 65 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE I 75 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL I 67 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY I 73 " --> pdb=" O VAL I 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY O 73 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL O 67 " --> pdb=" O GLY O 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE O 75 " --> pdb=" O LEU O 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU O 65 " --> pdb=" O PHE O 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE O 93 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N CYS P 82 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE O 36 " --> pdb=" O CYS P 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP O 38 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR P 86 " --> pdb=" O ASP O 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 81 " --> pdb=" O ASN P 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR P 48 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE V 5 " --> pdb=" O ASN P 17 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA P 19 " --> pdb=" O ILE V 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.516A pdb=" N CYS I 21 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR I 48 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 81 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LEU H 34 " --> pdb=" O CYS I 82 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N SER I 84 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE H 36 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR I 86 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP H 38 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ASN I 88 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 93 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 65 " --> pdb=" O PHE H 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE H 75 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL H 67 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 73 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY U 73 " --> pdb=" O VAL U 67 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL U 67 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE U 75 " --> pdb=" O LEU U 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU U 65 " --> pdb=" O PHE U 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE U 93 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS O 82 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE U 36 " --> pdb=" O CYS O 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP U 38 " --> pdb=" O SER O 84 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR O 86 " --> pdb=" O ASP U 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU O 81 " --> pdb=" O ASN O 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR O 48 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE b 5 " --> pdb=" O ASN O 17 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA O 19 " --> pdb=" O ILE b 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 4 through 5 removed outlier: 3.542A pdb=" N CYS H 21 " --> pdb=" O ILE U 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR H 48 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU H 81 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N CYS H 82 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE N 36 " --> pdb=" O CYS H 82 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE N 93 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 65 " --> pdb=" O PHE N 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE N 75 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL N 67 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY N 73 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY T 73 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL T 67 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE T 75 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 65 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE T 93 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N CYS U 82 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE T 36 " --> pdb=" O CYS U 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP T 38 " --> pdb=" O SER U 84 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR U 86 " --> pdb=" O ASP T 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU U 81 " --> pdb=" O ASN U 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR U 48 " --> pdb=" O SER U 110 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE a 5 " --> pdb=" O ASN U 17 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA U 19 " --> pdb=" O ILE a 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 4 through 5 removed outlier: 3.658A pdb=" N CYS N 21 " --> pdb=" O ILE T 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR N 48 " --> pdb=" O SER N 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU N 81 " --> pdb=" O ASN N 53 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LEU M 34 " --> pdb=" O CYS N 82 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N SER N 84 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE M 36 " --> pdb=" O SER N 84 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR N 86 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP M 38 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N ASN N 88 " --> pdb=" O ASP M 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE M 93 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU M 65 " --> pdb=" O PHE M 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE M 75 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL M 67 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY M 73 " --> pdb=" O VAL M 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY S 73 " --> pdb=" O VAL S 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL S 67 " --> pdb=" O GLY S 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE S 75 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU S 65 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE S 93 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N CYS T 82 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE S 36 " --> pdb=" O CYS T 82 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP S 38 " --> pdb=" O SER T 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR T 86 " --> pdb=" O ASP S 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU T 81 " --> pdb=" O ASN T 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR T 48 " --> pdb=" O SER T 110 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE Z 5 " --> pdb=" O ASN T 17 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA T 19 " --> pdb=" O ILE Z 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.535A pdb=" N CYS M 21 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR M 48 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU M 81 " --> pdb=" O ASN M 53 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LEU L 34 " --> pdb=" O CYS M 82 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N SER M 84 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE L 36 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR M 86 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP L 38 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ASN M 88 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE L 93 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 65 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE L 75 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL L 67 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 73 " --> pdb=" O VAL L 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'V' and resid 14 through 26 removed outlier: 3.768A pdb=" N THR V 48 " --> pdb=" O SER V 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU V 81 " --> pdb=" O ASN V 53 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N CYS V 82 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE b 36 " --> pdb=" O CYS V 82 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE b 93 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU b 65 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE b 75 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL b 67 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY b 73 " --> pdb=" O VAL b 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY V 73 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL V 67 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE V 75 " --> pdb=" O LEU V 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU V 65 " --> pdb=" O PHE V 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE V 93 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LEU V 34 " --> pdb=" O CYS W 82 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N SER W 84 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE V 36 " --> pdb=" O SER W 84 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR W 86 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP V 38 " --> pdb=" O THR W 86 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N ASN W 88 " --> pdb=" O ASP V 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU W 81 " --> pdb=" O ASN W 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR W 48 " --> pdb=" O SER W 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY W 73 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL W 67 " --> pdb=" O GLY W 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE W 75 " --> pdb=" O LEU W 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU W 65 " --> pdb=" O PHE W 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE W 93 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU W 34 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N SER X 84 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE W 36 " --> pdb=" O SER X 84 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR X 86 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP W 38 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N ASN X 88 " --> pdb=" O ASP W 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 81 " --> pdb=" O ASN X 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR X 48 " --> pdb=" O SER X 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY X 73 " --> pdb=" O VAL X 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL X 67 " --> pdb=" O GLY X 73 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE X 75 " --> pdb=" O LEU X 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU X 65 " --> pdb=" O PHE X 75 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE X 93 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LEU X 34 " --> pdb=" O CYS Y 82 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N SER Y 84 " --> pdb=" O LEU X 34 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE X 36 " --> pdb=" O SER Y 84 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR Y 86 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASP X 38 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ASN Y 88 " --> pdb=" O ASP X 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Y 81 " --> pdb=" O ASN Y 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR Y 48 " --> pdb=" O SER Y 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 70 through 77 removed outlier: 8.691A pdb=" N GLY Y 73 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE Y 75 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Y 65 " --> pdb=" O PHE Y 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Y 93 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU Y 34 " --> pdb=" O CYS Z 82 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N SER Z 84 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE Y 36 " --> pdb=" O SER Z 84 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N THR Z 86 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP Y 38 " --> pdb=" O THR Z 86 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N ASN Z 88 " --> pdb=" O ASP Y 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Z 81 " --> pdb=" O ASN Z 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR Z 48 " --> pdb=" O SER Z 110 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY Z 73 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL Z 67 " --> pdb=" O GLY Z 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE Z 75 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Z 65 " --> pdb=" O PHE Z 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE Z 93 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU Z 34 " --> pdb=" O CYS a 82 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N SER a 84 " --> pdb=" O LEU Z 34 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE Z 36 " --> pdb=" O SER a 84 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR a 86 " --> pdb=" O ILE Z 36 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP Z 38 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N ASN a 88 " --> pdb=" O ASP Z 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU a 81 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR a 48 " --> pdb=" O SER a 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 70 through 77 removed outlier: 8.690A pdb=" N GLY a 73 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL a 67 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE a 75 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU a 65 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE a 93 " --> pdb=" O ILE a 36 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N LEU a 34 " --> pdb=" O CYS b 82 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N SER b 84 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE a 36 " --> pdb=" O SER b 84 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR b 86 " --> pdb=" O ILE a 36 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP a 38 " --> pdb=" O THR b 86 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N ASN b 88 " --> pdb=" O ASP a 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU b 81 " --> pdb=" O ASN b 53 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR b 48 " --> pdb=" O SER b 110 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.707A pdb=" N CYS B 21 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 48 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 81 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N LEU A 34 " --> pdb=" O CYS B 82 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N SER B 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 36 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR B 86 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 38 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N ASN B 88 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 93 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 65 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 75 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL A 67 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY A 73 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.767A pdb=" N THR C 48 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 81 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N LEU B 34 " --> pdb=" O CYS C 82 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N SER C 84 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 36 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR C 86 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 38 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ASN C 88 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 93 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 65 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE B 75 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL B 67 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 73 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.560A pdb=" N CYS D 21 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 48 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 81 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N LEU C 34 " --> pdb=" O CYS D 82 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N SER D 84 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 36 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR D 86 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP C 38 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N ASN D 88 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 93 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 65 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE C 75 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL C 67 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY C 73 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.768A pdb=" N THR E 48 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 81 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N LEU D 34 " --> pdb=" O CYS E 82 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N SER E 84 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE D 36 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR E 86 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP D 38 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 88 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 93 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 65 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE D 75 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 67 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY D 73 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.571A pdb=" N CYS F 21 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F 48 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 81 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N LEU E 34 " --> pdb=" O CYS F 82 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N SER F 84 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 36 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR F 86 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP E 38 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N ASN F 88 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 93 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 65 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE E 75 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL E 67 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 73 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.535A pdb=" N CYS G 21 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR G 48 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 81 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N LEU F 34 " --> pdb=" O CYS G 82 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N SER G 84 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE F 36 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR G 86 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP F 38 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N ASN G 88 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE F 93 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 65 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE F 75 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL F 67 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY F 73 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.569A pdb=" N CYS A 21 " --> pdb=" O ILE N 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 48 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 81 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N CYS A 82 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE G 36 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 86 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE G 93 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 65 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE G 75 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL G 67 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY G 73 " --> pdb=" O VAL G 67 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 2961 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: 10.73 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20244 1.03 - 1.23: 379 1.23 - 1.43: 8469 1.43 - 1.62: 13412 1.62 - 1.82: 308 Bond restraints: 42812 Sorted by residual: bond pdb=" CA CYS A 9 " pdb=" C CYS A 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.10e-01 bond pdb=" CA CYS Q 9 " pdb=" C CYS Q 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.01e-01 bond pdb=" CA CYS D 9 " pdb=" C CYS D 9 " ideal model delta sigma weight residual 1.529 1.521 0.008 9.30e-03 1.16e+04 7.01e-01 bond pdb=" CA CYS B 9 " pdb=" C CYS B 9 " ideal model delta sigma weight residual 1.529 1.522 0.008 9.30e-03 1.16e+04 6.85e-01 bond pdb=" CA CYS S 9 " pdb=" C CYS S 9 " ideal model delta sigma weight residual 1.529 1.522 0.008 9.30e-03 1.16e+04 6.78e-01 ... (remaining 42807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 74714 1.33 - 2.65: 1642 2.65 - 3.98: 203 3.98 - 5.31: 49 5.31 - 6.63: 28 Bond angle restraints: 76636 Sorted by residual: angle pdb=" C CYS P 9 " pdb=" CA CYS P 9 " pdb=" CB CYS P 9 " ideal model delta sigma weight residual 116.54 109.91 6.63 1.15e+00 7.56e-01 3.33e+01 angle pdb=" C CYS W 9 " pdb=" CA CYS W 9 " pdb=" CB CYS W 9 " ideal model delta sigma weight residual 116.54 109.93 6.61 1.15e+00 7.56e-01 3.30e+01 angle pdb=" C CYS T 9 " pdb=" CA CYS T 9 " pdb=" CB CYS T 9 " ideal model delta sigma weight residual 116.54 109.94 6.60 1.15e+00 7.56e-01 3.29e+01 angle pdb=" C CYS S 9 " pdb=" CA CYS S 9 " pdb=" CB CYS S 9 " ideal model delta sigma weight residual 116.54 109.95 6.59 1.15e+00 7.56e-01 3.29e+01 angle pdb=" C CYS X 9 " pdb=" CA CYS X 9 " pdb=" CB CYS X 9 " ideal model delta sigma weight residual 116.54 109.95 6.59 1.15e+00 7.56e-01 3.29e+01 ... (remaining 76631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 17940 16.92 - 33.84: 2067 33.84 - 50.76: 565 50.76 - 67.68: 127 67.68 - 84.60: 28 Dihedral angle restraints: 20727 sinusoidal: 11179 harmonic: 9548 Sorted by residual: dihedral pdb=" CB CYS R 8 " pdb=" SG CYS R 8 " pdb=" SG CYS L 21 " pdb=" CB CYS L 21 " ideal model delta sinusoidal sigma weight residual 93.00 134.27 -41.27 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS K 8 " pdb=" SG CYS K 8 " pdb=" SG CYS E 21 " pdb=" CB CYS E 21 " ideal model delta sinusoidal sigma weight residual 93.00 134.10 -41.10 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS S 8 " pdb=" SG CYS S 8 " pdb=" SG CYS M 21 " pdb=" CB CYS M 21 " ideal model delta sinusoidal sigma weight residual 93.00 133.80 -40.80 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 20724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2347 0.031 - 0.061: 877 0.061 - 0.092: 220 0.092 - 0.122: 376 0.122 - 0.153: 128 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE M 49 " pdb=" N ILE M 49 " pdb=" C ILE M 49 " pdb=" CB ILE M 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE X 49 " pdb=" N ILE X 49 " pdb=" C ILE X 49 " pdb=" CB ILE X 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 3945 not shown) Planarity restraints: 6832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY T 60 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO T 61 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO T 61 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO T 61 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Z 60 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO Z 61 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO Z 61 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO Z 61 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 60 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO D 61 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.023 5.00e-02 4.00e+02 ... (remaining 6829 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 16445 2.39 - 2.94: 93271 2.94 - 3.49: 101768 3.49 - 4.05: 148846 4.05 - 4.60: 205775 Nonbonded interactions: 566105 Sorted by model distance: nonbonded pdb="HE22 GLN X 12 " pdb=" H LEU Y 13 " model vdw 1.836 2.100 nonbonded pdb="HE22 GLN K 12 " pdb=" H LEU L 13 " model vdw 1.860 2.100 nonbonded pdb=" OD1 ASP X 39 " pdb=" H THR X 41 " model vdw 1.866 2.450 nonbonded pdb=" OD1 ASP T 39 " pdb=" H THR T 41 " model vdw 1.866 2.450 nonbonded pdb=" OD1 ASP B 39 " pdb=" H THR B 41 " model vdw 1.866 2.450 ... (remaining 566100 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: 0.11 Found NCS groups: ncs_group { reference = chain 'R' selection = chain 'Q' selection = chain 'P' selection = chain 'O' selection = chain 'U' selection = chain 'T' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 32.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.012 0.625 22617 Z= 0.592 Angle : 0.670 12.679 30982 Z= 0.407 Chirality : 0.051 0.153 3948 Planarity : 0.004 0.041 4004 Dihedral : 15.290 84.603 7560 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 35.59 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.95 (0.13), residues: 1400 loop : 0.32 (0.17), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 83 TYR 0.002 0.001 TYR D 113 PHE 0.005 0.001 PHE I 109 TRP 0.003 0.001 TRP D 37 Details of bonding type rmsd covalent geometry : bond 0.00240 (22540) covalent geometry : angle 0.60401 (30828) SS BOND : bond 0.19874 ( 77) SS BOND : angle 4.16972 ( 154) hydrogen bonds : bond 0.10705 ( 1127) hydrogen bonds : angle 6.48835 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 ASP cc_start: 0.7795 (t0) cc_final: 0.7519 (t0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2959 time to fit residues: 97.6172 Evaluate side-chains 187 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 12 GLN R 46 ASN Q 12 GLN Q 46 ASN Q 91 ASN P 12 GLN P 91 ASN O 12 GLN O 46 ASN U 12 GLN U 46 ASN T 12 GLN T 46 ASN S 12 GLN V 12 GLN W 12 GLN X 12 GLN Y 12 GLN Z 12 GLN a 12 GLN b 12 GLN b 46 ASN H 12 GLN H 46 ASN I 12 GLN J 12 GLN J 91 ASN K 12 GLN L 12 GLN L 91 ASN M 12 GLN M 46 ASN D 12 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.027263 restraints weight = 532139.689| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 6.22 r_work: 0.2578 rms_B_bonded: 5.50 restraints_weight: 2.0000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 22617 Z= 0.227 Angle : 0.589 4.827 30982 Z= 0.315 Chirality : 0.051 0.149 3948 Planarity : 0.003 0.022 4004 Dihedral : 4.309 16.939 3220 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.70 % Allowed : 33.79 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.85 (0.13), residues: 1428 loop : 0.39 (0.17), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 83 TYR 0.003 0.001 TYR b 113 PHE 0.022 0.001 PHE b 115 TRP 0.007 0.002 TRP M 37 Details of bonding type rmsd covalent geometry : bond 0.00486 (22540) covalent geometry : angle 0.58696 (30828) SS BOND : bond 0.00667 ( 77) SS BOND : angle 0.90594 ( 154) hydrogen bonds : bond 0.03010 ( 1127) hydrogen bonds : angle 5.79954 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 145 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 GLU cc_start: 0.9017 (tp30) cc_final: 0.8710 (mp0) REVERT: O 11 GLU cc_start: 0.9121 (tp30) cc_final: 0.8831 (mp0) REVERT: U 11 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8098 (mp0) REVERT: T 11 GLU cc_start: 0.9118 (tp30) cc_final: 0.8816 (mp0) REVERT: X 11 GLU cc_start: 0.9104 (tp30) cc_final: 0.8800 (mp0) REVERT: Y 11 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8456 (mp0) REVERT: Z 11 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8490 (mp0) REVERT: a 11 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8514 (mp0) REVERT: b 11 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8567 (mp0) REVERT: b 87 MET cc_start: 0.8656 (mtp) cc_final: 0.8383 (mtm) REVERT: H 50 MET cc_start: 0.9552 (ttp) cc_final: 0.8953 (tmm) REVERT: I 11 GLU cc_start: 0.9142 (tp30) cc_final: 0.8915 (mp0) outliers start: 117 outliers final: 75 residues processed: 260 average time/residue: 0.2388 time to fit residues: 106.7493 Evaluate side-chains 213 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 41 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 41 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 41 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 75 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 282 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.035434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027368 restraints weight = 537011.223| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 6.21 r_work: 0.2576 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 22617 Z= 0.153 Angle : 0.510 4.507 30982 Z= 0.273 Chirality : 0.050 0.142 3948 Planarity : 0.002 0.015 4004 Dihedral : 4.182 27.805 3220 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 31.78 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.65 (0.13), residues: 1428 loop : 0.59 (0.17), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.002 0.000 TYR U 113 PHE 0.021 0.001 PHE W 115 TRP 0.003 0.001 TRP Q 37 Details of bonding type rmsd covalent geometry : bond 0.00324 (22540) covalent geometry : angle 0.50823 (30828) SS BOND : bond 0.00279 ( 77) SS BOND : angle 0.79477 ( 154) hydrogen bonds : bond 0.02588 ( 1127) hydrogen bonds : angle 5.44589 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9641 (OUTLIER) cc_final: 0.8760 (mp10) REVERT: R 11 GLU cc_start: 0.8990 (tp30) cc_final: 0.8689 (mp0) REVERT: O 11 GLU cc_start: 0.9152 (tp30) cc_final: 0.8882 (mp0) REVERT: T 11 GLU cc_start: 0.9138 (tp30) cc_final: 0.8847 (mp0) REVERT: S 4 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: V 4 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.8795 (mp10) REVERT: X 4 GLN cc_start: 0.9542 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: Y 4 GLN cc_start: 0.9608 (OUTLIER) cc_final: 0.8746 (mp10) REVERT: b 4 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: H 89 ASP cc_start: 0.9329 (t0) cc_final: 0.9081 (t0) REVERT: I 11 GLU cc_start: 0.9127 (tp30) cc_final: 0.8909 (mp0) REVERT: L 89 ASP cc_start: 0.9280 (t0) cc_final: 0.9032 (t0) outliers start: 68 outliers final: 54 residues processed: 208 average time/residue: 0.2926 time to fit residues: 104.2805 Evaluate side-chains 200 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 144 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN E 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.035279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.027392 restraints weight = 521354.793| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 6.22 r_work: 0.2563 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22617 Z= 0.168 Angle : 0.504 4.644 30982 Z= 0.269 Chirality : 0.050 0.157 3948 Planarity : 0.002 0.014 4004 Dihedral : 4.114 23.210 3220 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.69 % Allowed : 27.69 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.16), residues: 3108 helix: None (None), residues: 0 sheet: 0.60 (0.13), residues: 1428 loop : 0.62 (0.17), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 83 TYR 0.001 0.000 TYR Z 113 PHE 0.023 0.001 PHE b 115 TRP 0.004 0.001 TRP H 37 Details of bonding type rmsd covalent geometry : bond 0.00354 (22540) covalent geometry : angle 0.50265 (30828) SS BOND : bond 0.00255 ( 77) SS BOND : angle 0.70615 ( 154) hydrogen bonds : bond 0.02605 ( 1127) hydrogen bonds : angle 5.42980 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 129 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9636 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: R 11 GLU cc_start: 0.9105 (tp30) cc_final: 0.8832 (mp0) REVERT: Q 4 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.8592 (mp10) REVERT: P 4 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.8820 (mp10) REVERT: O 4 GLN cc_start: 0.9526 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: O 11 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: U 4 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.8641 (mp10) REVERT: T 4 GLN cc_start: 0.9544 (OUTLIER) cc_final: 0.8591 (mp10) REVERT: T 11 GLU cc_start: 0.9142 (tp30) cc_final: 0.8850 (mp0) REVERT: W 4 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.8750 (mp10) REVERT: Z 4 GLN cc_start: 0.9580 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: a 4 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: b 4 GLN cc_start: 0.9590 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: H 50 MET cc_start: 0.9632 (ttp) cc_final: 0.9105 (tmm) REVERT: I 4 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9236 (mp10) REVERT: I 11 GLU cc_start: 0.9202 (tp30) cc_final: 0.8964 (mp0) REVERT: J 4 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.8805 (mp10) REVERT: K 4 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9058 (mp10) REVERT: M 4 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.9014 (mp10) REVERT: A 50 MET cc_start: 0.9103 (tmm) cc_final: 0.8893 (tmm) REVERT: C 50 MET cc_start: 0.8942 (tmm) cc_final: 0.8713 (tmm) REVERT: G 50 MET cc_start: 0.8892 (tmm) cc_final: 0.8684 (tmm) outliers start: 92 outliers final: 67 residues processed: 218 average time/residue: 0.2384 time to fit residues: 88.7823 Evaluate side-chains 210 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 128 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 302 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 242 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 137 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 ASN A 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.034769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027018 restraints weight = 537768.540| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 6.17 r_work: 0.2550 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 22617 Z= 0.231 Angle : 0.525 4.741 30982 Z= 0.286 Chirality : 0.049 0.140 3948 Planarity : 0.002 0.017 4004 Dihedral : 4.388 24.280 3220 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.49 % Allowed : 24.76 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.34 (0.13), residues: 1428 loop : 0.37 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 83 TYR 0.002 0.001 TYR Z 113 PHE 0.029 0.002 PHE V 115 TRP 0.006 0.002 TRP V 37 Details of bonding type rmsd covalent geometry : bond 0.00478 (22540) covalent geometry : angle 0.52324 (30828) SS BOND : bond 0.00368 ( 77) SS BOND : angle 0.77929 ( 154) hydrogen bonds : bond 0.02780 ( 1127) hydrogen bonds : angle 5.58081 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 126 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9617 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: R 11 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8806 (mp0) REVERT: Q 4 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: P 4 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: O 4 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.8578 (mp10) REVERT: O 11 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8936 (mp0) REVERT: U 4 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: T 4 GLN cc_start: 0.9569 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: T 11 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8900 (mp0) REVERT: S 4 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: V 4 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.8730 (mp10) REVERT: W 4 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.8650 (mp10) REVERT: X 4 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.8590 (mp10) REVERT: Y 4 GLN cc_start: 0.9596 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: Z 4 GLN cc_start: 0.9597 (OUTLIER) cc_final: 0.8684 (mp10) REVERT: a 4 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: b 4 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: H 4 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.8717 (mp10) REVERT: H 50 MET cc_start: 0.9652 (ttp) cc_final: 0.9123 (tmm) REVERT: I 4 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.9022 (mp10) REVERT: I 11 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9031 (mp0) REVERT: J 4 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.8797 (mp10) REVERT: K 4 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.8940 (mp10) REVERT: L 4 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: M 4 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8943 (mp10) REVERT: N 4 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: A 12 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: A 50 MET cc_start: 0.9136 (tmm) cc_final: 0.8908 (tmm) REVERT: B 50 MET cc_start: 0.9095 (tmm) cc_final: 0.8851 (tmm) REVERT: C 50 MET cc_start: 0.8971 (tmm) cc_final: 0.8728 (tmm) REVERT: D 50 MET cc_start: 0.9001 (tmm) cc_final: 0.8769 (tmm) REVERT: G 50 MET cc_start: 0.9005 (tmm) cc_final: 0.8763 (tmm) outliers start: 112 outliers final: 83 residues processed: 233 average time/residue: 0.2511 time to fit residues: 100.6890 Evaluate side-chains 234 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 125 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 11 GLU Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 11 GLU Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 132 optimal weight: 0.0670 chunk 136 optimal weight: 9.9990 chunk 148 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 chunk 162 optimal weight: 9.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.035278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027510 restraints weight = 544184.903| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 6.03 r_work: 0.2560 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22617 Z= 0.122 Angle : 0.484 4.518 30982 Z= 0.259 Chirality : 0.051 0.147 3948 Planarity : 0.002 0.015 4004 Dihedral : 4.184 24.322 3220 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.81 % Allowed : 24.00 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.38 (0.13), residues: 1428 loop : 0.52 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.002 0.000 TYR W 113 PHE 0.025 0.001 PHE Y 115 TRP 0.002 0.001 TRP Q 37 Details of bonding type rmsd covalent geometry : bond 0.00263 (22540) covalent geometry : angle 0.48337 (30828) SS BOND : bond 0.00228 ( 77) SS BOND : angle 0.64371 ( 154) hydrogen bonds : bond 0.02551 ( 1127) hydrogen bonds : angle 5.41856 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 127 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 4 GLN cc_start: 0.9479 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: P 4 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8793 (mp10) REVERT: O 4 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: U 4 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.8641 (mp10) REVERT: T 4 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: T 11 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8920 (mp0) REVERT: S 4 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: V 4 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: W 4 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8622 (mp10) REVERT: Z 4 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.8645 (mp10) REVERT: a 4 GLN cc_start: 0.9527 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: H 4 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: H 50 MET cc_start: 0.9657 (ttp) cc_final: 0.9145 (tmm) REVERT: I 4 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.9123 (mp10) REVERT: I 50 MET cc_start: 0.9498 (tmm) cc_final: 0.9197 (tmm) REVERT: K 4 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8975 (mp10) REVERT: L 4 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.8618 (mp10) REVERT: M 4 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8880 (mp10) REVERT: N 4 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: A 50 MET cc_start: 0.9162 (tmm) cc_final: 0.8914 (tmm) REVERT: B 50 MET cc_start: 0.9127 (tmm) cc_final: 0.8857 (tmm) REVERT: C 50 MET cc_start: 0.9015 (tmm) cc_final: 0.8749 (tmm) REVERT: D 50 MET cc_start: 0.9036 (tmm) cc_final: 0.8787 (tmm) REVERT: G 12 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: G 50 MET cc_start: 0.9011 (tmm) cc_final: 0.8745 (tmm) outliers start: 95 outliers final: 70 residues processed: 218 average time/residue: 0.2610 time to fit residues: 97.6509 Evaluate side-chains 212 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 124 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 280 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 225 optimal weight: 30.0000 chunk 113 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.034771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027220 restraints weight = 529433.685| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 5.85 r_work: 0.2558 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22617 Z= 0.191 Angle : 0.494 5.011 30982 Z= 0.266 Chirality : 0.049 0.142 3948 Planarity : 0.002 0.017 4004 Dihedral : 4.199 23.065 3220 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.74 % Allowed : 22.11 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.41 (0.13), residues: 1400 loop : 0.55 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 83 TYR 0.001 0.000 TYR E 113 PHE 0.026 0.001 PHE Y 115 TRP 0.003 0.001 TRP Z 37 Details of bonding type rmsd covalent geometry : bond 0.00395 (22540) covalent geometry : angle 0.49279 (30828) SS BOND : bond 0.00273 ( 77) SS BOND : angle 0.62522 ( 154) hydrogen bonds : bond 0.02676 ( 1127) hydrogen bonds : angle 5.47142 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 124 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: Q 4 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: P 4 GLN cc_start: 0.9522 (OUTLIER) cc_final: 0.8842 (mp10) REVERT: O 4 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: U 4 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: T 4 GLN cc_start: 0.9536 (OUTLIER) cc_final: 0.8549 (mp10) REVERT: T 11 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8945 (mp0) REVERT: S 4 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.8599 (mp10) REVERT: V 4 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.8709 (mp10) REVERT: W 4 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.8657 (mp10) REVERT: X 4 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: Y 4 GLN cc_start: 0.9587 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: Z 4 GLN cc_start: 0.9580 (OUTLIER) cc_final: 0.8711 (mp10) REVERT: a 4 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.8547 (mp10) REVERT: b 4 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: H 4 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: H 50 MET cc_start: 0.9650 (ttp) cc_final: 0.9094 (tmm) REVERT: I 4 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9078 (mp10) REVERT: J 4 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.8762 (mp10) REVERT: K 4 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8968 (mp10) REVERT: L 4 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.8609 (mp10) REVERT: M 4 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8908 (mp10) REVERT: N 4 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: A 50 MET cc_start: 0.9150 (tmm) cc_final: 0.8897 (tmm) REVERT: B 50 MET cc_start: 0.9104 (tmm) cc_final: 0.8826 (tmm) REVERT: C 50 MET cc_start: 0.8979 (tmm) cc_final: 0.8708 (tmm) REVERT: D 50 MET cc_start: 0.9023 (tmm) cc_final: 0.8765 (tmm) REVERT: F 12 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: G 50 MET cc_start: 0.9008 (tmm) cc_final: 0.8732 (tmm) outliers start: 118 outliers final: 86 residues processed: 240 average time/residue: 0.2833 time to fit residues: 116.7983 Evaluate side-chains 232 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 123 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 12 GLN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 222 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 297 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.035082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027356 restraints weight = 531070.856| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 6.00 r_work: 0.2560 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22617 Z= 0.136 Angle : 0.480 4.540 30982 Z= 0.257 Chirality : 0.050 0.143 3948 Planarity : 0.002 0.017 4004 Dihedral : 4.109 23.069 3220 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.41 % Allowed : 22.23 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.34 (0.13), residues: 1428 loop : 0.48 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.002 0.000 TYR b 113 PHE 0.027 0.001 PHE b 115 TRP 0.002 0.001 TRP Q 37 Details of bonding type rmsd covalent geometry : bond 0.00289 (22540) covalent geometry : angle 0.47861 (30828) SS BOND : bond 0.00240 ( 77) SS BOND : angle 0.65886 ( 154) hydrogen bonds : bond 0.02568 ( 1127) hydrogen bonds : angle 5.39600 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 124 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9605 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: Q 4 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.8509 (mp10) REVERT: P 4 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.8829 (mp10) REVERT: O 4 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: U 4 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: T 4 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: T 11 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8942 (mp0) REVERT: S 4 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: V 4 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: W 4 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: X 4 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: Y 4 GLN cc_start: 0.9611 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: Z 4 GLN cc_start: 0.9575 (OUTLIER) cc_final: 0.8716 (mp10) REVERT: a 4 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: b 4 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: H 4 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: H 50 MET cc_start: 0.9643 (ttp) cc_final: 0.9090 (tmm) REVERT: I 4 GLN cc_start: 0.9476 (OUTLIER) cc_final: 0.9133 (mp10) REVERT: I 50 MET cc_start: 0.9472 (tmm) cc_final: 0.9198 (tmm) REVERT: K 4 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.8994 (mp10) REVERT: L 4 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8549 (mp10) REVERT: M 4 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8862 (mp10) REVERT: N 4 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8557 (mp10) REVERT: A 50 MET cc_start: 0.9147 (tmm) cc_final: 0.8891 (tmm) REVERT: B 50 MET cc_start: 0.9103 (tmm) cc_final: 0.8817 (tmm) REVERT: C 50 MET cc_start: 0.8987 (tmm) cc_final: 0.8704 (tmm) REVERT: D 50 MET cc_start: 0.9002 (tmm) cc_final: 0.8733 (tmm) REVERT: G 50 MET cc_start: 0.9012 (tmm) cc_final: 0.8729 (tmm) outliers start: 110 outliers final: 82 residues processed: 231 average time/residue: 0.2795 time to fit residues: 110.3223 Evaluate side-chains 227 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 124 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 226 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 290 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 91 ASN M 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.034716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.027048 restraints weight = 535982.764| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 5.96 r_work: 0.2554 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 22617 Z= 0.193 Angle : 0.495 4.613 30982 Z= 0.268 Chirality : 0.049 0.141 3948 Planarity : 0.002 0.020 4004 Dihedral : 4.175 22.606 3220 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.61 % Allowed : 21.79 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.35 (0.13), residues: 1400 loop : 0.52 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 83 TYR 0.002 0.000 TYR H 113 PHE 0.030 0.001 PHE b 115 TRP 0.004 0.001 TRP V 37 Details of bonding type rmsd covalent geometry : bond 0.00398 (22540) covalent geometry : angle 0.49354 (30828) SS BOND : bond 0.00323 ( 77) SS BOND : angle 0.75093 ( 154) hydrogen bonds : bond 0.02706 ( 1127) hydrogen bonds : angle 5.48136 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 123 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9621 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: Q 4 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: P 4 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.8819 (mp10) REVERT: O 4 GLN cc_start: 0.9478 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: U 4 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: T 4 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: S 4 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: V 4 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.8692 (mp10) REVERT: W 4 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.8531 (mp10) REVERT: X 4 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: Y 4 GLN cc_start: 0.9564 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: Z 4 GLN cc_start: 0.9577 (OUTLIER) cc_final: 0.8708 (mp10) REVERT: a 4 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.8523 (mp10) REVERT: b 4 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: H 4 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: H 50 MET cc_start: 0.9658 (ttp) cc_final: 0.9110 (tmm) REVERT: I 4 GLN cc_start: 0.9456 (OUTLIER) cc_final: 0.9026 (mp10) REVERT: J 4 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: K 4 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.8948 (mp10) REVERT: L 4 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: M 4 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8886 (mp10) REVERT: N 4 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: A 50 MET cc_start: 0.9176 (tmm) cc_final: 0.8917 (tmm) REVERT: B 50 MET cc_start: 0.9133 (tmm) cc_final: 0.8842 (tmm) REVERT: C 50 MET cc_start: 0.9029 (tmm) cc_final: 0.8748 (tmm) REVERT: D 50 MET cc_start: 0.9022 (tmm) cc_final: 0.8743 (tmm) REVERT: E 50 MET cc_start: 0.9101 (tmm) cc_final: 0.8821 (tmm) REVERT: G 50 MET cc_start: 0.9035 (tmm) cc_final: 0.8738 (tmm) outliers start: 115 outliers final: 87 residues processed: 236 average time/residue: 0.2458 time to fit residues: 99.7795 Evaluate side-chains 230 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 122 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 43 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN O 91 ASN U 91 ASN S 91 ASN I 91 ASN N 91 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.034456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.026829 restraints weight = 540668.810| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 5.96 r_work: 0.2546 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 22617 Z= 0.237 Angle : 0.518 5.162 30982 Z= 0.281 Chirality : 0.049 0.137 3948 Planarity : 0.002 0.022 4004 Dihedral : 4.332 22.866 3220 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.49 % Allowed : 21.47 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.23 (0.13), residues: 1400 loop : 0.37 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 83 TYR 0.002 0.001 TYR a 113 PHE 0.032 0.001 PHE Y 115 TRP 0.006 0.001 TRP N 37 Details of bonding type rmsd covalent geometry : bond 0.00485 (22540) covalent geometry : angle 0.51550 (30828) SS BOND : bond 0.00363 ( 77) SS BOND : angle 0.86240 ( 154) hydrogen bonds : bond 0.02866 ( 1127) hydrogen bonds : angle 5.60954 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 119 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 4 GLN cc_start: 0.9616 (OUTLIER) cc_final: 0.8607 (mp10) REVERT: Q 4 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: P 4 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.8837 (mp10) REVERT: O 4 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: U 4 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: T 4 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: S 4 GLN cc_start: 0.9544 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: V 4 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: W 4 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.8578 (mp10) REVERT: X 4 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: Y 4 GLN cc_start: 0.9577 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: Z 4 GLN cc_start: 0.9591 (OUTLIER) cc_final: 0.8718 (mp10) REVERT: a 4 GLN cc_start: 0.9544 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: b 4 GLN cc_start: 0.9537 (OUTLIER) cc_final: 0.8605 (mp10) REVERT: H 4 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.8626 (mp10) REVERT: H 50 MET cc_start: 0.9660 (ttp) cc_final: 0.9063 (tmm) REVERT: I 4 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.8980 (mp10) REVERT: J 4 GLN cc_start: 0.9421 (OUTLIER) cc_final: 0.8706 (mp10) REVERT: K 4 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.8915 (mp10) REVERT: L 4 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: M 4 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8904 (mp10) REVERT: N 4 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: A 50 MET cc_start: 0.9168 (tmm) cc_final: 0.8904 (tmm) REVERT: B 50 MET cc_start: 0.9118 (tmm) cc_final: 0.8826 (tmm) REVERT: C 50 MET cc_start: 0.9027 (tmm) cc_final: 0.8758 (tmm) REVERT: D 50 MET cc_start: 0.9023 (tmm) cc_final: 0.8743 (tmm) REVERT: E 50 MET cc_start: 0.9103 (tmm) cc_final: 0.8825 (tmm) REVERT: F 50 MET cc_start: 0.9059 (tmm) cc_final: 0.8759 (tmm) REVERT: G 50 MET cc_start: 0.9049 (tmm) cc_final: 0.8750 (tmm) outliers start: 112 outliers final: 88 residues processed: 229 average time/residue: 0.2548 time to fit residues: 100.1500 Evaluate side-chains 227 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 118 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 4 GLN Chi-restraints excluded: chain R residue 21 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 82 CYS Chi-restraints excluded: chain Q residue 4 GLN Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 21 CYS Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 82 CYS Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 82 CYS Chi-restraints excluded: chain O residue 4 GLN Chi-restraints excluded: chain O residue 5 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 82 CYS Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 82 CYS Chi-restraints excluded: chain T residue 4 GLN Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 82 CYS Chi-restraints excluded: chain S residue 4 GLN Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 21 CYS Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 82 CYS Chi-restraints excluded: chain V residue 4 GLN Chi-restraints excluded: chain V residue 46 ASN Chi-restraints excluded: chain V residue 82 CYS Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 5 ILE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 82 CYS Chi-restraints excluded: chain X residue 4 GLN Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 82 CYS Chi-restraints excluded: chain Y residue 4 GLN Chi-restraints excluded: chain Y residue 46 ASN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 82 CYS Chi-restraints excluded: chain Z residue 4 GLN Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 82 CYS Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 82 CYS Chi-restraints excluded: chain b residue 4 GLN Chi-restraints excluded: chain b residue 70 THR Chi-restraints excluded: chain b residue 82 CYS Chi-restraints excluded: chain H residue 4 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain I residue 4 GLN Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 82 CYS Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 21 CYS Chi-restraints excluded: chain J residue 82 CYS Chi-restraints excluded: chain K residue 4 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 82 CYS Chi-restraints excluded: chain L residue 4 GLN Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 82 CYS Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 82 CYS Chi-restraints excluded: chain N residue 4 GLN Chi-restraints excluded: chain N residue 5 ILE Chi-restraints excluded: chain N residue 21 CYS Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 82 CYS Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 82 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 CYS Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 21 CYS Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 CYS Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 99 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 272 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.034735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.027094 restraints weight = 536504.239| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 5.90 r_work: 0.2550 rms_B_bonded: 5.26 restraints_weight: 2.0000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22617 Z= 0.161 Angle : 0.493 5.097 30982 Z= 0.264 Chirality : 0.050 0.137 3948 Planarity : 0.002 0.020 4004 Dihedral : 4.216 24.277 3220 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.33 % Allowed : 21.47 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3108 helix: None (None), residues: 0 sheet: 0.25 (0.13), residues: 1400 loop : 0.46 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 83 TYR 0.002 0.000 TYR W 113 PHE 0.028 0.001 PHE b 115 TRP 0.002 0.001 TRP Q 37 Details of bonding type rmsd covalent geometry : bond 0.00336 (22540) covalent geometry : angle 0.48922 (30828) SS BOND : bond 0.00305 ( 77) SS BOND : angle 0.96374 ( 154) hydrogen bonds : bond 0.02672 ( 1127) hydrogen bonds : angle 5.52024 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.18 seconds wall clock time: 134 minutes 2.47 seconds (8042.47 seconds total)